%% Papers Published
@article{fds368496,
Author = {Wagner, MR and Mitchell-Olds, T},
Title = {Soil variation among natural habitats alters glucosinolate
content in a wild perennial mustard.},
Journal = {Journal of experimental botany},
Volume = {74},
Number = {5},
Pages = {1723-1740},
Year = {2023},
Month = {March},
url = {http://dx.doi.org/10.1093/jxb/erac520},
Abstract = {Baseline levels of glucosinolates-important defensive
phytochemicals in brassicaceous plants-are determined by
both genotype and environment. However, the ecological
causes of glucosinolate plasticity are not well
characterized. Fertilization is known to alter glucosinolate
content of Brassica crops, but the effect of naturally
occurring soil variation on glucosinolate content of wild
plants is unknown. Here, we conducted greenhouse experiments
using Boechera stricta to ask (i) whether soil variation
among natural habitats shapes leaf and root glucosinolate
profiles; (ii) whether such changes are caused by abiotic
soil properties, soil microbes, or both; and (iii) whether
soil-induced glucosinolate plasticity is genetically
variable. Total glucosinolate quantity differed up to 2-fold
between soils from different natural habitats, while the
relative amounts of different compounds were less
responsive. This effect was due to physico-chemical soil
properties rather than microbial communities. We detected
modest genetic variation for glucosinolate plasticity in
response to soil. In addition, glucosinolate composition,
but not quantity, of field-grown plants could be accurately
predicted from measurements from greenhouse-grown plants. In
summary, soil alone is sufficient to cause plasticity of
baseline glucosinolate levels in natural plant populations,
which may have implications for the evolution of this
important trait across complex landscapes.},
Doi = {10.1093/jxb/erac520},
Key = {fds368496}
}
@article{fds367398,
Author = {Carley, LN and Morris, WF and Walsh, R and Riebe, D and Mitchell-Olds,
T},
Title = {Are genetic variation and demographic performance
linked?},
Journal = {Evolutionary applications},
Volume = {15},
Number = {11},
Pages = {1888-1906},
Year = {2022},
Month = {November},
url = {http://dx.doi.org/10.1111/eva.13487},
Abstract = {Quantifying relationships between genetic variation and
population viability is important from both basic biological
and applied conservation perspectives, yet few populations
have been monitored with both long-term demographic and
population genetics approaches. To empirically test whether
and how genetic variation and population dynamics are
related, we present one such paired approach. First, we use
eight years of historical demographic data from five
populations of <i>Boechera fecunda</i> (Brassicaceae), a
rare, self-compatible perennial plant endemic to Montana,
USA, and use integral projection models to estimate the
stochastic population growth rate (<i>λ</i> <sub>S</sub>)
and extinction risk of each population. We then combine
these demographic estimates with previously published
metrics of genetic variation in the same populations to test
whether genetic diversity within populations is linked to
demographic performance. Our results show that in this
predominantly inbred species, standing genetic variation and
demography are weakly positively correlated. However, the
inbreeding coefficient was not strongly correlated with
demographic performance, suggesting that more inbred
populations are not necessarily less viable or at higher
extinction risk than less inbred populations. A contemporary
re-census of these populations revealed that neither genetic
nor demographic parameters were consistently strong
predictors of current population density, although
populations showing lower probabilities of extinction in
demographic models had larger population sizes at present.
In the absence of evidence for inbreeding depression
decreasing population viability in this species, we
recommend conservation of distinct, potentially locally
adapted populations of <i>B. fecunda</i> rather than
alternatives such as translocations or reintroductions.},
Doi = {10.1111/eva.13487},
Key = {fds367398}
}
@article{fds367858,
Author = {Rushworth, CA and Wagner, MR and Mitchell-Olds, T and Anderson,
JT},
Title = {The Boechera model system for evolutionary
ecology.},
Journal = {American journal of botany},
Volume = {109},
Number = {11},
Pages = {1939-1961},
Year = {2022},
Month = {November},
url = {http://dx.doi.org/10.1002/ajb2.16090},
Abstract = {Model systems in biology expand the research capacity of
individuals and the community. Closely related to
Arabidopsis, the genus Boechera has emerged as an important
ecological model owing to the ability to integrate across
molecular, functional, and eco-evolutionary approaches.
