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Duke University

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Publications of Gregory A. Wray    :chronological  alphabetical  combined listing:

%% Books   
@book{fds29611,
   Author = {Ettensohn, C.A. and G. M. Wessell and G. A. Wray},
   Title = {Development of Sea Urchins, Ascidians, and Other
             Invertebrate Deuterostomes: Experimental
             Approaches},
   Publisher = {Academic Press, San Diego CA},
   Year = {2004},
   Key = {fds29611}
}


%% Papers Published   
@article{fds346768,
   Author = {Edsall, LE and Berrio, A and Majoros, WH and Swain-Lenz, D and Morrow,
             S and Shibata, Y and Safi, A and Wray, GA and Crawford, GE and Allen,
             AS},
   Title = {Evaluating Chromatin Accessibility Differences Across
             Multiple Primate Species Using a Joint Modeling
             Approach.},
   Journal = {Genome Biology and Evolution},
   Volume = {11},
   Number = {10},
   Pages = {3035-3053},
   Year = {2019},
   Month = {October},
   url = {http://dx.doi.org/10.1093/gbe/evz218},
   Abstract = {Changes in transcriptional regulation are thought to be a
             major contributor to the evolution of phenotypic traits, but
             the contribution of changes in chromatin accessibility to
             the evolution of gene expression remains almost entirely
             unknown. To address this important gap in knowledge, we
             developed a new method to identify DNase I Hypersensitive
             (DHS) sites with differential chromatin accessibility
             between species using a joint modeling approach. Our method
             overcomes several limitations inherent to conventional
             threshold-based pairwise comparisons that become
             increasingly apparent as the number of species analyzed
             rises. Our approach employs a single quantitative test which
             is more sensitive than existing pairwise methods. To
             illustrate, we applied our joint approach to DHS sites in
             fibroblast cells from five primates (human, chimpanzee,
             gorilla, orangutan, and rhesus macaque). We identified
             89,744 DHS sites, of which 41% are identified as
             differential between species using the joint model compared
             with 33% using the conventional pairwise approach. The joint
             model provides a principled approach to distinguishing
             single from multiple chromatin accessibility changes among
             species. We found that nondifferential DHS sites are
             enriched for nucleotide conservation. Differential DHS sites
             with decreased chromatin accessibility relative to rhesus
             macaque occur more commonly near transcription start sites
             (TSS), while those with increased chromatin accessibility
             occur more commonly distal to TSS. Further, differential DHS
             sites near TSS are less cell type-specific than more distal
             regulatory elements. Taken together, these results point to
             distinct classes of DHS sites, each with distinct
             characteristics of selection, genomic location, and cell
             type specificity.},
   Doi = {10.1093/gbe/evz218},
   Key = {fds346768}
}

@article{fds343523,
   Author = {Davidson, PL and Thompson, JW and Foster, MW and Moseley, MA and Byrne,
             M and Wray, GA},
   Title = {A comparative analysis of egg provisioning using mass
             spectrometry during rapid life history evolution in sea
             urchins.},
   Journal = {Evol Dev},
   Volume = {21},
   Number = {4},
   Pages = {188-204},
   Year = {2019},
   Month = {July},
   url = {http://dx.doi.org/10.1111/ede.12289},
   Abstract = {A dramatic life history switch that has evolved numerous
             times in marine invertebrates is the transition from
             planktotrophic (feeding) to lecithotrophic (nonfeeding)
             larval development-an evolutionary tradeoff with many
             important developmental and ecological consequences. To
             attain a more comprehensive understanding of the molecular
             basis for this switch, we performed untargeted lipidomic and
             proteomic liquid chromatography-tandem mass spectrometry on
             eggs and larvae from three sea urchin species: the
             lecithotroph Heliocidaris erythrogramma, the closely related
             planktotroph Heliocidaris tuberculata, and the distantly
             related planktotroph Lytechinus variegatus. We identify
             numerous molecular-level changes possibly associated with
             the evolution of lecithotrophy in H. erythrogramma. We find
             the massive lipid stores of H. erythrogramma eggs are
             largely composed of low-density, diacylglycerol ether lipids
             that, contrary to expectations, appear to support
             postmetamorphic development and survivorship. Rapid
             premetamorphic development in this species may instead be
             powered by upregulated carbohydrate metabolism or
             triacylglycerol metabolism. We also find proteins involved
             in oxidative stress regulation are upregulated in H.
             erythrogramma eggs, and apoB-like lipid transfer proteins
             may be important for echinoid oogenic nutrient provisioning.
             These results demonstrate how mass spectrometry can enrich
             our understanding of life history evolution and organismal
             diversity by identifying specific molecules associated with
             distinct life history strategies and prompt new hypotheses
             about how and why these adaptations evolve.},
   Doi = {10.1111/ede.12289},
   Key = {fds343523}
}

