Publications of Thomas Mitchell-Olds    :chronological  alphabetical  combined listing:

%% Papers Published   
@article{fds343685,
   Author = {Wang, B and Mojica, JP and Perera, N and Lee, C-R and Lovell, JT and Sharma, A and Adam, C and Lipzen, A and Barry, K and Rokhsar, DS and Schmutz, J and Mitchell-Olds, T},
   Title = {Ancient polymorphisms contribute to genome-wide variation by
             long-term balancing selection and divergent sorting in
             Boechera stricta.},
   Journal = {Genome Biology},
   Volume = {20},
   Number = {1},
   Pages = {126},
   Year = {2019},
   Month = {June},
   url = {http://dx.doi.org/10.1186/s13059-019-1729-9},
   Abstract = {BACKGROUND:Genomic variation is widespread, and both neutral
             and selective processes can generate similar patterns in the
             genome. These processes are not mutually exclusive, so it is
             difficult to infer the evolutionary mechanisms that govern
             population and species divergence. Boechera stricta is a
             perennial relative of Arabidopsis thaliana native to largely
             undisturbed habitats with two geographic and ecologically
             divergent subspecies. Here, we delineate the evolutionary
             processes driving the genetic diversity and population
             differentiation in this species. RESULTS:Using whole-genome
             re-sequencing data from 517 B. stricta accessions, we
             identify four genetic groups that diverged around 30-180
             thousand years ago, with long-term small effective
             population sizes and recent population expansion after the
             Last Glacial Maximum. We find three genomic regions with
             elevated nucleotide diversity, totaling about 10% of the
             genome. These three regions of elevated nucleotide diversity
             show excess of intermediate-frequency alleles, higher
             absolute divergence (dXY), and lower relative divergence
             (FST) than genomic background, and significant enrichment in
             immune-related genes, reflecting long-term balancing
             selection. Scattered across the genome, we also find regions
             with both high FST and dXY among the groups, termed
             FST-islands. Population genetic signatures indicate that
             FST-islands with elevated divergence, which have experienced
             directional selection, are derived from divergent sorting of
             ancient polymorphisms. CONCLUSIONS:Our results suggest that
             long-term balancing selection on disease resistance genes
             may have maintained ancestral haplotypes across different
             geographical lineages, and unequal sorting of balanced
             polymorphisms may have generated genomic regions with
             elevated divergence. This study highlights the importance of
             ancestral balanced polymorphisms as crucial components of
             genome-wide variation.},
   Doi = {10.1186/s13059-019-1729-9},
   Key = {fds343685}
}

@article{fds342544,
   Author = {Keith, RA and Mitchell-Olds, T},
   Title = {Antagonistic selection and pleiotropy constrain the
             evolution of plant chemical defenses.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {73},
   Number = {5},
   Pages = {947-960},
   Year = {2019},
   Month = {May},
   url = {http://dx.doi.org/10.1111/evo.13728},
   Abstract = {When pleiotropy is present, genetic correlations may
             constrain the evolution of ecologically important traits. We
             used a quantitative genetics approach to investigate
             constraints on the evolution of secondary metabolites in a
             wild mustard, Boechera stricta. Much of the genetic
             variation in chemical composition of glucosinolates in B.
             stricta is controlled by a single locus, BCMA1/3. In a
             large-scale common garden experiment under natural
             conditions, we quantified fitness and glucosinolate profile
             in two leaf types and in fruits. We estimated genetic
             variances and covariances (the G-matrix) and selection on
             chemical profile in each tissue. Chemical composition of
             defenses was strongly genetically correlated between
             tissues. We found antagonistic selection between defense
             composition in leaves and fruits: compounds that were
             favored in leaves were disadvantageous in fruits. The
             positive genetic correlations and antagonistic selection led
             to strong constraints on the evolution of defenses in leaves
             and fruits. In a hypothetical population with no genetic
             variation at BCMA1/3, we found no evidence for genetic
             constraints, indicating that pleiotropy affecting chemical
             profile in multiple tissues drives constraints on the
             evolution of secondary metabolites.},
   Doi = {10.1111/evo.13728},
   Key = {fds342544}
}

@article{fds340458,
   Author = {Rushworth, CA and Windham, MD and Keith, RA and Mitchell-Olds,
             T},
   Title = {Ecological differentiation facilitates fine-scale
             coexistence of sexual and asexual Boechera.},
   Journal = {American Journal of Botany},
   Volume = {105},
   Number = {12},
   Pages = {2051-2064},
   Year = {2018},
   Month = {December},
   url = {http://dx.doi.org/10.1002/ajb2.1201},
   Abstract = {PREMISE OF THE STUDY:Ecological differentiation (ED) between
             sexual and asexual organisms may permit the maintenance of
             reproductive polymorphism. Several studies of sexual/asexual
             ED in plants have shown that the geographic ranges of
             asexuals extend beyond those of sexuals, often in areas of
             higher latitude or elevation. But very little is known about
             ED at fine scales, wherein coexistence of sexuals and
             asexuals may be permitted by differential niche occupation.
             METHODS:We used 149 populations of sexual and apomictic
             lineages in the genus Boechera (rock cress) collected across
             a portion of this mustard's vast range. We characterized
             reproductive mode, ploidy, and species identity or hybrid
             parentage of each individual, and then used a multipronged
             statistical approach to (1) identify ED between sexuals and
             asexuals; (2) investigate the impacts of two confounding
             factors, polyploidy and hybridization, on ED; and (3)
             determine the environmental variables underlying ED. KEY
             RESULTS:We found that sexuals and asexuals are significantly
             ecologically differentiated across the landscape, despite
             fine-scale interdigitation of these two reproductive forms.
             Asexual reproduction was strongly associated with greater
             disturbance, reduced slope, and greater environmental
             variability. Although ploidy had little effect on the
             patterns observed, hybridization has a unique impact on the
             relationships between asexual reproduction and specific
             environmental variables. CONCLUSIONS:Ecological
             differentiation along the axes of disturbance, slope, and
             climatic variability, as well as the effects of
             heterozygosity, may contribute to the maintenance of
             sexuality and asexuality across the landscape, ultimately
             impacting the establishment and spread of asexual
             lineages.},
   Doi = {10.1002/ajb2.1201},
   Key = {fds340458}
}

@article{fds335255,
   Author = {Arisz, SA and Heo, J-Y and Koevoets, IT and Zhao, T and van Egmond, P and Meyer, AJ and Zeng, W and Niu, X and Wang, B and Mitchell-Olds, T and Schranz, ME and Testerink, C},
   Title = {DIACYLGLYCEROL ACYLTRANSFERASE1 Contributes to Freezing
             Tolerance.},
   Journal = {Plant Physiology},
   Volume = {177},
   Number = {4},
   Pages = {1410-1424},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1104/pp.18.00503},
   Abstract = {Freezing limits plant growth and crop productivity, and
             plant species in temperate zones have the capacity to
             develop freezing tolerance through complex modulation of
             gene expression affecting various aspects of metabolism and
             physiology. While many components of freezing tolerance have
             been identified in model species under controlled laboratory
             conditions, little is known about the mechanisms that impart
             freezing tolerance in natural populations of wild species.
             Here, we performed a quantitative trait locus (QTL) study of
             acclimated freezing tolerance in seedlings of Boechera
             stricta, a highly adapted relative of Arabidopsis
             (Arabidopsis thaliana) native to the Rocky Mountains. A
             single QTL was identified that contained the gene encoding
             ACYL-COENZYME A:DIACYLGLYCEROL ACYLTRANSFERASE1 (BstDGAT1),
             whose expression is highly cold responsive. The primary
             metabolic enzyme DGAT1 catalyzes the final step in assembly
             of triacylglycerol (TAG) by acyl transfer from acyl-CoA to
             diacylglycerol. Freezing tolerant plants showed higher DGAT1
             expression during cold acclimation than more sensitive
             plants, and this resulted in increased accumulation of TAG
             in response to subsequent freezing. Levels of
             oligogalactolipids that are produced by SFR2 (SENSITIVE TO
             FREEZING2), an indispensable element of freezing tolerance
             in Arabidopsis, were also higher in freezing-tolerant
             plants. Furthermore, overexpression of AtDGAT1 led to
             increased freezing tolerance. We propose that DGAT1 confers
             freezing tolerance in plants by supporting SFR2-mediated
             remodeling of chloroplast membranes.},
   Doi = {10.1104/pp.18.00503},
   Key = {fds335255}
}

@article{fds336999,
   Author = {Grondin, A and Dixit, S and Torres, R and Venkateshwarlu, C and Rogers,
             E and Mitchell-Olds, T and Benfey, PN and Kumar, A and Henry,
             A},
   Title = {Physiological mechanisms contributing to the QTL qDTY3.2
             effects on improved performance of rice Moroberekan x Swarna
             BC2F3:4 lines under drought.},
   Journal = {Rice (New York, N.Y.)},
   Volume = {11},
   Number = {1},
   Pages = {43},
   Year = {2018},
   Month = {July},
   url = {http://dx.doi.org/10.1186/s12284-018-0234-1},
   Abstract = {Traditional rice (Oryza sativa) varieties are valuable
             resources for the improvement of drought resistance. qDTY3.2
             is a drought-yield quantitative trait locus that was
             identified in a population derived from the traditional
             variety Moroberekan and the drought-susceptible variety
             Swarna. In this study, our aim was to characterize the
             physiological mechanisms associated with qDTY3.2. Our
             approach was to phenotype fifteen BC2F3:4 lines for shoot
             and root drought resistance-related traits as compared to
             Swarna in the field under well-watered and drought stress
             conditions. Four BC2F3:4 lines contrasting for yield under
             drought were selected for detailed characterization of shoot
             morphology, water use related traits, flowering time and
             root system architecture in the field as well as in
             controlled environments (lysimeters in a greenhouse, and gel
             imaging platform in a growth chamber).Across five field
             experiments, grain yield correlated significantly with root
             growth along the soil profile, flowering time, and canopy
             temperature under drought conditions. The four selected
             BC2F3:4 lines showed earlier flowering time, reduced
             distribution of root growth to shallow soil layers which
             resulted in lower water uptake (between 0 and 30 cm) and
             drought-induced increased distribution of root growth to
             deep soil layers (between 30 and 60 cm) as compared to
             Swarna in the field. Root system architecture phenotypes
             were confirmed in whole root systems in lysimeters, and
             corresponded to higher numbers of root tips in a gel imaging
             platform, highlighting the potential stability of some root
             traits across different growth stages and systems.We
             conclude that earlier flowering time, reduced shallow root
             growth, and drought-induced increased deep root growth are
             associated with the presence of qDTY3.2 since these
             phenotypes were consistently observed in the selected QTL
             lines with full introgression of qDTY3.2. We hypothesize
             that the qDTY3.2 associated RSA phenotypes led to better use
             of water and metabolic resources which, combined with
             earlier flowering time, improved yield under
             drought.},
   Doi = {10.1186/s12284-018-0234-1},
   Key = {fds336999}
}

@article{fds335256,
   Author = {Wagner, MR and Mitchell-Olds, T},
   Title = {Plasticity of plant defense and its evolutionary
             implications in wild populations of Boechera
             stricta.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {72},
   Number = {5},
   Pages = {1034-1049},
   Year = {2018},
   Month = {May},
   url = {http://dx.doi.org/10.1111/evo.13469},
   Abstract = {Phenotypic plasticity is thought to impact evolutionary
             trajectories by shifting trait values in a direction that is
             either favored by natural selection ("adaptive" plasticity)
             or disfavored ("nonadaptive" plasticity). However, it is
             unclear how commonly each of these types of plasticity
             occurs in natural populations. To answer this question, we
             measured glucosinolate defensive chemistry and reproductive
             fitness in over 1500 individuals of the wild perennial
             mustard Boechera stricta, planted in four common gardens
             across central Idaho, United States. Glucosinolate
             profiles-including total glucosinolate concentration as well
             as the relative abundances and overall diversity of
             different compounds-were strongly plastic both among
             habitats and within habitats. Patterns of glucosinolate
             plasticity varied greatly among genotypes. Plasticity among
             sites was predicted to affect fitness in 27.1% of cases;
             more often than expected by chance, glucosinolate plasticity
             increased rather than decreased relative fitness. In
             contrast, we found no evidence for within-habitat selection
             on glucosinolate reaction norm slopes (i.e., plasticity
             along a continuous environmental gradient). Together, our
             results indicate that glucosinolate plasticity may improve
             the ability of B. stricta populations to persist after
             migration to new habitats.},
   Doi = {10.1111/evo.13469},
   Key = {fds335256}
}

@article{fds333742,
   Author = {Kliver, S and Rayko, M and Komissarov, A and Bakin, E and Zhernakova, D and Prasad, K and Rushworth, C and Baskar, R and Smetanin, D and Schmutz, J and Rokhsar, DS and Mitchell-Olds, T and Grossniklaus, U and Brukhin,
             V},
   Title = {Assembly of the Boechera retrofracta Genome and Evolutionary
             Analysis of Apomixis-Associated Genes.},
   Journal = {Genes},
   Volume = {9},
   Number = {4},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.3390/genes9040185},
   Abstract = {Closely related to the model plant Arabidopsis thaliana, the
             genus Boechera is known to contain both sexual and apomictic
             species or accessions. Boechera retrofracta is a diploid
             sexually reproducing species and is thought to be an
             ancestral parent species of apomictic species. Here we
             report the de novo assembly of the B. retrofracta genome
             using short Illumina and Roche reads from 1 paired-end and 3
             mate pair libraries. The distribution of 23-mers from the
             paired end library has indicated a low level of
             heterozygosity and the presence of detectable duplications
             and triplications. The genome size was estimated to be equal
             227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a
             hybrid approach that combines homology-based and de novo
             methods 27,048 protein-coding genes were predicted. Also
             repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes
             were annotated. Finally, genes of B. retrofracta and 6 other
             Brassicaceae species were used for phylogenetic tree
             reconstruction. In addition, we explored the histidine
             exonuclease APOLLO locus, related to apomixis in Boechera,
             and proposed model of its evolution through the series of
             duplications. An assembled genome of B. retrofracta will
             help in the challenging assembly of the highly heterozygous
             genomes of hybrid apomictic species.},
   Doi = {10.3390/genes9040185},
   Key = {fds333742}
}

@article{fds337382,
   Author = {Lee, C-R and Hsieh, J-W and Schranz, ME and Mitchell-Olds,
             T},
   Title = {The Functional Change and Deletion of FLC Homologs
             Contribute to the Evolution of Rapid Flowering in Boechera
             stricta.},
   Journal = {Frontiers in Plant Science},
   Volume = {9},
   Pages = {1078},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.3389/fpls.2018.01078},
   Abstract = {Differences in the timing of vegetative-to-reproductive
             phase transition have evolved independently and repeatedly
             in different plant species. Due to their specific biological
             functions and positions in pathways, some genes are
             important targets of repeated evolution - independent
             mutations on these genes caused the evolution of similar
             phenotypes in distantly related organisms. While many
             studies have investigated these genes, it remains unclear
             how gene duplications influence repeated phenotypic
             evolution. Here we characterized the genetic architecture
             underlying a novel rapid-flowering phenotype in Boechera
             stricta and investigated the candidate genes BsFLC1 and
             BsFLC2. The expression patterns of BsFLC1 suggested its
             function in flowering time suppression, and the deletion of
             BsFLC1 is associated with rapid flowering and loss of
             vernalization requirement. In contrast, BsFLC2 did not
             appear to be associated with flowering and had accumulated
             multiple amino acid substitutions in the relatively short
             evolutionary timeframe after gene duplication. These
             non-synonymous substitutions greatly changed the
             physicochemical properties of the original amino acids,
             concentrated non-randomly near a protein-interacting domain,
             and had greater substitution rate than synonymous changes.
             Here we suggested that, after recent gene duplication of the
             FLC gene, the evolution of rapid phenology was made possible
             by the change of BsFLC2 expression pattern or protein
             sequences and the deletion of BsFLC1.},
   Doi = {10.3389/fpls.2018.01078},
   Key = {fds337382}
}

@article{fds331573,
   Author = {Wang, B and Mitchell-Olds, T},
   Title = {Balancing selection and trans-specific polymorphisms.},
   Journal = {Genome Biology},
   Volume = {18},
   Number = {1},
   Pages = {231},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1186/s13059-017-1365-1},
   Abstract = {Balancing selection maintains variation for evolution. A
             recent study investigated the extent of balancing selection
             in two Brassicaceae species and highlighted its importance
             for adaptation.},
   Doi = {10.1186/s13059-017-1365-1},
   Key = {fds331573}
}

@article{fds330826,
   Author = {Lee, C-R and Wang, B and Mojica, JP and Mandáková, T and Prasad, KVSK and Luis Goicoechea and J and Perera, N and Hellsten, U and Hundley, HN and Johnson, J and Grimwood, J and Barry, K and Fairclough, S and Jenkins,
             JW and Yu, Y and Kudrna, D and Zhang, J and Talag, J and Golser, W and Ghattas, K and Schranz, ME and Wing, R and Lysak, MA and Schmutz, J and Rokhsar, DS and Mitchell-Olds, T},
   Title = {Publisher correction: Young inversion with multiple linked
             QTLs under selection in a hybrid zone.},
   Journal = {Nature Ecology and Evolution},
   Volume = {1},
   Number = {10},
   Pages = {1585},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1038/s41559-017-0310-8},
   Abstract = {In Fig. 5 of the version of this Article originally
             published, the final number on the x axes of each panel was
             incorrectly written as 1.5; it should have read 7.5. This
             has now been corrected in all versions of the
             Article.},
   Doi = {10.1038/s41559-017-0310-8},
   Key = {fds330826}
}

@article{fds331574,
   Author = {Lee, C-R and Wang, B and Mojica, JP and Mandáková, T and Prasad, KVSK and Goicoechea, JL and Perera, N and Hellsten, U and Hundley, HN and Johnson, J and Grimwood, J and Barry, K and Fairclough, S and Jenkins,
             JW and Yu, Y and Kudrna, D and Zhang, J and Talag, J and Golser, W and Ghattas, K and Schranz, ME and Wing, R and Lysak, MA and Schmutz, J and Rokhsar, DS and Mitchell-Olds, T},
   Title = {Erratum: Young inversion with multiple linked QTLs under
             selection in a hybrid zone},
   Journal = {Nature Ecology and Evolution},
   Volume = {1},
   Number = {6},
   Pages = {0166-0166},
   Publisher = {Springer Science and Business Media LLC},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1038/s41559-017-0166},
   Doi = {10.1038/s41559-017-0166},
   Key = {fds331574}
}

@article{fds326984,
   Author = {Lee, C-R and Wang, B and Mojica, JP and Mandáková, T and Prasad, KVSK and Goicoechea, JL and Perera, N and Hellsten, U and Hundley, HN and Johnson, J and Grimwood, J and Barry, K and Fairclough, S and Jenkins,
             JW and Yu, Y and Kudrna, D and Zhang, J and Talag, J and Golser, W and Ghattas, K and Schranz, ME and Wing, R and Lysak, MA and Schmutz, J and Rokhsar, DS and Mitchell-Olds, T},
   Title = {Young inversion with multiple linked QTLs under selection in
             a hybrid zone.},
   Journal = {Nature Ecology and Evolution},
   Volume = {1},
   Number = {5},
   Pages = {119},
   Year = {2017},
   Month = {April},
   url = {http://dx.doi.org/10.1038/s41559-017-0119},
   Abstract = {Fixed chromosomal inversions can reduce gene flow and
             promote speciation in two ways: by suppressing recombination
             and by carrying locally favoured alleles at multiple loci.
             However, it is unknown whether favoured mutations slowly
             accumulate on older inversions or if young inversions spread
             because they capture pre-existing adaptive quantitative
             trait loci (QTLs). By genetic mapping, chromosome painting
             and genome sequencing, we have identified a major inversion
             controlling ecologically important traits in Boechera
             stricta. The inversion arose since the last glaciation and
             subsequently reached local high frequency in a hybrid
             speciation zone. Furthermore, the inversion shows signs of
             positive directional selection. To test whether the
             inversion could have captured existing, linked QTLs, we
             crossed standard, collinear haplotypes from the hybrid zone
             and found multiple linked phenology QTLs within the
             inversion region. These findings provide the first direct
             evidence that linked, locally adapted QTLs may be captured
             by young inversions during incipient speciation.},
   Doi = {10.1038/s41559-017-0119},
   Key = {fds326984}
}

@article{fds327559,
   Author = {Keith, RA and Mitchell-Olds, T},
   Title = {Testing the optimal defense hypothesis in nature: Variation
             for glucosinolate profiles within plants.},
   Journal = {Plos One},
   Volume = {12},
   Number = {7},
   Pages = {e0180971},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0180971},
   Abstract = {Plants employ highly variable chemical defenses against a
             broad community of herbivores, which vary in their
             susceptibilities to specific compounds. Variation in
             chemical defenses within the plant has been found in many
             species; the ecological and evolutionary influences on this
             variation, however, are less well-understood. One central
             theory describing the allocation of defenses in the plant is
             the Optimal Defense Hypothesis (ODH), which predicts that
             defenses will be concentrated in tissues that are of high
             fitness value to the plant. Although the ODH has been
             repeatedly supported within vegetative tissues, few studies
             have compared vegetative and reproductive tissues, and the
             results have not been conclusive. We quantified variation in
             glucosinolate profile and tissue value between vegetative
             and reproductive tissues in Boechera stricta, a close
             relative of Arabidopsis. B. stricta manufactures
             glucosinolates, a set of defensive compounds that vary
             genetically and are straightforward to quantify. Genetic
             diversity in glucosinolate profile has been previously
             demonstrated to be important to both herbivory and fitness
             in B. stricta; however, the importance of glucosinolate
             variation among tissues has not. Here, we investigate
             whether allocation of glucosinolates within the plant is
             consistent with the ODH. We used both clipping experiments
             on endogenous plants and ambient herbivory in a large-scale
             transplant experiment at three sites to quantify fitness
             effects of loss of rosette leaves, cauline leaves, and
             flowers and fruits. We measured glucosinolate concentration
             in leaves and fruits in the transplant experiment, and asked
             whether more valuable tissues were more defended. We also
             investigated within-plant variation in other aspects of the
             glucosinolate profile. Our results indicated that damage to
             fruits had a significantly larger effect on overall fitness
             than damage to leaves, and that fruits had much higher
             concentrations of glucosinolates, supporting the ODH. This
             is, to the best of our knowledge, the first study to
             explicitly compare both tissue value and chemical defense
             concentrations between vegetative and reproductive tissues
             under natural conditions.},
   Doi = {10.1371/journal.pone.0180971},
   Key = {fds327559}
}

@article{fds318042,
   Author = {Wagner, MR and Lundberg, DS and Del Rio and TG and Tringe, SG and Dangl,
             JL and Mitchell-Olds, T},
   Title = {Host genotype and age shape the leaf and root microbiomes of
             a wild perennial plant.},
   Journal = {Nature Communications},
   Volume = {7},
   Pages = {12151},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1038/ncomms12151},
   Abstract = {Bacteria living on and in leaves and roots influence many
             aspects of plant health, so the extent of a plant's genetic
             control over its microbiota is of great interest to crop
             breeders and evolutionary biologists. Laboratory-based
             studies, because they poorly simulate true environmental
             heterogeneity, may misestimate or totally miss the influence
             of certain host genes on the microbiome. Here we report a
             large-scale field experiment to disentangle the effects of
             genotype, environment, age and year of harvest on bacterial
             communities associated with leaves and roots of Boechera
             stricta (Brassicaceae), a perennial wild mustard. Host
             genetic control of the microbiome is evident in leaves but
             not roots, and varies substantially among sites. Microbiome
             composition also shifts as plants age. Furthermore, a large
             proportion of leaf bacterial groups are shared with roots,
             suggesting inoculation from soil. Our results demonstrate
             how genotype-by-environment interactions contribute to the
             complexity of microbiome assembly in natural
             environments.},
   Doi = {10.1038/ncomms12151},
   Key = {fds318042}
}

@article{fds326985,
   Author = {Yao, N and Lee, C-R and Semagn, K and Sow, M and Nwilene, F and Kolade, O and Bocco, R and Oyetunji, O and Mitchell-Olds, T and Ndjiondjop,
             M-N},
   Title = {QTL Mapping in Three Rice Populations Uncovers Major Genomic
             Regions Associated with African Rice Gall Midge
             Resistance.},
   Journal = {Plos One},
   Volume = {11},
   Number = {8},
   Pages = {e0160749},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1371/journal.pone.0160749},
   Abstract = {African rice gall midge (AfRGM) is one of the most
             destructive pests of irrigated and lowland African
             ecologies. This study aimed to identify the quantitative
             trait loci (QTL) associated with AfRGM pest incidence and
             resistance in three independent bi-parental rice populations
             (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to
             conduct meta QTL (mQTL) analysis to explore whether any
             genomic regions are conserved across different genetic
             backgrounds. Composite interval mapping (CIM) conducted on
             the three populations independently uncovered a total of 28
             QTLs associated with pest incidence (12) and pest severity
             (16). The number of QTLs per population associated with
             AfRGM resistance varied from three in the ITA306xBW348-1
             population to eight in the ITA306xTOG7106 population. Each
             QTL individually explained 1.3 to 34.1% of the phenotypic
             variance. The major genomic region for AfRGM resistance had
             a LOD score and R2 of 60.0 and 34.1% respectively, and
             mapped at 111 cM on chromosome 4 (qAfrGM4) in the
             ITA306xTOS14519 population. The meta-analysis reduced the
             number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to
             24.5% of phenotypic variance, and narrowed the confidence
             intervals by 2.2 cM. There was only one minor effect mQTL on
             chromosome 1 that was common in the TOS14519 and TOG7106
             genetic backgrounds; all other mQTLs were background
             specific. We are currently fine-mapping and validating the
             major effect genomic region on chromosome 4 (qAfRGM4). This
             is the first report in mapping the genomic regions
             associated with the AfRGM resistance, and will be highly
             useful for rice breeders.},
   Doi = {10.1371/journal.pone.0160749},
   Key = {fds326985}
}

@article{fds229115,
   Author = {Manzaneda, AJ and Rey, PJ and Anderson, JT and Raskin, E and Weiss-Lehman, C and Mitchell-Olds, T},
   Title = {Natural variation, differentiation, and genetic trade-offs
             of ecophysiological traits in response to water limitation
             in Brachypodium distachyon and its descendent allotetraploid
             B. hybridum (Poaceae).},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {69},
   Number = {10},
   Pages = {2689-2704},
   Year = {2015},
   Month = {October},
   ISSN = {0014-3820},
   url = {http://dx.doi.org/10.1111/evo.12776},
   Abstract = {Differences in tolerance to water stress may underlie
             ecological divergence of closely related ploidy lineages.
             However, the mechanistic basis of physiological variation
             governing ecogeographical cytotype segregation is not well
             understood. Here, using Brachypodium distachyon and its
             derived allotetraploid B. hybridum as model, we test the
             hypothesis that, for heteroploid annuals, ecological
             divergence of polyploids in drier environments is based on
             trait differentiation enabling drought escape. We
             demonstrate that under water limitation allotetraploids
             maintain higher photosynthesis and stomatal conductance and
             show earlier flowering than diploids, concordant with a
             drought-escape strategy to cope with water stress. Increased
             heterozygosity and greater genetic variability and
             plasticity of polyploids could confer a superior adaptive
             capability. Consistent with these predictions, we document
             (1) greater standing within-population genetic variation in
             water-use efficiency (WUE) and flowering time in
             allotetraploids, and (2) the existence of (nonlinear)
             environmental clines in physiology across allotetraploid
             populations. Increased gas exchange and diminished WUE
             occurred at the driest end of the gradient, consistent with
             a drought-escape strategy. Finally, we found that
             allotetraploids showed weaker genetic correlations than
             diploids congruous with the expectation of relaxed
             pleiotropic constraints in polyploids. Our results suggest
             evolutionary divergence of ecophysiological traits in each
             ploidy lineage.},
   Doi = {10.1111/evo.12776},
   Key = {fds229115}
}

@article{fds229116,
   Author = {Anderson, JT and Perera, N and Chowdhury, B and Mitchell-Olds,
             T},
   Title = {Microgeographic Patterns of Genetic Divergence and
             Adaptation across Environmental Gradients in Boechera
             stricta (Brassicaceae).},
   Journal = {The American Naturalist},
   Volume = {186 Suppl 1},
   Number = {S1},
   Pages = {S60-S73},
   Year = {2015},
   Month = {October},
   ISSN = {0003-0147},
   url = {http://dx.doi.org/10.1086/682404},
   Abstract = {Abiotic and biotic conditions often vary continuously across
             the landscape, imposing divergent selection on local
             populations. We used a provenance trial approach to examine
             microgeographic variation in local adaptation in Boechera
             stricta (Brassicaceae), a perennial forb native to the Rocky
             Mountains. In montane ecosystems, environmental conditions
             change considerably over short spatial scales, such that
             neighboring populations can be subject to different
             selective pressures. Using accessions from southern
             (Colorado) and northern (Idaho) populations, we
             characterized spatial variation in genetic similarity via
             microsatellite markers. We then transplanted genotypes from
             multiple local populations into common gardens in both
             regions. Continuous variation in local adaptation emerged
             for several components of fitness. In Idaho, genotypes from
             warmer environments (low-elevation or south-facing sites)
             were poorly adapted to the north-facing garden. In high- and
             low-elevation Colorado gardens, susceptibility to insect
             herbivory increased with source elevation. In the
             high-elevation Colorado garden, germination success peaked
             for genotypes that evolved at elevations similar to that of
             the garden and decreased for genotypes from higher and lower
             elevations. We also found evidence for local maladaptation
             in survival and fecundity components of fitness in the
             low-elevation Colorado garden. This approach is a first step
             in predicting how global change could affect evolutionary
             dynamics.},
   Doi = {10.1086/682404},
   Key = {fds229116}
}

@article{fds303161,
   Author = {Wagner, MR and Lundberg, DS and del Rio, TG and Tringe, SG and Dangl,
             JL and Mitchell-Olds, T},
   Title = {Age, genotype, and environment shape the root and leaf
             microbiomes of a wild perennial plant},
   Publisher = {Nature Communications},
   Year = {2015},
   Month = {September},
   Key = {fds303161}
}

@article{fds229117,
   Author = {Olson-Manning, CF and Strock, CF and Mitchell-Olds,
             T},
   Title = {Flux Control in a Defense Pathway in Arabidopsis thaliana Is
             Robust to Environmental Perturbations and Controls Variation
             in Adaptive Traits.},
   Journal = {G3 (Bethesda, Md.)},
   Volume = {5},
   Number = {11},
   Pages = {2421-2427},
   Year = {2015},
   Month = {September},
   url = {http://dx.doi.org/10.1534/g3.115.021816},
   Abstract = {The connections leading from genotype to fitness are not
             well understood, yet they are crucial for a diverse set of
             disciplines. Uncovering the general properties of
             biochemical pathways that influence ecologically important
             traits is an effective way to understand these connections.
             Enzyme flux control (or, control over pathway output) is one
             such pathway property. The flux-controlling enzyme in the
             antiherbivory aliphatic glucosinolate pathway of Arabidopsis
             thaliana has majority flux control under benign greenhouse
             conditions and has evidence of nonneutral evolution.
             However, it is unknown how patterns of flux control may
             change in different environments, or if insect herbivores
             respond to differences in pathway flux. We test this, first
             through genetic manipulation of the loci that code for the
             aliphatic glucosinolate pathway enzymes under a variety of
             environments (reduced water, reduced soil nutrients, leaf
             wounding and methyl jasmonate treatments), and find that
             flux control is consistently in the first enzyme of the
             pathway. We also find that a generalist herbivore,
             Trichoplusia ni, modifies its feeding behavior depending on
             the flux through the glucosinolate pathway. The influence
             over herbivore behavior combined with the consistency of
             flux control suggests that genes controlling flux might be
             repeatedly targeted by natural selection in diverse
             environments and species.},
   Doi = {10.1534/g3.115.021816},
   Key = {fds229117}
}

@article{fds229118,
   Author = {Dixit, S and Grondin, A and Lee, C-R and Henry, A and Olds, T-M and Kumar,
             A},
   Title = {Understanding rice adaptation to varying agro-ecosystems:
             trait interactions and quantitative trait
             loci.},
   Journal = {Bmc Genetics},
   Volume = {16},
   Number = {1},
   Pages = {86},
   Year = {2015},
   Month = {August},
   url = {http://dx.doi.org/10.1186/s12863-015-0249-1},
   Abstract = {Interaction and genetic control for traits influencing the
             adaptation of the rice crop to varying environments was
             studied in a mapping population derived from parents
             (Moroberekan and Swarna) contrasting for drought tolerance,
             yield potential, lodging resistance, and adaptation to dry
             direct seeding. A BC2F3-derived mapping population for
             traits related to these four trait groups was phenotyped to
             understand the interactions among traits and to map and
             align QTLs using composite interval mapping (CIM). The study
             also aimed to identify QTLs for the four trait groups as
             composite traits using multivariate least square interval
             mapping (MLSIM) to further understand the genetic control of
             these traits.Significant correlations between drought- and
             yield-related traits at seedling and reproductive stages
             respectively with traits for adaptation to dry direct-seeded
             conditions were observed. CIM and MLSIM methods were applied
             to identify QTLs for univariate and composite traits. QTL
             clusters showing alignment of QTLs for several traits within
             and across trait groups were detected at chromosomes 3, 4,
             and 7 through CIM. The largest number of QTLs related to
             traits belonging to all four trait groups were identified on
             chromosome 3 close to the qDTY 3.2 locus. These included
             QTLs for traits such as bleeding rate, shoot biomass, stem
             strength, and spikelet fertility. Multivariate QTLs were
             identified at loci supported by univariate QTLs such as on
             chromosomes 3 and 4 as well as at distinctly different loci
             on chromosome 8 which were undetected through CIM.Rice
             requires better adaptation across a wide range of
             environments and cultivation practices to adjust to climate
             change. Understanding the genetics and trade-offs related to
             each of these environments and cultivation practices thus
             becomes highly important to develop varieties with stability
             of yield across them. This study provides a wider picture of
             the genetics and physiology of adaptation of rice to wide
             range of environments. With a complete understanding of the
             processes and relationships between traits and trait groups,
             marker-assisted breeding can be used more efficiently to
             develop plant types that can combine all or most of the
             beneficial traits and show high stability across
             environments, ecosystems, and cultivation
             practices.},
   Doi = {10.1186/s12863-015-0249-1},
   Key = {fds229118}
}

@article{fds229124,
   Author = {Wagner, MR and Lundberg, DS and Coleman-Derr, D and Tringe, SG and Dangl, JL and Mitchell-Olds, T},
   Title = {Corrigendum to Wagner et al.: Natural soil microbes alter
             flowering phenology and the intensity of selection on
             flowering time in a wild Arabidopsis relative [Ecology
             Letters 18(2), (2014) 218-220]},
   Journal = {Ecology Letters},
   Volume = {18},
   Number = {2},
   Pages = {218-220},
   Publisher = {WILEY},
   Year = {2015},
   Month = {January},
   ISSN = {1461-023X},
   url = {http://dx.doi.org/10.1111/ele.12400},
   Doi = {10.1111/ele.12400},
   Key = {fds229124}
}

@article{fds229128,
   Author = {Heo, J-Y and Feng, D and Niu, X and Mitchell-Olds, T and Van Tienderen,
             PH and Tomes, D and Schranz, ME},
   Title = {Identification of quantitative trait loci and a candidate
             locus for freezing tolerance in controlled and outdoor
             environments in the overwintering crucifer Boechera
             stricta.},
   Journal = {Plant, Cell & Environment},
   Volume = {37},
   Number = {11},
   Pages = {2459-2469},
   Year = {2014},
   Month = {November},
   ISSN = {0140-7791},
   url = {http://dx.doi.org/10.1111/pce.12365},
   Abstract = {Development of chilling and freezing tolerance is complex
             and can be affected by photoperiod, temperature and
             photosynthetic performance; however, there has been limited
             research on the interaction of these three factors. We
             evaluated 108 recombinant inbred lines of Boechera stricta,
             derived from a cross between lines originating from Montana
             and Colorado, under controlled long day (LD), short-day (SD)
             and in an outdoor environment (OE). We measured maximum
             quantum yield of photosystem II, lethal temperature for 50%
             survival and electrolyte leakage of leaves. Our results
             revealed significant variation for chilling and freezing
             tolerance and photosynthetic performance in different
             environments. Using both single- and multi-trait analyses,
             three main-effect quantitative trait loci (QTL) were
             identified. QTL on linkage group (LG)3 were SD specific,
             whereas QTL on LG4 were found under both LD and SD. Under
             all conditions, QTL on LG7 were identified, but were
             particularly predictive for the outdoor experiment. The
             co-localization of photosynthetic performance and freezing
             tolerance effects supports these traits being co-regulated.
             Finally, the major QTL on LG7 is syntenic to the Arabidopsis
             C-repeat binding factor locus, known regulators of chilling
             and freezing responses in Arabidopsis thaliana and other
             species.},
   Doi = {10.1111/pce.12365},
   Key = {fds229128}
}

@article{fds229125,
   Author = {Lee, C-R and Anderson, JT and Mitchell-Olds, T},
   Title = {Unifying genetic canalization, genetic constraint, and
             genotype-by-environment interaction: QTL by genomic
             background by environment interaction of flowering time in
             Boechera stricta.},
   Journal = {Plos Genetics},
   Volume = {10},
   Number = {10},
   Pages = {e1004727},
   Year = {2014},
   Month = {October},
   ISSN = {1553-7390},
   url = {http://dx.doi.org/10.1371/journal.pgen.1004727},
   Abstract = {Natural populations exhibit substantial variation in
             quantitative traits. A quantitative trait is typically
             defined by its mean and variance, and to date most genetic
             mapping studies focus on loci altering trait means but not
             (co)variances. For single traits, the control of trait
             variance across genetic backgrounds is referred to as
             genetic canalization. With multiple traits, the genetic
             covariance among different traits in the same environment
             indicates the magnitude of potential genetic constraint,
             while genotype-by-environment interaction (GxE) concerns the
             same trait across different environments. While some have
             suggested that these three attributes of quantitative traits
             are different views of similar concepts, it is not yet
             clear, however, whether they have the same underlying
             genetic mechanism. Here, we detect quantitative trait loci
             (QTL) influencing the (co)variance of phenological traits in
             six distinct environments in Boechera stricta, a close
             relative of Arabidopsis. We identified nFT as the QTL
             altering the magnitude of phenological trait canalization,
             genetic constraint, and GxE. Both the magnitude and
             direction of nFT's canalization effects depend on the
             environment, and to our knowledge, this reversibility of
             canalization across environments has not been reported
             previously. nFT's effects on trait covariance structure
             (genetic constraint and GxE) likely result from the variable
             and reversible canalization effects across different traits
             and environments, which can be explained by the interaction
             among nFT, genomic backgrounds, and environmental stimuli.
             This view is supported by experiments demonstrating
             significant nFT by genomic background epistatic interactions
             affecting phenological traits and expression of the
             candidate gene, FT. In contrast to the well-known
             canalization gene Hsp90, the case of nFT may exemplify an
             alternative mechanism: Our results suggest that (at least in
             traits with major signal integrators such as flowering time)
             genetic canalization, genetic constraint, and GxE may have
             related genetic mechanisms resulting from interactions among
             major QTL, genomic backgrounds, and environments.},
   Doi = {10.1371/journal.pgen.1004727},
   Key = {fds229125}
}