Boechera species are broadly distributed in relatively
undisturbed habitats predominantly in western North America
and provide one of the few experimental systems for
identification of ecologically important genes through
genome-wide association studies and investigations of
selection with plants in their native habitats. The
ecologically, evolutionarily, and agriculturally important
trait of apomixis (asexual reproduction via seeds) is common
in the genus, and field experiments suggest that abiotic and
biotic environments shape the evolution of sex. To date,
population genetic studies have focused on the widespread
species B. stricta, detailing population divergence and
demographic history. Molecular and ecological studies show
that balancing selection maintains genetic variation in ~10%
of the genome, and ecological trade-offs contribute to
complex trait variation for herbivore resistance, flowering
phenology, and drought tolerance. Microbiome analyses have
shown that host genotypes influence leaf and root microbiome
composition, and the soil microbiome influences flowering
phenology and natural selection. Furthermore, Boechera
offers numerous opportunities for investigating biological
responses to global change. In B. stricta, climate change
has induced a shift of >2 weeks in the timing of first
flowering since the 1970s, altered patterns of natural
selection, generated maladaptation in previously
locally-adapted populations, and disrupted life history
trade-offs. Here we review resources and results for this
eco-evolutionary model system and discuss future research
directions.},
Doi = {10.1002/ajb2.16090},
Key = {fds367858}
}
@article{fds362966,
Author = {Han, T-S and Hu, Z-Y and Du, Z-Q and Zheng, Q-J and Liu, J and Mitchell-Olds, T and Xing, Y-W},
Title = {Adaptive responses drive the success of polyploid
yellowcresses (Rorippa, Brassicaceae) in the Hengduan
Mountains, a temperate biodiversity hotspot.},
Journal = {Plant diversity},
Volume = {44},
Number = {5},
Pages = {455-467},
Year = {2022},
Month = {September},
url = {http://dx.doi.org/10.1016/j.pld.2022.02.002},
Abstract = {Polyploids contribute substantially to plant evolution and
biodiversity; however, the mechanisms by which they succeed
are still unclear. According to the <i>polyploid adaptation
hypothesis</i>, successful polyploids spread by repeated
adaptive responses to new environments. Here, we tested this
hypothesis using two tetraploid yellowcresses
(<i>Rorippa</i>), the endemic <i>Rorippa elata</i> and the
widespread <i>Rorippa palustris</i>, in the temperate
biodiversity hotspot of the Hengduan Mountains. Speciation
modes were resolved by phylogenetic modeling using 12
low-copy nuclear loci. Phylogeographical patterns were then
examined using haplotypes phased from four plastid and ITS
markers, coupled with historical niche reconstruction by
ecological niche modeling. We inferred the time of hybrid
origins for both species as the mid-Pleistocene, with shared
glacial refugia within the southern Hengduan Mountains.
Phylogeographic and ecological niche reconstruction
indicated recurrent northward colonization by both species
after speciation, possibly tracking denuded habitats created
by glacial retreat during interglacial periods. Common
garden experiment involving perennial <i>R. elata</i>
conducted over two years revealed significant changes in
fitness-related traits across source latitudes or altitudes,
including latitudinal increases in survival rate and
compactness of plant architecture, suggesting gradual
adaptation during range expansion. These findings support
the <i>polyploid adaptation hypothesis</i> and suggest that
the spread of polyploids was aided by adaptive responses to
environmental changes during the Pleistocene. Our results
thus provide insight into the evolutionary success of
polyploids in high-altitude environments.},
Doi = {10.1016/j.pld.2022.02.002},
Key = {fds362966}
}
@article{fds362770,
Author = {Liang, Y-Y and Chen, X-Y and Zhou, B-F and Mitchell-Olds, T and Wang,
B},
Title = {Globally Relaxed Selection and Local Adaptation in Boechera
stricta.},
Journal = {Genome biology and evolution},
Volume = {14},
Number = {4},
Pages = {evac043},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1093/gbe/evac043},
Abstract = {The strength of selection varies among populations and
across the genome, but the determinants of efficacy of
selection remain unclear. In this study, we used
whole-genome sequencing data from 467 Boechera stricta
accessions to quantify the strength of selection and
characterize the pattern of local adaptation. We found low
genetic diversity on 0-fold degenerate sites and conserved
non-coding sites, indicating functional constraints on these
regions. The estimated distribution of fitness effects and
the proportion of fixed substitutions suggest relaxed
negative and positive selection in B. stricta. Among the
four population groups, the NOR and WES groups have smaller
effective population size (Ne), higher proportions of
effectively neutral sites, and lower rates of adaptive
evolution compared with UTA and COL groups, reflecting the
effect of Ne on the efficacy of natural selection. We also
found weaker selection on GC-biased sites compared with
GC-conservative (unbiased) sites, suggested that GC-biased
gene conversion has affected the strength of selection in B.
stricta. We found mixed evidence for the role of the
recombination rate on the efficacy of selection. The
positive and negative selection was stronger in
high-recombination regions compared with low-recombination
regions in COL but not in other groups. By scanning the
genome, we found different subsets of selected genes
suggesting differential adaptation among B. stricta groups.