@article{fds346004,
   Author = {Swain-Lenz, D and Berrio, A and Safi, A and Crawford, GE and Wray,
             GA},
   Title = {Comparative Analyses of Chromatin Landscape in White Adipose
             Tissue Suggest Humans May Have Less Beigeing Potential than
             Other Primates.},
   Journal = {Genome Biology and Evolution},
   Volume = {11},
   Number = {7},
   Pages = {1997-2008},
   Year = {2019},
   Month = {July},
   url = {http://dx.doi.org/10.1093/gbe/evz134},
   Abstract = {Humans carry a much larger percentage of body fat than other
             primates. Despite the central role of adipose tissue in
             metabolism, little is known about the evolution of white
             adipose tissue in primates. Phenotypic divergence is often
             caused by genetic divergence in cis-regulatory regions. We
             examined the cis-regulatory landscape of fat during human
             origins by performing comparative analyses of chromatin
             accessibility in human and chimpanzee adipose tissue using
             rhesus macaque as an outgroup. We find that many regions
             that have decreased accessibility in humans are enriched for
             promoter and enhancer sequences, are depleted for signatures
             of negative selection, are located near genes involved with
             lipid metabolism, and contain a short sequence motif
             involved in the beigeing of fat, the process in which
             lipid-storing white adipocytes are transdifferentiated into
             thermogenic beige adipocytes. The collective closing of many
             putative regulatory regions associated with beigeing of fat
             suggests a mechanism that increases body fat in
             humans.},
   Doi = {10.1093/gbe/evz134},
   Key = {fds346004}
}

@article{fds341866,
   Author = {Wray, GA and Haag, ES},
   Title = {Rudolf A. Raff (1941-2019).},
   Journal = {Nature Ecology and Evolution},
   Volume = {3},
   Number = {4},
   Pages = {518-519},
   Year = {2019},
   Month = {April},
   url = {http://dx.doi.org/10.1038/s41559-019-0844-z},
   Doi = {10.1038/s41559-019-0844-z},
   Key = {fds341866}
}

@article{fds340750,
   Author = {Oulhen, N and Foster, S and Wray, G and Wessel, G},
   Title = {Identifying gene expression from single cells to single
             genes.},
   Journal = {Methods in Cell Biology},
   Volume = {151},
   Pages = {127-158},
   Publisher = {Elsevier},
   Year = {2019},
   Month = {January},
   url = {http://dx.doi.org/10.1016/bs.mcb.2018.11.018},
   Abstract = {Gene regulatory networks reveal how transcription factors
             contribute to a dynamic cascade of cellular information
             processing. Recent advances in technologies have enhanced
             the toolkit for testing GRN mechanisms and connections. Here
             we emphasize three approaches that we have found important
             for interrogating transcriptional mechanisms in echinoderms:
             single cell mRNA sequencing (drop-seq), nascent RNA
             detection and identification, and chromatin
             immunoprecipitation (ChIP). We present these applications in
             order since it is a logical experimental protocol. With
             preliminary information from bulk mRNA transcriptome
             analysis and differential gene expression studies (DE-seq),
             one may need to test in what specific cells important genes
             may be expressed and to use single cell sequencing to define
             such links. Nascent RNA analysis with the Click-iT chemistry
             allows the investigator to deduce when the RNA was
             transcribed, not just identify its presence, and ChIP allows
             the investigator to study direct interactions of putative
             transcriptional regulators with the gene promoter of
             interest. This flow of thinking, and the technologies to
             support it, is presented here for echinoderms. While many of
             the procedures are general and applicable to many organisms
             and cell types, we emphasize unique aspects of the protocols
             for consideration in using echinoderm embryos, larvae, and
             adult tissues.},
   Doi = {10.1016/bs.mcb.2018.11.018},
   Key = {fds340750}
}