@article{fds229126,
   Author = {Leamy, LJ and Lee, C-R and Cousins, V and Mujacic, I and Manzaneda, AJ and Prasad, K and Mitchell-Olds, T and Song, B-H},
   Title = {Large-scale adaptive divergence in Boechera fecunda, an
             endangered wild relative of Arabidopsis.},
   Journal = {Ecology and Evolution},
   Volume = {4},
   Number = {16},
   Pages = {3175-3186},
   Year = {2014},
   Month = {August},
   url = {http://dx.doi.org/10.1002/ece3.1148},
   Abstract = {Many biological species are threatened with extinction
             because of a number of factors such as climate change and
             habitat loss, and their preservation depends on an accurate
             understanding of the extent of their genetic variability
             within and among populations. In this study, we assessed the
             genetic divergence of five quantitative traits in 10
             populations of an endangered cruciferous species, Boechera
             fecunda, found in only several populations in each of two
             geographic regions (WEST and EAST) in southwestern Montana.
             We analyzed variation in quantitative traits, neutral
             molecular markers, and environmental factors and provided
             evidence that despite the restricted geographical
             distribution of this species, it exhibits a high level of
             genetic variation and regional adaptation. Conservation
             efforts therefore should be directed to the preservation of
             populations in each of these two regions without attempting
             transplantation between regions. Heritabilities and genetic
             coefficients of variation estimated from nested ANOVAs were
             generally high for leaf and rosette traits, although lower
             (and not significantly different from 0) for water-use
             efficiency. Measures of quantitative genetic
             differentiation, Q ST, were calculated for each trait from
             each pair of populations. For three of the five traits,
             these values were significantly higher between regions
             compared with those within regions (after adjustment for
             neutral genetic variation, F ST). This suggested that
             natural selection has played an important role in producing
             regional divergence in this species. Our analysis also
             revealed that the B. fecunda populations appear to be
             locally adapted due, at least in part, to differences in
             environmental conditions in the EAST and WEST
             regions.},
   Doi = {10.1002/ece3.1148},
   Key = {fds229126}
}

@article{fds229127,
   Author = {Gordon, SP and Priest, H and Des Marais and DL and Schackwitz, W and Figueroa, M and Martin, J and Bragg, JN and Tyler, L and Lee, C-R and Bryant, D and Wang, W and Messing, J and Manzaneda, AJ and Barry, K and Garvin, DF and Budak, H and Tuna, M and Mitchell-Olds, T and Pfender,
             WF and Juenger, TE and Mockler, TC and Vogel, JP},
   Title = {Genome diversity in Brachypodium distachyon: deep sequencing
             of highly diverse inbred lines.},
   Journal = {The Plant Journal : for Cell and Molecular
             Biology},
   Volume = {79},
   Number = {3},
   Pages = {361-374},
   Year = {2014},
   Month = {August},
   ISSN = {0960-7412},
   url = {http://dx.doi.org/10.1111/tpj.12569},
   Abstract = {Brachypodium distachyon is small annual grass that has been
             adopted as a model for the grasses. Its small genome,
             high-quality reference genome, large germplasm collection,
             and selfing nature make it an excellent subject for studies
             of natural variation. We sequenced six divergent lines to
             identify a comprehensive set of polymorphisms and analyze
             their distribution and concordance with gene expression.
             Multiple methods and controls were utilized to identify
             polymorphisms and validate their quality. mRNA-Seq
             experiments under control and simulated drought-stress
             conditions, identified 300 genes with a genotype-dependent
             treatment response. We showed that large-scale sequence
             variants had extremely high concordance with altered
             expression of hundreds of genes, including many with
             genotype-dependent treatment responses. We generated a deep
             mRNA-Seq dataset for the most divergent line and created a
             de novo transcriptome assembly. This led to the discovery of
             >2400 previously unannotated transcripts and hundreds of
             genes not present in the reference genome. We built a public
             database for visualization and investigation of sequence
             variants among these widely used inbred lines.},
   Doi = {10.1111/tpj.12569},
   Key = {fds229127}
}

@article{fds229129,
   Author = {Wagner, MR and Lundberg, DS and Coleman-Derr, D and Tringe, SG and Dangl, JL and Mitchell-Olds, T},
   Title = {Natural soil microbes alter flowering phenology and the
             intensity of selection on flowering time in a wild
             Arabidopsis relative.},
   Journal = {Ecology Letters},
   Volume = {17},
   Number = {6},
   Pages = {717-726},
   Year = {2014},
   Month = {June},
   ISSN = {1461-023X},
   url = {http://dx.doi.org/10.1111/ele.12276},
   Abstract = {Plant phenology is known to depend on many different
             environmental variables, but soil microbial communities have
             rarely been acknowledged as possible drivers of flowering
             time. Here, we tested separately the effects of four
             naturally occurring soil microbiomes and their constituent
             soil chemistries on flowering phenology and reproductive
             fitness of Boechera stricta, a wild relative of Arabidopsis.
             Flowering time was sensitive to both microbes and the
             abiotic properties of different soils; varying soil
             microbiota also altered patterns of selection on flowering
             time. Thus, soil microbes potentially contribute to
             phenotypic plasticity of flowering time and to differential
             selection observed between habitats. We also describe a
             method to dissect the microbiome into single axes of
             variation that can help identify candidate organisms whose
             abundance in soil correlates with flowering time. This
             approach is broadly applicable to search for microbial
             community members that alter biological characteristics of
             interest.},
   Doi = {10.1111/ele.12276},
   Key = {fds229129}
}

@article{fds229130,
   Author = {Anderson, JT and Lee, C-R and Mitchell-Olds, T},
   Title = {Strong selection genome-wide enhances fitness trade-offs
             across environments and episodes of selection.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {68},
   Number = {1},
   Pages = {16-31},
   Year = {2014},
   Month = {January},
   ISSN = {0014-3820},
   url = {http://dx.doi.org/10.1111/evo.12259},
   Abstract = {Fitness trade-offs across episodes of selection and
             environments influence life-history evolution and adaptive
             population divergence. Documenting these trade-offs remains
             challenging as selection can vary in magnitude and direction
             through time and space. Here, we evaluate fitness trade-offs
             at the levels of the whole organism and the quantitative
             trait locus (QTL) in a multiyear field study of Boechera
             stricta (Brassicaceae), a genetically tractable mustard
             native to the Rocky Mountains. Reciprocal local adaptation
             was pronounced for viability, but not for reproductive
             components of fitness. Instead, local genomes had a
             fecundity advantage only in the high latitude garden. By
             estimating realized selection coefficients from
             individual-level data on viability and reproductive success
             and permuting the data to infer significance, we examined
             the genetic basis of fitness trade-offs. This analytical
             approach (Conditional Neutrality-Antagonistic Pleiotropy,
             CNAP) identified genetic trade-offs at a flowering phenology
             QTL (costs of adaptation) and revealed genetic trade-offs
             across fitness components (costs of reproduction). These
             patterns would not have emerged from traditional ANOVA-based
             QTL mapping. Our analytical framework can be applied to
             other systems to investigate fitness trade-offs. This task
             is becoming increasingly important as climate change may
             alter fitness landscapes, potentially disrupting fitness
             trade-offs that took many generations to
             evolve.},
   Doi = {10.1111/evo.12259},
   Key = {fds229130}
}

@article{fds229132,
   Author = {Anderson, JT and Wagner, MR and Rushworth, CA and Prasad, KVSK and Mitchell-Olds, T},
   Title = {The evolution of quantitative traits in complex
             environments.},
   Journal = {Heredity},
   Volume = {112},
   Number = {1},
   Pages = {4-12},
   Year = {2014},
   Month = {January},
   ISSN = {0018-067X},
   url = {http://dx.doi.org/10.1038/hdy.2013.33},
   Abstract = {Species inhabit complex environments and respond to
             selection imposed by numerous abiotic and biotic conditions
             that vary in both space and time. Environmental
             heterogeneity strongly influences trait evolution and
             patterns of adaptive population differentiation. For
             example, heterogeneity can favor local adaptation, or can
             promote the evolution of plastic genotypes that alter their
             phenotypes based on the conditions they encounter. Different
             abiotic and biotic agents of selection can act
             synergistically to either accelerate or constrain trait
             evolution. The environmental context has profound effects on
             quantitative genetic parameters. For instance,
             heritabilities measured in controlled conditions often
             exceed those measured in the field; thus, laboratory
             experiments could overestimate the potential for a
             population to respond to selection. Nevertheless, most
             studies of the genetic basis of ecologically relevant traits
             are conducted in simplified laboratory environments, which
             do not reflect the complexity of nature. Here, we advocate
             for manipulative field experiments in the native ranges of
             plant species that differ in mating system, life-history
             strategy and growth form. Field studies are vital to
             evaluate the roles of disparate agents of selection, to
             elucidate the targets of selection and to develop a nuanced
             perspective on the evolution of quantitative traits.
             Quantitative genetics field studies will also shed light on
             the potential for natural populations to adapt to novel
             climates in highly fragmented landscapes. Drawing from our
             experience with the ecological model system Boechera
             (Brassicaceae), we discuss advancements possible through
             dedicated field studies, highlight future research
             directions and examine the challenges associated with field
             studies.},
   Doi = {10.1038/hdy.2013.33},
   Key = {fds229132}
}

@article{fds229131,
   Author = {Keith, R and Mitchell-Olds, T},
   Title = {Genetic variation for resistance to herbivores and plant
             pathogens: Hypotheses, mechanisms and evolutionary
             implications},
   Journal = {Plant Pathology},
   Volume = {62},
   Number = {S1},
   Pages = {122-132},
   Year = {2013},
   Month = {December},
   ISSN = {0032-0862},
   url = {http://dx.doi.org/10.1111/ppa.12134},
   Abstract = {The interactions between plants and enemies employ a variety
             of mechanisms, which in turn affect the long-term
             evolutionary histories of the interacting species. Different
             patterns of interactions determine not only the selective
             forces acting on individual genes, but also the flexibility
             and rapidity of evolution in response to new threats. New
             genomic techniques allowing large-scale comparisons within
             and between species demonstrate that defence genes are
             highly variable and experience very different selective
             patterns even in recently diverged species. Similar and even
             shared pathways for defence against diverse taxa of enemies
             reveal the variability and flexibility of plant defence. ©
             2013 British Society for Plant Pathology.},
   Doi = {10.1111/ppa.12134},
   Key = {fds229131}
}

@article{fds229133,
   Author = {Lovell, JT and Aliyu, OM and Mau, M and Schranz, ME and Koch, M and Kiefer,
             C and Song, B-H and Mitchell-Olds, T and Sharbel,
             TF},
   Title = {On the origin and evolution of apomixis in
             Boechera.},
   Journal = {Plant Reproduction},
   Volume = {26},
   Number = {4},
   Pages = {309-315},
   Year = {2013},
   Month = {December},
   ISSN = {2194-7953},
   url = {http://dx.doi.org/10.1007/s00497-013-0218-7},
   Abstract = {The genetic mechanisms causing seed development by
             gametophytic apomixis in plants are predominantly unknown.
             As apomixis is consistently associated with hybridity and
             polyploidy, these confounding factors may either (a) be the
             underlying mechanism for the expression of apomixis, or (b)
             obscure the genetic factors which cause apomixis. To
             distinguish between these hypotheses, we analyzed the
             population genetic patterns of diploid and triploid
             apomictic lineages and their sexual progenitors in the genus
             Boechera (Brassicaceae). We find that while triploid
             apomixis is associated with hybridization, the majority of
             diploid apomictic lineages are likely the product of
             intra-specific crosses. We then show that these diploid
             apomicts are more likely to sire triploid apomictic lineages
             than conspecific sexuals. Combined with flow cytometric seed
             screen phenotyping for male and female components of
             apomixis, our analyses demonstrate that hybridization is an
             indirect correlate of apomixis in Boechera.},
   Doi = {10.1007/s00497-013-0218-7},
   Key = {fds229133}
}

@article{fds229134,
   Author = {Mitchell-Olds, T},
   Title = {Selection on QTL and complex traits in complex
             environments.},
   Journal = {Molecular Ecology},
   Volume = {22},
   Number = {13},
   Pages = {3427-3429},
   Year = {2013},
   Month = {July},
   ISSN = {0962-1083},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000320942000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Abstract = {Understanding genetic variation for complex traits in
             heterogeneous environments is a fundamental problem in
             biology. In this issue of Molecular Ecology, Fournier-Level
             et al. (2013) analyse quantitative trait loci
             (QTL)influencing ecologically important phenotypes in
             mapping populations of Arabidopsis thaliana grown in four
             habitats across its native European range. They used causal
             modelling to quantify the selective consequences of life
             history and morphological traits and QTL on components of
             fitness. They found phenology QTL colocalizing with known
             flowering time genes as well as novel loci. Most QTL
             influenced fitness via life history and size traits, rather
             than QTL having direct effects on fitness.Comparison of
             phenotypes among environments found no evidence for genetic
             trade-offs for phenology or growth traits, but genetic
             trade-offs for fitness resulted because flowering time had
             opposite fitness effects in different environments. These
             changes in QTL effects and selective consequences may
             maintain genetic variation among populations.},
   Doi = {10.1111/mec.12345},
   Key = {fds229134}
}

@article{fds229135,
   Author = {Topp, CN and Iyer-Pascuzzi, AS and Anderson, JT and Lee, C-R and Zurek,
             PR and Symonova, O and Zheng, Y and Bucksch, A and Mileyko, Y and Galkovskyi, T and Moore, BT and Harer, J and Edelsbrunner, H and Mitchell-Olds, T and Weitz, JS and Benfey, PN},
   Title = {3D phenotyping and quantitative trait locus mapping identify
             core regions of the rice genome controlling root
             architecture.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {110},
   Number = {18},
   Pages = {E1695-E1704},
   Year = {2013},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23580618},
   Abstract = {Identification of genes that control root system
             architecture in crop plants requires innovations that enable
             high-throughput and accurate measurements of root system
             architecture through time. We demonstrate the ability of a
             semiautomated 3D in vivo imaging and digital phenotyping
             pipeline to interrogate the quantitative genetic basis of
             root system growth in a rice biparental mapping population,
             Bala × Azucena. We phenotyped >1,400 3D root models and
             >57,000 2D images for a suite of 25 traits that quantified
             the distribution, shape, extent of exploration, and the
             intrinsic size of root networks at days 12, 14, and 16 of
             growth in a gellan gum medium. From these data we identified
             89 quantitative trait loci, some of which correspond to
             those found previously in soil-grown plants, and provide
             evidence for genetic tradeoffs in root growth allocations,
             such as between the extent and thoroughness of exploration.
             We also developed a multivariate method for generating and
             mapping central root architecture phenotypes and used it to
             identify five major quantitative trait loci (r(2) = 24-37%),
             two of which were not identified by our univariate analysis.
             Our imaging and analytical platform provides a means to
             identify genes with high potential for improving root traits
             and agronomic qualities of crops.},
   Doi = {10.1073/pnas.1304354110},
   Key = {fds229135}
}

@article{fds285171,
   Author = {Lee, C-R and Mitchell-Olds, T},
   Title = {Complex trait divergence contributes to environmental niche
             differentiation in ecological speciation of Boechera
             stricta.},
   Journal = {Molecular Ecology},
   Volume = {22},
   Number = {8},
   Pages = {2204-2217},
   Year = {2013},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23432437},
   Abstract = {Ecological factors may contribute to reproductive isolation
             if differential local adaptation causes immigrant or hybrid
             fitness reduction. Because local adaptation results from the
             interaction between natural selection and adaptive traits,
             it is crucial to investigate both to understand ecological
             speciation. Previously, we used niche modelling to identify
             local water availability as an environmental correlate of
             incipient ecological speciation between two subspecies in
             Boechera stricta, a close relative of Arabidopsis. Here, we
             performed several large-scale glasshouse experiments to
             investigate the divergence of various physiological,
             phenological and morphological traits. Although we found no
             significant difference in physiological traits, the Western
             subspecies has significantly faster growth rate, larger leaf
             area, less succulent leaves, delayed reproductive time and
             longer flowering duration. These trait differences are
             concordant with previous results that habitats of the
             Western genotypes have more consistent water availability,
             while Eastern genotypes inhabit locations with more
             ephemeral water supplies. In addition, by comparing
             univariate and multivariate divergence of complex traits
             (Q(ST)) to the genomewide distribution of SNP FST , we
             conclude that the aspects of phenology and morphology (but
             not physiology) are under divergent selection. In addition,
             we also identified several highly diverged traits without
             obvious water-related functions.},
   Doi = {10.1111/mec.12250},
   Key = {fds285171}
}

@article{fds229181,
   Author = {Anderson, JT and Lee, C-R and Rushworth, CA and Colautti, RI and Mitchell-Olds, T},
   Title = {Genetic trade-offs and conditional neutrality contribute to
             local adaptation.},
   Journal = {Molecular Ecology},
   Volume = {22},
   Number = {3},
   Pages = {699-708},
   Year = {2013},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22420446},
   Abstract = {Divergent natural selection promotes local adaptation and
             can lead to reproductive isolation of populations in
             contrasting environments; however, the genetic basis of
             local adaptation remains largely unresolved in natural
             populations. Local adaptation might result from antagonistic
             pleiotropy, where alternate alleles are favoured in distinct
             habitats, and polymorphism is maintained by selection.
             Alternatively, under conditional neutrality some alleles may
             be favoured in one environment but neutral at other
             locations. Antagonistic pleiotropy maintains genetic
             variation across the landscape; however, there is a
             systematic bias against discovery of antagonistic pleiotropy
             because the fitness benefits of local alleles need to be
             significant in at least two environments. Here, we develop a
             generally applicable method to investigate polygenic local
             adaptation and identify loci that are the targets of
             selection. This approach evaluates allele frequency changes
             after selection at loci across the genome to distinguish
             antagonistic pleiotropy from conditional neutrality and
             deleterious variation. We investigate local adaptation at
             the qualitative trait loci (QTL) level in field experiments,
             in which we expose 177 F(6) recombinant inbred lines and
             parental lines of Boechera stricta (Brassicaceae) to their
             parental environments over two seasons. We demonstrate
             polygenic selection for native alleles in both environments,
             with 2.8% of the genome exhibiting antagonistic pleiotropy
             and 8% displaying conditional neutrality. Our study strongly
             supports antagonistic pleiotropy at one large-effect
             flowering phenology QTL (nFT): native homozygotes had
             significantly greater probabilities of flowering than
             foreign homozygotes in both parental environments. Such
             large-scale field studies are essential to elucidate the
             genetic basis of adaptation in natural populations.},
   Doi = {10.1111/j.1365-294X.2012.05522.x},
   Key = {fds229181}
}

@article{fds229146,
   Author = {Olson-Manning, CF and Lee, C-R and Rausher, MD and Mitchell-Olds,
             T},
   Title = {Evolution of flux control in the glucosinolate pathway in
             Arabidopsis thaliana.},
   Journal = {Molecular Biology and Evolution},
   Volume = {30},
   Number = {1},
   Pages = {14-23},
   Year = {2013},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22923463},
   Abstract = {Network characteristics of biochemical pathways are believed
             to influence the rate of evolutionary change in constituent
             enzymes. One characteristic that may affect rate
             heterogeneity is control of the amount of product produced
             by a biochemical pathway or flux control. In particular,
             theoretical analyses suggest that adaptive substitutions
             should be concentrated in the enzyme(s) that exert the
             greatest control over flux. Although a handful of studies
             have found a correlation between position in a pathway and
             evolutionary rate, these investigations have not examined
             the relationship between evolutionary rate and flux control.
             Given that genes with greater control will experience
             stronger selection and that the probability of fixation is
             proportional to the selective advantage, we ask the
             following: 1) do upstream enzymes have majority flux
             control, 2) do enzymes with majority flux control accumulate
             adaptive substitutions, and 3) are upstream enzymes under
             higher selective constraint? First, by perturbing the
             enzymes in the aliphatic glucosinolate pathway in
             Arabidopsis thaliana with gene insertion lines, we show that
             flux control is focused in the first enzyme in the pathway.
             Next, by analyzing several sequence signatures of selection,
             we also show that this enzyme is the only one in the pathway
             that shows convincing evidence of selection. Our results
             support the hypothesis that natural selection preferentially
             acts on enzymes with high flux control.},
   Doi = {10.1093/molbev/mss204},
   Key = {fds229146}
}

@article{fds229172,
   Author = {Vigueira, CC and Rauh, B and Mitchell-Olds, T and Lawton-Rauh,
             AL},
   Title = {Signatures of demography and recombination at coding genes
             in naturally-distributed populations of Arabidopsis lyrata
             subsp. petraea.},
   Journal = {Plos One},
   Volume = {8},
   Number = {3},
   Pages = {e58916},
   Year = {2013},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23554957},
   Abstract = {Demography impacts the observed standing level of genetic
             diversity present in populations. Distinguishing the
             relative impacts of demography from selection requires a
             baseline of expressed gene variation in naturally occurring
             populations. Six nuclear genes were sequenced to estimate
             the patterns and levels of genetic diversity in natural
             Arabidopsis lyrata subsp. petraea populations that differ in
             demographic histories since the Pleistocene. As expected,
             northern European populations have genetic signatures of a
             strong population bottleneck likely due to glaciation during
             the Pleistocene. Levels of diversity in the northern
             populations are about half of that in central European
             populations. Bayesian estimates of historical population
             size changes indicate that central European populations also
             have signatures of population size change since the last
             glacial maxima, suggesting that these populations are not as
             stable as previously thought. Time since divergence amongst
             northern European populations is higher than amongst central
             European populations, suggesting that the northern European
             populations were established before the Pleistocene and
             survived glaciation in small separated refugia. Estimates of
             demography based on expressed genes are complementary to
             estimates based on microsatellites and transposable
             elements, elucidating temporal shifts in population dynamics
             and confirming the importance of marker selection for tests
             of demography.},
   Doi = {10.1371/journal.pone.0058916},
   Key = {fds229172}
}

@article{fds285172,
   Author = {Yang, R and Jarvis, DE and Chen, H and Beilstein, MA and Grimwood, J and Jenkins, J and Shu, S and Prochnik, S and Xin, M and Ma, C and Schmutz, J and Wing, RA and Mitchell-Olds, T and Schumaker, KS and Wang,
             X},
   Title = {The Reference Genome of the Halophytic Plant Eutrema
             salsugineum.},
   Journal = {Frontiers in Plant Science},
   Volume = {4},
   Pages = {46},
   Year = {2013},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23518688},
   Abstract = {Halophytes are plants that can naturally tolerate high
             concentrations of salt in the soil, and their tolerance to
             salt stress may occur through various evolutionary and
             molecular mechanisms. Eutrema salsugineum is a halophytic
             species in the Brassicaceae that can naturally tolerate
             multiple types of abiotic stresses that typically limit crop
             productivity, including extreme salinity and cold. It has
             been widely used as a laboratorial model for stress biology
             research in plants. Here, we present the reference genome
             sequence (241 Mb) of E. salsugineum at 8× coverage
             sequenced using the traditional Sanger sequencing-based
             approach with comparison to its close relative Arabidopsis
             thaliana. The E. salsugineum genome contains 26,531
             protein-coding genes and 51.4% of its genome is composed of
             repetitive sequences that mostly reside in pericentromeric
             regions. Comparative analyses of the genome structures,
             protein-coding genes, microRNAs, stress-related pathways,
             and estimated translation efficiency of proteins between E.
             salsugineum and A. thaliana suggest that halophyte
             adaptation to environmental stresses may occur via a global
             network adjustment of multiple regulatory mechanisms. The E.
             salsugineum genome provides a resource to identify naturally
             occurring genetic alterations contributing to the adaptation
             of halophytic plants to salinity and that might be
             bioengineered in related crop species.},
   Doi = {10.3389/fpls.2013.00046},
   Key = {fds285172}
}

@article{fds229171,
   Author = {Topp, and CN, and Iyer-Pascuzzi, AS and Anderson, JT and Lee, C-R and Zurek, PR and Symonova, O and Zheng, Y and Bucksch, A and Milyeko, Y and Galkovskyi, T and Moore, BT and Harer, J and Edelsbrunner, H and Mitchell-Olds, T and Weitz, JS and Benfey, PN},
   Title = {3-dimensional phenotyping of growing root systems and QTL
             mapping identifies core regions of the rice genome
             controlling root architecture},
   Journal = {Pnas},
   Volume = {110},
   Pages = {E1695-1704},
   Year = {2013},
   url = {http://dx.doi.org/10.1073/pnas.1304354110},
   Doi = {10.1073/pnas.1304354110},
   Key = {fds229171}
}

@article{fds229147,
   Author = {Anderson, JT and Panetta, AM and Mitchell-Olds,
             T},
   Title = {Evolutionary and ecological responses to anthropogenic
             climate change: update on anthropogenic climate
             change.},
   Journal = {Plant Physiology},
   Volume = {160},
   Number = {4},
   Pages = {1728-1740},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23043078},
   Doi = {10.1104/pp.112.206219},
   Key = {fds229147}
}

@article{fds229160,
   Author = {Laluk, K and Prasad, KVSK and Savchenko, T and Celesnik, H and Dehesh,
             K and Levy, M and Mitchell-Olds, T and Reddy, ASN},
   Title = {The calmodulin-binding transcription factor SIGNAL
             RESPONSIVE1 is a novel regulator of glucosinolate metabolism
             and herbivory tolerance in Arabidopsis.},
   Journal = {Plant & Cell Physiology},
   Volume = {53},
   Number = {12},
   Pages = {2008-2015},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23072934},
   Abstract = {The Arabidopsis Ca(2+)/calmodulin (CaM)-binding
             transcription factor SIGNAL RESPONSIVE1 (AtSR1/CAMTA3) was
             previously identified as a key negative regulator of plant
             immune responses. Here, we report a new role for AtSR1 as a
             critical component of plant defense against insect
             herbivory. Loss of AtSR1 function impairs tolerance to
             feeding by the generalist herbivore Trichoplusia ni as well
             as wound-induced jasmonate accumulation. The susceptibility
             of the atsr1 mutant is associated with decreased total
             glucosinolate (GS) levels. The two key herbivory deterrents,
             indol-3-ylmethyl (I3M) and 4-methylsulfinylbutyl (4MSOB),
             showed the most significant reductions in atsr1 plants.
             Further, changes in AtSR1 transcript levels led to altered
             expression of several genes involved in GS metabolism
             including IQD1, MYB51 and AtST5a. Overall, our results
             establish AtSR1 as an important component of plant
             resistance to insect herbivory as well as one of only three
             described proteins involved in Ca(2+)/CaM-dependent
             signaling to function in the regulation of GS metabolism,
             providing a novel avenue for future investigations of
             plant-insect interactions.},
   Doi = {10.1093/pcp/pcs143},
   Key = {fds229160}
}

@article{fds229175,
   Author = {Olson-Manning, CF and Wagner, MR and Mitchell-Olds,
             T},
   Title = {Adaptive evolution: evaluating empirical support for
             theoretical predictions.},
   Journal = {Nature Reviews. Genetics},
   Volume = {13},
   Number = {12},
   Pages = {867-877},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23154809},
   Abstract = {Adaptive evolution is shaped by the interaction of
             population genetics, natural selection and underlying
             network and biochemical constraints. Variation created by
             mutation, the raw material for evolutionary change, is
             translated into phenotypes by flux through metabolic
             pathways and by the topography and dynamics of molecular
             networks. Finally, the retention of genetic variation and
             the efficacy of selection depend on population genetics and
             demographic history. Emergent high-throughput experimental
             methods and sequencing technologies allow us to gather more
             evidence and to move beyond the theory in different systems
             and populations. Here we review the extent to which recent
             evidence supports long-established theoretical principles of
             adaptation.},
   Doi = {10.1038/nrg3322},
   Key = {fds229175}
}

@article{fds229176,
   Author = {Lee, C-R and Mitchell-Olds, T},
   Title = {Environmental adaptation contributes to gene polymorphism
             across the Arabidopsis thaliana genome.},
   Journal = {Molecular Biology and Evolution},
   Volume = {29},
   Number = {12},
   Pages = {3721-3728},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22798389},
   Abstract = {The level of within-species polymorphism differs greatly
             among genes in a genome. Many genomic studies have
             investigated the relationship between gene polymorphism and
             factors such as recombination rate or expression pattern.
             However, the polymorphism of a gene is affected not only by
             its physical properties or functional constraints but also
             by natural selection on organisms in their environments.
             Specifically, if functionally divergent alleles enable
             adaptation to different environments, locus-specific
             polymorphism may be maintained by spatially heterogeneous
             natural selection. To test this hypothesis and estimate the
             extent to which environmental selection shapes the pattern
             of genome-wide polymorphism, we define the "environmental
             relevance" of a gene as the proportion of genetic variation
             explained by environmental factors, after controlling for
             population structure. We found substantial effects of
             environmental relevance on patterns of polymorphism among
             genes. In addition, the correlation between environmental
             relevance and gene polymorphism is positive, consistent with
             the expectation that balancing selection among heterogeneous
             environments maintains genetic variation at ecologically
             important genes. Comparison of the gene ontology annotations
             shows that genes with high environmental relevance are
             enriched in unknown function categories. These results
             suggest an important role for environmental factors in
             shaping genome-wide patterns of polymorphism and indicate
             another direction of genomic study.},
   Doi = {10.1093/molbev/mss174},
   Key = {fds229176}
}

@article{fds229159,
   Author = {Anderson, JT and Inouye, DW and McKinney, AM and Colautti, RI and Mitchell-Olds, T},
   Title = {Phenotypic plasticity and adaptive evolution contribute to
             advancing flowering phenology in response to climate
             change.},
   Journal = {Proceedings of the Royal Society B: Biological
             Sciences},
   Volume = {279},
   Number = {1743},
   Pages = {3843-3852},
   Year = {2012},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22787021},
   Abstract = {Anthropogenic climate change has already altered the timing
             of major life-history transitions, such as the initiation of
             reproduction. Both phenotypic plasticity and adaptive
             evolution can underlie rapid phenological shifts in response
             to climate change, but their relative contributions are
             poorly understood. Here, we combine a continuous 38 year
             field survey with quantitative genetic field experiments to
             assess adaptation in the context of climate change. We
             focused on Boechera stricta (Brassicaeae), a mustard native
             to the US Rocky Mountains. Flowering phenology advanced
             significantly from 1973 to 2011, and was strongly associated
             with warmer temperatures and earlier snowmelt dates. Strong
             directional selection favoured earlier flowering in
             contemporary environments (2010-2011). Climate change could
             drive this directional selection, and promote even earlier
             flowering as temperatures continue to increase. Our
             quantitative genetic analyses predict a response to
             selection of 0.2 to 0.5 days acceleration in flowering per
             generation, which could account for more than 20 per cent of
             the phenological change observed in the long-term dataset.
             However, the strength of directional selection and the
             predicted evolutionary response are likely much greater now
             than even 30 years ago because of rapidly changing climatic
             conditions. We predict that adaptation will likely be
             necessary for long-term in situ persistence in the context
             of climate change.},
   Doi = {10.1098/rspb.2012.1051},
   Key = {fds229159}
}

@article{fds229174,
   Author = {Prasad, KVSK and Song, B-H and Olson-Manning, C and Anderson, JT and Lee, C-R and Schranz, ME and Windsor, AJ and Clauss, MJ and Manzaneda,
             AJ and Naqvi, I and Reichelt, M and Gershenzon, J and Rupasinghe, SG and Schuler, MA and Mitchell-Olds, T},
   Title = {A gain-of-function polymorphism controlling complex traits
             and fitness in nature.},
   Journal = {Science (New York, N.Y.)},
   Volume = {337},
   Number = {6098},
   Pages = {1081-1084},
   Year = {2012},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22936775},
   Abstract = {Identification of the causal genes that control complex
             trait variation remains challenging, limiting our
             appreciation of the evolutionary processes that influence
             polymorphisms in nature. We cloned a quantitative trait
             locus that controls plant defensive chemistry, damage by
             insect herbivores, survival, and reproduction in the natural
             environments where this polymorphism evolved. These
             ecological effects are driven by duplications in the BCMA
             (branched-chain methionine allocation) loci controlling this
             variation and by two selectively favored amino acid changes
             in the glucosinolate-biosynthetic cytochrome P450 proteins
             that they encode. These changes cause a gain of novel enzyme
             function, modulated by allelic differences in catalytic rate
             and gene copy number. Ecological interactions in diverse
             environments likely contribute to the widespread
             polymorphism of this biochemical function.},
   Doi = {10.1126/science.1221636},
   Key = {fds229174}
}

@article{fds229179,
   Author = {Colautti, RI and Lee, C-R and Mitchell-Olds, T},
   Title = {Origin, fate, and architecture of ecologically relevant
             genetic variation.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {15},
   Number = {2},
   Pages = {199-204},
   Year = {2012},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22341792},
   Abstract = {Recent advances in molecular genetics combined with field
             manipulations are yielding new insight into the origin,
             evolutionary fate, and genetic architecture of phenotypic
             variation in natural plant populations, with two surprising
             implications for the evolution of plant genomes. First,
             genetic loci exhibiting antagonistic pleiotropy across
             natural environments appear rare relative to loci that are
             adaptive in one or more environments and neutral elsewhere.
             These 'conditionally neutral' alleles should sweep to
             fixation when they arise, yet genome comparisons find little
             evidence for such selective sweeps. Second, genes under
             biotic selection tend to be of larger effect than genes
             under abiotic selection. Recent theory suggests this may be
             a consequence of high gene flow among populations under
             selection for local adaptation.},
   Doi = {10.1016/j.pbi.2012.01.016},
   Key = {fds229179}
}

@article{fds229178,
   Author = {Manzaneda, AJ and Rey, PJ and Bastida, JM and Weiss-Lehman, C and Raskin, E and Mitchell-Olds, T},
   Title = {Environmental aridity is associated with cytotype
             segregation and polyploidy occurrence in Brachypodium
             distachyon (Poaceae).},
   Journal = {The New Phytologist},
   Volume = {193},
   Number = {3},
   Pages = {797-805},
   Year = {2012},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22150799},
   Abstract = {• The ecological and adaptive significance of plant
             polyploidization is not well understood and no clear pattern
             of association between polyploid frequency and environment
             has emerged. Climatic factors are expected to predict
             cytotype distribution. However, the relationship among
             climate, cytotype distribution and variation of abiotic
             stress tolerance traits has rarely been examined. • Here,
             we use flow cytometry and root-tip squashes to examine the
             cytotype distribution in the temperate annual grass
             Brachypodium distachyon in 57 natural populations
             distributed across an aridity gradient in the Iberian
             Peninsula. We further investigate the link between
             environmental aridity, ploidy, and variation of drought
             tolerance and drought avoidance (flowering time) traits. •
             Distribution of diploids (2n = 10) and allotetraploids (2n =
             30) in this species is geographically structured throughout
             its range in the Iberian Peninsula, and is associated with
             aridity gradients. Importantly, after controlling for
             geographic and altitudinal effects, the link between aridity
             and polyploidization occurrence persisted. Water-use
             efficiency varied between ploidy levels, with tetraploids
             being more efficient in the use of water than diploids under
             water-restricted growing conditions. • Our results
             indicate that aridity is an important predictor of polyploid
             occurrence in B. distachyon, suggesting a possible adaptive
             origin of the cytotype segregation.},
   Doi = {10.1111/j.1469-8137.2011.03988.x},
   Key = {fds229178}
}

@article{fds207104,
   Author = {Anderson, Jill and DW Inouye and A McKinney and T
             Mitchell-Olds},
   Title = {Anderson, JT, DW Inouye, A. McKinney, and T. Mitchell-Olds.
             2012. Phenotypic plasticity and adaptive evolution
             contribute to advancing flowering phenology in response to
             climate change. Proceedings of the Royal Society
             B},
   Journal = {Proc. Roy. Soc. B.},
   Volume = {279},
   Pages = {3843-52},
   Year = {2012},
   Key = {fds207104}
}

@article{fds229173,
   Author = {Yang, R and Chen, H and Jarvi, D and Beilstein, M and Grimwood, J and Jenkins, J and Shu, SQ and Prochnik, S and Schmutz, J and Mitchell Olds,
             T and Wing, R and Schumaker, K and Wang, X},
   Title = {Distinct Dynamics of Transposable Elements in the Genome
             Evolution of the Salt-Tolerant Eutrema salsugineum and
             Related Brassicaceae Species},
   Journal = {Plant Cell},
   Year = {2012},
   url = {http://www.frontiersin.org/Journal/Abstract.aspx?s=905&name=plant},
   Doi = {10.3389/fpls.2013.00046},
   Key = {fds229173}
}

@article{fds229177,
   Author = {Lee, CR and Mitchell Olds and T},
   Title = {Ecological trait divergence confirms niche modeling
             predictions in ecological speciation of Boechera
             stricta},
   Journal = {Molecular Ecology},
   Volume = {22},
   Pages = {2204–2217},
   Year = {2012},
   Key = {fds229177}
}

@article{fds229180,
   Author = {Rushworth, CA and Song, B-H and Lee, C-R and Mitchell-Olds,
             T},
   Title = {Boechera, a model system for ecological genomics.},
   Journal = {Molecular Ecology},
   Volume = {20},
   Number = {23},
   Pages = {4843-4857},
   Year = {2011},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22059452},
   Abstract = {The selection and development of a study system for
             evolutionary and ecological functional genomics (EEFG)
             depend on a variety of factors. Here, we present the genus
             Boechera as an exemplary system with which to address
             ecological and evolutionary questions. Our focus on Boechera
             is based on several characteristics as follows: (i) native
             populations in undisturbed habitats where current
             environments reflect historical conditions over several
             thousand years; (ii) functional genomics benefitting from
             its close relationship to Arabidopsis thaliana; (iii)
             inbreeding tolerance enabling development of recombinant
             inbred lines, near-isogenic lines and positional cloning;
             (iv) interspecific crosses permitting mapping for genetic
             analysis of speciation; (v) apomixis (asexual reproduction
             by seeds) in a genetically tractable diploid; and (vi) broad
             geographic distribution in North America, permitting
             ecological genetics for a large research community. These
             characteristics, along with the current sequencing of three
             Boechera species by the Joint Genome Institute, position
             Boechera as a rapidly advancing system for EEFG
             studies.},
   Doi = {10.1111/j.1365-294X.2011.05340.x},
   Key = {fds229180}
}