These results show that differences in effective population
size, nucleotide composition, and recombination rate are
important determinants of the efficacy of selection. This
study enriches our understanding of the roles of natural
selection and local adaptation in shaping genomic
variation.},
Doi = {10.1093/gbe/evac043},
Key = {fds362770}
}
@article{fds357293,
Author = {Carley, LN and Mojica, JP and Wang, B and Chen, C-Y and Lin, Y-P and Prasad, KVSK and Chan, E and Hsu, C-W and Keith, R and Nuñez, CL and Olson-Manning, CF and Rushworth, CA and Wagner, MR and Wang, J and Yeh,
P-M and Reichelt, M and Ghattas, K and Gershenzon, J and Lee, C-R and Mitchell-Olds, T},
Title = {Ecological factors influence balancing selection on leaf
chemical profiles of a wildflower.},
Journal = {Nature ecology & evolution},
Volume = {5},
Number = {8},
Pages = {1135-1144},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1038/s41559-021-01486-0},
Abstract = {Balancing selection is frequently invoked as a mechanism
that maintains variation within and across populations.
However, there are few examples of balancing selection
operating on loci underpinning complex traits, which
frequently display high levels of variation. We investigated
mechanisms that may maintain variation in a focal
polymorphism-leaf chemical profiles of a perennial
wildflower (Boechera stricta, Brassicaceae)-explicitly
interrogating multiple ecological and genetic processes
including spatial variation in selection, antagonistic
pleiotropy and frequency-dependent selection. A suite of
common garden and greenhouse experiments showed that the
alleles underlying variation in chemical profile have
contrasting fitness effects across environments, implicating
two ecological drivers of selection on chemical profile:
herbivory and drought. Phenotype-environment associations
and molecular genetic analyses revealed additional evidence
of past selection by these drivers. Together, these data are
consistent with balancing selection on chemical profile,
probably caused by pleiotropic effects of secondary chemical
biosynthesis genes on herbivore defence and drought
response.},
Doi = {10.1038/s41559-021-01486-0},
Key = {fds357293}
}
@article{fds355595,
Author = {Castano-Duque, L and Ghosal, S and Quilloy, FA and Mitchell-Olds, T and Dixit, S},
Title = {An epigenetic pathway in rice connects genetic variation to
anaerobic germination and seedling establishment.},
Journal = {Plant physiology},
Volume = {186},
Number = {2},
Pages = {1042-1059},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1093/plphys/kiab100},
Abstract = {Rice production is shifting from transplanting seedlings to
direct sowing of seeds. Following heavy rains, directly sown
seeds may need to germinate under anaerobic environments,
but most rice (Oryza sativa) genotypes cannot survive these
conditions. To identify the genetic architecture of complex
traits, we quantified percentage anaerobic germination (AG)
in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice
genotypes and performed genome-wide association studies
(GWAS) using 693,502 single nucleotide polymorphisms. This
was followed by post-GWAS analysis with a generalized
SNP-to-gene set analysis, meta-analysis, and network
analysis. We determined that percentage AG is
intermediate-to-high among indica subpopulations, and AG is
a polygenic trait associated with transcription factors
linked to ethylene responses or genes involved in metabolic
processes that are known to be associated with AG. Our
post-GWAS analysis identified several genes involved in a
wide variety of metabolic processes. We subsequently
performed functional analysis focused on the small RNA and
methylation pathways. We selected CLASSY 1 (CLSY1), a gene
involved in the RNA-directed DNA methylation (RdDm) pathway,
for further analyses under AG and found several lines of
evidence that CLSY1 influences AG. We propose that the RdDm
pathway plays a role in rice responses to water status
during germination and seedling establishment developmental
stages.},
Doi = {10.1093/plphys/kiab100},
Key = {fds355595}
}
@article{fds354753,
Author = {Yan, W and Wang, B and Chan, E and Mitchell-Olds,
T},
Title = {Genetic architecture and adaptation of flowering time among
environments.},
Journal = {The New phytologist},
Volume = {230},
Number = {3},
Pages = {1214-1227},
Year = {2021},
Month = {May},
url = {http://dx.doi.org/10.1111/nph.17229},
Abstract = {The genetic basis of flowering time changes across
environments, and pleiotropy may limit adaptive evolution of
populations in response to local conditions. However, little
information is known about how genetic architecture changes
among environments. We used genome-wide association studies
(GWAS) in Boechera stricta (Graham) Al-Shehbaz, a relative
of Arabidopsis, to examine flowering variation among
environments and associations with climate conditions in
home environments. Also, we used molecular population
genetics to search for evidence of historical natural
selection. GWAS found 47 significant quantitative trait loci
(QTLs) that influence flowering time in one or more
environments, control plastic changes in phenology between
experiments, or show associations with climate in sites of
origin. Genetic architecture of flowering varied
substantially among environments. We found that some pairs
of QTLs showed similar patterns of pleiotropy across
environments. A large-effect QTL showed molecular signatures
of adaptive evolution and is associated with climate in home