@article{fds346769,
   Author = {Li, M and Santpere, G and Imamura Kawasawa and Y and Evgrafov, OV and Gulden, FO and Pochareddy, S and Sunkin, SM and Li, Z and Shin, Y and Zhu,
             Y and Sousa, AMM and Werling, DM and Kitchen, RR and Kang, HJ and Pletikos,
             M and Choi, J and Muchnik, S and Xu, X and Wang, D and Lorente-Galdos, B and Liu, S and Giusti-Rodríguez, P and Won, H and de Leeuw, CA and Pardiñas, AF and BrainSpan Consortium, and PsychENCODE
             Consortium, and PsychENCODE Developmental Subgroup, and Hu, M and Jin, F and Li, Y and Owen, MJ and O'Donovan, MC and Walters, JTR and Posthuma, D and Reimers, MA and Levitt, P and Weinberger, DR and Hyde,
             TM and Kleinman, JE and Geschwind, DH and Hawrylycz, MJ and State, MW and Sanders, SJ and Sullivan, PF and Gerstein, MB and Lein, ES and Knowles,
             JA and Sestan, N},
   Title = {Integrative functional genomic analysis of human brain
             development and neuropsychiatric risks.},
   Journal = {Science (New York, N.Y.)},
   Volume = {362},
   Number = {6420},
   Year = {2018},
   Month = {December},
   url = {http://dx.doi.org/10.1126/science.aat7615},
   Abstract = {To broaden our understanding of human neurodevelopment, we
             profiled transcriptomic and epigenomic landscapes across
             brain regions and/or cell types for the entire span of
             prenatal and postnatal development. Integrative analysis
             revealed temporal, regional, sex, and cell type-specific
             dynamics. We observed a global transcriptomic cup-shaped
             pattern, characterized by a late fetal transition associated
             with sharply decreased regional differences and changes in
             cellular composition and maturation, followed by a reversal
             in childhood-adolescence, and accompanied by epigenomic
             reorganizations. Analysis of gene coexpression modules
             revealed relationships with epigenomic regulation and
             neurodevelopmental processes. Genes with genetic
             associations to brain-based traits and neuropsychiatric
             disorders (including MEF2C, SATB2, SOX5, TCF4, and TSHZ3)
             converged in a small number of modules and distinct cell
             types, revealing insights into neurodevelopment and the
             genomic basis of neuropsychiatric risks.},
   Doi = {10.1126/science.aat7615},
   Key = {fds346769}
}

@article{fds339391,
   Author = {Eisthen, HL and Halanych, KM and Kelley, DB and White, SA and Phelps,
             SM and 66 additional authors},
   Title = {New NSF policy will stifle innovation.},
   Journal = {Science (New York, N.Y.)},
   Volume = {362},
   Number = {6412},
   Pages = {297-298},
   Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
   Year = {2018},
   Month = {October},
   url = {http://dx.doi.org/10.1126/science.aav4793},
   Doi = {10.1126/science.aav4793},
   Key = {fds339391}
}