@article{fds229182,
   Author = {Lee, C-R and Mitchell-Olds, T},
   Title = {Quantifying effects of environmental and geographical
             factors on patterns of genetic differentiation.},
   Journal = {Molecular Ecology},
   Volume = {20},
   Number = {22},
   Pages = {4631-4642},
   Year = {2011},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21999331},
   Abstract = {Elucidating the factors influencing genetic differentiation
             is an important task in biology, and the relative
             contribution from natural selection and genetic drift has
             long been debated. In this study, we used a regression-based
             approach to simultaneously estimate the quantitative
             contributions of environmental adaptation and isolation by
             distance on genetic variation in Boechera stricta, a wild
             relative of Arabidopsis. Patterns of discrete and continuous
             genetic differentiation coexist within this species. For the
             discrete differentiation between two major genetic groups,
             environment has larger contribution than geography, and we
             also identified a significant environment-by-geography
             interaction effect. Elsewhere in the species range, we found
             a latitudinal cline of genetic variation reflecting only
             isolation by distance. To further confirm the effect of
             environmental selection on genetic divergence, we identified
             the specific environmental variables predicting local
             genotypes in allopatric and sympatric regions. Water
             availability was identified as the possible cause of
             differential local adaptation in both geographical regions,
             confirming the role of environmental adaptation in driving
             and maintaining genetic differentiation between the two
             major genetic groups. In addition, the environment-by-geography
             interaction is further confirmed by the finding that water
             availability is represented by different environmental
             factors in the allopatric and sympatric regions. In
             conclusion, this study shows that geographical and
             environmental factors together created stronger and more
             discrete genetic differentiation than isolation by distance
             alone, which only produced a gradual, clinal pattern of
             genetic variation. These findings emphasize the importance
             of environmental selection in shaping patterns of
             species-wide genetic variation in the natural
             environment.},
   Doi = {10.1111/j.1365-294X.2011.05310.x},
   Key = {fds229182}
}

@article{fds229183,
   Author = {Brkljacic, J and Grotewold, E and Scholl, R and Mockler, T and Garvin,
             DF and Vain, P and Brutnell, T and Sibout, R and Bevan, M and Budak, H and Caicedo, AL and Gao, C and Gu, Y and Hazen, SP and Holt, BF and Hong, S-Y and Jordan, M and Manzaneda, AJ and Mitchell-Olds, T and Mochida, K and Mur,
             LAJ and Park, C-M and Sedbrook, J and Watt, M and Zheng, SJ and Vogel,
             JP},
   Title = {Brachypodium as a model for the grasses: today and the
             future.},
   Journal = {Plant Physiology},
   Volume = {157},
   Number = {1},
   Pages = {3-13},
   Year = {2011},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21771916},
   Doi = {10.1104/pp.111.179531},
   Key = {fds229183}
}

@article{fds229184,
   Author = {Wagner, MR and Mitchell-Olds, T},
   Title = {Repeated phenotypic changes highlight molecular targets of
             convergent evolution.},
   Journal = {Genome Biology},
   Volume = {12},
   Number = {8},
   Pages = {124},
   Year = {2011},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21861848},
   Abstract = {How predictable is evolution at the molecular level? An
             example of repeated evolution in rice and Brassica
             illustrates how selection might preferentially target
             certain genes and mutations.},
   Doi = {10.1186/gb-2011-12-8-124},
   Key = {fds229184}
}

@article{fds229185,
   Author = {Anderson, JT and Willis, JH and Mitchell-Olds,
             T},
   Title = {Evolutionary genetics of plant adaptation.},
   Journal = {Trends in Genetics : Tig},
   Volume = {27},
   Number = {7},
   Pages = {258-266},
   Year = {2011},
   Month = {July},
   ISSN = {0168-9525},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21550682},
   Abstract = {Plants provide unique opportunities to study the mechanistic
             basis and evolutionary processes of adaptation to diverse
             environmental conditions. Complementary laboratory and field
             experiments are important for testing hypotheses reflecting
             long-term ecological and evolutionary history. For example,
             these approaches can infer whether local adaptation results
             from genetic tradeoffs (antagonistic pleiotropy), where
             native alleles are best adapted to local conditions, or if
             local adaptation is caused by conditional neutrality at many
             loci, where alleles show fitness differences in one
             environment, but not in a contrasting environment.
             Ecological genetics in natural populations of perennial or
             outcrossing plants can also differ substantially from model
             systems. In this review of the evolutionary genetics of
             plant adaptation, we emphasize the importance of field
             studies for understanding the evolutionary dynamics of model
             and nonmodel systems, highlight a key life history trait
             (flowering time) and discuss emerging conservation
             issues.},
   Doi = {10.1016/j.tig.2011.04.001},
   Key = {fds229185}
}

@article{fds229186,
   Author = {Anderson, JT and Mitchell-Olds, T},
   Title = {Ecological genetics and genomics of plant defenses: Evidence
             and approaches.},
   Journal = {Functional Ecology.},
   Volume = {25},
   Number = {2},
   Pages = {312-324},
   Year = {2011},
   Month = {April},
   ISSN = {0269-8463},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21532968},
   Abstract = {Herbivores exert significant selection on plants, and plants
             have evolved a variety of constitutive and inducible
             defenses to resist and tolerate herbivory. Assessing the
             genetic mechanisms that influence defenses against
             herbivores will deepen our understanding of the evolution of
             essential phenotypic traits.Ecogenomics is a powerful
             interdisciplinary approach that can address fundamental
             questions about the ecology and evolutionary biology of
             species, such as: which evolutionary forces maintain
             variation within a population? and What is the genetic
             architecture of adaptation? This field seeks to identify
             gene regions that influence ecologically-important traits,
             assess the fitness consequences under natural conditions of
             alleles at key quantitative trait loci (QTLs), and test how
             the abiotic and biotic environment affects gene
             expression.Here, we review ecogenomics techniques and
             emphasize how this framework can address long-standing and
             emerging questions relating to anti-herbivore defenses in
             plants. For example, ecogenomics tools can be used to
             investigate: inducible vs. constitutive defenses; tradeoffs
             between resistance and tolerance; adaptation to the local
             herbivore community; selection on alleles that confer
             resistance and tolerance in natural populations; and whether
             different genes are activated in response to specialist vs.
             generalist herbivores and to different types of
             damage.Ecogenomic studies can be conducted with model
             species, such as Arabidopsis, or their relatives, in which
             case myriad molecular tools are already available.
             Burgeoning sequence data will also facilitate ecogenomic
             studies of non-model species. Throughout this paper, we
             highlight approaches that are particularly suitable for
             ecological studies of non-model organisms, discuss the
             benefits and disadvantages of specific techniques, and
             review bioinformatic tools for analyzing data.We focus on
             established and promising techniques, such as QTL mapping
             with pedigreed populations, genome wide association studies,
             transcription profiling strategies, population genomics, and
             transgenic methodologies. Many of these techniques are
             complementary and can be used jointly to investigate the
             genetic architecture of defense traits and selection on
             alleles in nature.},
   Doi = {10.1111/j.1365-2435.2010.01785.x},
   Key = {fds229186}
}

@article{fds229188,
   Author = {Anderson, JT and Lee, C-R and Mitchell-Olds, T},
   Title = {Life-history QTLS and natural selection on flowering time in
             Boechera stricta, a perennial relative of
             Arabidopsis.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {65},
   Number = {3},
   Pages = {771-787},
   Year = {2011},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21083662},
   Abstract = {Plants must precisely time flowering to capitalize on
             favorable conditions. Although we know a great deal about
             the genetic basis of flowering phenology in model species
             under controlled conditions, the genetic architecture of
             this ecologically important trait is poorly understood in
             nonmodel organisms. Here, we evaluated the transition from
             vegetative growth to flowering in Boechera stricta, a
             perennial relative of Arabidopsis thaliana. We examined
             flowering time QTLs using 7920 recombinant inbred
             individuals, across seven laboratory and field environments
             differing in vernalization, temperature, and photoperiod.
             Genetic and environmental factors strongly influenced the
             transition to reproduction. We found directional selection
             for earlier flowering in the field. In the growth chamber
             experiment, longer winters accelerated flowering, whereas
             elevated ambient temperatures delayed flowering. Our
             analyses identified one large effect QTL (nFT), which
             influenced flowering time in the laboratory and the
             probability of flowering in the field. In Montana,
             homozygotes for the native allele at nFT showed a selective
             advantage of 6.6%. Nevertheless, we found relatively low
             correlations between flowering times in the field and the
             growth chambers. Additionally, we detected flowering-related
             QTLs in the field that were absent across the full range of
             laboratory conditions, thus emphasizing the need to conduct
             experiments in natural environments.},
   Doi = {10.1111/j.1558-5646.2010.01175.x},
   Key = {fds229188}
}

@article{fds229187,
   Author = {Song, B-H and Mitchell-Olds, T},
   Title = {Evolutionary and Ecological Genomics of Non-Model
             Plants.},
   Journal = {Journal of Systematics and Evolution},
   Volume = {49},
   Number = {1},
   Pages = {17-24},
   Year = {2011},
   Month = {January},
   ISSN = {1674-4918},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21394233},
   Abstract = {Dissecting evolutionary dynamics of ecologically important
             traits is a long-term challenge for biologists. Attempts to
             understand natural variation and molecular mechanisms have
             motivated a move from laboratory model systems to non-model
             systems in diverse natural environments. Next generation
             sequencing methods, along with an expansion of genomic
             resources and tools, have fostered new links between diverse
             disciplines, including molecular biology, evolution, and
             ecology, and genomics. Great progress has been made in a few
             non-model wild plants, such as Arabidopsis relatives, monkey
             flowers, and wild sunflowers. Until recently, the lack of
             comprehensive genomic information has limited evolutionary
             and ecological studies to larger QTL regions rather than
             single gene resolution, and has hindered recognition of
             general patterns of natural variation and local adaptation.
             Further efforts in accumulating genomic data and developing
             bioinformatic and biostatistical tools are now poised to
             move this field forward. Integrative national and
             international collaborations and research communities are
             needed to facilitate development in the field of
             evolutionary and ecological genomics.},
   Doi = {10.1111/j.1759-6831.2010.00111.x},
   Key = {fds229187}
}

@article{fds229193,
   Author = {Anderson, JT and Mitchell-Olds, T},
   Title = {Beyond QTL cloning.},
   Journal = {Plos Genetics},
   Volume = {6},
   Number = {11},
   Pages = {e1001197},
   Year = {2010},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21085636},
   Doi = {10.1371/journal.pgen.1001197},
   Key = {fds229193}
}

@article{fds229194,
   Author = {Manzaneda, AJ and Prasad, KVSK and Mitchell-Olds,
             T},
   Title = {Variation and fitness costs for tolerance to different types
             of herbivore damage in Boechera stricta genotypes with
             contrasting glucosinolate structures.},
   Journal = {The New Phytologist},
   Volume = {188},
   Number = {2},
   Pages = {464-477},
   Year = {2010},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20663059},
   Abstract = {• Analyses of plant tolerance in response to different
             modes of herbivory are essential to an understanding of
             plant defense evolution, yet are still scarce. Allocation
             costs and trade-offs between tolerance and plant chemical
             defenses may influence genetic variation for tolerance.
             However, variation in defenses also occurs for the presence
             or absence of discrete chemical structures; yet, the effects
             of intraspecific polymorphisms on tolerance to multiple
             herbivores have not been evaluated. • Here, in a
             glasshouse experiment, we investigated the variation for
             tolerance to different types of herbivore damage, and direct
             allocation costs, in 10 genotypes of Boechera stricta
             (Brassicaceae), a wild relative of Arabidopsis, with
             contrasting foliar glucosinolate chemical structures
             (methionine-derived glucosinolates vs glucosinolates derived
             from branched-chain amino acids). • We found significant
             genetic variation for tolerance to different types of
             herbivore. Structural variations in the glucosinolate
             profile did not influence tolerance to damage, but predicted
             plant fitness. Levels of constitutive and induced
             glucosinolates varied between genotypes with different
             structural profiles, but we did not detect any cost of
             tolerance explaining the genetic variation in tolerance
             among genotypes. • Trade-offs between plant tolerance to
             multiple herbivores may not explain the existence of
             intermediate levels of tolerance to damage in plants with
             contrasting chemical defensive profiles.},
   Doi = {10.1111/j.1469-8137.2010.03385.x},
   Key = {fds229194}
}

@article{fds229189,
   Author = {Heidel, AJ and Ramos-Onsins, SE and Wang, W-K and Chiang, T-Y and Mitchell-Olds, T},
   Title = {Population history in Arabidopsis halleri using multilocus
             analysis.},
   Journal = {Molecular Ecology},
   Volume = {19},
   Number = {16},
   Pages = {3364-3379},
   Year = {2010},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20670364},
   Abstract = {A. halleri is a psuedometallophyte with a patchy
             distribution in Europe and is often spread by human
             activity. To determine the population history and whether
             this history is consistent with potential human effects, we
             surveyed nucleotide variation using 24 loci from 12
             individuals in a large A. halleri population. The means of
             total and silent nucleotide variation (theta(W)) are within
             the range expected for the species. The population genetic
             neutrality tests Tajima's D and Wall's B had significant
             composite results rejecting panmixia, and Approximate
             Bayesian Computation analysis revealed that a subdivision
             model better explained the variation than the standard
             neutral model, refugia (or admixture), bottleneck or change
             of population size models. A categorical regression analysis
             further supports the subdivision model, and under the
             subdivision model, the neutrality tests are no longer
             significant. The best support was for two source
             populations, a situation consistent with the mixing of two
             populations possibly mediated by human activity. This
             scenario might limit the genetic diversity and adaptive
             potential of the population. The non-neutral population
             variation described here should be considered in
             bioinformatic searches for adaptation.},
   Doi = {10.1111/j.1365-294X.2010.04761.x},
   Key = {fds229189}
}

@article{fds229195,
   Author = {Gossmann, TI and Song, B-H and Windsor, AJ and Mitchell-Olds, T and Dixon, CJ and Kapralov, MV and Filatov, DA and Eyre-Walker,
             A},
   Title = {Genome wide analyses reveal little evidence for adaptive
             evolution in many plant species.},
   Journal = {Molecular Biology and Evolution},
   Volume = {27},
   Number = {8},
   Pages = {1822-1832},
   Year = {2010},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20299543},
   Abstract = {The relative contribution of advantageous and neutral
             mutations to the evolutionary process is a central problem
             in evolutionary biology. Current estimates suggest that
             whereas Drosophila, mice, and bacteria have undergone
             extensive adaptive evolution, hominids show little or no
             evidence of adaptive evolution in protein-coding sequences.
             This may be a consequence of differences in effective
             population size. To study the matter further, we have
             investigated whether plants show evidence of adaptive
             evolution using an extension of the McDonald-Kreitman test
             that explicitly models slightly deleterious mutations by
             estimating the distribution of fitness effects of new
             mutations. We apply this method to data from nine pairs of
             species. Altogether more than 2,400 loci with an average
             length of approximately 280 nucleotides were analyzed. We
             observe very similar results in all species; we find little
             evidence of adaptive amino acid substitution in any
             comparison except sunflowers. This may be because many plant
             species have modest effective population
             sizes.},
   Doi = {10.1093/molbev/msq079},
   Key = {fds229195}
}

@article{fds229197,
   Author = {Schwartz, CJ and Doyle, MR and Manzaneda, AJ and Rey, PJ and Mitchell-Olds, T and Amasino, RM},
   Title = {Natural variation of flowering time and vernalization
             responsiveness in Brachypodium distachyon},
   Journal = {Bioenergy Research},
   Volume = {3},
   Number = {1},
   Pages = {38-46},
   Publisher = {Springer Nature},
   Year = {2010},
   Month = {February},
   ISSN = {1939-1234},
   url = {http://dx.doi.org/10.1007/s12155-009-9069-3},
   Abstract = {Dedicated bioenergy crops require certain characteristics to
             be economically viable and environmentally sustainable.
             Perennial grasses, which can provide large amounts of
             biomass over multiple years, are one option being
             investigated to grow on marginal agricultural land.
             Recently, a grass species (Brachypodium distachyon) has been
             developed as a model to better understand grass physiology
             and ecology. Here, we report on the flowering time
             variability of natural Brachypodium accessions in response
             to temperature and light cues. Changes in both environmental
             parameters greatly influence when a given accession will
             flower, and natural Brachypodium accessions broadly group
             into winter and spring annuals. Similar to what has been
             discovered in wheat and barley, we find that a portion of
             the phenotypic variation is associated with changes in
             expression of orthologs of VRN genes, and thus, VRN genes
             are a possible target for modifying flowering time in grass
             family bioenergy crops. © Springer Science+Business Media,
             LLC. 2010.},
   Doi = {10.1007/s12155-009-9069-3},
   Key = {fds229197}
}

@article{fds229196,
   Author = {Mitchell-Olds, T},
   Title = {Complex-trait analysis in plants.},
   Journal = {Genome Biology},
   Volume = {11},
   Number = {4},
   Pages = {113},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20409352},
   Abstract = {Two recent studies in Arabidopsis have identified
             quantitative trait loci (QTLs) by population- association
             and family-based studies, respectively, providing further
             data on the genetic architecture of complex-trait variation
             in plants.},
   Doi = {10.1186/gb-2010-11-4-113},
   Key = {fds229196}
}

@article{fds229200,
   Author = {Metcalf, CJE and Mitchell-Olds, T},
   Title = {Life history in a model system: opening the black box with
             Arabidopsis thaliana.},
   Journal = {Ecology Letters},
   Volume = {12},
   Number = {7},
   Pages = {593-600},
   Year = {2009},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19473216},
   Abstract = {A broad research programme in Arabidopsis thaliana has
             provided estimates of selection on specific alleles in
             specific contexts, and identified geographic patterns of
             alleles in genes linked to timing of flowering. A closely
             related field has successfully captured many key axes of the
             evolution of timing of flowering in other monocarpic species
             through statistical and demographic modelling of large
             empirical databases. There has as yet been no synthesis
             between these two fields. Here we examine ways in which the
             two fields inform each other, and how this synergy will
             shape our knowledge of life-history evolution as a
             whole.},
   Doi = {10.1111/j.1461-0248.2009.01320.x},
   Key = {fds229200}
}

@article{fds229199,
   Author = {Leinonen, PH and Sandring, S and Quilot, B and Clauss, MJ and Mitchell-Olds, T and Agren, J and Savolainen, O},
   Title = {Local adaptation in European populations of Arabidopsis
             lyrata (Brassicaceae).},
   Journal = {American Journal of Botany},
   Volume = {96},
   Number = {6},
   Pages = {1129-1137},
   Year = {2009},
   Month = {June},
   ISSN = {0002-9122},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21628263},
   Abstract = {We studied local adaptation to contrasting environments
             using an organism that is emerging as a model for
             evolutionary plant biology-the outcrossing, perennial herb
             Arabidopsis lyrata subsp. petraea (Brassicaceae). With
             reciprocal transplant experiments, we found variation in
             cumulative fitness, indicating adaptive differentiation
             among populations. Nonlocal populations did not have
             significantly higher fitness than the local population.
             Experimental sites were located in Norway (alpine), Sweden
             (coastal), and Germany (continental). At all sites after one
             year, the local population had higher cumulative fitness, as
             quantified by survival combined with rosette area, than at
             least one of the nonlocal populations. At the Norwegian
             site, measurements were done for two additional years, and
             fitness differences persisted. The fitness components that
             contributed most to differences in cumulative fitness varied
             among sites. Relatively small rosette area combined with a
             large number of inflorescences produced by German plants may
             reflect differentiation in life history. The results of the
             current study demonstrate adaptive population
             differentiation in A. lyrata along a climatic gradient in
             Europe. The studied populations harbor considerable
             variation in several characters contributing to adaptive
             population differentiation. The wealth of genetic
             information available makes A. lyrata a highly attractive
             system also for examining the functional and genetic basis
             of local adaptation in plants.},
   Doi = {10.3732/ajb.0800080},
   Key = {fds229199}
}

@article{fds229198,
   Author = {Schranz, ME and Manzaneda, AJ and Windsor, AJ and Clauss, MJ and Mitchell-Olds, T},
   Title = {Ecological genomics of Boechera stricta: identification of a
             QTL controlling the allocation of methionine- vs
             branched-chain amino acid-derived glucosinolates and levels
             of insect herbivory.},
   Journal = {Heredity},
   Volume = {102},
   Number = {5},
   Pages = {465-474},
   Year = {2009},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19240753},
   Abstract = {In the Brassicaceae, glucosinolates influence the feeding,
             reproduction and development of many insect herbivores.
             Glucosinolate production and effects on herbivore feeding
             have been extensively studied in the model species,
             Arabidopsis thaliana and Brassica crops, both of which
             constitutively produce leaf glucosinolates mostly derived
             from the amino acid, methionine. Much less is known about
             the regulation or role in defense of glucosinolates derived
             from other aliphatic amino acids, such as the branched-chain
             amino acids (BCAA), valine and isoleucine. We have
             identified a glucosinolate polymorphism in Boechera stricta
             controlling the allocation to BCAA- vs methionine-derived
             glucosinolates in both leaves and seeds. B. stricta is a
             perennial species that grows in mostly undisturbed habitats
             of western North America. We have measured glucosinolate
             profiles and concentrations in 192 F(2) lines that have
             earlier been used for genetic map construction. We also
             performed herbivory assays on six F(3) replicates per F(2)
             line using the generalist lepidopteran, Trichoplusia ni.
             Quantitative trait locus (QTL) analysis identified a single
             locus controlling both glucosinolate profile and levels of
             herbivory, the branched chain-methionine allocation or BCMA
             QTL. We have delimited this QTL to a small genomic region
             with a 1.0 LOD confidence interval just 1.9 cm wide, which,
             in A. thaliana, contains approximately 100 genes. We also
             found that methionine-derived glucosinolates provided
             significantly greater defense than the BCAA-derived
             glucosinolates against feeding by this generalist insect
             herbivore. The future positional cloning of this locus will
             allow for testing various adaptive explanations.},
   Doi = {10.1038/hdy.2009.12},
   Key = {fds229198}
}

@article{fds229201,
   Author = {Song, B-H and Windsor, AJ and Schmid, KJ and Ramos-Onsins, S and Schranz, ME and Heidel, AJ and Mitchell-Olds, T},
   Title = {Multilocus patterns of nucleotide diversity, population
             structure and linkage disequilibrium in Boechera stricta, a
             wild relative of Arabidopsis.},
   Journal = {Genetics},
   Volume = {181},
   Number = {3},
   Pages = {1021-1033},
   Year = {2009},
   Month = {March},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19104077},
   Abstract = {Information about polymorphism, population structure, and
             linkage disequilibrium (LD) is crucial for association
             studies of complex trait variation. However, most genomewide
             studies have focused on model systems, with very few
             analyses of undisturbed natural populations. Here, we
             sequenced 86 mapped nuclear loci for a sample of 46
             genotypes of Boechera stricta and two individuals of B.
             holboellii, both wild relatives of Arabidopsis. Isolation by
             distance was significant across the species range of B.
             stricta, and three geographic groups were identified by
             structure analysis, principal coordinates analysis, and
             distance-based phylogeny analyses. The allele frequency
             spectrum indicated a genomewide deviation from an
             equilibrium neutral model, with silent nucleotide diversity
             averaging 0.004. LD decayed rapidly, declining to background
             levels in approximately 10 kb or less. For tightly linked
             SNPs separated by <1 kb, LD was dependent on the reference
             population. LD was lower in the specieswide sample than
             within populations, suggesting that low levels of LD found
             in inbreeding species such as B. stricta, Arabidopsis
             thaliana, and barley may result from broad geographic
             sampling that spans heterogeneous genetic groups. Finally,
             analyses also showed that inbreeding B. stricta and A.
             thaliana have approximately 45% higher recombination per
             kilobase than outcrossing A. lyrata.},
   Doi = {10.1534/genetics.108.095364},
   Key = {fds229201}
}

@article{fds229191,
   Author = {McKay, JK and Richards, JH and Nemali, KS and Sen, S and Mitchell-Olds,
             T and Boles, S and Stahl, EA and Wayne, T and Juenger,
             TE},
   Title = {Genetics of drought adaptation in Arabidopsis thaliana II.
             QTL analysis of a new mapping population, KAS-1 x
             TSU-1.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {62},
   Number = {12},
   Pages = {3014-3026},
   Year = {2008},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18691264},
   Abstract = {Despite compelling evidence that adaptation to local climate
             is common in plant populations, little is known about the
             evolutionary genetics of traits that contribute to climatic
             adaptation. A screen of natural accessions of Arabidopsis
             thaliana revealed Tsu-1 and Kas-1 to be opposite extremes
             for water-use efficiency and climate at collection sites for
             these accessions differs greatly. To provide a tool to
             understand the genetic basis of this putative adaptation,
             Kas-1 and Tsu-1 were reciprocally crossed to create a new
             mapping population. Analysis of F(3) families showed
             segregating variation in both delta(13)C and transpiration
             rate, and as expected these traits had a negative genetic
             correlation (r(g)=- 0.3). 346 RILs, 148 with Kas-1 cytoplasm
             and 198 with Tsu-1 cytoplasm, were advanced to the F(9) and
             genotyped using 48 microsatellites and 55 SNPs for a total
             of 103 markers. This mapping population was used for QTL
             analysis of delta(13)C using F(9) RIL means. Analysis of
             this reciprocal cross showed a large effect of cytoplasmic
             background, as well as two QTL for delta(13)C. The Kas-1 x
             Tsu-1 mapping population provides a powerful new resource
             for mapping QTL underlying natural variation and for
             dissecting the genetic basis of water-use efficiency
             differences.},
   Doi = {10.1111/j.1558-5646.2008.00474.x},
   Key = {fds229191}
}

@article{fds229202,
   Author = {Hansen, BG and Kerwin, RE and Ober, JA and Lambrix, VM and Mitchell-Olds, T and Gershenzon, J and Halkier, BA and Kliebenstein,
             DJ},
   Title = {A novel 2-oxoacid-dependent dioxygenase involved in the
             formation of the goiterogenic 2-hydroxybut-3-enyl
             glucosinolate and generalist insect resistance in
             Arabidopsis,.},
   Journal = {Plant Physiology},
   Volume = {148},
   Number = {4},
   Pages = {2096-2108},
   Year = {2008},
   Month = {December},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18945935},
   Abstract = {Glucosinolates are secondary metabolites found almost
             exclusively in the order Brassicales. They are synthesized
             from a variety of amino acids and can have numerous side
             chain modifications that control biological function. We
             investigated the biosynthesis of 2-hydroxybut-3-enyl
             glucosinolate, which has biological activities including
             toxicity to Caenorhabditis elegans, inhibition of seed
             germination, induction of goiter disease in mammals, and
             production of bitter flavors in Brassica vegetable crops.
             Arabidopsis (Arabidopsis thaliana) accessions contain three
             different patterns of 2-hydroxybut-3-enyl glucosinolate
             accumulation (present in leaves and seeds, seeds only, or
             absent) corresponding to three different alleles at a single
             locus, GSL-OH. Fine-scale mapping of the GSL-OH locus
             identified a 2-oxoacid-dependent dioxygenase encoded by
             At2g25450 required for the formation of both 2R- and
             2S-2-hydroxybut-3-enyl glucosinolate from the precursor
             3-butenyl glucosinolate precursor. Naturally occurring null
             mutations and T-DNA insertional mutations in At2g25450
             exhibit a complete absence of 2-hydroxybut-3-enyl
             glucosinolate accumulation. Analysis of herbivory by the
             generalist lepidopteran Trichoplusia ni showed that
             production of 2-hydroxybut-3-enyl glucosinolate provides
             increased resistance. These results show that At2g25450 is
             necessary for the hydroxylation of but-3-enyl glucosinolate
             to 2-hydroxybut-3-enyl glucosinolate in planta and that this
             metabolite increases resistance to generalist
             herbivory.},
   Doi = {10.1104/pp.108.129981},
   Key = {fds229202}
}

@article{fds229192,
   Author = {Oyama, RK and Clauss, MJ and Formanová, N and Kroymann, J and Schmid,
             KJ and Vogel, H and Weniger, K and Windsor, AJ and Mitchell-Olds,
             T},
   Title = {The shrunken genome of Arabidopsis thaliana},
   Journal = {Plant Systematics and Evolution},
   Volume = {273},
   Number = {3-4},
   Pages = {257-271},
   Publisher = {Springer Nature},
   Year = {2008},
   Month = {July},
   ISSN = {0378-2697},
   url = {http://dx.doi.org/10.1007/s00606-008-0017-z},
   Abstract = {This paper examines macro and micro-level patterns of genome
             size evolution in the Brassicaceae. A phylogeny of 25
             relatives of Arabidopsis thaliana was reconstructed using
             four molecular markers under both parsimony and Bayesian
             methods. Reconstruction of genome size (C value) evolution
             as a discrete character and as a continuous character was
             also performed. In addition, size dynamics in small
             chromosomal regions were assessed by comparing genomic
             clones generated for Arabidopsis lyrata and for Boechera
             stricta to the fully sequenced genome of A. thaliana. The
             results reveal a sevenfold variation in genome size among
             the taxa investigated and that the small genome size of A.
             thaliana is derived. Our results also indicate that the
             genome is free to increase or decrease in size across these
             evolutionary lineages without a directional bias. These
             changes are accomplished by insertions and deletions at both
             large and small-scales occurring mostly in intergenic
             regions, with repetitive sequences and transposable elements
             implicated in genome size increases. The focus upon taxa
             relatively closely related to the model organism A.
             thaliana, and the combination of complementary approaches,
             allows for unique insights into the processes driving genome
             size changes. © 2008 The Author(s).},
   Doi = {10.1007/s00606-008-0017-z},
   Key = {fds229192}
}

@article{fds229204,
   Author = {Ming, R and Hou, S and Feng, Y and Yu, Q and Dionne-Laporte, A and Saw, JH and Senin, P and Wang, W and Ly, BV and Lewis, KLT and Salzberg, SL and Feng,
             L and Jones, MR and Skelton, RL and Murray, JE and Chen, C and Qian, W and Shen, J and Du, P and Eustice, M and Tong, E and Tang, H and Lyons, E and Paull, RE and Michael, TP and Wall, K and Rice, DW and Albert, H and Wang,
             M-L and Zhu, YJ and Schatz, M and Nagarajan, N and Acob, RA and Guan, P and Blas, A and Wai, CM and Ackerman, CM and Ren, Y and Liu, C and Wang, J and Wang, J and Na, J-K and Shakirov, EV and Haas, B and Thimmapuram, J and Nelson, D and Wang, X and Bowers, JE and Gschwend, AR and Delcher, AL and Singh, R and Suzuki, JY and Tripathi, S and Neupane, K and Wei, H and Irikura, B and Paidi, M and Jiang, N and Zhang, W and Presting, G and Windsor, A and Navajas-Pérez, R and Torres, MJ and Feltus, FA and Porter, B and Li, Y and Burroughs, AM and Luo, M-C and Liu, L and Christopher, DA and Mount, SM and Moore, PH and Sugimura, T and Jiang,
             J and Schuler, MA and Friedman, V and Mitchell-Olds, T and Shippen, DE and dePamphilis, CW and Palmer, JD and Freeling, M and Paterson, AH and Gonsalves, D and Wang, L and Alam, M},
   Title = {The draft genome of the transgenic tropical fruit tree
             papaya (Carica papaya Linnaeus).},
   Journal = {Nature},
   Volume = {452},
   Number = {7190},
   Pages = {991-996},
   Year = {2008},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18432245},
   Abstract = {Papaya, a fruit crop cultivated in tropical and subtropical
             regions, is known for its nutritional benefits and medicinal
             applications. Here we report a 3x draft genome sequence of
             'SunUp' papaya, the first commercial virus-resistant
             transgenic fruit tree to be sequenced. The papaya genome is
             three times the size of the Arabidopsis genome, but contains
             fewer genes, including significantly fewer
             disease-resistance gene analogues. Comparison of the five
             sequenced genomes suggests a minimal angiosperm gene set of
             13,311. A lack of recent genome duplication, atypical of
             other angiosperm genomes sequenced so far, may account for
             the smaller papaya gene number in most functional groups.
             Nonetheless, striking amplifications in gene number within
             particular functional groups suggest roles in the evolution
             of tree-like habit, deposition and remobilization of starch
             reserves, attraction of seed dispersal agents, and
             adaptation to tropical daylengths. Transgenesis at three
             locations is closely associated with chloroplast insertions
             into the nuclear genome, and with topoisomerase I
             recognition sites. Papaya offers numerous advantages as a
             system for fruit-tree functional genomics, and this draft
             genome sequence provides the foundation for revealing the
             basis of Carica's distinguishing morpho-physiological,
             medicinal and nutritional properties.},
   Doi = {10.1038/nature06856},
   Key = {fds229204}
}

@article{fds229205,
   Author = {Benfey, PN and Mitchell-Olds, T},
   Title = {From genotype to phenotype: systems biology meets natural
             variation.},
   Journal = {Science (New York, N.Y.)},
   Volume = {320},
   Number = {5875},
   Pages = {495-497},
   Year = {2008},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18436781},
   Abstract = {The promise that came with genome sequencing was that we
             would soon know what genes do, particularly genes involved
             in human diseases and those of importance to agriculture. We
             now have the full genomic sequence of human, chimpanzee,
             mouse, chicken, dog, worm, fly, rice, and cress, as well as
             those for a wide variety of other species, and yet we still
             have a lot of trouble figuring out what genes do. Mapping
             genes to their function is called the "genotype-to-phenotype
             problem," where phenotype is whatever is changed in the
             organism when a gene's function is altered.},
   Doi = {10.1126/science.1153716},
   Key = {fds229205}
}

@article{fds229207,
   Author = {Mitchell-Olds, T and Feder, M and Wray, G},
   Title = {Evolutionary and ecological functional genomics.},
   Journal = {Heredity},
   Volume = {100},
   Number = {2},
   Pages = {101-102},
   Year = {2008},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18212796},
   Doi = {10.1038/sj.hdy.6801015},
   Key = {fds229207}
}

@article{fds229190,
   Author = {Wheat, CW and Vogel, H and Wittstock, U and Braby, MF and Underwood, D and Mitchell-Olds, T},
   Title = {The genetic basis of a plant-insect coevolutionary key
             innovation.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {104},
   Number = {51},
   Pages = {20427-20431},
   Year = {2007},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18077380},
   Abstract = {Ehrlich and Raven formally introduced the concept of
             stepwise coevolution using butterfly and angiosperm
             interactions in an attempt to account for the impressive
             biological diversity of these groups. However, many
             biologists currently envision butterflies evolving 50 to 30
             million years (Myr) after the major angiosperm radiation and
             thus reject coevolutionary origins of butterfly
             biodiversity. The unresolved central tenet of Ehrlich and
             Raven's theory is that evolution of plant chemical defenses
             is followed closely by biochemical adaptation in insect
             herbivores, and that newly evolved detoxification mechanisms
             result in adaptive radiation of herbivore lineages. Using
             one of their original butterfly-host plant systems, the
             Pieridae, we identify a pierid glucosinolate detoxification
             mechanism, nitrile-specifier protein (NSP), as a key
             innovation. Larval NSP activity matches the distribution of
             glucosinolate in their host plants. Moreover, by using five
             different temporal estimates, NSP seems to have evolved
             shortly after the evolution of the host plant group
             (Brassicales) ( approximately 10 Myr). An adaptive radiation
             of these glucosinolate-feeding Pierinae followed, resulting
             in significantly elevated species numbers compared with
             related clades. Mechanistic understanding in its proper
             historical context documents more ancient and dynamic
             plant-insect interactions than previously envisioned.
             Moreover, these mechanistic insights provide the tools for
             detailed molecular studies of coevolution from both the
             plant and insect perspectives.},
   Doi = {10.1073/pnas.0706229104},
   Key = {fds229190}
}

@article{fds229161,
   Author = {Mitchell-Olds, T and Willis, JH and Goldstein,
             DB},
   Title = {Which evolutionary processes influence natural genetic
             variation for phenotypic traits?},
   Journal = {Nature Reviews. Genetics},
   Volume = {8},
   Number = {11},
   Pages = {845-856},
   Year = {2007},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17943192},
   Abstract = {Although many studies provide examples of evolutionary
             processes such as adaptive evolution, balancing selection,
             deleterious variation and genetic drift, the relative
             importance of these selective and stochastic processes for
             phenotypic variation within and among populations is
             unclear. Theoretical and empirical studies from humans as
             well as natural animal and plant populations have made
             progress in examining the role of these evolutionary forces
             within species. Tentative generalizations about evolutionary
             processes across species are beginning to emerge, as well as
             contrasting patterns that characterize different groups of
             organisms. Furthermore, recent technical advances now allow
             the combination of ecological measurements of selection in
             natural environments with population genetic analysis of
             cloned QTLs, promising advances in identifying the
             evolutionary processes that influence natural genetic
             variation.},
   Doi = {10.1038/nrg2207},
   Key = {fds229161}
}

@article{fds229208,
   Author = {Song, B-H and Mitchell-Olds, T},
   Title = {High genetic diversity and population differentiation in
             Boechera fecunda, a rare relative of Arabidopsis.},
   Journal = {Molecular Ecology},
   Volume = {16},
   Number = {19},
   Pages = {4079-4088},
   Year = {2007},
   Month = {October},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17784916},
   Abstract = {Conservation of endangered species becomes a critical issue
             with the increasing rates of extinction. In this study, we
             use 13 microsatellite loci and 27 single-copy nuclear loci
             to investigate the population genetics of Boechera fecunda,
             a rare relative of Arabidopsis thaliana, known from only 21
             populations in Montana. We investigated levels of genetic
             diversity and population structure in comparison to its
             widespread congener, Boechera stricta, which shares similar
             life history and mating system. Despite its rarity, B.
             fecunda had levels of genetic diversity similar to B.
             stricta for both microsatellites and nucleotide
             polymorphism. Populations of B. fecunda are highly
             differentiated, with a majority of genetic diversity
             existing among populations (F(ST) = 0.57). Differences in
             molecular diversity and allele frequencies between western
             and eastern population groups suggest they experienced very
             different evolutionary histories.},
   Doi = {10.1111/j.1365-294x.2007.03500.x},
   Key = {fds229208}
}