environments. The derived allele at this locus causes later
flowering and predominates in sites with greater water
availability. This work shows that GWAS of climate
associations and ecologically important traits across
diverse environments can be combined with molecular
signatures of natural selection to elucidate ecological
genetics of adaptive evolution.},
Doi = {10.1111/nph.17229},
Key = {fds354753}
}
@article{fds356013,
Author = {Lin, Y-P and Mitchell-Olds, T and Lee, C-R},
Title = {The ecological, genetic and genomic architecture of local
adaptation and population differentiation in Boechera
stricta.},
Journal = {Proceedings. Biological sciences},
Volume = {288},
Number = {1949},
Pages = {20202472},
Year = {2021},
Month = {April},
url = {http://dx.doi.org/10.1098/rspb.2020.2472},
Abstract = {Differential local adaptation restricts gene flow between
populations inhabiting distinct environments, resulting in
isolation by adaptation. In addition to the statistical
inferences of genotype-environment associations, an
integrative approach is needed to investigate the effect of
local adaptation on population divergence at the ecological,
genetic and genomic scale. Here, we combine reciprocal
transplant, genome-environment association and QTL mapping
to investigate local adaptation in <i>Boechera stricta</i>
(Drummond's rockcress). With reciprocal transplant
experiment, we found local genetic groups exhibit phenotypic
characteristics corresponding to the distinct selection
forces from different water availability. At the genetic
level, the local allele of a major fitness QTL confers
higher and sturdier flowering stalks, maximizing the
fecundity fitness component under sufficient water supply,
and its genetic variation is associated with precipitation
across the landscape. At the genomewide scale, we further
showed that multiple loci associated with precipitation are
highly differentiated between genetic groups, suggesting
that local adaptation has a widespread effect on reducing
gene flow. This study provides one of the few comprehensive
examples demonstrating how local adaptation facilitates
population divergence at the trait, gene and genome
level.},
Doi = {10.1098/rspb.2020.2472},
Key = {fds356013}
}
@article{fds353936,
Author = {Rushworth, CA and Mitchell-Olds, T},
Title = {The Evolution of Sex is Tempered by Costly Hybridization in
Boechera (Rock Cress).},
Journal = {The Journal of heredity},
Volume = {112},
Number = {1},
Pages = {67-77},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1093/jhered/esaa041},
Abstract = {Despite decades of research, the evolution of sex remains an
enigma in evolutionary biology. Typically, research
addresses the costs of sex and asexuality to characterize
the circumstances favoring one reproductive mode.
Surprisingly few studies address the influence of common
traits that are, in many organisms, obligately correlated
with asexuality, including hybridization and polyploidy.
These characteristics have substantial impacts on traits
under selection. In particular, the fitness consequences of
hybridization (i.e., reduced fitness due to interspecific
reproductive isolation) will influence the evolution of sex.
This may comprise a cost of either sex or asexuality due to
the link between hybridity and asexuality. We examined
reproductive isolation in the formation of de novo hybrid
lineages between 2 widespread species in the ecological
model system Boechera. Seventeen percent of 664 crosses
produced F1 fruits, and only 10% of these were viable,
suggesting that postmating prezygotic and postzygotic
barriers inhibit hybrid success in this system. The
postmating prezygotic barrier was asymmetrical, with 110 of
115 total F1 fruits produced when Boechera stricta acted as
maternal parent. This asymmetry was confirmed in
wild-collected lineages, using a chloroplast phylogeny of
wild-collected B. stricta, Boechera retrofracta, and
hybrids. We next compared fitness of F2 hybrids and selfed
parental B. stricta lines, finding that F2 fitness was
reduced by substantial hybrid sterility. Multiple
reproductively isolating barriers influence the formation
and fitness of hybrid lineages in the wild, and the costs of
hybridization likely have profound impacts on the evolution
of sex in the natural environment.},
Doi = {10.1093/jhered/esaa041},
Key = {fds353936}
}
@article{fds353935,
Author = {Rushworth, CA and Brandvain, Y and Mitchell-Olds,
T},
Title = {Identifying the fitness consequences of sex in complex
natural environments.},
Journal = {Evolution letters},
Volume = {4},
Number = {6},
Pages = {516-529},
Publisher = {WILEY},
Year = {2020},
Month = {December},
url = {http://dx.doi.org/10.1002/evl3.194},
Abstract = {In the natural world, sex prevails, despite its costs.
Although much effort has been dedicated to identifying the
intrinsic costs of sex (e.g., the cost of males), few
studies have identified the ecological fitness consequences
of sex. Furthermore, correlated biological traits that
differ between sexuals and asexuals may alter these costs,
or even render the typical costs of sex irrelevant. We
conducted a large-scale, multisite, reciprocal transplant
using multiple sexual and asexual genotypes of a native
North American wildflower to show that sexual genotypes have
reduced lifetime fitness, despite lower herbivory. We
separated the effects of sex from those of hybridity,
finding that overwinter survival is elevated in asexuals
regardless of hybridity, but herbivores target hybrid
asexuals more than nonhybrid asexual or sexual genotypes.