@article{fds337324,
   Author = {Bryois, J and Garrett, ME and Song, L and Safi, A and Giusti-Rodriguez,
             P and Johnson, GD and Shieh, AW and Buil, A and Fullard, JF and Roussos, P and Sklar, P and Akbarian, S and Haroutunian, V and Stockmeier, CA and Wray,
             GA and White, KP and Liu, C and Reddy, TE and Ashley-Koch, A and Sullivan,
             PF and Crawford, GE},
   Title = {Evaluation of chromatin accessibility in prefrontal cortex
             of individuals with schizophrenia.},
   Journal = {Nature Communications},
   Volume = {9},
   Number = {1},
   Pages = {3121},
   Year = {2018},
   Month = {August},
   url = {http://dx.doi.org/10.1038/s41467-018-05379-y},
   Abstract = {Schizophrenia genome-wide association studies have
             identified >150 regions of the genome associated with
             disease risk, yet there is little evidence that coding
             mutations contribute to this disorder. To explore the
             mechanism of non-coding regulatory elements in
             schizophrenia, we performed ATAC-seq on adult prefrontal
             cortex brain samples from 135 individuals with schizophrenia
             and 137 controls, and identified 118,152 ATAC-seq peaks.
             These accessible chromatin regions in the brain are highly
             enriched for schizophrenia SNP heritability. Accessible
             chromatin regions that overlap evolutionarily conserved
             regions exhibit an even higher heritability enrichment,
             indicating that sequence conservation can further refine
             functional risk variants. We identify few differences in
             chromatin accessibility between cases and controls, in
             contrast to thousands of age-related differential accessible
             chromatin regions. Altogether, we characterize chromatin
             accessibility in the human prefrontal cortex, the effect of
             schizophrenia and age on chromatin accessibility, and
             provide evidence that our dataset will allow for fine
             mapping of risk variants.},
   Doi = {10.1038/s41467-018-05379-y},
   Key = {fds337324}
}

@article{fds335282,
   Author = {Pizzollo, J and Nielsen, WJ and Shibata, Y and Safi, A and Crawford, GE and Wray, GA and Babbitt, CC},
   Title = {Comparative Serum Challenges Show Divergent Patterns of Gene
             Expression and Open Chromatin in Human and
             Chimpanzee.},
   Journal = {Genome Biology and Evolution},
   Volume = {10},
   Number = {3},
   Pages = {826-839},
   Year = {2018},
   Month = {March},
   url = {http://dx.doi.org/10.1093/gbe/evy041},
   Abstract = {Humans experience higher rates of age-associated diseases
             than our closest living evolutionary relatives, chimpanzees.
             Environmental factors can explain many of these increases in
             disease risk, but species-specific genetic changes can also
             play a role. Alleles that confer increased disease
             susceptibility later in life can persist in a population in
             the absence of selective pressure if those changes confer
             positive adaptation early in life. One age-associated
             disease that disproportionately affects humans compared with
             chimpanzees is epithelial cancer. Here, we explored genetic
             differences between humans and chimpanzees in a well-defined
             experimental assay that mimics gene expression changes that
             happen during cancer progression: A fibroblast serum
             challenge. We used this assay with fibroblasts isolated from
             humans and chimpanzees to explore species-specific
             differences in gene expression and chromatin state with
             RNA-Seq and DNase-Seq. Our data reveal that human
             fibroblasts increase expression of genes associated with
             wound healing and cancer pathways; in contrast, chimpanzee
             gene expression changes are not concentrated around
             particular functional categories. Chromatin accessibility
             dramatically increases in human fibroblasts, yet decreases
             in chimpanzee cells during the serum response. Many regions
             of opening and closing chromatin are in close proximity to
             genes encoding transcription factors or genes involved in
             wound healing processes, further supporting the link between
             changes in activity of regulatory elements and changes in
             gene expression. Together, these expression and open
             chromatin data show that humans and chimpanzees have
             dramatically different responses to the same physiological
             stressor, and how a core physiological process can evolve
             quickly over relatively short evolutionary time
             scales.},
   Doi = {10.1093/gbe/evy041},
   Key = {fds335282}
}