@article{fds229209,
   Author = {Kantama, L and Sharbel, TF and Schranz, ME and Mitchell-Olds, T and de
             Vries, S and de Jong, H},
   Title = {Diploid apomicts of the Boechera holboellii complex display
             large-scale chromosome substitutions and aberrant
             chromosomes.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {104},
   Number = {35},
   Pages = {14026-14031},
   Year = {2007},
   Month = {August},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17704257},
   Abstract = {We conducted a cytogenetic study of sexual lines of Boechera
             stricta and Boechera holboellii (2n = 14) and seven diploid
             apomictic accessions of their interspecific hybrid Boechera
             divaricarpa and B. holboellii (2n = 14 or 15). By studying
             chromosome morphology, rDNA repeats, genome painting, male
             meiosis, pollen morphology, and flow-cytometry seed screens,
             we revealed an unexpected plethora of chromosome forms,
             pairing behavior, and hybrid composition in all apomictic
             lines. Genome painting demonstrated that the apomicts are
             alloploid with variable numbers of B. stricta and B.
             holboellii-like chromosomes. We assume that large-scale
             homeologous chromosome substitutions took place in the
             apomictic hybrids that resulted from recurrent
             diploid-polyploid transitions through restitutional meiosis
             and polyploidy-diploid transitions through reductional
             meiosis. A second peculiarity was the presence of a largely
             heterochromatic chromosome (Het) in all apomictic accessions
             (2n = 14 and 15) and an additional smaller chromosome (Del)
             in the aneuploids (2n = 15). Both chromosomes share
             repetitive pericentromere repeats with those from the sexual
             B. stricta, suggesting that they originated from this
             species. Pairing and behavior at meiosis I of the Het share
             features with both Y and B chromosomes and suggest that the
             Del arose from a translocation event or homeologous
             recombination between a B. holboellii (or related taxon) and
             a B. stricta chromosome. Based on its presence exclusively
             in apomictic accessions, we propose that the Het chromosome
             plays a role in the genetic control of apomixis.},
   Doi = {10.1073/pnas.0706647104},
   Key = {fds229209}
}

@article{fds229206,
   Author = {Ramos-Onsins, SE and Mousset, S and Mitchell-Olds, T and Stephan,
             W},
   Title = {Population genetic inference using a fixed number of
             segregating sites: a reassessment.},
   Journal = {Genetical Research},
   Volume = {89},
   Number = {4},
   Pages = {231-244},
   Year = {2007},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18208629},
   Abstract = {Coalescent theory is commonly used to perform population
             genetic inference at the nucleotide level. Here, we examine
             the procedure that fixes the number of segregating sites
             (henceforth the FS procedure). In this approach a fixed
             number of segregating sites (S) are placed on a coalescent
             tree (independently of the total and internode lengths of
             the tree). Thus, although widely used, the FS procedure does
             not strictly follow the assumptions of coalescent theory and
             must be considered an approximation of (i) the standard
             procedure that uses a fixed population mutation parameter
             theta, and (ii) procedures that condition on the number of
             segregating sites. We study the differences in the false
             positive rate for nine statistics by comparing the FS
             procedure with the procedures (i) and (ii), using several
             evolutionary models with single-locus and multilocus data.
             Our results indicate that for single-locus data the FS
             procedure is accurate for the equilibrium neutral model, but
             problems arise under the alternative models studied;
             furthermore, for multilocus data, the FS procedure becomes
             inaccurate even for the standard neutral model. Therefore,
             we recommend a procedure that fixes the theta value (or
             alternatively, procedures that condition on S and take into
             account the uncertainty of theta) for analysing evolutionary
             models with multilocus data. With single-locus data, the FS
             procedure should not be employed for models other than the
             standard neutral model.},
   Doi = {10.1017/s0016672307008877},
   Key = {fds229206}
}

@article{fds229158,
   Author = {Schranz, ME and Windsor, AJ and Song, B and Lawton-Rauh, A and Mitchell-Olds, T},
   Title = {Erratum: Comparative genetic mapping in Boechera stricta, a
             close relative of arabidopsis (Plant Physiology (2007) 144,
             (286-298))},
   Journal = {Plant Physiology},
   Volume = {144},
   Number = {3},
   Pages = {1690},
   Publisher = {American Society of Plant Biologists (ASPB)},
   Year = {2007},
   Month = {July},
   ISSN = {0032-0889},
   url = {http://dx.doi.org/10.1104/pp.104.900229},
   Doi = {10.1104/pp.104.900229},
   Key = {fds229158}
}

@article{fds229212,
   Author = {Pfalz, M and Vogel, H and Mitchell-Olds, T and Kroymann,
             J},
   Title = {Mapping of QTL for resistance against the crucifer
             specialist herbivore Pieris brassicae in a new Arabidopsis
             inbred line population, Da(1)-12 x Ei-2.},
   Journal = {Plos One},
   Volume = {2},
   Number = {6},
   Pages = {e578},
   Year = {2007},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17593977},
   Abstract = {In Arabidopsis thaliana and other crucifers, the
             glucosinolate-myrosinase system contributes to resistance
             against herbivory by generalist insects. As yet, it is
             unclear how crucifers defend themselves against
             crucifer-specialist insect herbivores.We analyzed natural
             variation for resistance against two crucifer specialist
             lepidopteran herbivores, Pieris brassicae and Plutella
             xylostella, among Arabidopsis thaliana accessions and in a
             new Arabidopsis recombinant inbred line (RIL) population
             generated from the parental accessions Da(1)-12 and Ei-2.
             This RIL population consists of 201 individual F(8) lines
             genotyped with 84 PCR-based markers. We identified six QTL
             for resistance against Pieris herbivory, but found only one
             weak QTL for Plutella resistance. To elucidate potential
             factors causing these resistance QTL, we investigated leaf
             hair (trichome) density, glucosinolates and myrosinase
             activity, traits known to influence herbivory by generalist
             insects. We identified several previously unknown QTL for
             these traits, some of which display a complex pattern of
             epistatic interactions.Although some trichome, glucosinolate
             or myrosinase QTL co-localize with Pieris QTL, none of these
             traits explained the resistance QTL convincingly, indicating
             that resistance against specialist insect herbivores is
             influenced by other traits than resistance against
             generalists.},
   Doi = {10.1371/journal.pone.0000578},
   Key = {fds229212}
}

@article{fds229157,
   Author = {Schranz, ME and Windsor, AJ and Song, B-H and Lawton-Rauh, A and Mitchell-Olds, T},
   Title = {Comparative genetic mapping in Boechera stricta, a close
             relative of Arabidopsis.},
   Journal = {Plant Physiology},
   Volume = {144},
   Number = {1},
   Pages = {286-298},
   Year = {2007},
   Month = {May},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17369426},
   Abstract = {The angiosperm family Brassicaceae contains both the
             research model Arabidopsis (Arabidopsis thaliana) and the
             agricultural genus Brassica. Comparative genomics in the
             Brassicaceae has largely focused on direct comparisons
             between Arabidopsis and the species of interest. However,
             the reduced genome size and chromosome number (n = 5) of
             Arabidopsis complicates comparisons. Arabidopsis shows
             extensive genome and chromosome reshuffling compared to its
             close relatives Arabidopsis lyrata and Capsella rubella,
             both with n = 8. To facilitate comparative genomics across
             the Brassicaceae we recently outlined a system of 24
             conserved chromosomal blocks based on their positions in an
             ancestral karyotype of n = 8, rather than by their position
             in Arabidopsis. In this report we use this system as a tool
             to understand genome structure and evolution in Boechera
             stricta (n = 7). B. stricta is a diploid, sexual, and highly
             self-fertilizing species occurring in mostly montane regions
             of western North America. We have created an F(2) genetic
             map of B. stricta based on 192 individuals scored at 196
             microsatellite and candidate gene loci. Single-nucleotide
             polymorphism genotyping of 94 of the loci was done
             simultaneously using an Illumina bead array. The total map
             length is 725.8 cM, with an average marker spacing of 3.9
             cM. There are no gaps greater than 19.3 cM. The chromosomal
             reduction from n = 8 to n = 7 and other genomic changes in
             B. stricta likely involved a pericentric inversion, a
             chromosomal fusion, and two reciprocal translocations that
             are easily visualized using the genomic blocks. Our genetic
             map will facilitate the analysis of ecologically relevant
             quantitative variation in Boechera. Sequence data from this
             article can be found in the GenBank/EMBL data libraries
             under accession numbers DU 667459 to DU 708532.},
   Doi = {10.1104/pp.107.096685},
   Key = {fds229157}
}

@article{fds229213,
   Author = {Schranz, ME and Song, B-H and Windsor, AJ and Mitchell-Olds,
             T},
   Title = {Comparative genomics in the Brassicaceae: a family-wide
             perspective.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {10},
   Number = {2},
   Pages = {168-175},
   Year = {2007},
   Month = {April},
   ISSN = {1369-5266},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17300984},
   Abstract = {Comparative genomics of Arabidopsis relatives has great
             potential to improve our understanding of molecular function
             and evolutionary processes. Recent studies of phylogenetic
             relationships within Brassicaceae and the publication of a
             new tribal classification scheme provide an important
             framework for comparative genomics research. Comparative
             linkage mapping and chromosome painting in the close
             relatives of Arabidopsis have inferred an ancestral
             karyotype of these species. In addition, comparative mapping
             to Brassica has identified genomic blocks that have been
             maintained since the divergence of the Arabidopsis and
             Brassica lineages. Several analyses of conserved non-coding
             regions have identified putative cis-regulatory sequences,
             and have highlighted the need for comparative sequencing at
             greater evolutionary distances. The development of new model
             species with novel physiological and ecological traits
             allows analysis of phenotypes that are not available in A.
             thaliana. Looking towards the future, we suggest a
             prioritized research agenda for comparative genomics in the
             Brassicaceae.},
   Doi = {10.1016/j.pbi.2007.01.014},
   Key = {fds229213}
}

@article{fds229203,
   Author = {Ramos-Onsins, SE and Mitchell-Olds, T},
   Title = {Mlcoalsim: multilocus coalescent simulations.},
   Journal = {Evolutionary Bioinformatics Online},
   Volume = {3},
   Pages = {41-44},
   Year = {2007},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19430603},
   Abstract = {Coalescent theory is a powerful tool for population
             geneticists as well as molecular biologists interested in
             understanding the patterns and levels of DNA variation.
             Using coalescent Monte Carlo simulations it is possible to
             obtain the empirical distributions for a number of
             statistics across a wide range of evolutionary models; these
             distributions can be used to test evolutionary hypotheses
             using experimental data. The mlcoalsim application presented
             here (based on a version of the ms program, Hudson, 2002)
             adds important new features to improve methodology
             (uncertainty and conditional methods for mutation and
             recombination), models (including strong positive selection,
             finite sites and heterogeneity in mutation and recombination
             rates) and analyses (calculating a number of statistics used
             in population genetics and P-values for observed data). One
             of the most important features of mlcoalsim is the analysis
             of multilocus data in linked and independent regions. In
             summary, mlcoalsim is an integrated software application
             aimed at researchers interested in molecular evolution.
             mlcoalsim is written in ANSI C and is available at:
             http://www.ub.es/softevol/mlcoalsim.},
   Key = {fds229203}
}

@article{fds229211,
   Author = {Vogel, H and Kroymann, J and Mitchell-Olds, T},
   Title = {Different transcript patterns in response to specialist and
             generalist herbivores in the wild Arabidopsis relative
             Boechera divaricarpa.},
   Journal = {Plos One},
   Volume = {2},
   Number = {10},
   Pages = {e1081},
   Year = {2007},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17957263},
   Abstract = {BACKGROUND: Plants defend themselves against herbivorous
             insects, utilizing both constitutive and inducible defenses.
             Induced defenses are controlled by several
             phytohormone-mediated signaling pathways. Here, we analyze
             transcriptional changes in the North American Arabidopsis
             relative Boechera divaricarpa in response to larval
             herbivory by the crucifer specialist lepidopteran Plutella
             xylostella (diamondback moth) and by the generalist
             lepidopteran Trichoplusia ni (cabbage semilooper), and
             compare them to wounding and exogenous phytohormone
             application. METHODOLOGY/PRINCIPAL FINDINGS: We use a custom
             macroarray constructed from B. divaricarpa
             herbivory-regulated cDNAs identified by suppression
             subtractive hybridization and from known stress-responsive
             A. thaliana genes for transcript profiling after insect
             herbivory, wounding and in response to jasmonate, salicylate
             and ethylene. In addition, we introduce path analysis as a
             novel approach to analyze transcript profiles. Path analyses
             reveal that transcriptional responses to the crucifer
             specialist P. xylostella are primarily determined by direct
             effects of the ethylene and salicylate pathways, whereas
             responses to the generalist T. ni are influenced by the
             ethylene and jasmonate pathways. Wound-induced
             transcriptional changes are influenced by all three
             pathways, with jasmonate having the strongest effect.
             CONCLUSIONS/SIGNIFICANCE: Our results show that insect
             herbivory is distinct from simple mechanical plant damage,
             and that different lepidopteran herbivores elicit different
             transcriptional responses.},
   Doi = {10.1371/journal.pone.0001081},
   Key = {fds229211}
}

@article{fds229215,
   Author = {de Meaux, J and Pop, A and Mitchell-Olds, T},
   Title = {Cis-regulatory evolution of chalcone-synthase expression in
             the genus Arabidopsis.},
   Journal = {Genetics},
   Volume = {174},
   Number = {4},
   Pages = {2181-2202},
   Year = {2006},
   Month = {December},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17028316},
   Abstract = {The contribution of cis-regulation to adaptive evolutionary
             change is believed to be essential, yet little is known
             about the evolutionary rules that govern regulatory
             sequences. Here, we characterize the short-term evolutionary
             dynamics of a cis-regulatory region within and among two
             closely related species, A. lyrata and A. halleri, and
             compare our findings to A. thaliana. We focused on the
             cis-regulatory region of chalcone synthase (CHS), a key
             enzyme involved in the synthesis of plant secondary
             metabolites. We observed patterns of nucleotide diversity
             that differ among species but do not depart from neutral
             expectations. Using intra- and interspecific F1 progeny, we
             have evaluated functional cis-regulatory variation in
             response to light and herbivory, environmental cues, which
             are known to induce CHS expression. We find that substantial
             cis-regulatory variation segregates within and among
             populations as well as between species, some of which
             results from interspecific genetic introgression. We further
             demonstrate that, in A. thaliana, CHS cis-regulation in
             response to herbivory is greater than in A. lyrata or A.
             halleri. Our work indicates that the evolutionary dynamics
             of a cis-regulatory region is characterized by pervasive
             functional variation, achieved mostly by modification of
             response modules to one but not all environmental cues. Our
             study did not detect the footprint of selection on this
             variation.},
   Doi = {10.1534/genetics.106.064543},
   Key = {fds229215}
}

@article{fds229214,
   Author = {Clauss, MJ and Dietel, S and Schubert, G and Mitchell-Olds,
             T},
   Title = {Glucosinolate and trichome defenses in a natural Arabidopsis
             lyrata population.},
   Journal = {Journal of Chemical Ecology},
   Volume = {32},
   Number = {11},
   Pages = {2351-2373},
   Year = {2006},
   Month = {November},
   ISSN = {0098-0331},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17089185},
   Abstract = {Glucosinolates (GS) and trichomes contribute to plant
             resistance against insect herbivores in the model
             Arabidopsis thaliana. The functional and genetic
             characteristics of herbivore defense, however, can differ
             even between closely related species. In a quantitative
             genetic experiment with the out-crossing perennial
             Arabidopsis lyrata spp. petraea, we measured constitutive GS
             composition, trichome density, leaf thickness, and plant
             resistance in four different herbivore interactions. In a
             single population of A. lyrata, we found heritable variation
             for trichome density as well as GS amount and carbon
             side-chain elongation ratios associated with activity in
             methylthioalkylmalate synthase (MAM). Unexpectedly,
             heritabilities for indole GS in A. lyrata were high and less
             affected by differences in plant age and environment than
             aliphatic GS. We found significant heritability in plant
             resistance to the specialist Plutella xylostella and
             generalist Trichoplusia ni, but not to the specialists
             Pieris brassicae and Phyllotreta cruciferae. Analyses of
             phenotypic and genetic correlations between candidate
             defense traits and insect resistance suggested that A.
             lyrata resistance was conferred by a combination of indole
             GS amount and trichome density, and, to a lesser extent,
             aliphatic GS ratios and leaf thickness. Variation in the
             most abundant compound, the aliphatic 3-hydroxypropyl GS,
             had little impact on A. lyrata herbivore resistance. The
             contribution of defense traits to resistance depended on the
             experimental herbivory context, and resistances were weakly
             correlated. A diversified defense strategy is likely to be
             important for long-lived individuals of A. lyrata that are
             subject to attack by many different herbivores in
             nature.},
   Doi = {10.1007/s10886-006-9150-8},
   Key = {fds229214}
}

@article{fds229216,
   Author = {Schranz, ME and Lysak, MA and Mitchell-Olds, T},
   Title = {The ABC's of comparative genomics in the Brassicaceae:
             building blocks of crucifer genomes.},
   Journal = {Trends in Plant Science},
   Volume = {11},
   Number = {11},
   Pages = {535-542},
   Year = {2006},
   Month = {November},
   ISSN = {1360-1385},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17029932},
   Abstract = {In this review we summarize recent advances in our
             understanding of phylogenetics, polyploidization and
             comparative genomics in the family Brassicaceae. These
             findings pave the way for a unified comparative genomic
             framework. We integrate several of these findings into a
             simple system of 24 conserved chromosomal blocks (labeled
             A-X). The naming, order, orientation and color-coding of
             these blocks are based on their positions in a proposed
             ancestral karyotype (n=8), rather than by their position in
             the reduced genome of Arabidopsis thaliana (n=5). We show
             how these crucifer building blocks can be rearranged to
             model the genome structures of A. thaliana, Arabidopsis
             lyrata, Capsella rubella and Brassica rapa. A framework for
             comparison between species is timely because several
             crucifer genome-sequencing projects are underway.},
   Doi = {10.1016/j.tplants.2006.09.002},
   Key = {fds229216}
}

@article{fds229217,
   Author = {Clauss, MJ and Mitchell-Olds, T},
   Title = {Population genetic structure of Arabidopsis lyrata in
             Europe.},
   Journal = {Molecular Ecology},
   Volume = {15},
   Number = {10},
   Pages = {2753-2766},
   Year = {2006},
   Month = {September},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16911198},
   Abstract = {Population genetic theory predicts that the
             self-incompatible and perennial herb, Arabidopsis lyrata,
             will have a genetic structure that differs from the
             self-fertilizing, annual Arabidopsis thaliana. We quantified
             the genetic structure for eight populations of A. lyrata
             ssp. petraea in historically nonglaciated regions of central
             Europe. Analysis of 20 microsatellite loci for 344
             individuals demonstrated that, in accordance with
             predictions, diploid populations had high genome-wide
             heterozygosity (H(O) = 0.48; H(E) = 0.52), high
             within-population diversity (83% of total) compatible with
             mutation-drift equilibrium, and moderate differentiation
             among populations (F(ST) = 0.17). Within a single
             population, the vast majority of genetic variability (92%)
             was found at the smallest spatial scale (< 3 m). Although
             there was no evidence of biparental inbreeding or clonal
             propagation at this scale (F(IS) = 0.003), significant
             fine-scale spatial autocorrelation indicated localized gene
             flow presumably due to gravity dispersed seeds (Sp = 0.018).
             Limited gene flow between isolated population clusters
             (regions) separated by hundreds of kilometres has given rise
             to an isolation by distance pattern of diversification, with
             low, but significant, differentiation among regions (F(ST) =
             0.05). The maintenance of geographically widespread
             polymorphisms and uniformly high diversity throughout
             central Europe is consistent with periglacial survival of A.
             lyrata ssp. petraea north of the Alps in steppe-tundra
             habitats during the last glacial maximum. As expected of
             northern and previously glaciated localities, A. lyrata in
             Iceland was genetically less diverse and highly
             differentiated from central Europe (H(E) = 0.37; F(ST) =
             0.27).},
   Doi = {10.1111/j.1365-294x.2006.02973.x},
   Key = {fds229217}
}

@article{fds229219,
   Author = {Heidel, AJ and Clauss, MJ and Kroymann, J and Savolainen, O and Mitchell-Olds, T},
   Title = {Natural variation in MAM within and between populations of
             Arabidopsis lyrata determines glucosinolate
             phenotype.},
   Journal = {Genetics},
   Volume = {173},
   Number = {3},
   Pages = {1629-1636},
   Year = {2006},
   Month = {July},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16702431},
   Abstract = {The genetic variation that underlies the glucosinolate
             phenotype of Arabidopsis lyrata ssp. petraea was
             investigated between and within populations. A candidate
             glucosinolate biosynthetic locus (MAM, containing
             methylthioalkylmalate synthase genes) was mapped in A.
             lyrata to a location on linkage group 6 corresponding to the
             homologous location for MAM in A. thaliana. In A. thaliana
             MAM is responsible for side chain elongation in aliphatic
             glucosinolates, and the MAM phenotype can be characterized
             by the ratios of long- to short-chain glucosinolates. A
             quantitative trait loci (QTL) analysis of glucosinolate
             ratios in an A. lyrata interpopulation cross found one QTL
             at MAM. Additional QTL were identified for total indolic
             glucosinolates and for the ratio of aliphatic to indolic
             glucosinolates. MAM was then used as the candidate gene for
             a within-population cosegregation analysis in a natural A.
             lyrata population from Germany. Extensive variation in
             microsatellite markers at MAM was found and this variation
             cosegregated with the same glucosinolate ratios as in the
             QTL study. The combined results indicate that both between-
             and within-population genetic variation in the MAM region
             determines phenotypic variation in glucosinolate side chains
             in A. lyrata.},
   Doi = {10.1534/genetics.106.056986},
   Key = {fds229219}
}

@article{fds229210,
   Author = {Benderoth, M and Textor, S and Windsor, AJ and Mitchell-Olds, T and Gershenzon, J and Kroymann, J},
   Title = {Positive selection driving diversification in plant
             secondary metabolism.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {103},
   Number = {24},
   Pages = {9118-9123},
   Year = {2006},
   Month = {June},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16754868},
   Abstract = {In Arabidopsis thaliana and related plants, glucosinolates
             are a major component in the blend of secondary metabolites
             and contribute to resistance against herbivorous insects.
             Methylthioalkylmalate synthases (MAM) encoded at the MAM
             gene cluster control an early step in the biosynthesis of
             glucosinolates and, therefore, are central to the
             diversification of glucosinolate metabolism. We sequenced
             bacterial artificial chromosomes containing the MAM cluster
             from several Arabidopsis relatives, conducted enzyme assays
             with heterologously expressed MAM genes, and analyzed MAM
             nucleotide variation patterns. Our results show that gene
             duplication, neofunctionalization, and positive selection
             provide the mechanism for biochemical adaptation in plant
             defense. These processes occur repeatedly in the history of
             the MAM gene family, indicating their fundamental importance
             for the evolution of plant metabolic diversity both within
             and among species.},
   Doi = {10.1073/pnas.0601738103},
   Key = {fds229210}
}

@article{fds229142,
   Author = {Lambrix, V and Reichelt, M and Mitchell-Olds, T and Kliebenstein, DJ and Gershenzon, J},
   Title = {The Arabidopsis epithiospecifier protein promotes the
             hydrolysis of glucosinolates to nitriles and influences
             Trichoplusia ni herbivory (vol 13, pg 2793,
             2001)},
   Journal = {The Plant Cell},
   Volume = {18},
   Number = {6},
   Pages = {1537-1537},
   Publisher = {AMER SOC PLANT BIOLOGISTS},
   Year = {2006},
   Month = {June},
   ISSN = {1040-4651},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000238088300018&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds229142}
}

@article{fds229156,
   Author = {Lambrix, V and Reichelt, M and Mitchell-Olds, T and Kliebenstein, DJ and Gershenzon, J},
   Title = {Erratum: The Arabidopsis epithiospecifier protein promotes
             the hydrolysis of glucosinolates to nitriles and influences
             Trichoplusia ni herbivory (Plant Cell (2001) 13
             (2793-2807))},
   Journal = {The Plant Cell},
   Volume = {18},
   Number = {6},
   Pages = {1537},
   Publisher = {American Society of Plant Biologists (ASPB)},
   Year = {2006},
   Month = {June},
   ISSN = {1040-4651},
   url = {http://dx.doi.org/10.1105/tpc.106.180660},
   Doi = {10.1105/tpc.106.180660},
   Key = {fds229156}
}

@article{fds229218,
   Author = {Mitchell-Olds, T and Schmitt, J},
   Title = {Genetic mechanisms and evolutionary significance of natural
             variation in Arabidopsis.},
   Journal = {Nature},
   Volume = {441},
   Number = {7096},
   Pages = {947-952},
   Year = {2006},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16791187},
   Abstract = {Genomic studies of natural variation in model organisms
             provide a bridge between molecular analyses of gene function
             and evolutionary investigations of adaptation and natural
             selection. In the model plant species Arabidopsis thaliana,
             recent studies of natural variation have led to the
             identification of genes underlying ecologically important
             complex traits, and provided new insights about the
             processes of genome evolution, geographic population
             structure, and the selective mechanisms shaping complex
             trait variation in natural populations. These advances
             illustrate the potential for a new synthesis to elucidate
             mechanisms for the adaptive evolution of complex traits from
             nucleotide sequences to real-world environments.},
   Doi = {10.1038/nature04878},
   Key = {fds229218}
}

@article{fds229221,
   Author = {Schranz, ME and Mitchell-Olds, T},
   Title = {Independent ancient polyploidy events in the sister families
             Brassicaceae and Cleomaceae.},
   Journal = {The Plant Cell},
   Volume = {18},
   Number = {5},
   Pages = {1152-1165},
   Year = {2006},
   Month = {May},
   ISSN = {1040-4651},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16617098},
   Abstract = {Recent studies have elucidated the ancient polyploid history
             of the Arabidopsis thaliana (Brassicaceae) genome. The
             studies concur that there was at least one polyploidy event
             occurring some 14.5 to 86 million years ago (Mya), possibly
             near the divergence of the Brassicaceae from its sister
             family, Cleomaceae. Using a comparative genomics approach,
             we asked whether this polyploidy event was unique to members
             of the Brassicaceae, shared with the Cleomaceae, or an
             independent polyploidy event in each lineage. We isolated
             and sequenced three genomic regions from diploid Cleome
             spinosa (Cleomaceae) that are each homoeologous to a
             duplicated region shared between At3 and At5, centered on
             the paralogs of SEPALLATA (SEP) and CONSTANS (CO).
             Phylogenetic reconstructions and analysis of synonymous
             substitution rates support the hypothesis that a genomic
             triplication in Cleome occurred independently of and more
             recently than the duplication event in the Brassicaceae.
             There is a strong correlation in the copy number (single
             versus duplicate) of individual genes, suggesting
             functionally consistent influences operating on gene copy
             number in these two independently evolving lineages.
             However, the amount of gene loss in Cleome is greater than
             in Arabidopsis. The genome of C. spinosa is only 1.9 times
             the size of A. thaliana, enabling comparative genome
             analysis of separate but related polyploidy
             events.},
   Doi = {10.1105/tpc.106.041111},
   Key = {fds229221}
}

@article{fds229154,
   Author = {Lee, CE and Mitchell-Olds, T},
   Title = {Preface to the special issue: ecological and evolutionary
             genomics of populations in nature.},
   Journal = {Molecular Ecology},
   Volume = {15},
   Number = {5},
   Pages = {1193-1196},
   Year = {2006},
   Month = {April},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16626447},
   Doi = {10.1111/j.1365-294x.2006.02945.x},
   Key = {fds229154}
}

@article{fds229155,
   Author = {Windsor, AJ and Schranz, ME and Formanová, N and Gebauer-Jung, S and Bishop, JG and Schnabelrauch, D and Kroymann, J and Mitchell-Olds,
             T},
   Title = {Partial shotgun sequencing of the Boechera stricta genome
             reveals extensive microsynteny and promoter conservation
             with Arabidopsis.},
   Journal = {Plant Physiology},
   Volume = {140},
   Number = {4},
   Pages = {1169-1182},
   Year = {2006},
   Month = {April},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16607030},
   Abstract = {Comparative genomics provides insight into the evolutionary
             dynamics that shape discrete sequences as well as whole
             genomes. To advance comparative genomics within the
             Brassicaceae, we have end sequenced 23,136 medium-sized
             insert clones from Boechera stricta, a wild relative of
             Arabidopsis (Arabidopsis thaliana). A significant proportion
             of these sequences, 18,797, are nonredundant and display
             highly significant similarity (BLASTn e-value < or =
             10(-30)) to low copy number Arabidopsis genomic regions,
             including more than 9,000 annotated coding sequences. We
             have used this dataset to identify orthologous gene pairs in
             the two species and to perform a global comparison of DNA
             regions 5' to annotated coding regions. On average, the 500
             nucleotides upstream to coding sequences display 71.4%
             identity between the two species. In a similar analysis,
             61.4% identity was observed between 5' noncoding sequences
             of Brassica oleracea and Arabidopsis, indicating that
             regulatory regions are not as diverged among these lineages
             as previously anticipated. By mapping the B. stricta end
             sequences onto the Arabidopsis genome, we have identified
             nearly 2,000 conserved blocks of microsynteny (bracketing
             26% of the Arabidopsis genome). A comparison of fully
             sequenced B. stricta inserts to their homologous Arabidopsis
             genomic regions indicates that indel polymorphisms >5 kb
             contribute substantially to the genome size difference
             observed between the two species. Further, we demonstrate
             that microsynteny inferred from end-sequence data can be
             applied to the rapid identification and cloning of genomic
             regions of interest from nonmodel species. These results
             suggest that among diploid relatives of Arabidopsis, small-
             to medium-scale shotgun sequencing approaches can provide
             rapid and cost-effective benefits to evolutionary and/or
             functional comparative genomic frameworks.},
   Doi = {10.1104/pp.105.073981},
   Key = {fds229155}
}

@article{fds229222,
   Author = {Windsor, AJ and Mitchell-Olds, T},
   Title = {Comparative genomics as a tool for gene discovery.},
   Journal = {Current Opinion in Biotechnology},
   Volume = {17},
   Number = {2},
   Pages = {161-167},
   Year = {2006},
   Month = {April},
   ISSN = {0958-1669},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16459073},
   Abstract = {With the increasing availability of data from multiple
             eukaryotic genome sequencing projects, attention has focused
             on interspecific comparisons to discover novel genes and
             transcribed genomic sequences. Generally, these extrinsic
             strategies combine ab initio gene prediction with expression
             and/or homology data to identify conserved gene candidates
             between two or more genomes. Interspecific sequence analyses
             have proven invaluable for the improvement of existing
             annotations, automation of annotation, and identification of
             novel coding regions and splice variants. Further,
             comparative genomic approaches hold the promise of improved
             prediction of terminal or small exons, microRNA precursors,
             and small peptide-encoding open reading frames--sequence
             elements that are difficult to identify through purely
             intrinsic methodologies in the absence of experimental
             data.},
   Doi = {10.1016/j.copbio.2006.01.007},
   Key = {fds229222}
}

@article{fds229224,
   Author = {Knight, CA and Vogel, H and Kroymann, J and Shumate, A and Witsenboer,
             H and Mitchell-Olds, T},
   Title = {Expression profiling and local adaptation of Boechera
             holboellii populations for water use efficiency across a
             naturally occurring water stress gradient.},
   Journal = {Molecular Ecology},
   Volume = {15},
   Number = {5},
   Pages = {1229-1237},
   Year = {2006},
   Month = {April},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16626450},
   Abstract = {We studied the physiological basis of local adaptation to
             drought in Boechera holboellii, a perennial relative of
             Arabidopsis thaliana, and used cDNA-AFLPs to identify
             candidate genes showing differential expression in these
             populations. We compared two populations of B. holboellii
             from contrasting water environments in a reciprocal
             transplant experiment, as well as in a laboratory dry-down
             experiment. We continuously measured the water content of
             soils using time domain reflectometery (TDR). We compared
             populations for their water use efficiency (WUE), root/shoot
             ratios (R:S) and leaf mass per unit area (LMA) in the field
             and in the laboratory, and identified candidate genes that
             (i) responded plastically to water stress and (ii) were
             differentially expressed between the two populations.
             Genotypes from the drier site had higher WUE, which was
             attributable to a large reduction in transpirational water
             loss. The xeric-adapted population also had increased
             investment in root biomass and greater leaf mass per unit
             area. Reciprocal transplants in the field had significantly
             greater survival in their native habitat. In total, 450
             cDNA-AFLP fragments showed significant changes between
             drought and control treatments. Furthermore, some genes
             showed genotype (population)-specific patterns of up- or
             down-regulation in response to drought. Three hundred
             cDNA-AFLP bands were sequenced leading to the identification
             of cDNAs coding for proteins involved in signal
             transduction, transcriptional regulation, redox regulation,
             oxidative stress and pathways involved in stress adaptation.
             Some of these proteins could contribute a physiological
             advantage under drought, making them potential targets for
             natural selection.},
   Doi = {10.1111/j.1365-294x.2006.02818.x},
   Key = {fds229224}
}

@article{fds229305,
   Author = {Song, B-H and Clauss, MJ and Pepper, A and Mitchell-Olds,
             T},
   Title = {Geographic patterns of microsatellite variation in Boechera
             stricta, a close relative of Arabidopsis.},
   Journal = {Molecular Ecology},
   Volume = {15},
   Number = {2},
   Pages = {357-369},
   Year = {2006},
   Month = {February},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16448406},
   Abstract = {The genus Boechera is a widespread North American group with
             great potential for studies of ecology and evolution:
             Boechera is closely related to Arabidopsis and exhibits
             different ecological and reproductive strategies. Boechera
             stricta (previously Arabis drummondii) is a morphologically
             and genetically well-defined, perennial crucifer species.
             Fifteen natural populations of diploid individuals from the
             Rocky Mountains were analysed using 21 microsatellite loci.
             In accordance with our expectation for this predominately
             inbreeding species, a high F IS value (0.89) was observed.
             Furthermore, populations of B. stricta were highly
             differentiated, as indicated by F ST = 0.56. Three clusters
             were identified using structure- the majority of populations
             belonged to either the Northern or Southern cluster.
             Together, the north-south partitioning and evenness of
             genetic variation across the two clusters suggested multiple
             refugia for this perennial herb in the Rocky Mountains.
             Pleistocene glaciation, together with the topographically
             and climatologically heterogeneous cordillera, has
             profoundly influenced the genetic architecture of B.
             stricta. Genetic population structure was also influenced by
             relatively recent genome admixture at two levels: within
             species (involving individuals from the Northern and
             Southern clusters) and between species (with the
             hybridization of B. stricta and Boechera holboellii). This
             complexity of population structure at presumably neutral
             microsatellite loci located throughout the genome in B.
             stricta provides a baseline against which to test whether
             functional genetic variation is undergoing local adaptive
             evolution throughout the natural species
             range.},
   Doi = {10.1111/j.1365-294x.2005.02817.x},
   Key = {fds229305}
}

@article{fds229220,
   Author = {Schranz, ME and Kantama, L and de Jong, H and Mitchell-Olds,
             T},
   Title = {Asexual reproduction in a close relative of Arabidopsis: a
             genetic investigation of apomixis in Boechera
             (Brassicaceae).},
   Journal = {The New Phytologist},
   Volume = {171},
   Number = {2},
   Pages = {425-438},
   Year = {2006},
   Month = {January},
   ISSN = {0028-646X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16866948},
   Abstract = {Understanding apomixis (asexual reproduction through seeds)
             is of great interest to both plant breeders and evolutionary
             biologists. The genus Boechera is an excellent system for
             studying apomixis because of its close relationship to
             Arabidopsis, the occurrence of apomixis at the diploid
             level, and its potentially simple inheritance by
             transmission of a heterochromatic (Het) chromosome. Diploid
             sexual Boechera stricta and diploid apomictic Boechera
             divaricarpa (carrying a Het chromosome) were crossed. Flow
             cytometry, karyotype analysis, genomic in situ
             hybridization, pollen staining and seed-production
             measurements were used to analyse the parents and resulting
             F1, F2 and selected F3 and test-cross (TC) generations. The
             F1 plant was a low-fertility triploid that produced a swarm
             of aneuploid and polyploid F2 progeny. Two of the F2 plants
             were fertile near-tetraploids, and analysis of their F3 and
             TC progeny revealed that they were sexual and genomically
             stabilized. The apomictic phenotype was not transmitted by
             genetic crossing as a single dominant locus on the Het
             chromosome, suggesting a complex genetic control of apomixis
             that has implications for future genetic and evolutionary
             analyses in this group.},
   Doi = {10.1111/j.1469-8137.2006.01765.x},
   Key = {fds229220}
}

@article{fds229223,
   Author = {Lee, CE and Mitchell Olds and T},
   Title = {Ecological and evolutionary genomics of populations in
             nature},
   Journal = {Molecular Ecology},
   Volume = {15},
   Pages = {1193-1195},
   Year = {2006},
   Key = {fds229223}
}

@article{fds229310,
   Author = {Schranz, ME and Dobes, C and Koch, MA and Mitchell-Olds,
             T},
   Title = {Sexual reproduction, hybridization, apomixis, and
             polyploidization in the genus Boechera (Brassicaceae).},
   Journal = {American Journal of Botany},
   Volume = {92},
   Number = {11},
   Pages = {1797-1810},
   Year = {2005},
   Month = {November},
   ISSN = {0002-9122},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21646097},
   Abstract = {Of the 340 genera in the Brassicaceae, apomictic
             reproduction is found only in the North American genus
             Boechera. We investigated phylogenetic relationships,
             ability to hybridize, mating system, and ploidy levels of 92
             lines sampled from 85 populations and representing 19
             Boechera species. Phylogenetic analyses based on chloroplast
             DNA sequences identified three lineages in the genus.
             Reciprocal crosses of each line were made to a common sexual
             diploid B. stricta tester. The resulting F(1) progeny were
             analyzed for the inheritance of polymorphic microsatellite
             loci, genome size, and seed production. Intraspecific B.
             stricta crosses confirmed that this species is mostly
             diploid and sexual. Interspecific crosses revealed many
             other species were diploid and sexual and could be
             successfully hybridized with the tester. We also found
             obligate and facultative apomictic diploid and triploid
             lines. De novo F(1) polyploids (either triploids or
             tetraploids) were derived from the union of nonreduced (from
             an apomictic parent) and reduced (from the tester) gametes.
             However, seed production of these F(1) plants was generally
             low, suggesting a failure in the transmission of apomixis.
             The creation of a wide array of segregating genetic
             populations will facilitate future research on the evolution
             and inheritance of quantitative variation in
             Boechera.},
   Doi = {10.3732/ajb.92.11.1797},
   Key = {fds229310}
}

@article{fds229225,
   Author = {Windsor, AJ and Reichelt, M and Figuth, A and Svatos, A and Kroymann, J and Kliebenstein, DJ and Gershenzon, J and Mitchell-Olds,
             T},
   Title = {Geographic and evolutionary diversification of
             glucosinolates among near relatives of Arabidopsis thaliana
             (Brassicaceae).},
   Journal = {Phytochemistry},
   Volume = {66},
   Number = {11},
   Pages = {1321-1333},
   Year = {2005},
   Month = {June},
   ISSN = {0031-9422},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15913672},
   Abstract = {Glucosinolates are biologically active secondary metabolites
             that display both intra- and interspecific variation in the
             order Brassicales. Glucosinolate profiles have not been
             interpreted within a phylogenic framework and little is
             known regarding the processes that influence the evolution
             of glucosinolate diversity at a macroevolutionary scale. We
             have analyzed leaf glucosinolate profiles from members of
             the Brassicaceae that have diverged from Arabidopsis
             thaliana within the last 15 million years and interpreted
             our findings relative to the phylogeny of this group. We
             identified several interspecific polymorphisms in
             glucosinolate composition. A majority of these polymorphisms
             are lineage-specific secondary losses of glucosinolate
             characters, but a gain-of-character polymorphism was also
             detected. The genetic basis of most observed polymorphisms
             appears to be regulatory. In the case of A. lyrata,
             geographic distribution is also shown to contribute to
             glucosinolate metabolic diversity. Further, we observed
             evidence of gene-flow between sympatric species, parallel
             evolution, and the existence of genetic constraints on the
             evolution of glucosinolates within the Brassicaceae.},
   Doi = {10.1016/j.phytochem.2005.04.016},
   Key = {fds229225}
}