Survival is lowest in homozygous sexual lineages,
implicating inbreeding depression as a cost of sex. Our
results show that the consequences of sex are shaped not
just by sex itself, but by complex natural environments,
correlated traits, and the identity and availability of
mates.},
Doi = {10.1002/evl3.194},
Key = {fds353935}
}
@article{fds359766,
Author = {Zhang, H and Mitchell-Olds, T and Mujacic, I and Song,
BH},
Title = {De novo Genome Assembly, Annotation, and SNP Identification
of an Endangered Rockcress, Boechera fecunda},
Journal = {Frontiers in Ecology and Evolution},
Volume = {8},
Year = {2020},
Month = {October},
url = {http://dx.doi.org/10.3389/fevo.2020.550936},
Doi = {10.3389/fevo.2020.550936},
Key = {fds359766}
}
@article{fds350201,
Author = {Mandáková, T and Hloušková, P and Windham, MD and Mitchell-Olds,
T and Ashby, K and Price, B and Carman, J and Lysak,
MA},
Title = {Chromosomal Evolution and Apomixis in the Cruciferous Tribe
Boechereae.},
Journal = {Frontiers in plant science},
Volume = {11},
Pages = {514},
Year = {2020},
Month = {January},
url = {http://dx.doi.org/10.3389/fpls.2020.00514},
Abstract = {The mustard family (Brassicaceae) comprises several dozen
monophyletic clades usually ranked as tribes. The tribe
Boechereae plays a prominent role in plant research due to
the incidence of apomixis and its close relationship to
<i>Arabidopsis</i>. This tribe, largely confined to western
North America, harbors nine genera and c. 130 species, with
>90% of species belonging to the genus <i>Boechera</i>.
Hundreds of apomictic diploid and triploid <i>Boechera</i>
hybrids have spurred interest in this genus, but the
remaining Boechereae genomes remain virtually unstudied.
Here we report on comparative genome structure of six genera
(<i>Borodinia</i>, <i>Cusickiella</i>, <i>Phoenicaulis</i>,
<i>Polyctenium</i>, <i>Nevada</i>, and <i>Sandbergia</i>)
and three <i>Boechera</i> species as revealed by comparative
chromosome painting (CCP). All analyzed taxa shared the same
seven-chromosome genome structure. Comparisons with the
sister Halimolobeae tribe (<i>n</i> = 8) showed that the
ancestral Boechereae genome (<i>n</i> = 7) was derived from
an older <i>n</i> = 8 genome by descending dysploidy
followed by the divergence of extant Boechereae taxa. As
tribal divergence post-dated the origin of four
tribe-specific chromosomes, it is proposed that these
chromosomal rearrangements were a key evolutionary
innovation underlaying the origin and diversification of the
Boechereae in North America. Although most Boechereae genera
exhibit genomic conservatism, intra-tribal cladogenesis has
occasionally been accompanied by chromosomal rearrangements
(particularly inversions). Recently, apomixis was reported
in the Boechereae genera <i>Borodinia</i> and
<i>Phoenicaulis</i>. Here, we report sexual reproduction in
diploid <i>Nevada</i>, diploid <i>Sandbergia</i>, and
tetraploid <i>Cusickiella</i> and aposporous apomixis in
tetraploids of <i>Polyctenium</i> and <i>Sandbergia</i>. In
sum, apomixis is now known to occur in five of the nine
Boechereae genera.},
Doi = {10.3389/fpls.2020.00514},
Key = {fds350201}
}
@article{fds345713,
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 = {Correction to: 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 = {161},
Year = {2019},
Month = {August},
url = {http://dx.doi.org/10.1186/s13059-019-1781-5},
Abstract = {Following publication of the original article [1], the
authors reported that the Availability of data and materials
section required updating. The updated text reads as
follows.},
Doi = {10.1186/s13059-019-1781-5},
Key = {fds345713}
}
@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 = {<h4>Background</h4>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.<h4>Results</h4>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
(d<sub>XY</sub>), and lower relative divergence
(F<sub>ST</sub>) 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 F<sub>ST</sub> and
d<sub>XY</sub> among the groups, termed F<sub>ST</sub>-islands.
Population genetic signatures indicate that
F<sub>ST</sub>-islands with elevated divergence, which have
experienced directional selection, are derived from
divergent sorting of ancient polymorphisms.<h4>Conclusions</h4>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 = {<h4>Premise of the study</h4>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.<h4>Methods</h4>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.<h4>Key results</h4>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.<h4>Conclusions</h4>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 <i>Boechera
stricta</i>, a highly adapted relative of Arabidopsis
(<i>Arabidopsis thaliana</i>) native to the Rocky Mountains.