@article{fds330379,
   Author = {Byrne, M and Koop, D and Morris, VB and Chui, J and Wray, GA and Cisternas,
             P},
   Title = {Expression of genes and proteins of the pax-six-eya-dach
             network in the metamorphic sea urchin: Insights into
             development of the enigmatic echinoderm body plan and
             sensory structures.},
   Journal = {Developmental Dynamics : an Official Publication of the
             American Association of Anatomists},
   Volume = {247},
   Number = {1},
   Pages = {239-249},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1002/dvdy.24584},
   Abstract = {Photoreception-associated genes of the Pax-Six-Eya-Dach
             network (PSEDN) are deployed for many roles in addition to
             photoreception development. In this first study of PSEDN
             genes during development of the pentameral body in sea
             urchins, we investigated their spatial expression in
             Heliocidaris erythrogramma.Expression of PSEDN genes in the
             hydrocoele of early (Dach, Eya, Six1/2) and/or late (Pax6,
             Six3/6) larvae, and the five hydrocoele lobes, the first
             morphological expression of pentamery, supports a role in
             body plan development. Pax6, Six1/2, and Six3/6 were
             localized to the primary and/or secondary podia and putative
             sensory/neuronal cells. Six1/2 and Six3/6 were expressed in
             the neuropil region in the terminal disc of the podia. Dach
             was localized to spines. Sequential up-regulation of gene
             expression as new podia and spines formed was evident.
             Rhabdomeric opsin and pax6 protein were localized to cells
             in the primary podia and spines.Our results support roles
             for PSEDN genes in development of the pentameral body plan,
             contributing to our understanding of how the most unusual
             body plan in the Bilateria may have evolved. Development of
             sensory cells within the Pax-Six expression field is
             consistent with the role of these genes in sensory cell
             development in diverse species. Developmental Dynamics
             247:239-249, 2018. © 2017 Wiley Periodicals,
             Inc.},
   Doi = {10.1002/dvdy.24584},
   Key = {fds330379}
}

@article{fds339223,
   Author = {Singh, A and Pinto, L and Martin, C and Rutherford, N and Ragunathan, A and Upadhyay, U and Kapoor, P and McRae, M and Siddiqui, A and Cantelmi, D and Heyland, A and Wray, G and Stone, JR},
   Title = {Rudiment resorption as a response to starvation during
             larval development in the sea urchin Strongylocentrotus
             droebachiensis},
   Journal = {Canadian Journal of Zoology},
   Volume = {96},
   Number = {10},
   Pages = {1178-1185},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1139/cjz-2017-0261},
   Abstract = {© 2018, Canadian Science Publishing. All rights reserved.
             Phenotypic flexibility (reversible phenotypic change)
             enables organisms to couple internal, ontogenetic responses
             with external, environmental cues. Phenotypic flexibility
             also provides organisms with the capacity to buffer
             stereotypical internal, developmental processes from
             unpredictable external, ecological events. Echinoids exhibit
             dramatic phenotypic flexibility in response to variation in
             exogenous nutrient supplies. The extent to which echinoids
             display this flexibility has been explored incompletely and
             research hitherto has been conducted predominantly on larval
             structures and morphologies. We investigated experimentally
             the extent to which the primordial juvenile, the developing
             rudiment, can exhibit the first phase in phenotypic
             flexibility among individuals. We report for the first time
             on rudiment regression and complete resorption as a response
             to starvation during larval development in the sea urchin
             Strongylocentrotus droebachiensis (O.F. Müller, 1776) and
             identify a developmental “window of opportunity” within
             which this can occur. Based on our observations and previous
             suggestions, we speculate that sea urchin rudiments might
             provide means of buffering development during unfavorable
             conditions.},
   Doi = {10.1139/cjz-2017-0261},
   Key = {fds339223}
}