@article{fds229308,
   Author = {Kliebenstein, DJ and Kroymann, J and Mitchell-Olds,
             T},
   Title = {The glucosinolate-myrosinase system in an ecological and
             evolutionary context.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {8},
   Number = {3},
   Pages = {264-271},
   Year = {2005},
   Month = {June},
   ISSN = {1369-5266},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15860423},
   Abstract = {Functional analysis of natural variation in the model
             species Arabidopsis thaliana has enabled the cloning of many
             glucosinolate biosynthesis and hydrolysis genes. Variation
             in these genes is central to understanding the ecological
             role of the glucosinolate-myrosinase defense system, and
             allows us to dissect the evolutionary and ecological forces
             that shape polymorphism at underlying loci. These same genes
             are also variable in other crucifer species, suggesting the
             presence of recurring selection, possibly mediated by
             insects. By utilizing the genomic tools available in A.
             thaliana to investigate these loci fully, it might be
             possible to generate detailed evolutionary or ecological
             models to apply to other species.},
   Doi = {10.1016/j.pbi.2005.03.002},
   Key = {fds229308}
}

@article{fds229309,
   Author = {Kroymann, J and Mitchell-Olds, T},
   Title = {Epistasis and balanced polymorphism influencing complex
             trait variation.},
   Journal = {Nature},
   Volume = {435},
   Number = {7038},
   Pages = {95-98},
   Year = {2005},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15875023},
   Abstract = {Complex traits such as human disease, growth rate, or crop
             yield are polygenic, or determined by the contributions from
             numerous genes in a quantitative manner. Although progress
             has been made in identifying major quantitative trait loci
             (QTL), experimental constraints have limited our knowledge
             of small-effect QTL, which may be responsible for a large
             proportion of trait variation. Here, we identified and
             dissected a one-centimorgan chromosome interval in
             Arabidopsis thaliana without regard to its effect on growth
             rate, and examined the signature of historical sequence
             polymorphism among Arabidopsis accessions. We found that the
             interval contained two growth rate QTL within 210 kilobases.
             Both QTL showed epistasis; that is, their phenotypic effects
             depended on the genetic background. This amount of
             complexity in such a small area suggests a highly polygenic
             architecture of quantitative variation, much more than
             previously documented. One QTL was limited to a single gene.
             The gene in question displayed a nucleotide signature
             indicative of balancing selection, and its phenotypic
             effects are reversed depending on genetic background. If
             this region typifies many complex trait loci, then
             non-neutral epistatic polymorphism may be an important
             contributor to genetic variation in complex
             traits.},
   Doi = {10.1038/nature03480},
   Key = {fds229309}
}

@article{fds229304,
   Author = {Koch, MA and Dobes, C and Matschinger, M and Bleeker, W and Vogel, J and Kiefer, M and Mitchell-Olds, T},
   Title = {Evolution of the trnF(GAA) gene in Arabidopsis relatives and
             the brassicaceae family: monophyletic origin and subsequent
             diversification of a plastidic pseudogene.},
   Journal = {Molecular Biology and Evolution},
   Volume = {22},
   Number = {4},
   Pages = {1032-1043},
   Year = {2005},
   Month = {April},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15689533},
   Abstract = {Recently, we used the 5'-trnL(UAA)-trnF(GAA) region of the
             chloroplast DNA for phylogeographic reconstructions and
             phylogenetic analysis among the genera Arabidopsis,
             Boechera, Rorippa, Nasturtium, and Cardamine. Despite the
             fact that extensive gene duplications are rare among the
             chloroplast genome of higher plants, within these taxa the
             anticodon domain of the trnF(GAA) gene exhibit extensive
             gene duplications with one to eight tandemly repeated copies
             in close 5' proximity of the functional gene. Interestingly,
             even in Arabidopsis thaliana we found six putative
             pseudogenic copies of the functional trnF gene within the
             5'-intergenic trnL-trnF spacer. A reexamination of
             trnL(UAA)-trnF(GAA) regions from numerous published
             phylogenetic studies among halimolobine, cardaminoid, and
             other cruciferous taxa revealed not only extensive trnF gene
             duplications but also favor the hypothesis about a single
             origin of trnF pseudogene formation during evolution of the
             Brassicaceae family 16-21 MYA. Conserved sequence motifs
             from this tandemly repeated region are codistributed
             nonrandomly throughout the plastome, and we found some
             similarities with a DNA sequence duplication in the rps7
             gene and its adjacent spacer. Our results demonstrate the
             potential evolutionary dynamics of a plastidic region
             generally regarded as highly conserved and probably
             cotranscribed and, as shown here for several genera among
             cruciferous plants, greatly characterized by parallel gains
             and losses of duplicated trnF copies.},
   Doi = {10.1093/molbev/msi092},
   Key = {fds229304}
}

@article{fds229307,
   Author = {Schmid, KJ and Ramos-Onsins, S and Ringys-Beckstein, H and Weisshaar,
             B and Mitchell-Olds, T},
   Title = {A multilocus sequence survey in Arabidopsis thaliana reveals
             a genome-wide departure from a neutral model of DNA sequence
             polymorphism.},
   Journal = {Genetics},
   Volume = {169},
   Number = {3},
   Pages = {1601-1615},
   Year = {2005},
   Month = {March},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15654111},
   Abstract = {The simultaneous analysis of multiple genomic loci is a
             powerful approach to studying the effects of population
             history and natural selection on patterns of genetic
             variation of a species. By surveying nucleotide sequence
             polymorphism at 334 randomly distributed genomic regions in
             12 accessions of Arabidopsis thaliana, we examined whether a
             standard neutral model of nucleotide sequence polymorphism
             is consistent with observed data. The average nucleotide
             diversity was 0.0071 for total sites and 0.0083 for silent
             sites. Although levels of diversity are variable among loci,
             no correlation with local recombination rate was observed,
             but polymorphism levels were correlated for physically
             linked loci (<250 kb). We found that observed distributions
             of Tajima's D- and D/D(min)- and of Fu and Li's D-, D*- and
             F-, F*-statistics differed significantly from the expected
             distributions under a standard neutral model due to an
             excess of rare polymorphisms and high variances. Observed
             and expected distributions of Fay and Wu's H were not
             different, suggesting that demographic processes and not
             selection at multiple loci are responsible for the deviation
             from a neutral model. Maximum-likelihood comparisons of
             alternative demographic models like logistic population
             growth, glacial refugia, or past bottlenecks did not produce
             parameter estimates that were more consistent with observed
             patterns. However, exclusion of highly polymorphic "outlier
             loci" resulted in a fit to the logistic growth model.
             Various tests of neutrality revealed a set of candidate loci
             that may evolve under selection.},
   Doi = {10.1534/genetics.104.033795},
   Key = {fds229307}
}

@article{fds304287,
   Author = {de Meaux, J and Goebel, U and Pop, A and Mitchell-Olds,
             T},
   Title = {Allele-specific assay reveals functional variation in the
             chalcone synthase promoter of Arabidopsis thaliana that is
             compatible with neutral evolution.},
   Journal = {The Plant Cell},
   Volume = {17},
   Number = {3},
   Pages = {676-690},
   Year = {2005},
   Month = {March},
   ISSN = {1040-4651},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15705952},
   Abstract = {Promoters are thought to play a major role in adaptive
             evolution, yet little is known about the regulatory
             diversity within species, where microevolutionary processes
             take place. To investigate the potential for evolutionary
             change in the promoter of a gene, we examined nucleotide and
             functional variation of the Chalcone Synthase (CHS)
             cis-regulatory region in Arabidopsis thaliana. CHS is the
             branch point enzyme of a biosynthetic pathway that leads to
             the production of secondary metabolites influencing the
             interaction between the plant and its environment. We found
             that nucleotide diversity in the intergenic region
             encompassing the CHS promoter (pi=0.003) is compatible with
             neutral expectations. To quantify functional variation
             specifically as a result of cis-regulation of CHS mRNA
             levels, we developed an assay using F1 individuals in which
             distinct promoter alleles are compared within a common
             trans-regulatory background. We examined functional
             cis-regulatory variation in response to different stimuli
             representing a variety of CHS transcriptional environments
             (dark, light, and insect feeding). We observed extensive
             functional variation, some of which appeared to be
             independent of the trans-regulatory background. Comparison
             of functional and nucleotide diversity suggested a candidate
             point mutation that may explain cis-regulatory differences
             in light response. Our results indicate that functional
             changes in promoters can arise from a few mutations,
             pointing to promoter regions as a fundamental determinant of
             functional genetic variation.},
   Doi = {10.1105/tpc.104.027839},
   Key = {fds304287}
}

@article{fds229152,
   Author = {Stranger, BE and Mitchell-Olds, T},
   Title = {Nucleotide variation at the myrosinase-encoding locus, TGG1,
             and quantitative myrosinase enzyme activity variation in
             Arabidopsis thaliana.},
   Journal = {Molecular Ecology},
   Volume = {14},
   Number = {1},
   Pages = {295-309},
   Year = {2005},
   Month = {January},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15643972},
   Abstract = {The Arabidopsis thaliana TGG1 gene encodes thioglucoside
             glucohydrolase (myrosinase), an enzyme catalysing the
             hydrolysis of glucosinolate compounds. The enzyme is
             involved in plant defence against some insect herbivores,
             and is present in species of the order Capparales
             (Brassicales). Nucleotide variation was surveyed by
             sequencing c. 2.4 kb of the TGG1 locus in a sample of 28
             worldwide A. thaliana accessions, and one Arabidopsis lyrata
             ssp. lyrata individual. Myrosinase activity was quantified
             for 27 of these same A. thaliana accessions, plus five
             additional others. Overall, estimated nucleotide diversity
             in A. thaliana was low compared to other published A.
             thaliana surveys, and the frequency distribution was skewed
             toward an excess of low-frequency variants. Furthermore,
             comparison to the outgroup species A. lyrata demonstrated
             that A. thaliana exhibited an excess of high-frequency
             derived variants relative to a neutral equilibrium model,
             suggesting a selective sweep. A. thaliana accessions
             differed significantly in total myrosinase activity, but
             analysis of variance detected no statistical evidence for an
             association between quantitative enzyme activity and alleles
             at the TGG1 myrosinase-encoding locus. We thus conclude that
             other, unsurveyed factors primarily affect the observed
             myrosinase activity levels in this species. The pattern of
             nucleotide variation was consistent with a model of positive
             selection but might also be compatible with a completely
             neutral model that takes into account the metapopulation
             behaviour of this highly inbreeding species which
             experienced a relatively recent worldwide
             expansion.},
   Doi = {10.1111/j.1365-294x.2004.02403.x},
   Key = {fds229152}
}

@article{fds229303,
   Author = {Sharbel, TF and Mitchell-Olds, T and Dobes, C and Kantama, L and de
             Jong, H},
   Title = {Biogeographic distribution of polyploidy and B chromosomes
             in the apomictic Boechera holboellii complex.},
   Journal = {Cytogenetic and Genome Research},
   Volume = {109},
   Number = {1-3},
   Pages = {283-292},
   Year = {2005},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15753588},
   Abstract = {The Boechera holboellii complex comprises B. holboellii and
             B. drummondii, both of which can reproduce through sex or
             apomixis. Sexuality is associated with diploid individuals,
             whereas apomictic individuals are diploid or triploid and
             may additionally have B chromosomes. Using flow cytometry
             and karyotype analysis, we have shown that B chromosomes (a)
             occur in both diploid and triploid apomictic B. holboellii,
             (b) may occur in triploid B. drummondii, and (c) are
             dispensable for the plant. Both diploid and triploid
             karyotypes are found in multiple chloroplast haplotypes of
             both species, suggesting that triploid forms have originated
             multiple times during the evolution of this complex. B
             chromosome carriers are found in geographically and
             genetically distinct populations, but it is unknown whether
             the extra chromosomes are shared by common descent (single
             origin) or have originated via introgressive hybridization
             and repeated transitions from diploidy to triploidy. Diploid
             plants containing the Bs reproduce apomictically, suggesting
             that the supernumerary elements are associated with
             apomixis. Finally, our analyses of pollen size and viability
             suggest that irregular chromosome segregation in some
             triploid lineages may lead to the generation of diploid
             individuals which carry the B chromosomes.},
   Doi = {10.1159/000082411},
   Key = {fds229303}
}

@article{fds229306,
   Author = {de Meaux, J and Goebel, U and Pop, A and Mitchell Olds,
             T},
   Title = {The potential for adaptive evolution in Arabidopsis thaliana
             CHS promoter region revealed by an allele-specific
             functional assay},
   Journal = {Plant Cell},
   Volume = {17},
   Number = {3},
   Pages = {676-690},
   Year = {2005},
   ISSN = {1040-4651},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15705952},
   Abstract = {Promoters are thought to play a major role in adaptive
             evolution, yet little is known about the regulatory
             diversity within species, where microevolutionary processes
             take place. To investigate the potential for evolutionary
             change in the promoter of a gene, we examined nucleotide and
             functional variation of the Chalcone Synthase (CHS)
             cis-regulatory region in Arabidopsis thaliana. CHS is the
             branch point enzyme of a biosynthetic pathway that leads to
             the production of secondary metabolites influencing the
             interaction between the plant and its environment. We found
             that nucleotide diversity in the intergenic region
             encompassing the CHS promoter (pi=0.003) is compatible with
             neutral expectations. To quantify functional variation
             specifically as a result of cis-regulation of CHS mRNA
             levels, we developed an assay using F1 individuals in which
             distinct promoter alleles are compared within a common
             trans-regulatory background. We examined functional
             cis-regulatory variation in response to different stimuli
             representing a variety of CHS transcriptional environments
             (dark, light, and insect feeding). We observed extensive
             functional variation, some of which appeared to be
             independent of the trans-regulatory background. Comparison
             of functional and nucleotide diversity suggested a candidate
             point mutation that may explain cis-regulatory differences
             in light response. Our results indicate that functional
             changes in promoters can arise from a few mutations,
             pointing to promoter regions as a fundamental determinant of
             functional genetic variation.},
   Doi = {10.1105/tpc.104.027839},
   Key = {fds229306}
}

@article{fds229297,
   Author = {Dobes, C and Mitchell-Olds, T and Koch, MA},
   Title = {Intraspecific diversification in North American Boechera
             stricta (= Arabis drummondii), Boechera xdivaricarpa, and
             Boechera holboellii (Brassicaceae) inferred from nuclear and
             chloroplast molecular markers--an integrative
             approach.},
   Journal = {American Journal of Botany},
   Volume = {91},
   Number = {12},
   Pages = {2087-2101},
   Year = {2004},
   Month = {December},
   ISSN = {0002-9122},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21652357},
   Abstract = {We performed a combined evolutionary analysis of North
             American Boechera stricta, Boechera holboellii, and their
             hybrid Boechera ×divaricarpa using information on ploidy
             level estimators, allelic microsatellite variation,
             noncoding regions of the plastidic genome (cpDNA), and
             sequences of the internal transcribed spacers 1 and 2 of the
             nuclear ribosomal DNA (ITS). Somatic ploidy levels of
             herbarium specimens were estimated based on comparison of
             pollen size and the number of alleles per locus at seven
             microsatellites. Results indicate that B. stricta and B.
             holboellii are genetically distinct from each other,
             although we also find evidence for occasional introgression
             between both parental species. Microsatellite patterns for
             B. stricta from northeastern North America are genetically
             distinct from western populations, suggesting isolation in
             glacial refugia along the southeastern margin of the
             continuous ice shield. Microsatellites supported recent
             origin of B. ×divaricarpa. Correspondence of nrDNA with
             cpDNA genetic variation for the majority of diploid B.
             holboellii accessions suggests a basal, sexual evolutionary
             unit within a polymorphic B. holboellii group. Hybridization
             of genetically distinct lineage(s) evidently played an
             important role in the establishment of polyploid B.
             holboellii. Frequency of polyploid B. holboellii is
             substantially higher in the southern United States. This
             trend corresponds to a southerly distribution of derived
             chloroplast haplotypes, suggesting an evolutionary advantage
             of polyploidy and associated apomixis in the colonization of
             the Sierra Nevada and the Southern Rocky
             Mountains.},
   Doi = {10.3732/ajb.91.12.2087},
   Key = {fds229297}
}

@article{fds304286,
   Author = {Kuittinen, H and de Haan, AA and Vogl, C and Oikarinen, S and Leppälä,
             J and Koch, M and Mitchell-Olds, T and Langley, CH and Savolainen,
             O},
   Title = {Comparing the linkage maps of the close relatives
             Arabidopsis lyrata and A. thaliana.},
   Journal = {Genetics},
   Volume = {168},
   Number = {3},
   Pages = {1575-1584},
   Year = {2004},
   Month = {November},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15579708},
   Abstract = {We have constructed a genetic map of Arabidopsis lyrata, a
             self-incompatible relative of the plant model species A.
             thaliana. A. lyrata is a diploid (n = 8) species that
             diverged from A. thaliana (n = 5) approximately 5 MYA.
             Mapping was conducted in a full-sib progeny of two unrelated
             F(1) hybrids between two European populations of A. lyrata
             ssp. petraea. We used the least-squares method of the
             Joinmap program for map construction. The gross chromosomal
             differences between the two species were most parsimoniously
             explained with three fusions, two reciprocal translocations,
             and one inversion. The total map length was 515 cM, and the
             distances were 12% larger than those between corresponding
             markers in the linkage map of A. thaliana. The 72 markers,
             consisting of microsatellites and gene-based markers, were
             spaced on average every 8 cM. Transmission ratio distortion
             was extensive, and most distortions were specific to each
             reciprocal cross, suggesting cytoplasmic interactions. We
             estimate locations and most probable genotype frequencies of
             transmission ratio distorting loci (TRDL) with a Bayesian
             method and discuss the possible reasons for the observed
             distortions.},
   Doi = {10.1534/genetics.103.022343},
   Key = {fds304286}
}

@article{fds229143,
   Author = {Ramos-Onsins, SE and Stranger, BE and Mitchell-Olds, T and Aguade,
             M},
   Title = {Multilocus analysis of variation and speciation in the
             closely related species Arabidopsis halleri and A. lyrata
             (vol 166, pg 373, 2004)},
   Journal = {Genetics},
   Volume = {167},
   Number = {4},
   Pages = {2143-2143},
   Publisher = {GENETICS},
   Year = {2004},
   Month = {August},
   ISSN = {0016-6731},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000223720300056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds229143}
}

@article{fds229150,
   Author = {Ramos-Onsins, SE and Stranger, BE and Mitchell-Olds, T and Aguadé,
             M},
   Title = {Erratum: Multilocus analysis of variation and speciation in
             the closely related species Arabidopsis halleri and A.
             lyrata (Genetics 166 (373-388))},
   Journal = {Genetics},
   Volume = {167},
   Number = {4},
   Pages = {2143},
   Year = {2004},
   Month = {August},
   Key = {fds229150}
}

@article{fds229300,
   Author = {Schein, M and Yang, Z and Mitchell-Olds, T and Schmid,
             KJ},
   Title = {Rapid evolution of a pollen-specific oleosin-like gene
             family from Arabidopsis thaliana and closely related
             species.},
   Journal = {Molecular Biology and Evolution},
   Volume = {21},
   Number = {4},
   Pages = {659-669},
   Year = {2004},
   Month = {April},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14739246},
   Abstract = {It has been shown in a variety of species that genes
             expressed in reproductive tissues evolve rapidly, which
             often appears to be the result of positive Darwinian
             selection. We investigated the evolution of a family of
             seven pollen-specific oleosin-like proteins (or
             oleopollenins) in Arabidopsis thaliana and two closely
             related species. More than 30 kb of a genomic region that
             harbors the complete, tandemly repeated oleopollenin cluster
             were sequenced from Arabidopsis lyrata ssp. lyrata, and
             Boechera drummondii. A phylogenetic analysis of the complete
             gene cluster from these three species and from Brassica
             oleracea confirmed its rapid evolution resulting from gene
             duplication and gene loss events, numerous amino acid
             substitutions, and insertions/deletions in the coding
             sequence. Independent duplications were inferred in the
             lineages leading to Arabidopsis and to Brassica, and gene
             loss was inferred in the lineage leading to B. drummondii.
             Comparisons of the ratio of nonsynonymous (d(N)) and
             synonymous (d(S)) divergence revealed that the oleopollenins
             are among the most rapidly evolving proteins currently known
             from Arabidopsis and that they may evolve under positive
             Darwinian selection. Reverse transcriptase polymerase chain
             reaction analysis demonstrated the expression of
             oleopollenins in flowers of the outcrossing A. lyrata, the
             selfing B. drummondii, and the apomictic Boechera
             holboellii, suggesting that oleopollenins play an important
             role in species with different breeding systems. These
             results are consistent with a putative function in species
             recognition, but further analyses of protein function and
             sequence variation in species with different breeding
             systems are necessary to reveal the underlying causes for
             the rapid evolution of oleopollenins.},
   Doi = {10.1093/molbev/msh059},
   Key = {fds229300}
}

@article{fds229302,
   Author = {Wittstock, U and Agerbirk, N and Stauber, EJ and Olsen, CE and Hippler,
             M and Mitchell-Olds, T and Gershenzon, J and Vogel,
             H},
   Title = {Successful herbivore attack due to metabolic diversion of a
             plant chemical defense.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {101},
   Number = {14},
   Pages = {4859-4864},
   Year = {2004},
   Month = {April},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15051878},
   Abstract = {Plants protect themselves against herbivory with a diverse
             array of repellent or toxic secondary metabolites. However,
             many herbivorous insects have developed counteradaptations
             that enable them to feed on chemically defended plants
             without apparent negative effects. Here, we present evidence
             that larvae of the specialist insect, Pieris rapae (cabbage
             white butterfly, Lepidoptera: Pieridae), are biochemically
             adapted to the glucosinolate-myrosinase system, the major
             chemical defense of their host plants. The defensive
             function of the glucosinolate-myrosinase system results from
             the toxic isothiocyanates that are released when
             glucosinolates are hydrolyzed by myrosinases on tissue
             disruption. We show that the hydrolysis reaction is
             redirected toward the formation of nitriles instead of
             isothiocyanates if plant material is ingested by P. rapae
             larvae, and that the nitriles are excreted with the feces.
             The ability to form nitriles is due to a larval gut protein,
             designated nitrile-specifier protein, that by itself has no
             hydrolytic activity on glucosinolates and that is unrelated
             to any functionally characterized protein. Nitrile-specifier
             protein appears to be the key biochemical counteradaptation
             that allows P. rapae to feed with impunity on plants
             containing glucosinolates and myrosinases. This finding
             sheds light on the ecology and evolution of plant-insect
             interactions and suggests novel highly selective pest
             management strategies.},
   Doi = {10.1073/pnas.0308007101},
   Key = {fds229302}
}

@article{fds229294,
   Author = {Clauss, MJ and Mitchell-Olds, T},
   Title = {Functional divergence in tandemly duplicated Arabidopsis
             thaliana trypsin inhibitor genes.},
   Journal = {Genetics},
   Volume = {166},
   Number = {3},
   Pages = {1419-1436},
   Year = {2004},
   Month = {March},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15082560},
   Abstract = {In multigene families, variation among loci and alleles can
             contribute to trait evolution. We explored patterns of
             functional and genetic variation in six duplicated
             Arabidopsis thaliana trypsin inhibitor (ATTI) loci. We
             demonstrate significant variation in constitutive and
             herbivore-induced transcription among ATTI loci that show,
             on average, 65% sequence divergence. Significant variation
             in ATTI expression was also found between two molecularly
             defined haplotype classes. Population genetic analyses for
             17 accessions of A. thaliana showed that six ATTI loci
             arranged in tandem within 10 kb varied 10-fold in nucleotide
             diversity, from 0.0009 to 0.0110, and identified a minimum
             of six recombination events throughout the tandem array. We
             observed a significant peak in nucleotide and indel
             polymorphism spanning ATTI loci in the interior of the
             array, due primarily to divergence between the two haplotype
             classes. Significant deviation from the neutral equilibrium
             model for individual genes was interpreted within the
             context of intergene linkage disequilibrium and correlated
             patterns of functional differentiation. In contrast to the
             outcrosser Arabidopsis lyrata for which recombination is
             observed even within ATTI loci, our data suggest that
             response to selection was slowed in the inbreeding, annual
             A. thaliana because of interference among functionally
             divergent ATTI loci.},
   Doi = {10.1534/genetics.166.3.1419},
   Key = {fds229294}
}

@article{fds229296,
   Author = {Dobes, CH and Mitchell-Olds, T and Koch, MA},
   Title = {Extensive chloroplast haplotype variation indicates
             Pleistocene hybridization and radiation of North American
             Arabis drummondii, A. x divaricarpa, and A. holboellii
             (Brassicaceae).},
   Journal = {Molecular Ecology},
   Volume = {13},
   Number = {2},
   Pages = {349-370},
   Year = {2004},
   Month = {February},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14717892},
   Abstract = {Arabis drummondii, A. holboellii and their hybrid A. x
             divaricarpa are widespread perennials of open habitats in
             North America. A phylogenetic analysis based on noncoding
             chloroplast DNA sequences (trnL intron and trnL/F intergenic
             spacer) resolved A. drummondii as a monophyletic taxon, but
             found A. holboellii to bear chloroplast haplotypes from
             highly diverged evolutionary lineages. This raised the
             question of a possible polyphyletic origin of A. holboellii.
             Arabis x divaricarpa was found to be of recent and polytopic
             origin, a result consistent with its presumed hybrid origin.
             One hundred and three chloroplast haplotypes were detected
             within 719 Arabis accessions investigated. The majority of
             chloroplast-types were estimated to have arisen prior to the
             Wisconsin glaciation. Phylogeographical analysis using
             nested clade analysis, suggested for A. holboellii (i). past
             fragmentation events, partitioning genetic variation in
             several instances between the Sierra Nevada, the Southern
             Rocky Mountains and the Colorado Plateau on the one hand and
             the Central to Northern Rockies of the United States and
             adjacent Cascades on the other; and for both parental
             species (ii). recolonization of major areas formerly covered
             by the Wisconsin glaciation by three haplotypes; and (iii).
             restricted gene flow indicating isolation by distance in
             areas south of the last glacial maximum. Arabis x
             divaricarpa is closely codistributed with its parental
             species and resampled their haplotypes. The highest genetic
             diversity was found in the Rocky Mountains from Idaho and
             Montana south to Utah and Colorado. This area was further
             hypothesized to have played a major role in the origin of
             both parental species and probably represented an important
             glacial refugium. However, evidence for glacial refugia was
             also found in arctic and boreal regions of Alaska and near
             the Great Lakes. In comparison to nuclear ribosomal internal
             transcribed spacer data, chloroplast DNA divergence was very
             high and evidently predated the origin of A. drummondii and
             possibly A. holboellii. Divergence of major chloroplast
             lineages dates back to the middle of the Pleistocene at
             least. Extensive hybridization is the most likely
             evolutionary factor working on A. holboellii to explain the
             revealed discrepancy in nuclear DNA and chloroplast DNA
             diversification.},
   Doi = {10.1046/j.1365-294x.2003.02064.x},
   Key = {fds229296}
}

@article{fds229139,
   Author = {Windsor, AJ and Shumate, AM and Forrnanova, N and Mitchell-Olds,
             T},
   Title = {ECOLOGICAL GENOMICS OF GLUCOSINOLATES IN RELATIVES OF
             ARABIDOPSIS},
   Journal = {Acta Physiologiae Plantarum},
   Volume = {26},
   Number = {3},
   Pages = {60-60},
   Publisher = {SPRINGER HEIDELBERG},
   Year = {2004},
   Month = {January},
   ISSN = {0137-5881},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000205415400154&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds229139}
}

@article{fds229299,
   Author = {Ramos-Onsins, SE and Stranger, BE and Mitchell-Olds, T and Aguadé,
             M},
   Title = {Multilocus analysis of variation and speciation in the
             closely related species Arabidopsis halleri and A.
             lyrata.},
   Journal = {Genetics},
   Volume = {166},
   Number = {1},
   Pages = {373-388},
   Year = {2004},
   Month = {January},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15020431},
   Abstract = {Nucleotide variation in eight effectively unlinked genes was
             surveyed in species-wide samples of the closely related
             outbreeding species Arabidopsis halleri and A. lyrata ssp.
             petraea and in three of these genes in A. lyrata ssp. lyrata
             and A. thaliana. Significant genetic differentiation was
             observed more frequently in A. l. petraea than in A.
             halleri. Average estimates of nucleotide variation were
             highest in A. l. petraea and lowest in A. l. lyrata,
             reflecting differences among species in effective population
             size. The low level of variation in A. l. lyrata is
             concordant with a bottleneck effect associated with its
             origin. The A. halleri/A. l. petraea speciation process was
             studied, considering the orthologous sequences of an
             outgroup species (A. thaliana). The high number of ancestral
             mutations relative to exclusive polymorphisms detected in A.
             halleri and A. l. petraea, the significant results of the
             multilocus Fay and Wu H tests, and haplotype sharing between
             the species indicate introgression subsequent to speciation.
             Average among-population variation in A. halleri and A. l.
             petraea was approximately 1.5- and 3-fold higher than that
             in the inbreeder A. thaliana. The detected reduction of
             variation in A. thaliana is less than that expected from
             differences in mating system alone, and therefore from
             selective processes related to differences in the effective
             recombination rate, but could be explained by differences in
             population structure.},
   Doi = {10.1534/genetics.166.1.373},
   Key = {fds229299}
}

@article{fds229301,
   Author = {Sharbel, TF and Voigt, ML and Mitchell-Olds, T and Kantama, L and de
             Jong, H},
   Title = {Is the aneuploid chromosome in an apomictic Boechera
             holboellii a genuine B chromosome?},
   Journal = {Cytogenetic and Genome Research},
   Volume = {106},
   Number = {2-4},
   Pages = {173-183},
   Year = {2004},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15292588},
   Abstract = {The Boechera holboellii complex comprises B. holboellii and
             B. drummondii, both of which can reproduce through sex or
             apomixis. Sexuality is associated with diploidy, whereas
             apomictic individuals can either be diploid, aneuploid or
             triploid. Aneuploid individuals are found in geographically
             and genetically distinct populations and contain a single
             extra chromosome. It is unknown whether the supernumerary
             chromosomes are shared by common descent (single origin) or
             have originated via introgressive hybridizations associated
             with the repeated transition from diploidy to triploidy.
             Diploid plants containing the extra chromosome(s) reproduce
             apomictically, suggesting that the supernumerary elements
             are associated with apomixis. In this study we compared flow
             cytometry data, chromosome morphology, and DNA sequences of
             sexual diploid and apomictic aneuploids in order to
             establish whether the extra chromosome fits the classical
             concept of a B chromosome. Karyotype analyses revealed that
             the supernumerary chromosome in the metaphase complement is
             heterochromatic and often smaller than the A chromosomes,
             and differs in length between apomictic plants from
             different populations. DNA sequence analyses furthermore
             demonstrated elevated levels of non-synonymous substitutions
             in one of the alleles, likely that on the aneuploid
             chromosome. Although the extra chromosome in apomictic
             Boechera does not go through normal reductional meiosis, in
             which it may get eliminated or accumulated by a
             B-chromosome-specific process, its variable size and
             heterochromatic nature does meet the remaining criteria for
             a genuine B chromosome in other species. Its prevalence and
             conserved genetic composition nonetheless implies that this
             chromosome, if truly a B, may be atypical with respect to
             its influence on its carriers.},
   Doi = {10.1159/000079284},
   Key = {fds229301}
}

@article{fds45785,
   Author = {Dobeš, C. and T. Mitchell-Olds and M.A. Koch},
   Title = {Intraspecific diversification in North American A.
             drummondii, A. ×divaricarpa, and A. holboellii
             (Brassicaceae) inferred from nuclear and chloroplast
             molecular markers – an integrative approach},
   Journal = {Amer. J. Bot.},
   Volume = {91},
   Pages = {2087-2101},
   Year = {2004},
   Key = {fds45785}
}

@article{fds229298,
   Author = {Kuittinen, and H, and Haan, AD and Vogl, C and Oikarinen, S and Leppälä, J and Koch, M and Mitchell-Olds, T and Langley, C and Savolainen, O},
   Title = {Comparing the maps of close relatives Arabidopsis lyrata and
             Arabidopsis thaliana},
   Journal = {Genetics},
   Volume = {168},
   Number = {3},
   Pages = {1575-1584},
   Year = {2004},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15579708},
   Abstract = {We have constructed a genetic map of Arabidopsis lyrata, a
             self-incompatible relative of the plant model species A.
             thaliana. A. lyrata is a diploid (n = 8) species that
             diverged from A. thaliana (n = 5) approximately 5 MYA.
             Mapping was conducted in a full-sib progeny of two unrelated
             F(1) hybrids between two European populations of A. lyrata
             ssp. petraea. We used the least-squares method of the
             Joinmap program for map construction. The gross chromosomal
             differences between the two species were most parsimoniously
             explained with three fusions, two reciprocal translocations,
             and one inversion. The total map length was 515 cM, and the
             distances were 12% larger than those between corresponding
             markers in the linkage map of A. thaliana. The 72 markers,
             consisting of microsatellites and gene-based markers, were
             spaced on average every 8 cM. Transmission ratio distortion
             was extensive, and most distortions were specific to each
             reciprocal cross, suggesting cytoplasmic interactions. We
             estimate locations and most probable genotype frequencies of
             transmission ratio distorting loci (TRDL) with a Bayesian
             method and discuss the possible reasons for the observed
             distortions.},
   Doi = {10.1534/genetics.103.022343},
   Key = {fds229298}
}

@article{fds229289,
   Author = {Kroymann, J and Donnerhacke, S and Schnabelrauch, D and Mitchell-Olds, T},
   Title = {Evolutionary dynamics of an Arabidopsis insect resistance
             quantitative trait locus.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {100 Suppl 2},
   Pages = {14587-14592},
   Year = {2003},
   Month = {November},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14506289},
   Abstract = {Glucosinolate profiles differ among Arabidopsis thaliana
             ecotypes, caused by the composition of alleles at several
             glucosinolate biosynthetic loci. One of these, GS-Elong,
             harbors a family of methylthioalkylmalate synthase (MAM)
             genes that determine the side chain length of aliphatic
             glucosinolate structures. Fine mapping reveals that GS-Elong
             constitutes an insect resistance quantitative trait locus,
             caused by variation in glucosinolate profiles conferred by
             polymorphism of MAM alleles in this region. A sequence
             survey of randomly chosen ecotypes indicates that GS-Elong
             is highly variable among A. thaliana ecotypes: indel
             polymorphisms are frequent, as well as gene conversion
             events between gene copies arranged in tandem. Furthermore,
             statistical methods of molecular population genetics suggest
             that one of the genes, MAM2, is subject to balancing
             selection. This may be caused by ecological tradeoffs, i.e.,
             by contrasting physiological effects of glucosinolates on
             generalist vs. specialist insects.},
   Doi = {10.1073/pnas.1734046100},
   Key = {fds229289}
}

@article{fds229287,
   Author = {de Meaux, J and Mitchell-Olds, T},
   Title = {Evolution of plant resistance at the molecular level:
             ecological context of species interactions.},
   Journal = {Heredity},
   Volume = {91},
   Number = {4},
   Pages = {345-352},
   Year = {2003},
   Month = {October},
   ISSN = {0018-067X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14512948},
   Abstract = {Molecular data regarding the diversity of plant loci
             involved in resistance to herbivores or pathogens are
             becoming increasingly available. These genes demonstrate
             variable patterns of diversity, suggesting that they differ
             in their evolutionary history. In parallel, the study of
             natural variation for resistance, generally conducted at the
             phenotypic level, has shown that resistance does not evolve
             solely under selection pressures exerted by enemies.
             Metapopulation dynamics and other ecological characteristics
             of interacting species also appear to have a large impact on
             resistance evolution. Until now, studies of resistance at
             the molecular level have been conducted separately from
             ecological studies in extant populations. Future progress
             requires an evolutionary approach integrating both molecular
             and ecological aspects of resistance evolution. Such an
             approach will contribute greatly to our understanding of the
             evolution of molecular diversity at loci involved in biotic
             stress.},
   Doi = {10.1038/sj.hdy.6800342},
   Key = {fds229287}
}

@article{fds229293,
   Author = {Törjék, O and Berger, D and Meyer, RC and Müssig, C and Schmid, KJ and Rosleff Sörensen and T and Weisshaar, B and Mitchell-Olds, T and Altmann, T},
   Title = {Establishment of a high-efficiency SNP-based framework
             marker set for Arabidopsis.},
   Journal = {The Plant Journal : for Cell and Molecular
             Biology},
   Volume = {36},
   Number = {1},
   Pages = {122-140},
   Year = {2003},
   Month = {October},
   ISSN = {0960-7412},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12974817},
   Abstract = {The major goal of this project was the establishment of a
             tool for rapid mapping of new mutations and genotyping in
             Arabidopsis consisting of at least 100 evenly spaced
             framework markers. We assembled a single nucleotide
             polymorphism (SNP)-based marker set consisting of 112
             polymorphic sites with average spacing of 1.15 Mbp derived
             from an SNP database that we recently developed. This
             information was used to set up efficient SNP detection
             reactions based on multiplexed primer extension assays. The
             112 Columbia (Col-0)/C24 framework markers were used to
             assemble 18 multiplexed SNaPshot assays with which up to
             eight separate loci can be genotyped in a
             single-tube/single-capillary format. In addition, for 110
             framework markers matrix-assisted laser desorption/ionization
             time of flight (MALDI-ToF) assays have been established for
             high throughput analyses. We demonstrated the usefulness and
             the robustness of both procedures of this tool by genotyping
             48 BC3F1 individuals created between the accessions Col-0
             and C24. Subsets of 10-62 of the established markers
             discriminate between various combinations of the accessions
             Col-0, C24, Landsberg erecta (Ler), Cape Verdi Islands (Cvi)
             and Niederzenz (Nd). Using a subset of 17 evenly distributed
             and established SNP markers that are also polymorphic
             between Ler and Col-0, we were able to rapidly map a mutant
             gene (tbr1) to an interval of 2.3 Mbp in an Ler (tbr1) x
             Col-0 cross.},
   Doi = {10.1046/j.1365-313x.2003.01861.x},
   Key = {fds229293}
}