A single QTL was identified that contained the gene encoding
ACYL-COENZYME A:DIACYLGLYCEROL ACYLTRANSFERASE1
(<i>BstDGAT1</i>), 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 <i>DGAT1</i> 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
<i>AtDGAT1</i> 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 = {<h4>Background</h4>Traditional rice (Oryza sativa) varieties
are valuable resources for the improvement of drought
resistance. qDTY<sub>3.2</sub> 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 qDTY<sub>3.2</sub>. Our approach was to phenotype
fifteen BC<sub>2</sub>F<sub>3:4</sub> lines for shoot and
root drought resistance-related traits as compared to Swarna
in the field under well-watered and drought stress
conditions. Four BC<sub>2</sub>F<sub>3:4</sub> 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).<h4>Results</h4>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
BC<sub>2</sub>F<sub>3:4</sub> 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.<h4>Conclusions</h4>We conclude that earlier
flowering time, reduced shallow root growth, and
drought-induced increased deep root growth are associated
with the presence of qDTY<sub>3.2</sub> since these
phenotypes were consistently observed in the selected QTL
lines with full introgression of qDTY<sub>3.2</sub>. We
hypothesize that the qDTY<sub>3.2</sub> 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},
Pages = {E185},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.3390/genes9040185},
Abstract = {Closely related to the model plant <i>Arabidopsis
thaliana</i>, the genus <i>Boechera</i> is known to contain
both sexual and apomictic species or accessions. <i>Boechera
retrofracta</i> 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 <i>B. retrofracta</i> 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
<i>B. retrofracta</i> and 6 other Brassicaceae species were
used for phylogenetic tree reconstruction. In addition, we
explored the histidine exonuclease <i>APOLLO</i> locus,
related to apomixis in <i>Boechera</i>, and proposed model
of its evolution through the series of duplications. An
assembled genome of <i>B. retrofracta</i> will help in the
challenging assembly of the highly heterozygous genomes of
hybrid apomictic species<i>.</i>},
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 <i>Boechera
stricta</i> and investigated the candidate genes
<i>BsFLC1</i> and <i>BsFLC2</i>. The expression patterns of
<i>BsFLC1</i> suggested its function in flowering time
suppression, and the deletion of <i>BsFLC1</i> is associated
with rapid flowering and loss of vernalization requirement.
In contrast, <i>BsFLC2</i> 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 <i>FLC</i> gene, the
evolution of rapid phenology was made possible by the change
of <i>BsFLC2</i> expression pattern or protein sequences and
the deletion of <i>BsFLC1</i>.},
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 & 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 & Evolution},
Volume = {1},
Number = {6},
Pages = {0166-0166},
Publisher = {Springer Science and Business Media LLC},
Year = {2017},
Month = {April},
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 & 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, 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 = {Nat Commun},
Volume = {7},
Pages = {12151},
Publisher = {Nature Publishing Group, a division of Macmillan Publishers
Limited. All Rights Reserved.},
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 = {Andeson, JT and Perera, N and Chowdhury, B and Mitchell-Olds,
T},
Title = {Microgeographic patterns of genetic divergence and
adaptation across natural environments in Boechera stricta
(Brassicaceae)},
Journal = {American Naturalist},
Volume = {186 Suppl 1},
Number = {S1},
Pages = {S60-S73},
Publisher = {University of Chicago Press},
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-Manningq, CF and Strock, CF and Mitchell-Olds,
T},
Title = {Flux control in a plant defense pathway is robust to
environmental perturbations and controls variation in
adaptive traits},
Journal = {G3/Genes/Genomes/Gentics Early Online},
Volume = {5},
Number = {11},
Pages = {2421-2427},
Publisher = {Genetics Society of America},
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 = {<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusion</h4>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 = {February},
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{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{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. 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{fds229133,
Author = {Lovell, and JT, and Aliyu, W 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 = {New Phytologist},
Volume = {26},
Number = {4},
Pages = {309-315},
Year = {2012},
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{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{fds359855,
Author = {Anderson, and JT, and Lee, C-R and Mitchell-Olds,
T},
Title = {Strong selection genome-wide enhances fitness tradeoffs
across environments and episodes of selection},
Journal = {Evolution},
Year = {2012},
Key = {fds359855}
}
@article{fds359554,
Author = {Anderson, and JT, and Wagner, MR and Rushworth, C and Prasad, KVSK and Mitchell-Olds, T},
Title = {The evolution of quantitative traits in complex
environments},
Journal = {Heredity},
Year = {2012},
Key = {fds359554}
}
@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{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{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, A and Gao, C and Gu, Y and Hazen, S and Holt, B and Hong, SY and Jordan, M and Manzaneda, A and Mitchell Olds and T and Mochida, K and Mur,
L and Park, CM 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},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21771916},
Doi = {10.1104/pp.111.179531},