@article{fds328432,
   Author = {Linchangco, GV and Foltz, DW and Reid, R and Williams, J and Nodzak, C and Kerr, AM and Miller, AK and Hunter, R and Wilson, NG and Nielsen, WJ and Mah, CL and Rouse, GW and Wray, GA and Janies, DA},
   Title = {The phylogeny of extant starfish (Asteroidea: Echinodermata)
             including Xyloplax, based on comparative
             transcriptomics.},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {115},
   Pages = {161-170},
   Year = {2017},
   Month = {October},
   url = {http://dx.doi.org/10.1016/j.ympev.2017.07.022},
   Abstract = {Multi-locus phylogenetic studies of echinoderms based on
             Sanger and RNA-seq technologies and the fossil record have
             provided evidence for the Asterozoa-Echinozoa hypothesis.
             This hypothesis posits a sister relationship between
             asterozoan classes (Asteroidea and Ophiuroidea) and a
             similar relationship between echinozoan classes (Echinoidea
             and Holothuroidea). Despite this consensus around
             Asterozoa-Echinozoa, phylogenetic relationships within the
             class Asteroidea (sea stars or starfish) have been
             controversial for over a century. Open questions include
             relationships within asteroids and the status of the
             enigmatic taxon Xyloplax. Xyloplax is thought by some to
             represent a newly discovered sixth class of echinoderms -
             and by others to be an asteroid. To address these questions,
             we applied a novel workflow to a large RNA-seq dataset that
             encompassed a broad taxonomic and genomic sample. This study
             included 15 species sampled from all extant orders and 13
             families, plus four ophiuroid species as an outgroup. To
             expand the taxonomic coverage, the study also incorporated
             five previously published transcriptomes and one previously
             published expressed sequence tags (EST) dataset. We
             developed and applied methods that used a range of alignment
             parameters with increasing permissiveness in terms of gap
             characters present within an alignment. This procedure
             facilitated the selection of phylogenomic data subsets from
             large amounts of transcriptome data. The results included 19
             nested data subsets that ranged from 37 to 4,281loci. Tree
             searches on all data subsets reconstructed Xyloplax as a
             velatid asteroid rather than a new class. This result
             implies that asteroid morphology remains labile well beyond
             the establishment of the body plan of the group. In the
             phylogenetic tree with the highest average asteroid nodal
             support several monophyletic groups were recovered. In this
             tree, Forcipulatida and Velatida are monophyletic and form a
             clade that includes Brisingida as sister to Forcipulatida.
             Xyloplax is consistently recovered as sister to Pteraster.
             Paxillosida and Spinulosida are each monophyletic, with
             Notomyotida as sister to the Paxillosida. Valvatida is
             recovered as paraphyletic. The results from other data
             subsets are largely consistent with these results. Our
             results support the hypothesis that the earliest divergence
             event among extant asteroids separated Velatida and
             Forcipulatacea from Valvatacea and Spinulosida.},
   Doi = {10.1016/j.ympev.2017.07.022},
   Key = {fds328432}
}

@article{fds326814,
   Author = {Babbitt, CC and Haygood, R and Nielsen, WJ and Wray,
             GA},
   Title = {Gene expression and adaptive noncoding changes during human
             evolution.},
   Journal = {Bmc Genomics},
   Volume = {18},
   Number = {1},
   Pages = {435},
   Year = {2017},
   Month = {June},
   url = {http://dx.doi.org/10.1186/s12864-017-3831-2},
   Abstract = {Despite evidence for adaptive changes in both gene
             expression and non-protein-coding, putatively regulatory
             regions of the genome during human evolution, the
             relationship between gene expression and adaptive changes in
             cis-regulatory regions remains unclear.Here we present new
             measurements of gene expression in five tissues of humans
             and chimpanzees, and use them to assess this relationship.
             We then compare our results with previous studies of
             adaptive noncoding changes, analyzing correlations at the
             level of gene ontology groups, in order to gain statistical
             power to detect correlations.Consistent with previous
             studies, we find little correlation between gene expression
             and adaptive noncoding changes at the level of individual
             genes; however, we do find significant correlations at the
             level of biological function ontology groups. The types of
             function include processes regulated by specific
             transcription factors, responses to genetic or chemical
             perturbations, and differentiation of cell types within the
             immune system. Among functional categories co-enriched with
             both differential expression and noncoding adaptation,
             prominent themes include cancer, particularly epithelial
             cancers, and neural development and function.},
   Doi = {10.1186/s12864-017-3831-2},
   Key = {fds326814}
}