@article{fds229288,
   Author = {Feder, ME and Mitchell-Olds, T},
   Title = {Evolutionary and ecological functional genomics.},
   Journal = {Nature Reviews. Genetics},
   Volume = {4},
   Number = {8},
   Pages = {651-657},
   Year = {2003},
   Month = {August},
   ISSN = {1471-0056},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12897776},
   Abstract = {A unique combination of disciplines is emerging--evolutionary
             and ecological functional genomics--which focuses on the
             genes that affect ecological success and evolutionary
             fitness in natural environments and populations. Already
             this approach has provided new insights that were not
             available from its disciplinary components in isolation.
             However, future advances will necessitate the re-engineering
             of scientific attitudes, training and institutions, to
             achieve extensive multidisciplinarity.},
   Doi = {10.1038/nrg1128},
   Key = {fds229288}
}

@article{fds229292,
   Author = {Schmid, KJ and Sorensen, TR and Stracke, R and Torjek, O and Altmann, T and Mitchell-Olds, T and Weisshaar, B},
   Title = {Large-scale identification and analysis of genome-wide
             single-nucleotide polymorphisms for mapping in Arabidopsis
             thaliana.},
   Journal = {Genome Research},
   Volume = {13},
   Number = {6A},
   Pages = {1250-1257},
   Year = {2003},
   Month = {June},
   ISSN = {1088-9051},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12799357},
   Abstract = {Genetic markers such as single nucleotide polymorphisms
             (SNPs) are essential tools for positional cloning,
             association, or quantitative trait locus mapping and the
             determination of genetic relationships between individuals.
             We identified and characterized a genome-wide set of SNP
             markers by generating 10,706 expressed sequence tags (ESTs)
             from cDNA libraries derived from 6 different accessions, and
             by analysis of 606 sequence tagged sites (STS) from up to 12
             accessions of the model flowering plant Arabidopsis
             thaliana. The cDNA libraries for EST sequencing were made
             from individuals that were stressed by various means to
             enrich for transcripts from genes expressed under such
             conditions. SNPs discovered in these sequences may be useful
             markers for mapping genes involved in interactions with the
             biotic and abiotic environment. The STS loci are distributed
             randomly over the genome. By comparison with the Col-0
             genome sequence, we identified a total of 8051 SNPs and 637
             insertion/deletion polymorphisms (InDel). Analysis of
             STS-derived SNPs shows that most SNPs are rare, but that it
             is possible to identify intermediate frequency framework
             markers that can be used for genetic mapping in many
             different combinations of accessions. A substantial
             proportion of SNPs located in ORFs caused a change of the
             encoded amino acid. A comparison of the density of our SNP
             markers among accessions in both the EST and STS datasets,
             revealed that Cvi-0 is the most divergent accession from
             Col-0 among the 12 accessions studied. All of these markers
             are freely available via the internet.},
   Doi = {10.1101/gr.728603},
   Key = {fds229292}
}

@article{fds229286,
   Author = {Clauss, MJ and Mitchell-Olds, T},
   Title = {Population genetics of tandem trypsin inhibitor genes in
             Arabidopsis species with contrasting ecology and life
             history.},
   Journal = {Molecular Ecology},
   Volume = {12},
   Number = {5},
   Pages = {1287-1299},
   Year = {2003},
   Month = {May},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12694291},
   Abstract = {Duplicated genes are important in the evolution and ecology
             of plant-defences because herbivore and pathogen attack can
             be countered via functional diversification at two levels:
             among duplicated loci and within loci. We explore molecular
             sequence variation for two members of a defence-related gene
             family, Arabidopsis thaliana trypsin inhibitors (ATTI), in
             A. thaliana and a closely related species, A. lyrata subspp.
             petraea. A worldwide sample of the inbreeding annual A.
             thaliana had less genetic variation at two ATTI loci
             (piTOTAL <or= 0.0006) than observed previously at other
             functional loci. A significant excess of high frequency
             derived alleles in the signal sequence and 5' UTR of ATTI2
             was consistent with a model of positive selection. However,
             demographic processes such as population subdivision and
             expansion, both likely to have occurred in A. thaliana
             during the last 10 000 years, can also give rise to similar
             deviations from neutrality. A single population of A. lyrata
             subspp. petraea in Germany had up to an order of magnitude
             more standing genetic variation at ATTI loci than the
             species-wide sample of A. thaliana. Although the level of
             variability for ATTI1 and ATTI2 within this single
             population was similar to, or even greater than, observed
             species-wide diversity for other loci in A. lyrata, there
             was little evidence to reject an equilibrium neutral model.
             A spatially explicit sample of 87 A. lyrata subspp. petraea
             individuals detected outbreeding (FIS = -0.16; FIT = -0.15)
             but little population subdivision (FST = 0.006) in this
             self-incompatible perennial herb. Genetic differences
             between Arabidopsis species were consistent with, but not
             fully explained by, divergence in ecology and life history.
             Diversification appears to have occurred in different
             functional domains for the tandemly duplicated ATTI1 and
             ATTI2 genes; the majority of fixed replacements in ATTI1
             surround the enzyme binding site of the mature protein,
             whereas in ATTI2 most functional evolutionary change is
             located in the signal peptide. This pattern is consistent
             with a hypothesis of subfunctionalization in trypsin
             inhibitory function.},
   Doi = {10.1046/j.1365-294x.2003.01832.x},
   Key = {fds229286}
}

@article{fds229290,
   Author = {McKay, JK and Richards, JH and Mitchell-Olds, T},
   Title = {Genetics of drought adaptation in Arabidopsis thaliana: I.
             Pleiotropy contributes to genetic correlations among
             ecological traits.},
   Journal = {Molecular Ecology},
   Volume = {12},
   Number = {5},
   Pages = {1137-1151},
   Year = {2003},
   Month = {May},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12694278},
   Abstract = {We examined patterns of genetic variance and covariance in
             two traits (i) carbon stable isotope ratio delta13C
             (dehydration avoidance) and (ii) time to flowering (drought
             escape), both of which are putative adaptations to local
             water availability. Greenhouse screening of 39 genotypes of
             Arabidopsis thaliana native to habitats spanning a wide
             range of climatic conditions, revealed a highly significant
             positive genetic correlation between delta13C and flowering
             time. Studies in a range of C3 annuals have also reported
             large positive correlations, suggesting the presence of a
             genetically based trade-off between mechanisms of
             dehydration avoidance (delta13C) and drought escape (early
             flowering). We examined the contribution of pleiotropy by
             using a combination of mutant and near-isogenic lines to
             test for positive mutational covariance between delta13C and
             flowering time. Ecophysiological mutants generally showed
             variation in delta13C but not flowering time. However,
             flowering time mutants generally demonstrated pleiotropic
             effects consistent with natural variation. Mutations that
             caused later flowering also typically resulted in less
             negative delta13C and thus probably higher water use
             efficiency. We found strong evidence for pleiotropy using
             near-isogenic lines of Frigida and Flowering locus C, cloned
             loci known to be responsible for natural variation in
             flowering time. These data suggest the correlated evolution
             of delta13C and flowering time is explained in part by the
             fixation of pleiotropic alleles that alter both delta13C and
             time to flowering.},
   Doi = {10.1046/j.1365-294x.2003.01833.x},
   Key = {fds229290}
}

@article{fds229295,
   Author = {Koch, MA and Dobes, C and Mitchell-Olds, T},
   Title = {Multiple hybrid formation in natural populations: concerted
             evolution of the internal transcribed spacer of nuclear
             ribosomal DNA (ITS) in North American Arabis divaricarpa
             (Brassicaceae).},
   Journal = {Molecular Biology and Evolution},
   Volume = {20},
   Number = {3},
   Pages = {338-350},
   Year = {2003},
   Month = {March},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12644554},
   Abstract = {DNA sequence variation of the internal transcribed spacer
             (ITS) region of nuclear ribosomal DNA from Arabis
             holboellii, A. drummondii, and its putative hybrid A.
             divaricarpa was analyzed to study hybrid speciation in a
             species system geographically covering nearly the entire
             North American continent. Based on molecular systematics the
             investigated species are better combined under the genus
             Boechera. Multiple intraindividual ITS copies were detected
             in numerous accessions of A. divaricarpa, and, to a minor
             extent, in the parental taxa. Comparative phylogenetic
             analysis demonstrates that reticulate evolution is common.
             Consequently, concerted evolution of ITS regions resulted in
             different types of ITS fragments not only in hybrid
             populations but also in one of the parental taxa, A.
             holboellii. Hybrid formation often occurred independently at
             different sites and at different times, which is reflected
             by ITS copies resampling the original parental sequence
             variation in different ways. Some biogeographic structuring
             of genetic diversity is apparent and mirrors postglacial
             migration routes. Hybridization, reticulation, and apomixis
             are assumed to be the major forces driving speciation
             processes in this species complex. Analysis of conserved
             regions and secondary structures of the ITS region provided
             no evidence that, in this system, hybrid ITS evolution is
             predominantly driven in a particular direction. However, two
             regions in the ITS1 and ITS2, respectively, show higher
             mutation rates than expected from outgroup comparisons.
             Strong evidence for the occurrence of apomixis in A.
             holboellii and A. divaricarpa has come from pollen size
             measurements and estimations of pollen quality, which favor
             the hypothesis that A. drummondii served as paternal
             hybridization partner more frequently than A.
             holboellii.},
   Doi = {10.1093/molbev/msg046},
   Key = {fds229295}
}

@article{fds229291,
   Author = {Morin, and A, P and Luikart, G and Wayne, RK and group,
             TSNPW},
   Title = {Applications of SNPs in ecology, evolution, and
             conservation},
   Journal = {Trends in Ecology and Evolution},
   Volume = {19},
   Pages = {208-216},
   Year = {2003},
   Key = {fds229291}
}

@article{fds304285,
   Author = {Kuittinen, H and Aguade, M and Charlesworth, D and Haan, ADE and Lauga,
             B and Mitchell-Olds, T and Oikarinen, S and Ramos-Onsins, S and Stranger, B and Van Tienderen and P and Savolainen,
             O},
   Title = {Primers for 22 candidate genes for ecological adaptations in
             Brassicaceae},
   Journal = {Molecular Ecology Notes},
   Volume = {2},
   Number = {3},
   Pages = {258-262},
   Publisher = {BLACKWELL PUBLISHING LTD},
   Year = {2002},
   Month = {September},
   ISSN = {1471-8278},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000177964300021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1046/j.1471-8278.2002.00210.x},
   Key = {fds304285}
}

@article{fds229284,
   Author = {Ratzka, A and Vogel, H and Kliebenstein, DJ and Mitchell-Olds, T and Kroymann, J},
   Title = {Disarming the mustard oil bomb.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {99},
   Number = {17},
   Pages = {11223-11228},
   Year = {2002},
   Month = {August},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12161563},
   Abstract = {Plants are attacked by a broad array of herbivores and
             pathogens. In response, plants deploy an arsenal of
             defensive traits. In Brassicaceae, the glucosinolate-myrosinase
             complex is a sophisticated two-component system to ward off
             opponents. However, this so-called "mustard oil bomb" is
             disarmed by a glucosinolate sulfatase of a crucifer
             specialist insect, diamondback moth, Plutella xylostella
             (Lepidoptera: Plutellidae). Sulfatase activity of this
             enzyme largely prevents the formation of toxic hydrolysis
             products arising from this plant defense system.
             Importantly, the enzyme acts on all major classes of
             glucosinolates, thus enabling diamondback moths to use a
             broad range of cruciferous host plants.},
   Doi = {10.1073/pnas.172112899},
   Key = {fds229284}
}

@article{fds229280,
   Author = {Kliebenstein, DJ and Figuth, A and Mitchell-Olds,
             T},
   Title = {Genetic architecture of plastic methyl jasmonate responses
             in Arabidopsis thaliana.},
   Journal = {Genetics},
   Volume = {161},
   Number = {4},
   Pages = {1685-1696},
   Year = {2002},
   Month = {August},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12196411},
   Abstract = {The ability of a single genotype to generate different
             phenotypes in disparate environments is termed phenotypic
             plasticity, which reflects the interaction of genotype and
             environment on developmental processes. However, there is
             controversy over the definition of plasticity genes. The
             gene regulation model states that plasticity loci influence
             trait changes between environments without altering the
             means within a given environment. Alternatively, the allelic
             sensitivity model argues that plasticity evolves due to
             selection of phenotypic values expressed within particular
             environments; hence plasticity must be controlled by loci
             expressed within these environments. To identify genetic
             loci controlling phenotypic plasticity and address this
             controversy, we analyzed the plasticity of glucosinolate
             accumulation under methyl jasmonate (MeJa) treatment in
             Arabidopsis thaliana. We found genetic variation influencing
             multiple MeJa signal transduction pathways. Analysis of MeJa
             responses in the Landsberg erecta x Columbia recombinant
             inbred lines identified a number of quantitative trait loci
             (QTL) that regulate plastic MeJa responses. All significant
             plasticity QTL also impacted the mean trait value in at
             least one of the two "control" or "MeJa" environments,
             supporting the allelic sensitivity model. Additionally, we
             present an analysis of MeJa and salicylic acid cross-talk in
             glucosinolate regulation and describe the implications for
             glucosinolate physiology and functional understanding of
             Arabidopsis MeJa signal transduction.},
   Key = {fds229280}
}

@article{fds229278,
   Author = {Haubold, B and Kroymann, J and Ratzka, A and Mitchell-Olds, T and Wiehe,
             T},
   Title = {Recombination and gene conversion in a 170-kb genomic region
             of Arabidopsis thaliana.},
   Journal = {Genetics},
   Volume = {161},
   Number = {3},
   Pages = {1269-1278},
   Year = {2002},
   Month = {July},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12136029},
   Abstract = {Arabidopsis thaliana is a highly selfing plant that
             nevertheless appears to undergo substantial recombination.
             To reconcile its selfing habit with the observations of
             recombination, we have sampled the genetic diversity of A.
             thaliana at 14 loci of approximately 500 bp each, spread
             across 170 kb of genomic sequence centered on a QTL for
             resistance to herbivory. A total of 170 of the 6321
             nucleotides surveyed were polymorphic, with 169 being
             biallelic. The mean silent genetic diversity (pi(s)) varied
             between 0.001 and 0.03. Pairwise linkage disequilibria
             between the polymorphisms were negatively correlated with
             distance, although this effect vanished when only pairs of
             polymorphisms with four haplotypes were included in the
             analysis. The absence of a consistent negative correlation
             between distance and linkage disequilibrium indicated that
             gene conversion might have played an important role in
             distributing genetic diversity throughout the region. We
             tested this by coalescent simulations and estimate that up
             to 90% of recombination is due to gene conversion.},
   Key = {fds229278}
}

@article{fds229282,
   Author = {Mitchell-Olds, T and Knight, CA},
   Title = {Evolution. Chaperones as buffering agents?},
   Journal = {Science (New York, N.Y.)},
   Volume = {296},
   Number = {5577},
   Pages = {2348-2349},
   Year = {2002},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12089432},
   Doi = {10.1126/science.1073846},
   Key = {fds229282}
}

@article{fds229279,
   Author = {Kliebenstein, D and Pedersen, D and Barker, B and Mitchell-Olds,
             T},
   Title = {Comparative analysis of quantitative trait loci controlling
             glucosinolates, myrosinase and insect resistance in
             Arabidopsis thaliana.},
   Journal = {Genetics},
   Volume = {161},
   Number = {1},
   Pages = {325-332},
   Year = {2002},
   Month = {May},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12019246},
   Abstract = {Evolutionary interactions among insect herbivores and plant
             chemical defenses have generated systems where plant
             compounds have opposing fitness consequences for host
             plants, depending on attack by various insect herbivores.
             This interplay complicates understanding of fitness costs
             and benefits of plant chemical defenses. We are studying the
             role of the glucosinolate-myrosinase chemical defense system
             in protecting Arabidopsis thaliana from specialist and
             generalist insect herbivory. We used two Arabidopsis
             recombinant inbred populations in which we had previously
             mapped QTL controlling variation in the glucosinolate-myrosinase
             system. In this study we mapped QTL controlling resistance
             to specialist (Plutella xylostella) and generalist
             (Trichoplusia ni) herbivores. We identified a number of QTL
             that are specific to one herbivore or the other, as well as
             a single QTL that controls resistance to both insects.
             Comparison of QTL for herbivory, glucosinolates, and
             myrosinase showed that T. ni herbivory is strongly deterred
             by higher glucosinolate levels, faster breakdown rates, and
             specific chemical structures. In contrast, P. xylostella
             herbivory is uncorrelated with variation in the
             glucosinolate-myrosinase system. This agrees with
             evolutionary theory stating that specialist insects may
             overcome host plant chemical defenses, whereas generalists
             will be sensitive to these same defenses.},
   Key = {fds229279}
}

@article{fds229277,
   Author = {Clauss, MJ and Cobban, H and Mitchell-Olds, T},
   Title = {Cross-species microsatellite markers for elucidating
             population genetic structure in Arabidopsis and Arabis
             (Brassicaeae).},
   Journal = {Molecular Ecology},
   Volume = {11},
   Number = {3},
   Pages = {591-601},
   Year = {2002},
   Month = {March},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11918792},
   Abstract = {Species closely related to model organisms present the
             opportunity to efficiently apply molecular and functional
             tools developed by a large research community to taxa with
             different ecological and evolutionary histories. We complied
             42 microsatellite loci that amplify under common conditions
             in four closely related Arabidopsis: A. thaliana; A.
             halleri; A. lyrata ssp. lyrata; and A. lyrata ssp. petraea,
             as well as in one more distantly related crucifer; Arabis
             drummondii. Variation at these loci is amenable to a
             diversity of applications including population genetics,
             phylogeographical analyses, mapping of inter and
             intraspecific crosses, and recombination mapping. Our
             analysis of microsatellite variation illustrates significant
             differences in population genetic parameters among three
             Arabidopsis species. A population of A. thaliana, an
             inbreeding annual plant associated with disturbed habitats,
             was highly monomorphic (P = 8% percent polymorphic loci) and
             only 0.2% heterozygous for 648 locus-by-individual
             combinations. A population of the self-incompatible
             perennial herb, A. halleri, was more genetically variable (P
             = 71%) and had an excess of heterozygosity that may reflect
             a recent population bottleneck associated with
             human-mediated founder events. A population of the
             self-incompatible perennial herb, A. lyrata ssp. petraea,
             was even more genetically variable (P = 86%) and appeared to
             be at mutation-drift equilibrium. Population structure
             estimated from neutrally evolving loci provides an empirical
             expectation against which hypotheses of adaptive evolution
             at functional loci can be tested.},
   Doi = {10.1046/j.0962-1083.2002.01465.x},
   Key = {fds229277}
}

@article{fds229285,
   Author = {Reichelt, M and Brown, PD and Schneider, B and Oldham, NJ and Stauber,
             E and Tokuhisa, J and Kliebenstein, DJ and Mitchell-Olds, T and Gershenzon, J},
   Title = {Benzoic acid glucosinolate esters and other glucosinolates
             from Arabidopsis thaliana.},
   Journal = {Phytochemistry},
   Volume = {59},
   Number = {6},
   Pages = {663-671},
   Year = {2002},
   Month = {March},
   ISSN = {0031-9422},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11867099},
   Abstract = {The spectacular recent progress in Arabidopsis thaliana
             molecular genetics furnishes outstanding tools for studying
             the formation and function of all metabolites in this
             cruciferous species. One of the major groups of secondary
             metabolites in A. thaliana is the glucosinolates. These
             hydrophilic, sulfur-rich glycosides appear to serve as
             defenses against some generalist herbivores and pathogens,
             and as feeding and oviposition stimulants to specialist
             herbivores. To help study their biosynthesis and role in
             plant-insect interactions, we wanted to determine the
             complete glucosinolate content of A. thaliana. In previous
             studies, 24 glucosinolates had been identified from ecotype
             Columbia. We reinvestigated Columbia as well as additional
             ecotypes and mutant lines, and identified 12 further
             glucosinolates, including five novel compounds. Structures
             were elucidated by MS and NMR spectroscopy of their
             desulfated derivatives, and by enzymatic cleavage of the
             attached ester moieties. Four of the novel glucosinolates
             are benzoate esters isolated from the seeds. In all but one
             of these compounds, esterification is on the glucose moiety
             rather than the side chain, a very unusual feature for
             glucosinolates. Among additional glucosinolates identified
             were the first non-chain elongated, methionine-derived
             glucosinolate from A. thaliana and the first compounds that
             appear to be derived from leucine.},
   Doi = {10.1016/s0031-9422(02)00014-6},
   Key = {fds229285}
}

@article{fds229274,
   Author = {Siemens, DH and Garner, SH and Mitchell-Olds, T and Callaway,
             RM},
   Title = {Cost of defense in the context of plant competition:
             Brassica rapa may grow and defend},
   Journal = {Ecology},
   Volume = {83},
   Number = {2},
   Pages = {505-517},
   Publisher = {WILEY},
   Year = {2002},
   Month = {February},
   url = {http://dx.doi.org/10.1890/0012-9658(2002)083[0505:coditc]2.0.co;2},
   Abstract = {Theory on costs of plant defense against herbivory in
             stressful environments predicts that costs should increase
             when competition is intense. This amplifies a fundamental
             dilemma that plants are thought to face: allocate limited
             resources to grow fast enough to compete, or invest these
             resources in secondary metabolites to maintain defense. We
             studied costs associated with genetic and environmental
             variation in secondary metabolite production of Brassica
             rapa in the presence and absence of the generalist
             competitor Lolium perenne. We used experimental quantitative
             genetics (artificial selection) to manipulate genetic
             variation, and herbivore-induction treatments to produce
             environmental variation in myrosinase and glucosinolate
             concentrations and resistance. Glucosinolates, and their
             byproducts after breakdown by myrosinase, are known to
             affect herbivory on plants in the Brassicaceae family.
             Defense costs were significant in the absence of
             competitors, but in contrast to theoretical predictions,
             costs of constitutive defense (measured as growth rates)
             were not detectable and the cost of induced defense remained
             the same in the competitive environment. To understand what
             factors made constitutive defense costs not detectable under
             competition we conducted several experiments to assess the
             effects of limited resources and allelopathy on costs and
             benefits of the defense chemicals. None of the experiments
             involving nutrient supply and weak competition supported the
             hypothesis that the lack of defense costs in competitive
             environments was due to limited resources. Instead, the
             breakdown products of the glucosinolate-myrosinase reaction
             appeared to function as allelopathic agents, which may
             benefit B. rapa plants in competition, thereby reducing net
             costs of chemical defense. We found that: (1) the effects of
             exogenous glucosinolates on Lolium root length depended on
             the presence of myrosinase. (2) In the absence of nutrients,
             Lolium root lengths were shorter when seeds germinated with
             B. rapa. (3) Genetic increases in glucosinolate
             concentration negatively affected Lolium seedling growth
             only when there were simultaneous genetic increases in
             myrosinase concentration. Activated carbon treatments
             designed to neutralize allelopathic effects and restore
             costs in the competitive environments were, however, not
             statistically significant. When plant defenses also function
             to benefit plants in competitive interactions, plants may
             evolve to compete and defend.},
   Doi = {10.1890/0012-9658(2002)083[0505:coditc]2.0.co;2},
   Key = {fds229274}
}

@article{fds229275,
   Author = {Stotz, HU and Koch, T and Biedermann, A and Weniger, K and Boland, W and Mitchell-Olds, T},
   Title = {Evidence for regulation of resistance in Arabidopsis to
             Egyptian cotton worm by salicylic and jasmonic acid
             signaling pathways.},
   Journal = {Planta},
   Volume = {214},
   Number = {4},
   Pages = {648-652},
   Year = {2002},
   Month = {February},
   ISSN = {0032-0935},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11925049},
   Abstract = {Signaling cross-talk between wound- and pathogen-response
             pathways influences resistance of plants to insects and
             disease. To elucidate potential interactions between
             salicylic acid (SA) and jasmonic acid (JA) defense pathways,
             we exploited the availability of characterized mutants of
             Arabidopsis thaliana (L.) Heynh. and monitored resistance to
             Egyptian cotton worm (Spodoptera littoralis Boisd.;
             Lepidoptera: Noctuidae). This generalist herbivore is
             sensitive to induced plant defense pathways and is thus a
             useful model for a mechanistic analysis of insect
             resistance. As expected, treatment of wild-type Arabidopsis
             with JA enhanced resistance to Egyptian cotton worm.
             Conversely, the coil mutant, with a deficiency in the JA
             response pathway, was more susceptible to Egyptian cotton
             worm than wild-type Arabidopsis. By contrast, the nprl
             mutant, with defects in systemic disease resistance,
             exhibited enhanced resistance to Egyptian cotton worm.
             Pretreatment with SA significantly reduced this enhanced
             resistance of nprl plants but had no influence on the
             resistance of wild-type plants. However, exogenous SA
             reduced the amount of JA that Egyptian cotton worm induced
             in both npr1 mutant and wild-type plants. Thus, this
             generalist herbivore engages two different induced defense
             pathways that interact to mediate resistance in
             Arabidopsis.},
   Doi = {10.1007/s004250100656},
   Key = {fds229275}
}

@article{fds229283,
   Author = {Mitchell-Olds, T and Clauss, MJ},
   Title = {Plant evolutionary genomics.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {5},
   Number = {1},
   Pages = {74-79},
   Year = {2002},
   Month = {February},
   ISSN = {1369-5266},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11788312},
   Abstract = {Evolutionary genomics combines functional and evolutionary
             analyses of genome conservation and differentiation. Gene
             duplication and polyploidy have fundamentally shaped the
             genomes of Arabidopsis and all angiosperms. Recent
             comparative studies have focussed on gene regulation, the
             function of untranscribed genomic regions, and the effects
             of natural selection on protein function. A large fraction
             of interspecific protein divergence is probably adaptive,
             and may be useful for experimental studies of genes and
             proteins.},
   Doi = {10.1016/s1369-5266(01)00231-x},
   Key = {fds229283}
}

@article{fds229276,
   Author = {Berger, S and Mitchell-Olds, T and Stotz, HU},
   Title = {Local and differential control of vegetative storage protein
             expression in response to herbivore damage in Arabidopsis
             thaliana.},
   Journal = {Physiologia Plantarum},
   Volume = {114},
   Number = {1},
   Pages = {85-91},
   Year = {2002},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11982938},
   Abstract = {Vegetative storage proteins (VSPs) are thought to fulfil
             important nutritional roles during plant development and
             stress adaptation. Plant responses to mechanical wounding
             and herbivore damage include an activation of VSP
             expression. It was recently suggested that vsp is part of
             the systemic response of Arabidopsis to wounding. To test
             this proposal, we monitored the spatial regulation of vsp
             mRNAs and VSP proteins. Arabidopsis contains two vsp genes
             and real-time quantitative PCR allowed us to characterize
             their differential expression. The ratio of vsp1 to vsp2
             mRNA abundance increased when plants were challenged with
             diamondback moth larvae or Egyptian cotton worms, but not
             when they were mechanically wounded. We observed a dramatic
             increase of vsp1 and vsp2 mRNA as well as VSP protein levels
             in leaves that experienced herbivore damage. By contrast,
             there was a relatively minor increase of vsp mRNA and VSP
             protein levels in undamaged leaves of infested plants. These
             results clearly demonstrate that VSPs are part of the local
             plant response to herbivore attack. To obtain additional
             information on vsp regulation, we analysed a fusion of a
             soybean vspB promoter fragment to the beta-glucuronidase
             gene in transgenic Arabidopsis plants. The vspB promoter
             responded to both jasmonate and herbivore treatments,
             suggesting that similar signals regulate its expression in
             both plant species.},
   Doi = {10.1046/j.0031-9317.2001.1140112.x},
   Key = {fds229276}
}

@article{fds229281,
   Author = {Kuittinen, and H, and Aguadé, M and Charlesworth, D and Haan, AD and Lauga, B and Mitchell-Olds, T and Oikarinen, S and Ramos-Onsins, S and Stranger, B and Tienderen, PV and Savolainen, O},
   Title = {A set of primers for functional biodiversity screening and
             comparative genetics in Brassicaceae},
   Journal = {Molecular Ecology Notes},
   Volume = {2},
   Number = {3},
   Pages = {258-262},
   Year = {2002},
   ISSN = {1471-8278},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000177964300021&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1046/j.1471-8278.2002.00210.x},
   Key = {fds229281}
}

@article{fds229270,
   Author = {Lambrix, V and Reichelt, M and Mitchell-Olds, T and Kliebenstein, DJ and Gershenzon, J},
   Title = {The Arabidopsis epithiospecifier protein promotes the
             hydrolysis of glucosinolates to nitriles and influences
             Trichoplusia ni herbivory.},
   Journal = {The Plant Cell},
   Volume = {13},
   Number = {12},
   Pages = {2793-2807},
   Year = {2001},
   Month = {December},
   ISSN = {1040-4651},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11752388},
   Abstract = {Glucosinolates are anionic thioglucosides that have become
             one of the most frequently studied groups of defensive
             metabolites in plants. When tissue damage occurs, the
             thioglucoside linkage is hydrolyzed by enzymes known as
             myrosinases, resulting in the formation of a variety of
             products that are active against herbivores and pathogens.
             In an effort to learn more about the molecular genetic and
             biochemical regulation of glucosinolate hydrolysis product
             formation, we analyzed leaf samples of 122 Arabidopsis
             ecotypes. A distinct polymorphism was observed with all
             ecotypes producing primarily isothiocyanates or primarily
             nitriles. The ecotypes Columbia (Col) and Landsberg erecta
             (Ler) differed in their hydrolysis products; therefore, the
             Col x Ler recombinant inbred lines were used for mapping the
             genes controlling this polymorphism. The major quantitative
             trait locus (QTL) affecting nitrile versus isothiocyanate
             formation was found very close to a gene encoding a homolog
             of a Brassica napus epithiospecifier protein (ESP), which
             causes the formation of epithionitriles instead of
             isothiocyanates during glucosinolate hydrolysis in the seeds
             of certain Brassicaceae. The heterologously expressed
             Arabidopsis ESP was able to convert glucosinolates both to
             epithionitriles and to simple nitriles in the presence of
             myrosinase, and thus it was more versatile than previously
             described ESPs. The role of ESP in plant defense is
             uncertain, because the generalist herbivore Trichoplusia ni
             (the cabbage looper) was found to feed more readily on
             nitrile-producing than on isothiocyanate-producing
             Arabidopsis. However, isothiocyanates are frequently used as
             recognition cues by specialist herbivores, and so the
             formation of nitriles instead of isothiocyanates may allow
             Arabidopsis to be less apparent to specialists.},
   Doi = {10.1105/tpc.010261},
   Key = {fds229270}
}

@article{fds229272,
   Author = {Mitchell-Olds, T},
   Title = {Arabidopsis thaliana and its wild relatives: A model system
             for ecology and evolution},
   Journal = {Trends in Ecology and Evolution},
   Volume = {16},
   Number = {12},
   Pages = {693-700},
   Publisher = {Elsevier BV},
   Year = {2001},
   Month = {December},
   ISSN = {0169-5347},
   url = {http://dx.doi.org/10.1016/S0169-5347(01)02291-1},
   Abstract = {The postgenomics era will bring many changes to ecology and
             evolution. Information about genomic sequence and function
             provides a new foundation for organismal biology. The
             crucifer Arabidopsis thaliana and its wild relatives will
             play an important role in this synthesis of genomics and
             ecology. We discuss the need for model systems in ecology,
             the biology and relationships of crucifers, and the
             molecular resources available for these experiments. The
             scientific potential of this model system is illustrated by
             several recent studies in plant-insect interactions,
             developmental plasticity, comparative genomics and molecular
             evolution.},
   Doi = {10.1016/S0169-5347(01)02291-1},
   Key = {fds229272}
}

@article{fds229269,
   Author = {Kroymann, J and Textor, S and Tokuhisa, JG and Falk, KL and Bartram, S and Gershenzon, J and Mitchell-Olds, T},
   Title = {A gene controlling variation in Arabidopsis glucosinolate
             composition is part of the methionine chain elongation
             pathway.},
   Journal = {Plant Physiology},
   Volume = {127},
   Number = {3},
   Pages = {1077-1088},
   Year = {2001},
   Month = {November},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11706188},
   Abstract = {Arabidopsis and other Brassicaceae produce an enormous
             diversity of aliphatic glucosinolates, a group of methionine
             (Met)-derived plant secondary compounds containing a
             beta-thio-glucose moiety, a sulfonated oxime, and a variable
             side chain. We fine-scale mapped GSL-ELONG, a locus
             controlling variation in the side-chain length of aliphatic
             glucosinolates. Within this locus, a polymorphic gene was
             identified that determines whether Met is extended
             predominantly by either one or by two methylene groups to
             produce aliphatic glucosinolates with either three- or
             four-carbon side chains. Two allelic mutants deficient in
             four-carbon side-chain glucosinolates were shown to contain
             independent missense mutations within this gene. In
             cell-free enzyme assays, a heterologously expressed cDNA
             from this locus was capable of condensing
             2-oxo-4-methylthiobutanoic acid with acetyl-coenzyme A, the
             initial reaction in Met chain elongation. The gene
             methylthioalkylmalate synthase1 (MAM1) is a member of a gene
             family sharing approximately 60% amino acid sequence
             similarity with 2-isopropylmalate synthase, an enzyme of
             leucine biosynthesis that condenses 2-oxo-3-methylbutanoate
             with acetyl-coenzyme A.},
   Doi = {10.1104/pp.127.3.1077},
   Key = {fds229269}
}

@article{fds229267,
   Author = {Koch, MA and Weisshaar, B and Kroymann, J and Haubold, B and Mitchell-Olds, T},
   Title = {Comparative genomics and regulatory evolution: conservation
             and function of the Chs and Apetala3 promoters.},
   Journal = {Molecular Biology and Evolution},
   Volume = {18},
   Number = {10},
   Pages = {1882-1891},
   Year = {2001},
   Month = {October},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11557794},
   Abstract = {DNA sequence variations of chalcone synthase (Chs) and
             Apetala3 gene promoters from 22 cruciferous plant species
             were analyzed to identify putative conserved regulatory
             elements. Our comparative approach confirmed the existence
             of numerous conserved sequences which may act as regulatory
             elements in both investigated promoters. To confirm the
             correct identification of a well-conserved
             UV-light-responsive promoter region, a subset of Chs
             promoter fragments were tested in Arabidopsis thaliana
             protoplasts. All promoters displayed similar light
             responsivenesses, indicating the general functional
             relevance of the conserved regulatory element. In addition
             to known regulatory elements, other highly conserved regions
             were detected which are likely to be of functional
             importance. Phylogenetic trees based on DNA sequences from
             both promoters (gene trees) were compared with the
             hypothesized phylogenetic relationships (species trees) of
             these taxa. The data derived from both promoter sequences
             were congruent with the phylogenies obtained from coding
             regions of other nuclear genes and from chloroplast DNA
             sequences. This indicates that promoter sequence evolution
             generally is reflective of species phylogeny. Our study also
             demonstrates the great value of comparative genomics and
             phylogenetics as a basis for functional analysis of promoter
             action and gene regulation.},
   Doi = {10.1093/oxfordjournals.molbev.a003729},
   Key = {fds229267}
}

@article{fds229148,
   Author = {Wiehe, T and Gebauer-Jung, S and Mitchell-Olds, T and Guigó,
             R},
   Title = {SGP-1: prediction and validation of homologous genes based
             on sequence alignments.},
   Journal = {Genome Research},
   Volume = {11},
   Number = {9},
   Pages = {1574-1583},
   Year = {2001},
   Month = {September},
   ISSN = {1088-9051},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11544202},
   Abstract = {Conventional methods of gene prediction rely on the
             recognition of DNA-sequence signals, the coding potential or
             the comparison of a genomic sequence with a cDNA, EST, or
             protein database. Reasons for limited accuracy in many
             circumstances are species-specific training and the
             incompleteness of reference databases. Lately, comparative
             genome analysis has attracted increasing attention. Several
             analysis tools that are based on human/mouse comparisons are
             already available. Here, we present a program for the
             prediction of protein-coding genes, termed SGP-1 (Syntenic
             Gene Prediction), which is based on the similarity of
             homologous genomic sequences. In contrast to most existing
             tools, the accuracy of depends little on species-specific
             properties such as codon usage or the nucleotide
             distribution. may therefore be applied to nonstandard model
             organisms in vertebrates as well as in plants, without the
             need for extensive parameter training. In addition to
             predicting genes in large-scale genomic sequences, the
             program may be useful to validate gene structure annotations
             from databases. To this end, SGP-1 output also contains
             comparisons between predicted and annotated gene structures
             in HTML format. The program can be accessed via a Web server
             at http://soft.ice.mpg.de/sgp-1. The source code, written in
             ANSI C, is available on request from the
             authors.},
   Doi = {10.1101/gr.177401},
   Key = {fds229148}
}

@article{fds229264,
   Author = {Kliebenstein, DJ and Gershenzon, J and Mitchell-Olds,
             T},
   Title = {Comparative quantitative trait loci mapping of aliphatic,
             indolic and benzylic glucosinolate production in Arabidopsis
             thaliana leaves and seeds.},
   Journal = {Genetics},
   Volume = {159},
   Number = {1},
   Pages = {359-370},
   Year = {2001},
   Month = {September},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11560911},
   Abstract = {Secondary metabolites are a diverse set of plant compounds
             believed to have numerous functions in plant-environment
             interactions. Despite this importance, little is known about
             the regulation of secondary metabolite accumulation. We are
             studying the regulation of glucosinolates, a large group of
             secondary metabolites, in Arabidopsis to investigate how
             secondary metabolism is controlled. We utilized Ler and Cvi,
             two ecotypes of Arabidopsis that have striking differences
             in both the types and amounts of glucosinolates that
             accumulate in the seeds and leaves. QTL analysis identified
             six loci determining total aliphatic glucosinolate
             accumulation, six loci controlling total indolic
             glucosinolate concentration, and three loci regulating
             benzylic glucosinolate levels. Our results show that two of
             the loci controlling total aliphatic glucosinolates map to
             biosynthetic loci that interact epistatically to regulate
             aliphatic glucosinolate accumulation. In addition to the six
             loci regulating total indolic glucosinolate concentration,
             mapping of QTL for the individual indolic glucosinolates
             identified five additional loci that were specific to
             subsets of the indolic glucosinolates. These data show that
             there are a large number of variable loci controlling
             glucosinolate accumulation in Arabidopsis
             thaliana.},
   Key = {fds229264}
}

@article{fds229271,
   Author = {McKay, JK and Bishop, JG and Lin, JZ and Richards, JH and Sala, A and Mitchell-Olds, T},
   Title = {Local adaptation across a climatic gradient despite small
             effective population size in the rare sapphire
             rockcress.},
   Journal = {Proceedings of the Royal Society B: Biological
             Sciences},
   Volume = {268},
   Number = {1477},
   Pages = {1715-1721},
   Year = {2001},
   Month = {August},
   ISSN = {0962-8452},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11506685},
   Abstract = {When assigning conservation priorities in endangered
             species, two common management strategies seek to protect
             remnant populations that (i) are the most genetically
             divergent or (ii) possess the highest diversity at neutral
             genetic markers. These two approaches assume that variation
             in molecular markers reflects variation in ecologically
             important traits and ignore the possibility of local
             adaptation among populations that show little divergence or
             variation at marker loci. Using common garden experiments,
             we demonstrate that populations of the rare endemic plant
             Arabis fecunda are physiologically adapted to the local
             microclimate. Local adaptation occurs despite (i) the
             absence of divergence at almost all marker loci and (ii)
             very small effective population sizes, as evidenced by
             extremely low levels of allozyme and DNA sequence
             polymorphism. Our results provide empirical evidence that
             setting conservation priorities based exclusively on
             molecular marker diversity may lead to the loss of locally
             adapted populations.},
   Doi = {10.1098/rspb.2001.1715},
   Key = {fds229271}
}