Key = {fds229183}
}
@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 = Entwicklungsgeschichte und
Systematik der Pflanzen},
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.},
Doi = {10.1007/s00606-008-0017-z},
Key = {fds229192}
}
@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{fds229204,
Author = {Ming, R and Hou, S and Feng, Y and Yu, Q and Dionne Laporte and 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, D and Albert, H and Wang,
ML and Zhu, YJ and Schatz, M and Nagarajan, N and Agbayani, R and Guan, P and Blas, A and Wai, CM and Ackerman, CM and Ren, Y and Liu, C and Wang, J and Na,
JK 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 Pérez, RN and Torres, MJ and Feltus, FA and Porter, B and Li, Y and Burroughs, AM and Luo, MC 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, D 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},
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{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{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 = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17957263},
Abstract = {<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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{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{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{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 = {<h4>Background</h4>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.<h4>Methodology/principal
findings</h4>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.<h4>Conclusions/significance</h4>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{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 = {January},
ISSN = {0032-0889},
url = {http://dx.doi.org/10.1104/pp.104.900229},
Doi = {10.1104/pp.104.900229},
Key = {fds229158}
}
@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{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 = {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{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{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{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 = {Plant Cell},
Volume = {18},
Number = {6},
Pages = {1537},
Publisher = {American Society of Plant Biologists (ASPB)},
Year = {2006},
Month = {January},
ISSN = {1040-4651},
url = {http://dx.doi.org/10.1105/tpc.106.180660},
Doi = {10.1105/tpc.106.180660},
Key = {fds229156}
}
@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, M-L 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 Aguadé, 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 = {WILEY},
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},
Abstract = {There is an increasing interest in direct screening of
polymorphisms at candidate loci to associate them with
adaptations in natural situations. We report primers that
amplify regions at 22 putatively orthologous functional loci
in the family Brassicaceae: Arabidopsis thaliana, its two
wild outcrossing relatives, and Brassica oleracea. Four
groups of genes were known to have specific functions in the
model species A. thaliana in ecologically important traits:
timing of reproduction; metabolism of secondary compounds;
defence against pathogens or light perception. In addition,
genes of a fifth group were selected with no consideration
of their function, as reference loci.},
Doi = {10.1046/j.1471-8286.2002.00210.x},
Key = {fds304285}
}
@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.},
Doi = {10.1093/genetics/161.4.1685},
Key = {fds229280}
}
@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{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.},
Doi = {10.1093/genetics/161.3.1269},
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.},
Doi = {10.1093/genetics/161.1.325},
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 = {2793-2793},
Publisher = {JSTOR},
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 = {10.2307/3871535},
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.010416},
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.},
Doi = {10.1093/genetics/159.1.359},
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. 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 = {681-681},
Publisher = {JSTOR},
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 = {10.2307/3871415},
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},
Doi = {10.1016/s1369-5266(00)00079-0},
Key = {fds229145}
}
@article{fds229169,
Author = {Campos de Quiros and H and Magrath, R and McCallum, D and Kroymann, J and Scnabelrauch, D and Mitchell-0lds, T and Mithen,
R},
Title = {alpha-Keto acid elongation and glucosinolate biosynthesis in
Arabidopsis thaliana.},
Journal = {TAG. Theoretical and applied genetics. Theoretische und
angewandte Genetik},
Volume = {101},
Number = {3},
Pages = {429-437},
Publisher = {Springer Nature},
Year = {2000},
Month = {August},
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{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{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{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},
url = {http://dx.doi.org/10.1139/cjfr-29-9-1317},
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/cjfr-29-9-1317},
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{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},
Volume = {53},
Number = {4},
Pages = {1105-1113},
Year = {1999},
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 = {fds341080}
}
@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.},
Doi = {10.1093/genetics/149.2.739},
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/10.2307/176959},
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 = {10.2307/176959},
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{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{fds229250,
Author = {Mitchell-Olds, T},