@article{fds324886,
   Author = {Koop, D and Cisternas, P and Morris, VB and Strbenac, D and Yang, JYH and Wray, GA and Byrne, M},
   Title = {Nodal and BMP expression during the transition to pentamery
             in the sea urchin Heliocidaris erythrogramma: insights into
             patterning the enigmatic echinoderm body
             plan.},
   Journal = {Bmc Developmental Biology},
   Volume = {17},
   Number = {1},
   Pages = {4},
   Year = {2017},
   Month = {February},
   url = {http://dx.doi.org/10.1186/s12861-017-0145-1},
   Abstract = {BACKGROUND:The molecular mechanisms underlying the
             development of the unusual echinoderm pentameral body plan
             and their likeness to mechanisms underlying the development
             of the bilateral plans of other deuterostomes are of
             interest in tracing body plan evolution. In this first study
             of the spatial expression of genes associated with Nodal and
             BMP2/4 signalling during the transition to pentamery in sea
             urchins, we investigate Heliocidaris erythrogramma, a
             species that provides access to the developing adult
             rudiment within days of fertilization. RESULTS:BMP2/4, and
             the putative downstream genes, Six1/2, Eya, Tbx2/3 and Msx
             were expressed in the earliest morphological manifestation
             of pentamery during development, the five hydrocoele lobes.
             The formation of the vestibular ectoderm, the specialized
             region overlying the left coelom that forms adult ectoderm,
             involved the expression of putative Nodal target genes
             Chordin, Gsc and BMP2/4 and putative BMP2/4 target genes
             Dlx, Msx and Tbx. The expression of Nodal, Lefty and Pitx2
             in the right ectoderm, and Pitx2 in the right coelom, was as
             previously observed in other sea urchins. CONCLUSION:That
             genes associated with Nodal and BMP2/4 signalling are
             expressed in the hydrocoele lobes, indicates that they have
             a role in the developmental transition to pentamery,
             contributing to our understanding of how the most unusual
             body plan in the Bilateria may have evolved. We suggest that
             the Nodal and BMP2/4 signalling cascades might have been
             duplicated or split during the evolution to
             pentamery.},
   Doi = {10.1186/s12861-017-0145-1},
   Key = {fds324886}
}

@article{fds324077,
   Author = {Runcie, DE and Dorey, N and Garfield, DA and Stumpp, M and Dupont, S and Wray, GA},
   Title = {Genomic Characterization of the Evolutionary Potential of
             the Sea Urchin Strongylocentrotus droebachiensis Facing
             Ocean Acidification.},
   Journal = {Genome Biology and Evolution},
   Volume = {8},
   Number = {12},
   Pages = {3672-3684},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1093/gbe/evw272},
   Abstract = {Ocean acidification (OA) is increasing due to anthropogenic
             CO2 emissions and poses a threat to marine species and
             communities worldwide. To better project the effects of
             acidification on organisms' health and persistence, an
             understanding is needed of the 1) mechanisms underlying
             developmental and physiological tolerance and 2) potential
             populations have for rapid evolutionary adaptation. This is
             especially challenging in nonmodel species where targeted
             assays of metabolism and stress physiology may not be
             available or economical for large-scale assessments of
             genetic constraints. We used mRNA sequencing and a
             quantitative genetics breeding design to study mechanisms
             underlying genetic variability and tolerance to decreased
             seawater pH (-0.4 pH units) in larvae of the sea urchin
             Strongylocentrotus droebachiensis. We used a gene
             ontology-based approach to integrate expression profiles
             into indirect measures of cellular and biochemical traits
             underlying variation in larval performance (i.e., growth
             rates). Molecular responses to OA were complex, involving
             changes to several functions such as growth rates, cell
             division, metabolism, and immune activities. Surprisingly,
             the magnitude of pH effects on molecular traits tended to be
             small relative to variation attributable to segregating
             functional genetic variation in this species. We discuss how
             the application of transcriptomics and quantitative genetics
             approaches across diverse species can enrich our
             understanding of the biological impacts of climate
             change.},
   Doi = {10.1093/gbe/evw272},
   Key = {fds324077}
}