@article{fds229273,
   Author = {Sharbel, TF and Mitchell-Olds, T},
   Title = {Recurrent polyploid origins and chloroplast phylogeography
             in the Arabis holboellii complex (Brassicaceae).},
   Journal = {Heredity},
   Volume = {87},
   Number = {Pt 1},
   Pages = {59-68},
   Year = {2001},
   Month = {July},
   ISSN = {0018-067X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11678988},
   Abstract = {Arabis holboellii is a North American member of the
             Brassicaceae that can reproduce via sex or apomixis.
             Previous studies have shown sexual individuals to be
             diploid, whilst apomictic individuals can be diploid (and
             aneuploid) or polyploid (typically 3x). Apomictic
             individuals can furthermore be facultative (i.e. both sexual
             and apomictic seed production in a single individual). Using
             flow cytometry, ploidy variation in 245 accessions of A.
             holboellii and A. drummondii from western North America and
             Greenland has been examined. Additionally, the chloroplast
             trnL intron region from each accession was sequenced for
             phylogenetic analysis of ploidy variation. Based upon 17
             informative single nucleotide and insertion-deletion
             polymorphisms, we identified seven and 14 chloroplast
             haplotypes for A. drummondii and A. holboellii,
             respectively. Six of the haplotypes were found in both
             species. Ten of the chloroplast haplotypes were
             characterized by diploid, aneuploid, and triploid
             individuals, and thus we conclude that polyploidy has
             repeatedly and independently arisen within the species
             complex. As triploid individuals, which undergo normal
             meiosis, can only reproduce through apomixis, this may imply
             that the phenotype apomixis has also arisen multiple times.
             Arabis holboellii thus appears to have some predisposition
             to evolve apomictic reproduction.},
   Doi = {10.1046/j.1365-2540.2001.00908.x},
   Key = {fds229273}
}

@article{fds229265,
   Author = {Kliebenstein, DJ and Kroymann, J and Brown, P and Figuth, A and Pedersen, D and Gershenzon, J and Mitchell-Olds,
             T},
   Title = {Genetic control of natural variation in Arabidopsis
             glucosinolate accumulation.},
   Journal = {Plant Physiology},
   Volume = {126},
   Number = {2},
   Pages = {811-825},
   Year = {2001},
   Month = {June},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11402209},
   Abstract = {Glucosinolates are biologically active secondary metabolites
             of the Brassicaceae and related plant families that
             influence plant/insect interactions. Specific glucosinolates
             can act as feeding deterrents or stimulants, depending upon
             the insect species. Hence, natural selection might favor the
             presence of diverse glucosinolate profiles within a given
             species. We determined quantitative and qualitative
             variation in glucosinolates in the leaves and seeds of 39
             Arabidopsis ecotypes. We identified 34 different
             glucosinolates, of which the majority are chain-elongated
             compounds derived from methionine. Polymorphism at only five
             loci was sufficient to generate 14 qualitatitvely different
             leaf glucosinolate profiles. Thus, there appears to be a
             modular genetic system regulating glucosinolate profiles in
             Arabidopsis. This system allows the rapid generation of new
             glucosinolate combinations in response to changing herbivory
             or other selective pressures. In addition to the qualitative
             variation in glucosinolate profiles, we found a nearly
             20-fold difference in the quantity of total aliphatic
             glucosinolates and were able to identify a single locus that
             controls nearly three-quarters of this variation.},
   Doi = {10.1104/pp.126.2.811},
   Key = {fds229265}
}

@article{fds229141,
   Author = {Stotz, HU and Pittendrigh, BR and Kroymann, J and Weniger, K and Fritsche, J and Bauke, A and Mitchell-Olds, T},
   Title = {Induced plant defense responses against chewing insects.
             Ethylene signaling reduces resistance of arabidopsis against
             Egyptian cotton worm but not diamondback moth. (vol 124, pg
             1007, 2000)},
   Journal = {Plant Physiology},
   Volume = {125},
   Number = {4},
   Pages = {2203-2203},
   Publisher = {AMER SOC PLANT PHYSIOLOGISTS},
   Year = {2001},
   Month = {April},
   ISSN = {0032-0889},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000168215200068&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds229141}
}

@article{fds229266,
   Author = {Kliebenstein, DJ and Lambrix, VM and Reichelt, M and Gershenzon, J and Mitchell-Olds, T},
   Title = {Gene duplication in the diversification of secondary
             metabolism: tandem 2-oxoglutarate-dependent dioxygenases
             control glucosinolate biosynthesis in Arabidopsis.},
   Journal = {The Plant Cell},
   Volume = {13},
   Number = {3},
   Pages = {681-693},
   Year = {2001},
   Month = {March},
   ISSN = {1040-4651},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11251105},
   Abstract = {Secondary metabolites are a diverse set of plant compounds
             believed to have numerous functions in plant-environment
             interactions. The large chemical diversity of secondary
             metabolites undoubtedly arises from an equally diverse set
             of enzymes responsible for their biosynthesis. However,
             little is known about the evolution of enzymes involved in
             secondary metabolism. We are studying the biosynthesis of
             glucosinolates, a large group of secondary metabolites, in
             Arabidopsis to investigate the evolution of enzymes involved
             in secondary metabolism. Arabidopsis contains natural
             variations in the presence of methylsulfinylalkyl, alkenyl,
             and hydroxyalkyl glucosinolates. In this article, we report
             the identification of genes encoding two
             2-oxoglutarate--dependent dioxygenases that are responsible
             for this variation. These genes, AOP2 and AOP3, which map to
             the same position on chromosome IV, result from an apparent
             gene duplication and control the conversion of
             methylsulfinylalkyl glucosinolate to either the alkenyl or
             the hydroxyalkyl form. By heterologous expression in
             Escherichia and the correlation of gene expression patterns
             to the glucosinolate phenotype, we show that AOP2 catalyzes
             the conversion of methylsulfinylalkyl glucosinolates to
             alkenyl glucosinolates. Conversely, AOP3 directs the
             formation of hydroxyalkyl glucosinolates from
             methylsulfinylalkyl glucosinolates. No ecotype coexpressed
             both genes. Furthermore, the absence of functional AOP2 and
             AOP3 leads to the accumulation of the precursor
             methylsulfinylalkyl glucosinolates. A third member of this
             gene family, AOP1, is present in at least two forms and
             found in all ecotypes examined. However, its catalytic role
             is still uncertain.},
   Doi = {10.1105/tpc.13.3.681},
   Key = {fds229266}
}

@article{fds229268,
   Author = {Koch, M and Haubold, B and Mitchell-Olds, T},
   Title = {Molecular systematics of the Brassicaceae: evidence from
             coding plastidic matK and nuclear Chs sequences.},
   Journal = {American Journal of Botany},
   Volume = {88},
   Number = {3},
   Pages = {534-544},
   Year = {2001},
   Month = {March},
   ISSN = {0002-9122},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11250830},
   Abstract = {Phylogenetic relationships were inferred using nucleotide
             sequence variation of the nuclear-encoded chalcone synthase
             gene (Chs) and the chloroplast gene matK for members of five
             tribes from the family Brassicaceae to analyze tribal and
             subtribal structures. Phylogenetic trees from individual
             data sets are mostly in congruence with the results from a
             combined matK-Chs analysis with a total of 2721 base pairs,
             but with greater resolution and higher statistical support
             for deeper branching patterns. The analysis indicates that
             tribes Lepidieae, Arabideae, and Sisymbrieae are not
             monophyletic. Among taxa under study four different lineages
             each were detected in tribes Arabideae and Lepidieae,
             interspersed with taxa from tribes Sisymbrieae, Hesperideae,
             and Brassiceae. It is concluded that tribe Brassiceae might
             be the only monophyletic group of the traditional tribes.
             From our data we estimated several divergence times for
             different lineages among cruciferous plants: 5.8 mya
             (million years ago) for the Arabidopsis-Cardaminopsis split,
             20 mya for the Brassica-Arabidopsis split, and ∼40 mya for
             the age of the deepest split between the most basal crucifer
             Aethionema and remaining cruciferous taxa.},
   Doi = {10.2307/2657117},
   Key = {fds229268}
}

@article{fds229149,
   Author = {Stotz, HU and Pittendrigh, BR and Kroymann, J and Weniger, K and Fritsche, J and Bauke, A and Mitchell-Olds, T},
   Title = {Erratum: Induced plant defense responses against chewing
             insects. Ethylene signaling reduces resistance of
             arabidopsis against Egyptian cotton worm but not diamondback
             moth (Plant Physiology (2000) 124 (1007-1017))},
   Journal = {Plant Physiology},
   Volume = {125},
   Number = {4},
   Pages = {2203},
   Year = {2001},
   Month = {January},
   Key = {fds229149}
}

@article{fds229263,
   Author = {Sharbel, TF and Haubold, B and Mitchell-Olds, T},
   Title = {Genetic isolation by distance in Arabidopsis thaliana:
             biogeography and postglacial colonization of
             Europe.},
   Journal = {Molecular Ecology},
   Volume = {9},
   Number = {12},
   Pages = {2109-2118},
   Year = {2000},
   Month = {December},
   ISSN = {0962-1083},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11123622},
   Abstract = {Arabidopsis thaliana provides a useful model system for
             functional, evolutionary and ecological studies in plant
             biology. We have analysed natural genetic variation in A.
             thaliana in order to infer its biogeographical and
             historical distribution across Eurasia. We analysed 79
             amplified fragment length polymorphism (AFLP) markers in 142
             accessions from the species' native range, and found highly
             significant genetic isolation by distance among A. thaliana
             accessions from Eurasia and southern Europe. These spatial
             patterns of genetic variation suggest that A. thaliana
             colonized central and northern Europe from Asia and from
             Mediterranean Pleistocene refugia, a trend which has been
             identified in other species. Statistically significant
             levels of multilocus linkage disequilibrium suggest
             intermediate levels of disequilibrium among subsets of loci,
             and analysis of genetic relationships among accessions
             reveal a star or bush-like dendrogram with low bootstrap
             support. Taken together, it appears that there has been
             sufficient historical recombination in the A. thaliana
             genome such that accessions do not conform to a tree-like,
             bifurcating pattern of evolution - there is no 'ecotype
             phylogeny.' Nonetheless, significant isolation by distance
             provides a framework upon which studies of natural variation
             in A. thaliana may be designed and interpreted.},
   Doi = {10.1046/j.1365-294x.2000.01122.x},
   Key = {fds229263}
}

@article{fds229168,
   Author = {Stotz, HU and Pittendrigh, BR and Kroymann, J and Weniger, K and Fritsche, J and Bauke, A and Mitchell-Olds, T},
   Title = {Induced plant defense responses against chewing insects.
             Ethylene signaling reduces resistance of Arabidopsis against
             Egyptian cotton worm but not diamondback
             moth.},
   Journal = {Plant Physiology},
   Volume = {124},
   Number = {3},
   Pages = {1007-1018},
   Year = {2000},
   Month = {November},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11080278},
   Abstract = {The induction of plant defenses by insect feeding is
             regulated via multiple signaling cascades. One of them,
             ethylene signaling, increases susceptibility of Arabidopsis
             to the generalist herbivore Egyptian cotton worm (Spodoptera
             littoralis; Lepidoptera: Noctuidae). The hookless1 mutation,
             which affects a downstream component of ethylene signaling,
             conferred resistance to Egyptian cotton worm as compared
             with wild-type plants. Likewise, ein2, a mutant in a central
             component of the ethylene signaling pathway, caused enhanced
             resistance to Egyptian cotton worm that was similar in
             magnitude to hookless1. Moreover, pretreatment of plants
             with ethephon (2-chloroethanephosphonic acid), a chemical
             that releases ethylene, elevated plant susceptibility to
             Egyptian cotton worm. By contrast, these mutations in the
             ethylene-signaling pathway had no detectable effects on
             diamondback moth (Plutella xylostella) feeding. It is
             surprising that this is not due to nonactivation of defense
             signaling, because diamondback moth does induce genes that
             relate to wound-response pathways. Of these wound-related
             genes, jasmonic acid regulates a novel beta-glucosidase 1
             (BGL1), whereas ethylene controls a putative calcium-binding
             elongation factor hand protein. These results suggest that a
             specialist insect herbivore triggers general wound-response
             pathways in Arabidopsis but, unlike a generalist herbivore,
             does not react to ethylene-mediated physiological
             changes.},
   Doi = {10.1104/pp.124.3.1007},
   Key = {fds229168}
}

@article{fds229261,
   Author = {Koch, MA and Haubold, B and Mitchell-Olds, T},
   Title = {Comparative evolutionary analysis of chalcone synthase and
             alcohol dehydrogenase loci in Arabidopsis, Arabis, and
             related genera (Brassicaceae).},
   Journal = {Molecular Biology and Evolution},
   Volume = {17},
   Number = {10},
   Pages = {1483-1498},
   Year = {2000},
   Month = {October},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11018155},
   Abstract = {We analyzed sequence variation for chalcone synthase (Chs)
             and alcohol dehydrogenase (Adh) loci in 28 species in the
             genera Arabidopsis and Arabis and related taxa from tribe
             Arabideae. Chs was single-copy in nearly all taxa examined,
             while Adh duplications were found in several species.
             Phylogenies constructed from both loci confirmed that the
             closest relatives of Arabidopsis thaliana include
             Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis
             halleri (formerly in the genus Cardaminopsis). Slightly more
             distant are the North American n = 7 Arabis (Boechera)
             species. The genus Arabis is polyphyletic-some unrelated
             species appear within this taxonomic classification, which
             has little phylogenetic meaning. Fossil pollen data were
             used to compute a synonymous substitution rate of 1.5 x 10
             substitutions per site per year for both Chs and Adh.
             Arabidopsis thaliana diverged from its nearest relatives
             about 5 MYA, and from Brassica roughly 24 MYA. Independent
             molecular and fossil data from several sources all provide
             similar estimates of evolutionary timescale in the
             Brassicaceae.},
   Doi = {10.1093/oxfordjournals.molbev.a026248},
   Key = {fds229261}
}

@article{fds229145,
   Author = {Mitchell-Olds, T and Bergelson, J},
   Title = {Biotic interactions. Genomics and coevolution.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {3},
   Number = {4},
   Pages = {273-277},
   Year = {2000},
   Month = {August},
   ISSN = {1369-5266},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10939869},
   Key = {fds229145}
}

@article{fds229170,
   Author = {Bishop, JG and Dean, AM and Mitchell-Olds, T},
   Title = {Rapid evolution in plant chitinases: molecular targets of
             selection in plant-pathogen coevolution.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {97},
   Number = {10},
   Pages = {5322-5327},
   Year = {2000},
   Month = {May},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10805791},
   Abstract = {Many pathogen recognition genes, such as plant R-genes,
             undergo rapid adaptive evolution, providing evidence that
             these genes play a critical role in plant-pathogen
             coevolution. Surprisingly, whether rapid adaptive evolution
             also occurs in genes encoding other kinds of plant defense
             proteins is unknown. Unlike recognition proteins, plant
             chitinases attack pathogens directly, conferring disease
             resistance by degrading chitin, a component of fungal cell
             walls. Here, we show that nonsynonymous substitution rates
             in plant class I chitinase often exceed synonymous rates in
             the plant genus Arabis (Cruciferae) and in other dicots,
             indicating a succession of adaptively driven amino acid
             replacements. We identify individual residues that are
             likely subject to positive selection by using codon
             substitution models and determine the location of these
             residues on the three-dimensional structure of class I
             chitinase. In contrast to primate lysozymes and plant class
             III chitinases, structural and functional relatives of class
             I chitinase, the adaptive replacements of class I chitinase
             occur disproportionately in the active site cleft. This
             highly unusual pattern of replacements suggests that fungi
             directly defend against chitinolytic activity through
             enzymatic inhibition or other forms of chemical resistance
             and identifies target residues for manipulating chitinolytic
             activity. These data also provide empirical evidence that
             plant defense proteins not involved in pathogen recognition
             also evolve in a manner consistent with rapid coevolutionary
             interactions.},
   Doi = {10.1073/pnas.97.10.5322},
   Key = {fds229170}
}

@article{fds229138,
   Author = {Stotz, H and Kroymann, J and Tobler, M and Mitchell-Olds,
             T},
   Title = {Systematic genetic and molecular analysis of insect
             resistance in Arabidopsis},
   Journal = {Biology of Plant Microbe Interactions, Vol
             2},
   Volume = {2},
   Pages = {373-377},
   Booktitle = {Biology of Plant-Microbe Interactions},
   Publisher = {INTERNATIONAL SOC MOLECULAR PLANT-MICROBE
             INTERACTIONS},
   Editor = {DeWit, JGM and Bisseling, T and Stiekema, WJ},
   Year = {2000},
   Month = {January},
   ISBN = {0-9654625-1-X},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000167211400068&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds229138}
}

@article{fds229169,
   Author = {De Quiros and HC and Magrath, R and McCallum, D and Kroymann, J and Scnabelrauch, D and Mitchell-Olds, T and Mithen,
             R},
   Title = {α-Keto acid elongation and glucosinolate biosynthesis in
             Arabidopsis thaliana},
   Journal = {Tag Theoretical and Applied Genetics},
   Volume = {101},
   Number = {3},
   Pages = {429-437},
   Publisher = {Springer Nature},
   Year = {2000},
   Month = {January},
   url = {http://dx.doi.org/10.1007/s001220051500},
   Abstract = {QTL mapping of glucosinolates in a RI population derived
             from an F1 hybrid between the Arabidopsis thaliana ecotypes
             Columbia and Landsberg erecta identified a single major QTL
             coincident with the GSL-ELONG locus which regulates side
             chain elongation. Physical mapping and sequencing identified
             two members of an isopropylmalate synthase-like gene family
             within the region of maximum LOD score for the QTL and the
             GSL-ELONG non-recombinant region. These genes are prime
             candidates for regulating glucosinolate biosynthesis.},
   Doi = {10.1007/s001220051500},
   Key = {fds229169}
}

@article{fds45824,
   Author = {Stotz, H.U. and B.R. Pittendrigh and J. Kroymann and K. Weniger and J.
             Fritsche, A. Bauke and T. Mitchell-Olds},
   Title = {Ethylene signaling reduces resistance of Arabidopsis against
             Egyptian cotton worm but not diamondback
             moth},
   Journal = {Plant Physiology},
   Volume = {124},
   Pages = {1007-1026},
   Year = {2000},
   Key = {fds45824}
}

@article{fds229262,
   Author = {Mitchell Olds and T and Bergelson, J},
   Title = {Editorial Overview: Genomics and coevolution},
   Journal = {Current Opinion in Plant Biology},
   Volume = {3},
   Pages = {273-276},
   Year = {2000},
   Key = {fds229262}
}

@article{fds229259,
   Author = {Stotz, HU and Kroymann, J and Mitchell-Olds, T},
   Title = {Plant-insect interactions.},
   Journal = {Current Opinion in Plant Biology},
   Volume = {2},
   Number = {4},
   Pages = {268-272},
   Year = {1999},
   Month = {August},
   ISSN = {1369-5266},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10458997},
   Abstract = {Recent research shows partially overlapping signal
             transduction pathways controlling responses to wounding,
             insects, and pathogens. Chemical and behavioral assays show
             that plants release herbivore-specific volatiles, and that
             parasitic wasps can distinguish between these emission
             patterns. QTL mapping and candidate gene studies are
             beginning to identify polymorphic resistance genes, and
             ecological analyses provide information on the physiological
             and fitness costs of resistance. Such multidisciplinary
             approaches can elucidate the physiological causes and
             ecological consequences of plant-herbivore
             interactions.},
   Doi = {10.1016/s1369-5266(99)80048-x},
   Key = {fds229259}
}

@article{fds229260,
   Author = {Strauss, SY and Siemens, DH and Decher, MB and Mitchell-Olds,
             T},
   Title = {Ecological costs of plant resistance to herbivores in the
             currency of pollination},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {53},
   Number = {4},
   Pages = {1105-1113},
   Publisher = {JSTOR},
   Year = {1999},
   Month = {August},
   url = {http://dx.doi.org/10.2307/2640815},
   Abstract = {In this paper, we examine how ecological costs of resistance
             might be manifested through plant relationships with
             pollinators. If defensive compounds are incorporated into
             floral structures or if they are sufficiently costly that
             fewer rewards are offered to pollinators, pollinators may
             discriminate against more defended plants. Here we consider
             whether directional selection for increased resistance to
             herbivores could be constrained by opposing selection
             through pollinator discrimination against more defended
             plants. We used artificial selection to create two
             populations of Brassica rapa plants that had high and low
             myrosinase concentrations and, consequently, high and low
             resistance to flea beetle herbivores. We measured changes in
             floral characters of plants in both damaged and undamaged
             states from these populations with different resistances to
             flea beetle attack. We also measured pollinator visitation
             to plants, including numbers of pollinators and measures of
             visit quality (numbers of flowers visited and time spent per
             flower). Damage from herbivores resulted in reduced petal
             size, as did selection for high resistance to herbivores
             later in the plant lifetime. In addition, floral display
             (number of open flowers) was also altered by an interaction
             between these two effects. Changes in floral traits
             translated into overall greater use of low-resistance,
             undamaged plants based on total amount of time pollinators
             spent foraging on plants. Total numbers of pollinators
             attracted to plants did not differ among treatments;
             however, pollinators spent significantly more time per
             flower on plants from the low-resistance population and
             tended to visit more flowers on these plants as well.
             Previous work by other investigators on the same pollinator
             taxa has shown that longer visit times are associated with
             greater male and female plant fitness. Because initial
             numbers of pollinators did not differ between selection
             regimes, palatability and/or amount of rewards offered by
             high- and low-resistance populations are likely to be
             responsible for these patterns. During periods of pollinator
             limitation, less defended plants may have a selective
             advantage and pollinator preferences may mediate directional
             selection imposed by herbivores. In addition, if pollinator
             preferences limit seed set in highly defended plants, then
             lower seed set previously attributed to allocation costs of
             defense may also reflect greater pollinator limitation in
             these plants relative to less defended plants.},
   Doi = {10.2307/2640815},
   Key = {fds229260}
}

@article{fds341080,
   Author = {Strauss, SY and Siemens, DH and Decher, MB and Mitchell-Olds,
             T},
   Title = {ECOLOGICAL COSTS OF PLANT RESISTANCE TO HERBIVORES IN THE
             CURRENCY OF POLLINATION.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {53},
   Number = {4},
   Pages = {1105-1113},
   Year = {1999},
   Month = {August},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1999.tb04525.x},
   Abstract = {In this paper, we examine how ecological costs of resistance
             might be manifested through plant relationships with
             pollinators. If defensive compounds are incorporated into
             floral structures or if they are sufficiently costly that
             fewer rewards are offered to pollinators, pollinators may
             discriminate against more defended plants. Here we consider
             whether directional selection for increased resistance to
             herbivores could be constrained by opposing selection
             through pollinator discrimination against more defended
             plants. We used artificial selection to create two
             populations of Brassica rapa plants that had high and low
             myrosinase concentrations and, consequently, high and low
             resistance to flea beetle herbivores. We measured changes in
             floral characters of plants in both damaged and undamaged
             states from these populations with different resistances to
             flea beetle attack. We also measured pollinator visitation
             to plants, including numbers of pollinators and measures of
             visit quality (numbers of flowers visited and time spent per
             flower). Damage from herbivores resulted in reduced petal
             size, as did selection for high resistance to herbivores
             later in the plant lifetime. In addition, floral display
             (number of open flowers) was also altered by an interaction
             between these two effects. Changes in floral traits
             translated into overall greater use of low-resistance,
             undamaged plants based on total amount of time pollinators
             spent foraging on plants. Total numbers of pollinators
             attracted to plants did not differ among treatments;
             however, pollinators spent significantly more time per
             flower on plants from the low-resistance population and
             tended to visit more flowers on these plants as well.
             Previous work by other investigators on the same pollinator
             taxa has shown that longer visit times are associated with
             greater male and female plant fitness. Because initial
             numbers of pollinators did not differ between selection
             regimes, palatability and/or amount of rewards offered by
             high- and low-resistance populations are likely to be
             responsible for these patterns. During periods of pollinator
             limitation, less defended plants may have a selective
             advantage and pollinator preferences may mediate directional
             selection imposed by herbivores. In addition, if pollinator
             preferences limit seed set in highly defended plants, then
             lower seed set previously attributed to allocation costs of
             defense may also reflect greater pollinator limitation in
             these plants relative to less defended plants.},
   Doi = {10.1111/j.1558-5646.1999.tb04525.x},
   Key = {fds341080}
}

@article{fds229165,
   Author = {Koch, M and Bishop, J and Mitchell-Olds, T},
   Title = {Molecular systematics and evolution of Arabidopsis and
             Arabis},
   Journal = {Plant Biology},
   Volume = {1},
   Number = {5},
   Pages = {529-537},
   Publisher = {WILEY},
   Year = {1999},
   Month = {January},
   url = {http://dx.doi.org/10.1111/j.1438-8677.1999.tb00779.x},
   Abstract = {We provide a phylogenetic analysis of the genera Arabidopsis
             and Arabis based on nuclear ribosomal DNA sequences. We show
             that traditional taxonomical concepts within tribe
             Arabideae, which includes these genera, are highly
             artificial. Arabis and Arabidopsis are paraphyletic and
             consist of several different independent lineages. The genus
             Capsella, originally placed in tribe Lepideae, is related to
             North American Arabis and the Arabidopsis thaliana lineage.
             Other genera, including East Asian Yinshania, North American
             Halimolobus, cosmopolitan Barbarea and Cardamine, and
             European Aubrieta are positioned among different Arabis
             lineages. One Arabis species, Arabis pauciflora, is only
             distantly related to tribe Arabideae. Base chromosome number
             reduction from n = 8 to n = 5 to 7 occurred several times,
             suggesting that lower base chromosome numbers than n = 8 are
             derived in tribe Arabideae. Current knowledge on the
             evolution and systematics of the genera Arabis and
             Arabidopsis and relationships within the mustard family are
             summarized and discussed in the light of convergent
             evolution and transfer of knowledge from Arabidopsis
             thaliana as a molecular model plant to other species of the
             Cruciferae.},
   Doi = {10.1111/j.1438-8677.1999.tb00779.x},
   Key = {fds229165}
}

@article{fds229166,
   Author = {Marler, M and Pedersen, D and Mitchell-Olds, T and Callaway,
             RM},
   Title = {A polymerase chain reaction method for detecting dwarf
             mistletoe infection in douglas-fir and western
             larch},
   Journal = {Canadian Journal of Forest Research},
   Volume = {29},
   Number = {9},
   Pages = {1317-1321},
   Publisher = {Canadian Science Publishing},
   Year = {1999},
   Month = {January},
   url = {http://dx.doi.org/10.1139/x99-092},
   Abstract = {Early detection and management of dwarf mistletoe
             (Arceuthobium spp.) is currently limited by the inability to
             rapidly detect infection during the 2- to 5-year endophyte
             phase of the parasite. We describe a polymerase chain
             reaction (PCR) technique for detecting Arceuthobium
             douglasii Engelm. and Arceuthobium laricis Engelm. in
             tissues of its hosts, Pseudotsuga menziesii (Mirb.) Franco
             and Larix occidentalis Nutt. DNA was extracted from branches
             of 15 infected and 15 uninfected P. menziesii. The PCR
             product amplified by using the Arceuthobium specific primer
             in the rbcL gene from Arceuthobium template DNA was a
             fragment of 708 pairs of bases in length. This product was
             amplified from all branches that were visibly infected, but
             the fragment was not generated from any samples known to be
             uninfected. The PCR product from conifer DNA was a fragment
             of 385 pairs of bases in length and was not amplified from
             pure mistletoe DNA; this was amplified as an internal
             positive control. The primers developed for P. menziesii and
             A. douglasii also worked on L. occidentalis and A. laricis.
             This method detected mistletoe DNA in 7 of 29 P. menziesii
             branches and 3 of 21 L. occidentalis branches that did not
             have external symptoms of infection and are presumed to be
             the result of the endophyte phase. This method provides a
             useful tool for experimental applications and for managing
             the spread of dwarf mistletoe.},
   Doi = {10.1139/x99-092},
   Key = {fds229166}
}

@article{fds229167,
   Author = {Mitchell-Olds, T},
   Title = {Genetics and evolution of insect resistance in
             Arabidopsis.},
   Journal = {Insect Plant Interactions and Inducible Plant
             Defense},
   Volume = {223},
   Pages = {239-248},
   Booktitle = {Insect-Plant Interactions and Inducible Plant
             Defense},
   Publisher = {Novartis Foundation},
   Editor = {Chadwick, DJ},
   Year = {1999},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10549559},
   Abstract = {The genetic and molecular tools available in Arabidopsis
             allow identification of insect resistance genes. Many
             functional aspects of pest recognition and signal
             transduction are conserved in the defensive physiology of a
             broad range of plant species. Therefore, studies of insect
             resistance in Arabidopsis may be extended to functional
             genomics studies in many plant species of agricultural and
             ecological importance. Because of public concerns for field
             release of genetically modified organisms, naturally
             occurring genetic variation for resistance to insect
             herbivores will be valuable in plant breeding. Combined
             studies employing QTL mapping and candidate resistance genes
             are necessary to find and understand the genes responsible
             for variation in resistance. We review experiments showing
             that plant populations contain high levels of genetic
             variation for defensive physiology and disease and insect
             resistance, and that this variation can be manipulated to
             alter resistance and its components in a predictable
             fashion. In Arabidopsis, we can map the genes controlling
             physiological variation, and estimate the importance of
             regulatory or enzyme-encoding loci. Finally, we review
             functional genomics approaches for identification of insect
             resistance genes in Arabidopsis.},
   Key = {fds229167}
}

@article{fds229257,
   Author = {Mitchell-Olds, T and Gershenzon, J and Baldwin, I and Boland,
             W},
   Title = {Chemical ecology in the molecular era},
   Journal = {Trends in Plant Science},
   Volume = {3},
   Number = {9},
   Pages = {362-365},
   Publisher = {Elsevier BV},
   Year = {1998},
   Month = {September},
   url = {http://dx.doi.org/10.1016/S1360-1385(98)01296-5},
   Doi = {10.1016/S1360-1385(98)01296-5},
   Key = {fds229257}
}

@article{fds229256,
   Author = {Mitchell-Olds, T and Pedersen, D},
   Title = {The molecular basis of quantitative genetic variation in
             central and secondary metabolism in Arabidopsis.},
   Journal = {Genetics},
   Volume = {149},
   Number = {2},
   Pages = {739-747},
   Year = {1998},
   Month = {June},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/9611188},
   Abstract = {To find the genes controlling quantitative variation, we
             need model systems where functional information on
             physiology, development, and gene regulation can guide
             evolutionary inferences. We mapped quantitative trait loci
             (QTLs) influencing quantitative levels of enzyme activity in
             primary and secondary metabolism in Arabidopsis. All 10
             enzymes showed highly significant quantitative genetic
             variation. Strong positive genetic correlations were found
             among activity levels of 5 glycolytic enzymes, PGI, PGM,
             GPD, FBP, and G6P, suggesting that enzymes with closely
             related metabolic functions are coregulated. Significant
             QTLs were found influencing activity of most enzymes. Some
             enzyme activity QTLs mapped very close to known
             enzyme-encoding loci (e.g., hexokinase, PGI, and PGM). A
             hexokinase QTL is attributable to cis-acting regulatory
             variation at the AtHXK1 locus or a closely linked regulatory
             locus, rather than polypeptide sequence differences. We also
             found a QTL on chromosome IV that may be a joint regulator
             of GPD, PGI, and G6P activity. In addition, a QTL affecting
             PGM activity maps within 700 kb of the PGM-encoding locus.
             This QTL is predicted to alter starch biosynthesis by 3.4%,
             corresponding with theoretical models, suggesting that QTLs
             reflect pleiotropic effects of mutant alleles.},
   Key = {fds229256}
}

@article{fds229258,
   Author = {Siemens, DH and Mitchell-Olds, T},
   Title = {Evolution of pest-induced defenses in Brassica plants: Tests
             of theory},
   Journal = {Ecology},
   Volume = {79},
   Number = {2},
   Pages = {632-646},
   Publisher = {WILEY},
   Year = {1998},
   Month = {January},
   url = {http://dx.doi.org/10.1890/0012-9658(1998)079[0632:eopidi]2.0.co;2},
   Abstract = {Theory on the evolution of pest-induced defenses in plants
             predicts (1) a negative genetic correlation between induced
             and constitutive (basal) levels of secondary metabolites,
             and (2) costs of maintaining high constitutive levels of
             secondary metabolites. We tested these predictions with
             genetically diverged populations created by artificial
             selection on myrosinase and glucosinolate levels in Brassica
             rapa. Glucosinolates and their breakdown products from the
             action of the enzyme myrosinase are putative defensive
             compounds in brassicas. Theory also suggests that effects of
             genetic changes in secondary metabolites may depend on
             resource availability, so nitrogen, a main constituent of
             glucosinolates and myrosinase was added in fertilizer
             treatments to assess costs. We used the fungal pathogen
             Leptosphaeria maculans and diamondback moth larvae Plutella
             xylostella as induction agents in comparisons of the
             diverged myrosinase populations. We found pleiotropic
             effects among constitutive myrosinase levels and
             pathogen-induced levels of myrosinase, glucosinolates, and
             resistance to diamondback moth larvae. In field experiments,
             genetic increases in myrosinase production were associated
             with significant decreases in estimated seed production,
             despite potential benefits from increased resistance to flea
             beetles Phylotreta cruciferae. No genotype-by-nitrogen
             interaction was found. Although costs were detected, our
             results indicate, in contrast to theory, mainly positive
             pleiotropic effects between constitutive levels of secondary
             metabolites and induced responses.},
   Doi = {10.1890/0012-9658(1998)079[0632:eopidi]2.0.co;2},
   Key = {fds229258}
}

@article{fds229255,
   Author = {Karowe, DN and Seimens, DH and Mitchell-Olds, T},
   Title = {Species-specific response of glucosinolate content to
             elevated atmospheric CO2},
   Journal = {Journal of Chemical Ecology},
   Volume = {23},
   Number = {11},
   Pages = {2569-2582},
   Publisher = {Springer Nature},
   Year = {1997},
   Month = {January},
   ISSN = {0098-0331},
   url = {http://dx.doi.org/10.1023/B:JOEC.0000006667.81616.18},
   Abstract = {The carbon/nutrient balance hypothesis has recently been
             interpreted to predict that plants grown under elevated CO2
             environments will allocate excess carbon to defense,
             resulting in an increase in carbon-based secondary
             compounds. A related prediction is that, because plant
             growth will be increasingly nitrogen-limited under elevated
             CO2 environments, plants will allocate less nitrogen to
             defense, resulting in decreased levels of
             nitrogen-containing secondary compounds. We present the
             first evidence of decreased investment in
             nitrogen-containing secondary compounds for a plant grown
             under elevated CO2. We also present evidence that plant
             response is species-specific and is not correlated with
             changes in leaf nitrogen content or leaf carbon-nitrogen
             ratio. When three crucifers were grown at 724 ± 8 ppm CO2,
             total foliar glucosinolate content decreased significantly
             for mustard, but not for radish or turnip. Glucosinolate
             content of the second and fourth youngest mustard leaves
             decreased by 45% and 31%, respectively. In contrast, no
             significant change in total glucosinolate content was
             observed in turnip or radish leaves, despite significant
             decreases in leaf nitrogen content. Total glucosinolate
             content differed significantly among leaves of different
             age; however, the trend differed among species. For both
             mustard and turnip, glucosinolate content was significantly
             higher in older leaves, while the opposite was true for
             radish. No significant CO2 x leaf age interaction was
             observed, suggesting that intraplant patterns of allocation
             to defense will not change for these species. Changes in
             nitrogen allocation strategy are likely to be
             species-specific as plants experience increasing atmospheric
             CO2 levels. The ecological consequences of CO2-induced
             changes in plant defensive investment remain to be
             investigated.},
   Doi = {10.1023/B:JOEC.0000006667.81616.18},
   Key = {fds229255}
}

@article{fds229251,
   Author = {Mitchell-Olds, T},
   Title = {PLEIOTROPY CAUSES LONG-TERM GENETIC CONSTRAINTS ON
             LIFE-HISTORY EVOLUTION IN BRASSICA RAPA.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {50},
   Number = {5},
   Pages = {1849-1858},
   Publisher = {JSTOR},
   Year = {1996},
   Month = {October},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1996.tb03571.x},
   Abstract = {Fundamental, long-term genetic trade-offs constrain
             life-history evolution in wild crucifer populations. I
             studied patterns of genetic constraint in Brassica rapa by
             estimating genetic correlations among life-history
             components by quantitative genetic analyses among ten wild
             populations, and within four populations. Genetic
             correlations between age and size at first reproduction were
             always greater than +0.8 within and among all populations
             studied. Although quantitative genetics might provide
             insight about genetic constraints if genetic parameters
             remain approximately constant, little evidence has been
             available to determine the constancy of genetic
             correlations. I found strong and consistent estimates of
             genetic correlations between life-history components, which
             were very similar within four natural populations.
             Population differentiation also showed these same
             trade-offs, resulting from long-term genetic constraint. For
             some traits, evolutionary changes among populations were
             incompatible with a model of genetic drift. Historical
             patterns of natural selection were inferred from population
             differentiation, suggesting that correlated response to
             selection has caused some traits to evolve opposite to the
             direct forces of natural selection. Comparison with
             Arabidopsis suggests that these life-history trade-offs are
             caused by genes that regulate patterns of resource
             allocation to different components of fitness. Ecological
             and energetic models may correctly predict these trade-offs
             because there is little additive genetic variation for rates
             of resource acquisition, but resource allocation is
             genetically variable.},
   Doi = {10.1111/j.1558-5646.1996.tb03571.x},
   Key = {fds229251}
}