Title = {Genetic constraints on life-history evolution:
Quantitative-trait loci influencing growth and flowering in
Arabidopsis thaliana},
Journal = {Evolution},
Volume = {50},
Number = {1},
Pages = {140-145},
Publisher = {JSTOR},
Year = {1996},
url = {http://dx.doi.org/10.2307/2410788},
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 = {10.2307/2410788},
Key = {fds229250}
}
@article{fds229251,
Author = {Mitchell-Olds, T},
Title = {Pleiotropy causes long-term genetic constraints on
life-history evolution in Brassica rapa},
Journal = {Evolution},
Volume = {50},
Number = {5},
Pages = {1849-1858},
Publisher = {JSTOR},
Year = {1996},
url = {http://dx.doi.org/10.2307/2410742},
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 = {10.2307/2410742},
Key = {fds229251}
}
@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},
Volume = {50},
Number = {5},
Pages = {1859-1865},
Year = {1996},
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 = {fds341081}
}
@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{fds353937,
Author = {Shaw, RG and Mitchell-Olds, T},
Title = {Erratum: ANOVA for Unbalanced Data: An Overview},
Journal = {Ecology},
Volume = {76},
Number = {6},
Pages = {2000-2000},
Publisher = {Wiley},
Year = {1995},
Month = {September},
url = {http://dx.doi.org/10.2307/1940735},
Doi = {10.2307/1940735},
Key = {fds353937}
}
@article{fds229247,
Author = {Mitchell-Olds, T},
Title = {The molecular basis of quantitative genetic variation in
natural populations.},
Journal = {Trends in ecology & 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.},
Doi = {10.1093/genetics/140.3.1105},
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},
url = {http://dx.doi.org/10.1093/genetics/138.4.1293},
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.},
Doi = {10.1093/genetics/138.4.1293},
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/10.2307/2410489},
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 = {10.2307/2410489},
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 & 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},
Number = {1},
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},
Number = {1},
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},
ISBN = {0-931146-19-4},
Key = {fds229123}
}
@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.},
Doi = {10.1093/genetics/124.2.407},
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{fds229237,
Author = {Mitchell Olds and T and Shaw, RG},
Title = {Comments on the causes of natural selection},
Journal = {Evolution},
Volume = {44},
Number = {8},
Pages = {2158},
Publisher = {Oxford University Press (OUP)},
Year = {1990},
url = {http://dx.doi.org/10.2307/2409625},
Doi = {10.2307/2409625},
Key = {fds229237}
}
@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},
Publisher = {Oxford University Press (OUP)},
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{fds376355,
Author = {Mitchell-Olds, T and Shaw, RG},
Title = {Regression Analysis of Natural Selection: Statistical
Inference and Biological Interpretation},
Journal = {Evolution},
Volume = {41},
Number = {6},
Pages = {1149-1149},
Publisher = {Oxford University Press (OUP)},
Year = {1987},
Month = {November},
url = {http://dx.doi.org/10.2307/2409084},
Doi = {10.2307/2409084},
Key = {fds376355}
}
@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},
Number = {5},
Pages = {1548-1551},
Publisher = {WILEY},
Year = {1987},
url = {http://dx.doi.org/10.2307/1939238},
Doi = {10.2307/1939238},
Key = {fds229232}
}
@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},
Number = {6},
Pages = {942-946},
Publisher = {Canadian Science Publishing},
Year = {1986},
url = {http://dx.doi.org/10.1139/g86-131},
Abstract = {<jats:p> Lethal genetic load might be caused by a few lethal
genes or by large numbers of mildly deleterious polygenes.
The extent of this lethal load can be quantified as the
number of "lethal equivalents" in each individual. If there
are large numbers of deleterious genes scattered throughout
the genome then we might expect a correlation between the
number of lethal equivalents and the level of heterozygosity
at isozyme marker loci. Using data from 52 isozyme loci, we
estimated this correlation on 68 individuals in four conifer
species (Pinus ponderosa Laws., Pinus contorta Dougl., Picea
glauca (Moench) Voss., and Pseudotsuga menziesii (Mirb.)
Franco). No significant correlation was detected. We
interpret this consistent result in four species as
indicating that lethal equivalents do not represent large
numbers of mildly deleterious polygenes in these forest
trees.Key words: genetic load, lethal equivalent, Pinaceae,
heterozygosity. </jats:p>},
Doi = {10.1139/g86-131},
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},
Number = {4},
Pages = {1316-1318},
Publisher = {Institute of Mathematical Statistics},
Year = {1986},
url = {http://dx.doi.org/10.1214/aos/1176350151},
Doi = {10.1214/aos/1176350151},
Key = {fds229229}
}
@article{fds229230,
Author = {Mitchell Olds and T},
Title = {Quantitative genetics of survival and growth in Impatiens
capensis},
Journal = {Evolution},
Volume = {40},
Number = {1},
Pages = {107-116},
Publisher = {Oxford University Press (OUP)},
Year = {1986},
url = {http://dx.doi.org/10.2307/2408608},
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 = {10.2307/2408608},
Key = {fds229230}
}
@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},
Number = {3},
Pages = {379-402},
Publisher = {University of Chicago Press},
Year = {1986},
url = {http://dx.doi.org/10.1086/284490},
Doi = {10.1086/284490},
Key = {fds229231}
}
@article{fds229227,
Author = {MITCHELL-OLDS, T},
Title = {Relative performance of selfed and outcrossed progeny in
Impatiens capensis.},
Journal = {Evolution},
Volume = {39},
Number = {3},
Pages = {533-544},
Publisher = {JSTOR},
Year = {1985},
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}
}