@article{fds229252,
   Author = {Mitchell-Olds, T and Bradley, D},
   Title = {Genetics of Brassica rapa. 3. Costs of disease resistance to
             three fungal pathogens},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {50},
   Number = {5},
   Pages = {1859-1865},
   Publisher = {JSTOR},
   Year = {1996},
   Month = {October},
   url = {http://dx.doi.org/10.2307/2410743},
   Abstract = {Genetic costs of resistance to pathogens may be an important
             factor maintaining heritable variation for resistance in
             natural populations. Pleiotropic fitness trade-offs occur
             when genetic resistance causes reduction in other components
             of illness. Although costs of resistance have an important
             influence on plant-pathogen interactions, few previous
             studies have detected pleiotropic costs of resistance in the
             absence of confounding effects of linkage disequilibrium. To
             avoid this potential problem, we performed artificial
             selection experiments on resistance to two fungal pathogens,
             Leptosphaeria maculans, and Peronospora parasitica, and
             compared growth rates of resistant and susceptible genotypes
             of Brassica rapa in the absence of pathogens. Leptosphaeria
             resistance had no effect on growth rate, indicating cost
             free defense. In contrast, Peronospora-resistant genotypes
             grow 6% slower than Peronospora-susceptible genotypes in
             pathogen-free environments, indicating a significant genetic
             fitness cost to Peronospora resistance. Such genetic
             trade-offs could maintain genetic variation in the wild.
             Another factor that might explain heritable variation for
             resistance is ecological trade-offs, in which genetic
             resistance to one species causes susceptibility to another.
             Such ecological trade-offs do not exist for the pathogens
             studied in this system.},
   Doi = {10.2307/2410743},
   Key = {fds229252}
}

@article{fds341081,
   Author = {Mitchell-Olds, T and Bradley, D},
   Title = {GENETICS OF BRASSICA RAPA. 3. COSTS OF DISEASE RESISTANCE TO
             THREE FUNGAL PATHOGENS.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {50},
   Number = {5},
   Pages = {1859-1865},
   Year = {1996},
   Month = {October},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1996.tb03572.x},
   Abstract = {Genetic costs of resistance to pathogens may be an important
             factor maintaining heritable variation for resistance in
             natural populations. Pleiotropic fitness trade-offs occur
             when genetic resistance causes reduction in other components
             of fitness. Although costs of resistance have an important
             influence on plant-pathogen interactions, few previous
             studies have detected pleiotropic costs of resistance in the
             absence of confounding effects of linkage disequilibrium. To
             avoid this potential problem, we performed artificial
             selection experiments on resistance to two fungal pathogens,
             Leptosphaeria maculans, and Peronospora parasitica, and
             compared growth rates of resistant and susceptible genotypes
             of Brassica rapa in the absence of pathogens. Leptosphaeria
             resistance had no effect on growth rate, indicating
             cost-free defense. In contrast, Peronospora-resistant
             genotypes grow 6% slower than Peronospora-susceptible
             genotypes in pathogen-free environments, indicating a
             significant genetic fitness cost to Peronospora resistance.
             Such genetic trade-offs could maintain genetic variation in
             the wild. Another factor that might explain heritable
             variation for resistance is ecological trade-offs, in which
             genetic resistance to one species causes susceptibility to
             another. Such ecological trade-offs do not exist for the
             pathogens studied in this system.},
   Doi = {10.1111/j.1558-5646.1996.tb03572.x},
   Key = {fds341081}
}

@article{fds229250,
   Author = {Mitchell-Olds, T},
   Title = {GENETIC CONSTRAINTS ON LIFE-HISTORY EVOLUTION:
             QUANTITATIVE-TRAIT LOCI INFLUENCING GROWTH AND FLOWERING IN
             ARABIDOPSIS THALIANA.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {50},
   Number = {1},
   Pages = {140-145},
   Publisher = {JSTOR},
   Year = {1996},
   Month = {February},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1996.tb04480.x},
   Abstract = {We have mapped genes causing life-history trade-offs, and
             they behave as predicted by ecological theory. Energetic and
             quantitative-genetic models suggest a trade-off between age
             and size at first reproduction. Natural selection favored
             plants that flower early and attain large size at first
             reproduction. Response to selection was opposed by a genetic
             trade-off between these two components of fitness. Two
             quantitative-trait loci (QTLs) influencing flowering time
             were mapped in a recombinant inbred population of
             Arabidopsis. These QTLs also influenced size at first
             reproduction, but did not affect growth rate (resource
             acquisition). Substitutions of small chromosomal segments,
             which may represent allelic differences at flowering time
             loci, caused genetic trade-offs between life-history
             components. One QTL explained 22% of the genetic variation
             in flowering time. It is within a few centiMorgans (cM) of
             the gigantea (GI) locus, and may be allelic with GI. Sixteen
             percent of the genetic variation was explained by another
             QTL, FDR1, near 18 cM on chromosome II, which does not
             correspond to any previously identified flowering-time
             locus. These life-history genes regulate patterns of
             resource allocation and life-history trade-offs in this
             population.},
   Doi = {10.1111/j.1558-5646.1996.tb04480.x},
   Key = {fds229250}
}

@article{fds229253,
   Author = {Mitchell-Olds, T and Siemens, D and Pedersen, D},
   Title = {Physiology and costs of resistance to herbivory and disease
             in Brassica},
   Journal = {Entomologia Experimentalis Et Applicata},
   Volume = {80},
   Number = {1},
   Pages = {231-237},
   Publisher = {WILEY},
   Year = {1996},
   Month = {January},
   ISSN = {0013-8703},
   url = {http://dx.doi.org/10.1111/j.1570-7458.1996.tb00925.x},
   Abstract = {We used artificial selection experiments to study genetic
             allocation costs and physiological mechanisms of resistance
             to herbivory and fungal disease. Genetic costs to resistance
             were present in some instances and absent in others. Genetic
             resistance to the fungal pathogen, Leptosphaeria maculans
             was cost-free, while resistance to Peronospora parasitica
             showed a negative genetic correlation between disease
             resistance and growth rate. Leptosphaeria resistant
             genotypes had 13% higher chitinase activity. Genetic
             increases in myrosinase activity were correlated with
             increased resistance to flea beetles (Phyllotreta
             cruciferae), but resulted in lower plant fecundity,
             presumably due to production costs of myrosinase. Genetic
             costs of resistance may maintain genetic variation in
             natural plant populations. These studies demonstrate the
             predictive and explanatory power of a functional approach to
             plant-herbivore and plant-pathogen interactions.},
   Doi = {10.1111/j.1570-7458.1996.tb00925.x},
   Key = {fds229253}
}

@article{fds229254,
   Author = {Siemens, DH and Mitchell-Olds, T},
   Title = {Glucosinolates and Herbivory by Specialists (Coleoptera:
             Chrysomelidae, Lepidoptera: Plutellidae): Consequences of
             Concentration and Induced Resistance},
   Journal = {Environmental Entomology},
   Volume = {25},
   Number = {6},
   Pages = {1344-1353},
   Publisher = {Oxford University Press (OUP)},
   Year = {1996},
   Month = {January},
   url = {http://dx.doi.org/10.1093/ee/25.6.1344},
   Abstract = {Varied responses by specialist herbivores to glucosinolates
             could be a function of glucosinolate concentration or other
             correlated resistance factors. Herbivory by the specialist
             flea beetle Phyllotreta cruciferae (Goeze), and diamondback
             moth, Plutella xylostella (L.), varied curvilinearly with
             natural levels of glucosinolates in Brassica rapa (syn.
             campestris) (L.) such that maximum herbivory occurred at
             intermediate glucosinolate levels. Although the pattern was
             weak, decreases in herbivory at high concentrations of
             glucosinolates were enhanced by inoculating plants with the
             fungal pathogen Leptosphaeria maculans (Desm.) Ces. et de
             Not.(Ascomycetes), in laboratory experiments. This
             enhancement effect may have been caused by other correlated
             induced resistance factors produced by the plant or by
             resistance factors produced by the pathogen (independent of
             the host plant). Although specialist herbivores of mustards
             may have overcome glucosinolates, the apparent
             dose-dependent effect of glucosinolates suggest this
             herbivore counteradaptation may not have been complete,
             perhaps because of correlated resistance factors. Because a
             component of glucosinolate variation in B. rapa is heritable
             and because P. cruciferae can negatively affect plant
             fitness, the varied responses of specialist herbivores with
             glucosinolate concentrations reported here further suggest
             the possibility of disruptive selection on
             glucosinolates.},
   Doi = {10.1093/ee/25.6.1344},
   Key = {fds229254}
}

@article{fds229248,
   Author = {Mitchell-Olds, T and James, RV and Palmer, MJ and Williams,
             PH},
   Title = {Genetics of Brassica rapa (syn. campestris). 2. Multiple
             disease resistance to three fungal pathogens: Peronospora
             parasitica, Albugo candida and Leptosphaeria
             maculans.},
   Journal = {Heredity},
   Volume = {75 ( Pt 4)},
   Pages = {362-369},
   Year = {1995},
   Month = {October},
   ISSN = {0018-067X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/7591832},
   Abstract = {Although the genetic basis of multiple disease resistance
             (MDR) is poorly understood, it is of great value for
             understanding the evolution of disease resistance in natural
             plant populations and for increasing crop yields in
             agriculture. In Brassica rapa, we studied genetic
             correlations among levels of disease resistance to three
             fungal pathogens: Peronospora parasitica, Albugo candida and
             Leptosphaeria maculans. A large, replicated quantitative
             genetics experiment used artificial selection on resistance
             to individual pathogens, and examined correlated responses
             to selection for resistance to other, unselected pathogens.
             Data from 9518 plants, each measured simultaneously for
             resistance to three fungal pathogens, showed heritable
             genetic variation for resistance to each pathogen and a
             positive genetic correlation between resistance to P.
             parasitica and L. maculans. This indicates that some
             resistance genes provide defence against fundamental
             characteristics common to two taxonomic orders of fungal
             pathogens. Conceivably, such MDR could contribute to a
             durable defence that might not be easily circumvented by
             rapidly evolving fungal pathogens.},
   Doi = {10.1038/hdy.1995.147},
   Key = {fds229248}
}

@article{fds229247,
   Author = {Mitchell-Olds, T},
   Title = {The molecular basis of quantitative genetic variation in
             natural populations.},
   Journal = {Trends in Ecology and Evolution},
   Volume = {10},
   Number = {8},
   Pages = {324-328},
   Year = {1995},
   Month = {August},
   ISSN = {0169-5347},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21237056},
   Abstract = {DNA markers allow us to study quantitative trait loci (QTL)
             - the genes that control adaptation and quantitative
             variation. Experiments can map the genes responsible for
             quantitative variation and address the evolutionary and
             ecological significance of this variation. Recent studies
             suggest that major genes segregate within and among natural
             populations. It is now feasible to study the genes that
             cause morphological variation, life history trade-offs,
             heterosis and speciation. These methods can determine the
             role of epistasis and genotype-by-environment interaction in
             maintaining genetic variation. QTL mapping is an important
             tool used to address evolutionary and ecological questions
             of long-standing interest.},
   Doi = {10.1016/s0169-5347(00)89119-3},
   Key = {fds229247}
}

@article{fds229246,
   Author = {Mitchell-Olds, T},
   Title = {Interval mapping of viability loci causing heterosis in
             Arabidopsis.},
   Journal = {Genetics},
   Volume = {140},
   Number = {3},
   Pages = {1105-1109},
   Year = {1995},
   Month = {July},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/7672581},
   Abstract = {The genetic basis of heterosis has implications for many
             problems in genetics and evolution. Heterosis and inbreeding
             depression affect human genetic diseases, maintenance of
             genetic variation, evolution of breeding systems,
             agricultural productivity, and conservation biology. Despite
             decades of theoretical and empirical studies, the genetic
             basis of heterosis has remained unclear. I mapped viability
             loci contributing to heterosis in Arabidopsis. An
             overdominant factor with large effects on viability mapped
             to a short interval on chromosome I. Homozygotes had 50%
             lower viability than heterozygotes in this chromosomal
             region. Statistical analysis of viability data in this cross
             indicates that observed viability heterosis is better
             explained by functional overdominance than by
             pseudo-overdominance. Overdominance sometimes may be an
             important cause of hybrid vigor, especially in habitually
             inbreeding species. Finally, I developed a maximum
             likelihood interval mapping procedure that can be used to
             examine chromosomal regions showing segregation distortion
             or viability selection.},
   Key = {fds229246}
}

@article{fds229249,
   Author = {Nakamura, RR and Mitchell-Olds, T and Manasse, RS and Lello,
             D},
   Title = {Seed predation, pathogen infection and life-history traits
             in Brassica rapa.},
   Journal = {Oecologia},
   Volume = {102},
   Number = {3},
   Pages = {324-328},
   Year = {1995},
   Month = {June},
   ISSN = {0029-8549},
   url = {http://dx.doi.org/10.1007/bf00329799},
   Abstract = {Herbivory and disease can shape the evolution of plant
             populations, but their joint effects are rarely
             investigated. Families of plants of Brassica rapa
             (Brassicaceae) were grown from seeds collected in two
             naturalized populations in an experimental garden. We
             examined leaf infection by the fungus Alternaria, seed
             predation by a gall midge (Cecidomyiidae) and plant
             life-history traits. Plants from one population had heavier
             seeds, were more likely to flower, had less fungal
             infection, had more seed predation and were more fecund.
             Fungal infection score and seed predation rate increased
             with plant size, but large plants still had the greatest
             number of undamaged fruits. Spatial heterogeneity in the
             experimental garden was significant; seed predation rate and
             fecundity varied among blocks. An apparent tradeoff existed
             between susceptibility to disease and seed predation: plants
             with the highest fungal infection score had the lowest seed
             predation rate. Alternaria infection varied between
             populations, but the disease had no effect on fecundity.
             Seed predation did reduce fecundity. Damaged fruits had
             31.4% fewer intact seeds. However, evidence for additive
             genetic variation in resistance to seed predation was weak.
             Therefore, neither disease nor seed predation was likely to
             be a strong agent of genetically based fecundity
             selection.},
   Doi = {10.1007/bf00329799},
   Key = {fds229249}
}

@article{fds229243,
   Author = {Groover, A and Devey, M and Fiddler, T and Lee, J and Megraw, R and Mitchel-Olds, T and Sherman, B and Vujcic, S and Williams, C and Neale,
             D},
   Title = {Identification of quantitative trait loci influencing wood
             specific gravity in an outbred pedigree of loblolly
             pine.},
   Journal = {Genetics},
   Volume = {138},
   Number = {4},
   Pages = {1293-1300},
   Year = {1994},
   Month = {December},
   ISSN = {0016-6731},
   Abstract = {We report the identification of quantitative trait loci
             (QTL) influencing wood specific gravity (WSG) in an outbred
             pedigree of loblolly pine (Pinus taeda L.). QTL mapping in
             an outcrossing species is complicated by the presence of
             multiple alleles (> 2) at QTL and marker loci. Multiple
             alleles at QTL allow the examination of interaction among
             alleles at QTL (deviation from additive gene action).
             Restriction fragment length polymorphism (RFLP) marker
             genotypes and wood specific gravity phenotypes were
             determined for 177 progeny. Two RFLP linkage maps were
             constructed, representing maternal and paternal parent
             gamete segregations as inferred from diploid progeny RFLP
             genotypes. RFLP loci segregating for multiple alleles were
             vital for aligning the two maps. Each RFLP locus was assayed
             for cosegregation with WSG QTL using analysis of variance
             (ANOVA). Five regions of the genome contained one or more
             RFLP loci showing differences in mean WSG at or below the P
             = 0.05 level for progeny as grouped by RFLP genotype. One
             region contained a marker locus (S6a) whose QTL-associated
             effects were highly significant (P > 0.0002). Marker S6a
             segregated for multiple alleles, a prerequisite for
             determining the number of alleles segregating at the linked
             QTL and analyzing the interactions among QTL alleles. The
             QTL associated with marker S6a appeared to be segregating
             for multiple alleles which interacted with each other and
             with environments. No evidence for digenic epistasis was
             found among the five QTL.},
   Key = {fds229243}
}

@article{fds229245,
   Author = {McCall, C and Waller, DM and Mitchell-Olds, T},
   Title = {EFFECTS OF SERIAL INBREEDING ON FITNESS COMPONENTS IN
             IMPATIENS CAPENSIS.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {48},
   Number = {3},
   Pages = {818-827},
   Year = {1994},
   Month = {June},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1994.tb01364.x},
   Abstract = {Studies of inbreeding depression in wild plants customarily
             compare the fitness of outcrossed progeny to progeny derived
             from one generation of self-pollination. We compare levels
             of inbreeding depression in a greenhouse in two populations
             of jewelweed using progeny derived from random outcrosses,
             one generation of self-pollination, and three generations of
             selling. The progeny have expected inbreeding coefficients
             of, respectively, 0, 0.5, and 0.875. Seedling survivorship
             declined linearly with the level of inbreeding in both
             populations. Inbreeding also increased the variability of
             emergence date. Maternal family membership affected early
             seedling performance and often interacted significantly with
             the level of inbreeding. In contrast, path analyses reveal
             that inbreeding had both negative linear and positive
             quadratic direct effects on seed and final plant weight,
             causing the highly inbred progeny to outperform progeny
             derived from one generation of selfing. These results
             suggest either the rapid purging of deleterious alleles or
             diminishing epistasis among the loci affecting these
             characters. It is not clear why the loci affecting survival
             responded differently.},
   Doi = {10.1111/j.1558-5646.1994.tb01364.x},
   Key = {fds229245}
}

@article{fds229244,
   Author = {Hamilton, MB and Mitchell-Olds, T},
   Title = {The mating system and relative performance of selfed and
             outcrossed progeny in Arabis fecunda (Brassicaceae)},
   Journal = {American Journal of Botany},
   Volume = {81},
   Number = {10},
   Pages = {1252-1256},
   Publisher = {WILEY},
   Year = {1994},
   Month = {January},
   url = {http://dx.doi.org/10.2307/2445400},
   Doi = {10.2307/2445400},
   Key = {fds229244}
}

@article{fds229164,
   Author = {Chadchawan, S and Bishop, J and Thangstad, OP and Bones, AM and Mitchell-Olds, T and Bradley, D},
   Title = {Arabidopsis cDNA sequence encoding myrosinase.},
   Journal = {Plant Physiology},
   Volume = {103},
   Number = {2},
   Pages = {671},
   Year = {1993},
   Month = {October},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/8029343},
   Doi = {10.1104/pp.103.2.671},
   Key = {fds229164}
}

@article{fds229163,
   Author = {Machlin, S and Mitchell-Olds, T and Bradley, D},
   Title = {Sequence of a Brassica campestris myrosinase
             gene.},
   Journal = {Plant Physiology},
   Volume = {102},
   Number = {4},
   Pages = {1359-1360},
   Year = {1993},
   Month = {August},
   ISSN = {0032-0889},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/8278558},
   Doi = {10.1104/pp.102.4.1359},
   Key = {fds229163}
}

@article{fds229162,
   Author = {Shaw, RG and Mitchell-Olds, T},
   Title = {ANOVA for unbalanced data: an overview},
   Journal = {Ecology},
   Volume = {74},
   Number = {6},
   Pages = {1638-1645},
   Publisher = {WILEY},
   Year = {1993},
   Month = {January},
   url = {http://dx.doi.org/10.2307/1939922},
   Abstract = {When the response variables have continuous distributions
             and the conditions are discrete, whether inherently or by
             design, then it is appropriate to analyze the data using
             analysis of variance (ANOVA). When data conform to a
             complete, balanced design (equal numbers of observations in
             each experimental treatment), it is straightforward to
             conduct an ANOVA. This paper provides an overview of the
             consequences of lack of balance and gives some guidelines to
             analyzing unbalanced data for models involving fixed
             effects. -from Authors},
   Doi = {10.2307/1939922},
   Key = {fds229162}
}

@article{fds229241,
   Author = {Mitchell-Olds, T},
   Title = {Does environmental variation maintain genetic variation? A
             question of scale.},
   Journal = {Trends in Ecology and Evolution},
   Volume = {7},
   Number = {12},
   Pages = {397-398},
   Year = {1992},
   Month = {December},
   ISSN = {0169-5347},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21236077},
   Doi = {10.1016/0169-5347(92)90017-6},
   Key = {fds229241}
}

@article{fds229240,
   Author = {Leeper, D and Pavek, D and Walsh, R and Mitchell Olds,
             T},
   Title = {Management of Arabis fecunda, a threatened
             plant},
   Journal = {Northwest Environmental Journal},
   Volume = {8},
   Pages = {200-201},
   Year = {1992},
   Key = {fds229240}
}

@article{fds229242,
   Author = {Pavek, D and Mitchell Olds and T},
   Title = {Genetic diversity in plant species in Glacier National
             Park},
   Journal = {Northwest Environmental Journal},
   Volume = {8},
   Pages = {181-183},
   Year = {1992},
   Key = {fds229242}
}

@article{fds229238,
   Author = {Dorn, LA and Mitchell-Olds, T},
   Title = {GENETICS OF BRASSICA CAMPESTRIS. 1. GENETIC CONSTRAINTS ON
             EVOLUTION OF LIFE-HISTORY CHARACTERS.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {45},
   Number = {2},
   Pages = {371-379},
   Year = {1991},
   Month = {March},
   ISSN = {0014-3820},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1991.tb04411.x},
   Abstract = {Energy allocation arguments suggest a possible tradeoff
             between timing and magnitude of reproduction: plants that
             postpone reproduction may accumulate greater resources and
             consequently produce more offspring. However, early
             reproduction may be favored when adult mortality is high.
             Tradeoffs among life-history characters may be a consequence
             of constraints imposed by genetic and environmental
             covariation among traits. In this paper we examine the
             genetic basis of the relationship between timing and
             magnitude of reproduction in an annual plant, Brassica
             campestris, by selecting to change flowering date and plant
             size in each of four directions (early and large, late and
             large, early and small, or late and small). There is a
             strong positive relationship between flowering date and
             flowering height. The response to selection was greatest
             along the axis of positive genetic covariation. Populations
             may evolve to become early flowering and small or late
             flowering and tall, but there is little response for the
             alternative combinations of characters. In this instance,
             the constraints imposed by quantitative genetics are in
             striking accord with predictions that might be made on
             physiological, energetic, or ecological grounds.},
   Doi = {10.1111/j.1558-5646.1991.tb04411.x},
   Key = {fds229238}
}

@article{fds229239,
   Author = {McCall, C and Mitchell-Olds, T and Waller, DM},
   Title = {Distance between mates affects seedling characters in a
             population of Impatiens capensis (Balsaminaceae)},
   Journal = {American Journal of Botany},
   Volume = {78},
   Number = {7},
   Pages = {964-970},
   Publisher = {WILEY},
   Year = {1991},
   Month = {January},
   url = {http://dx.doi.org/10.2307/2445175},
   Abstract = {Tested for the presence of an optimal outcrossing distance
             in a population of Impatiens capensis, an annual herb that
             possesses a mixed mating system, by measuring fitness
             components for offspring of parents that were separated by
             distances of 2, 20 or 50 m. Heavier seed weights and later
             seed maturation enhanced probabilities of emergence and
             subsequent survival, but emergence and survival were
             unaffect by outcrossing distance. Seeds that were produced
             late in the season were heavier than early seeds, and late
             seeds germinated at later dates. Although late germination
             dates were associated with taller plants after 1 and 3
             months of growth, late germination resulted in lighter dry
             weights at maturity. Distance between parents had a negative
             direct effect on seed weight but a positive effect on height
             after 1 month. Data imply an optimal outcrossing distance
             for height at 1 month, estimated as 29 m, but path analysis
             suggests that the apparent optimum is due to a negative
             correlation between the interparent distance and seed
             weight. -from Authors},
   Doi = {10.2307/2445175},
   Key = {fds229239}
}

@article{fds229123,
   Author = {Mitchell-Olds, T},
   Title = {Quantitative genetic changes in small populations},
   Journal = {Proceedings of the Fourth International Congress of
             Systematic and Evolutionary Biology},
   Pages = {634-638},
   Booktitle = {Proceedings of the Fourth International Congress of
             Systematic and Evolutionary Biology},
   Publisher = {Dioscorides Press},
   Year = {1991},
   Key = {fds229123}
}

@article{fds229237,
   Author = {Mitchell-Olds, T and Shaw, RG},
   Title = {COMMENTS ON THE CAUSES OF NATURAL SELECTION.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {44},
   Number = {8},
   Pages = {2158},
   Year = {1990},
   Month = {December},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1990.tb04321.x},
   Doi = {10.1111/j.1558-5646.1990.tb04321.x},
   Key = {fds229237}
}

@article{fds229144,
   Author = {Mitchell-Olds, T and Bergelson, J},
   Title = {Statistical genetics of an annual plant, Impatiens capensis.
             II. Natural selection.},
   Journal = {Genetics},
   Volume = {124},
   Number = {2},
   Pages = {416-421},
   Year = {1990},
   Month = {February},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/2307362},
   Abstract = {Measurement of natural selection on correlated characters
             provides valuable information on fitness surfaces, patterns
             of directional, stabilizing, or disruptive selection,
             mechanisms of fitness variation operating in nature, and
             possible spatial variation in selective pressures. We
             examined effects of seed weight, germination date, plant
             size, early growth, and late growth on individual fitness.
             Path analysis showed that most characters had direct or
             indirect effects on individual fitness, indicating
             directional selection. For most early life-cycle characters,
             indirect effects via later characters exceed the direct
             causal effect on fitness. Selection gradients were uniform
             across the experimental site. There was no evidence for
             stabilizing or disruptive selection. We discuss several
             definitions of stabilizing and disruptive selection.
             Although early events in the life of an individual have
             important causal effects on subsequent characters and
             fitness, there is no detectable genetic variance for most of
             these characters, so little or no genetic response to
             natural selection is expected.},
   Key = {fds229144}
}

@article{fds229236,
   Author = {Mitchell-Olds, T and Bergelson, J},
   Title = {Statistical genetics of an annual plant, Impatiens capensis.
             I. Genetic basis of quantitative variation.},
   Journal = {Genetics},
   Volume = {124},
   Number = {2},
   Pages = {407-415},
   Year = {1990},
   Month = {February},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/2307361},
   Abstract = {Analysis of quantitative genetics in natural populations has
             been hindered by computational and methodological problems
             in statistical analysis. We developed and validated a
             jackknife procedure to test for existence of broad sense
             heritabilities and dominance or maternal effects influencing
             quantitative characters in Impatiens capensis. Early life
             cycle characters showed evidence of dominance and/or
             maternal effects, while later characters exhibited
             predominantly environmental variation. Monte Carlo
             simulations demonstrate that these jackknife tests of
             variance components are extremely robust to heterogeneous
             error variances. Statistical methods from human genetics
             provide evidence for either a major locus influencing
             germination date, or genes that affect phenotypic
             variability per se. We urge explicit consideration of
             statistical behavior of estimation and testing procedures
             for proper biological interpretation of statistical
             results.},
   Key = {fds229236}
}

@article{fds45861,
   Author = {Mitchell-Olds, T. and J. Bergelson},
   Title = {Statistical genetics of Impatiens capensis. II. Natural
             selection},
   Journal = {Genetics},
   Volume = {124},
   Pages = {417-421},
   Year = {1990},
   Key = {fds45861}
}

@article{fds229235,
   Author = {McCall, C and Mitchell-Olds, T and Waller, DM},
   Title = {FITNESS CONSEQUENCES OF OUTCROSSING IN IMPATIENS CAPENSIS:
             TESTS OF THE FREQUENCY-DEPENDENT AND SIB-COMPETITION
             MODELS.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {43},
   Number = {5},
   Pages = {1075-1084},
   Year = {1989},
   Month = {August},
   ISSN = {0014-3820},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1989.tb02552.x},
   Abstract = {Using field and greenhouse experiments, we tested two
             hypotheses that could account for the maintenance of
             outcrossing in Impatiens capensis. Seedlings derived from
             cleistogamous (CL) and chasmogamous (CH) flowers were grown
             under competitive conditions while flanked by neighbors that
             were either related or unrelated. In both experiments, CH
             progeny sometimes expressed more phenotypic variability than
             CL progeny. In the greenhouse experiment, CH progeny
             attained the same weight as CL progeny, and the relatedness
             of neighboring plants did not affect the growth of either
             type. In the field experiment, CL and CH progeny performed
             similarly when grown with related competitors. However, CH
             progeny were somewhat larger when planted with nonsibs,
             while CL progeny were somewhat smaller under those
             conditions. Thus, there is no evidence that either
             frequency-dependent selection or the avoidance of
             competition among siblings favors the maintenance of
             outcrossing in this species. We also modeled the relative
             variability of selfed and outcrossed progeny under several
             reproductive systems. When females mate with one male
             (progeny are full sibs), selfed progeny are often more
             variable than outcrossed progeny. When females engage in
             both selfing and outcrossing, variation among progeny is
             frequently maximized at an intermediate selfing rate. The
             sib-competition mechanism, under a range of genetic models,
             is not apt to promote outcrossing, since selfed progeny are
             commonly more variable than outcrossed progeny.},
   Doi = {10.1111/j.1558-5646.1989.tb02552.x},
   Key = {fds229235}
}

@article{fds229234,
   Author = {Mitchell-Olds, T and Shaw, RG},
   Title = {REGRESSION ANALYSIS OF NATURAL SELECTION: STATISTICAL
             INFERENCE AND BIOLOGICAL INTERPRETATION.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {41},
   Number = {6},
   Pages = {1149-1161},
   Year = {1987},
   Month = {November},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1987.tb02457.x},
   Abstract = {Recent theoretical work in quantitative genetics has fueled
             interest in measuring natural selection in the wild. We
             discuss statistical and biological issues that may arise in
             applications of Lande and Arnold's (1983)
             multiple-regression approach to measuring selection. We
             review assumptions involved in estimation and hypothesis
             testing in regression problems, and we note difficulties
             that frequently arise as a result of violation of these
             assumptions. In particular, multicollinearity (extreme
             intercorrelation of characters) and extrinsic, unmeasured
             factors affecting fitness may seriously complicate inference
             regarding selection. Further, violation of the assumption
             that residuals are normally distributed vitiates tests of
             significance. For this situation, we suggest applications of
             recently developed jackknife tests of significance. While
             fitness regression permits direct assessment of selection in
             a form suitable for predicting selection response, we
             suggest that the aim of inferring causal relationships about
             the effects of phenotypic characters on fitness is greatly
             facilitated by manipulative experiments. Finally, we discuss
             alternative definitions of stabilizing and disruptive
             selection.},
   Doi = {10.1111/j.1558-5646.1987.tb02457.x},
   Key = {fds229234}
}

@article{fds229233,
   Author = {Mitchell-Olds, T},
   Title = {Analysis of local variation in plant size.},
   Journal = {Ecology},
   Volume = {68},
   Number = {1},
   Pages = {82-87},
   Publisher = {WILEY},
   Year = {1987},
   Month = {January},
   url = {http://dx.doi.org/10.2307/1938807},
   Abstract = {Attempts to quantify local competitive interactions by
             examining size and growth of neighboring plants may suffer
             from several statistical difficulties: 1) when individuals
             are analyzed both as focal plants and as neighbors of other
             individuals, observations are not independent and tests of
             statistical significance may be invalid; 2) effects of
             competition and local site quality may be confounded. Path
             analysis and randomization tests may permit more accurate
             estimation and testing of influences on individual plant
             growth. Analysis of results of experiments with Impatiens
             capensis showed that conventional statistical tests may
             yield serious errors in estimates of significance, and that
             these errors are of unpredictable magnitude and direction.
             It is essential to measure or estimate the effects of site
             quality on variation in plant size. -from
             Author},
   Doi = {10.2307/1938807},
   Key = {fds229233}
}

@article{fds229232,
   Author = {Dixon, PM and Weiner, J and Mitchell Olds and T and Woodley,
             R},
   Title = {Bootstrapping the Gini coefficient of inequality},
   Journal = {Ecology},
   Volume = {68},
   Pages = {1548-1551},
   Year = {1987},
   Key = {fds229232}
}

@article{fds229230,
   Author = {Mitchell-Olds, T},
   Title = {QUANTITATIVE GENETICS OF SURVIVAL AND GROWTH IN IMPATIENS
             CAPENSIS.},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {40},
   Number = {1},
   Pages = {107-116},
   Year = {1986},
   Month = {January},
   url = {http://dx.doi.org/10.1111/j.1558-5646.1986.tb05722.x},
   Abstract = {When variation in life-history characters is caused by many
             genes of small effect, then quantitative-genetic parameters
             may quantify constraints on rate and direction of
             microevolutionary change. I estimated heritabilities and
             genetic correlations for 16 life-history and morphological
             characters in two populations of Impatiens capensis, a
             partially self-pollinating herbaceous annual. The Madison
             population had little or no additive genetic variance for
             any of these characters, while the Milwaukee population had
             significant narrowsense heritabilities and genetic
             correlations for several traits, including adult size, which
             is highly correlated with fitness. All genetic correlations
             among fitness components were positive, hence there is no
             evidence for antagonistic pleiotropy among these traits.
             Dissimilarity of heritabilities in the two populations
             supports theoretical predictions that long-term changes in
             genetic variance-covariance patterns may occur when
             population sizes are small and selection is strong, as may
             occur in many plant species.},
   Doi = {10.1111/j.1558-5646.1986.tb05722.x},
   Key = {fds229230}
}

@article{fds229228,
   Author = {Mitchell Olds and T and Guries, RP},
   Title = {Genetic load and heterozygosity in the Pinaceae},
   Journal = {Can. J. Genet. Cytol.},
   Volume = {28},
   Pages = {942-946},
   Year = {1986},
   Key = {fds229228}
}

@article{fds229229,
   Author = {Mitchell Olds and T},
   Title = {Discussion of C. F. J. Wu's "Jackknife, bootstrap, and other
             resampling methods in regression analysis"},
   Journal = {Ann. Statis.},
   Volume = {14},
   Pages = {1316-1318},
   Year = {1986},
   Key = {fds229229}
}

@article{fds229231,
   Author = {Mitchell Olds and T and Rutledge, JJ},
   Title = {Quantitative genetics in natural plant populations: A review
             of the theory},
   Journal = {American Naturalist},
   Volume = {127},
   Pages = {379-402},
   Year = {1986},
   Key = {fds229231}
}

@article{fds229227,
   Author = {Mitchell-Olds, T and Waller, DM},
   Title = {Relative Performance of Selfed and Outcrossed Progeny in
             Impatiens capensis},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {39},
   Number = {3},
   Pages = {533-533},
   Publisher = {JSTOR},
   Year = {1985},
   Month = {May},
   url = {http://dx.doi.org/10.2307/2408651},
   Abstract = {This study compares survival and growth of progeny derived
             from chasmogamous (CH) and cleistogamous (CL) flowers in
             Impatiens capensis, a forest annual. When progeny were grown
             in the field, CH seeds had significantly higher survival
             rates over winter (64% versus 56%), and the survival
             advantage of outcrossed progeny was not attributable to seed
             weight differences. No differences in seedling growth were
             detected. Greenhouse comparisons revealed no difference in
             seed survival but a 30% growth advantage to CH seedlings. We
             found no changes in developmental homeostasis of three leaf
             shape characters between inbred and outbred progeny, nor was
             there any difference in variability within CH and CL
             families. The outcrossing advantage observed in these
             experiments could not have been caused by avoidance of sib
             competition. Theory predicts that self-pollinated progenies
             may be more variable than outcrossed progenies if rare,
             recessive alleles are important contributors to genetic
             variances. Electrophoretic markers indicate that progeny
             derived from CH flowers are predominantly outcrossed (at
             least 54-97%).},
   Doi = {10.2307/2408651},
   Key = {fds229227}
}

@article{fds229226,
   Author = {Charnov, EL and Bull, JJ and Mitchell Olds and ST},
   Title = {A note on sex and life histories},
   Journal = {American Naturalist},
   Volume = {117},
   Pages = {814-818},
   Year = {1981},
   Key = {fds229226}
}


%% Papers Accepted   
@article{fds226369,
   Author = {Anderson, JT and N Perera and B Chowdhury and T
             Mitchell-Olds},
   Title = {Microgeographic patterns of genetic divergence and
             adaptation across natural environments in Boechera stricta
             (Brassicaceae)},
   Journal = {American Naturalist},
   Year = {2014},
   Key = {fds226369}
}


%% Papers Submitted   
@article{fds226373,
   Author = {Olson-Manning, CF and CF Strock and T Mitchell-Olds},
   Title = {Flux control in a plant defense pathway is robust to
             environmental perturbations and controls variation in
             adaptive traits},
   Journal = {PLoS Genetics},
   Year = {2015},
   Key = {fds226373}
}

@article{fds226370,
   Author = {Shalabh Dixit and Alexandre Grondin and Cheng-Ruei Lee and Amelia
             Henry, Thomas-Mitchell Olds and Arvind Kumar},
   Title = {Rice for 2020 and beyond: genetics of traits, trait
             interactions, quantitative trait loci, and epistatic
             interactions},
   Journal = {Journal of Experimental Botany},
   Year = {2015},
   Key = {fds226370}
}

@article{fds219211,
   Author = {Manzaneda, A. and P. Rey and J. Anderson and E. Raskin and C.
             Weiss-Lehman and T. Mitchell-Olds},
   Title = {Natural variation, plasticity and tradeoffs of drought
             tolerance-related traits in the Brachypodium distachyon
             (Poaceae) ploidy complex},
   Journal = {Evolution},
   Year = {2014},
   Key = {fds219211}
}


%% Book Chapters   
@misc{fds229119,
   Author = {Voigt, ML and Melzer, M and Rutten, T and Mitchell-Olds, T and Sharbel,
             TF},
   Title = {Gametogenesis in the apomictic Boechera holboellii complex:
             the male perspective},
   Booktitle = {Apomixis: Evolution, Mechanisms and Perspectives},
   Publisher = {International Association for Plant Taxonomy - Koeltz
             Scientific Books},
   Editor = {Horandl, E and Grossniklaus, U and van Dijk, P and Sharbel,
             TF},
   Year = {2007},
   Key = {fds229119}
}

@misc{fds229120,
   Author = {Mitchell-Olds, T and Al-Shehbaz, I and Koch, M and Sharbel,
             T},
   Title = {Crucifer Evolution in the Post-Genomic Era},
   Pages = {119-137},
   Booktitle = {Diversity and Evolution of Plants - genotype and phenotype
             variation in higher plants},
   Publisher = {CABI press},
   Editor = {Henry, R},
   Year = {2005},
   Key = {fds229120}
}

@misc{fds229121,
   Author = {Gurganus, M and Mitchell-Olds, T},
   Title = {Quantitative Trait Loci and Developmental
             Plasticity},
   Pages = {77-100},
   Booktitle = {Plant Evolutionary Genetics and the Biology of
             Weeds},
   Publisher = {Endemic Species Research Institute},
   Editor = {Schaal, BA and Chiang, TY and Chou, CH},
   Year = {2004},
   Key = {fds229121}
}

@misc{fds229122,
   Author = {Kroymann, J and Mitchell-Olds, T},
   Title = {Function and evolution of an Arabidopsis insect resistance
             QTL},
   Volume = {4},
   Pages = {259-262},
   Booktitle = {Biology of Molecular Plant-Microbe Interactions},
   Publisher = {. International Society of Molecular Plant Microbe
             Interactions, APS Press},
   Editor = {Lugtenberg, B and Tikhonovich, I and Provprov,
             N},
   Year = {2003},
   Key = {fds229122}
}