@article{fds322168,
   Author = {Israel, JW and Martik, ML and Byrne, M and Raff, EC and Raff, RA and McClay, DR and Wray, GA},
   Title = {Comparative Developmental Transcriptomics Reveals Rewiring
             of a Highly Conserved Gene Regulatory Network during a Major
             Life History Switch in the Sea Urchin Genus
             Heliocidaris.},
   Journal = {Plos Biology},
   Volume = {14},
   Number = {3},
   Pages = {e1002391},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1371/journal.pbio.1002391},
   Abstract = {The ecologically significant shift in developmental strategy
             from planktotrophic (feeding) to lecithotrophic (nonfeeding)
             development in the sea urchin genus Heliocidaris is one of
             the most comprehensively studied life history transitions in
             any animal. Although the evolution of lecithotrophy involved
             substantial changes to larval development and morphology, it
             is not known to what extent changes in gene expression
             underlie the developmental differences between species, nor
             do we understand how these changes evolved within the
             context of the well-defined gene regulatory network (GRN)
             underlying sea urchin development. To address these
             questions, we used RNA-seq to measure expression dynamics
             across development in three species: the lecithotroph
             Heliocidaris erythrogramma, the closely related planktotroph
             H. tuberculata, and an outgroup planktotroph Lytechinus
             variegatus. Using well-established statistical methods, we
             developed a novel framework for identifying, quantifying,
             and polarizing evolutionary changes in gene expression
             profiles across the transcriptome and within the GRN. We
             found that major changes in gene expression profiles were
             more numerous during the evolution of lecithotrophy than
             during the persistence of planktotrophy, and that genes with
             derived expression profiles in the lecithotroph displayed
             specific characteristics as a group that are consistent with
             the dramatically altered developmental program in this
             species. Compared to the transcriptome, changes in gene
             expression profiles within the GRN were even more pronounced
             in the lecithotroph. We found evidence for conservation and
             likely divergence of particular GRN regulatory interactions
             in the lecithotroph, as well as significant changes in the
             expression of genes with known roles in larval
             skeletogenesis. We further use coexpression analysis to
             identify genes of unknown function that may contribute to
             both conserved and derived developmental traits between
             species. Collectively, our results indicate that distinct
             evolutionary processes operate on gene expression during
             periods of life history conservation and periods of life
             history divergence, and that this contrast is even more
             pronounced within the GRN than across the transcriptome as a
             whole.},
   Doi = {10.1371/journal.pbio.1002391},
   Key = {fds322168}
}

@article{fds342449,
   Author = {Schierwater, B and Holland, PWH and Miller, DJ and Stadler, PF and Wiegmann, BM and Wörheide, G and Wray, GA and DeSalle,
             R},
   Title = {Never ending analysis of a century old evolutionary debate:
             "Unringing" the urmetazoon bell},
   Journal = {Frontiers in Ecology and Evolution},
   Volume = {4},
   Number = {FEB},
   Year = {2016},
   Month = {February},
   url = {http://dx.doi.org/10.3389/fevo.2016.00005},
   Abstract = {© 2016 Schierwater, Holland, Miller, Stadler, Wiegmann,
             Wörheide, Wray and DeSalle. Our understanding of the early
             evolution of animals will be greatly improved if a final
             solution can be found to the evolutionary relationships
             between Porifera, Placozoa, Ctenophora, Cnidaria, and
             Bilateria. There have been many recent attempts to solve
             this key issue at the base of the metazoan tree of life, and
             these have sparked heated discussions and highlighted
             fundamental analytical problems. We argue that solving this
             problem will necessitate analysis of disparate data types,
             including phylogenomic data, larger scale genomic
             characters, developmental data, and morphological
             characters. At the least, morphological and developmental
             data must be used to cross-validate phylogenomic
             conclusions, but ideally solutions should be sought to the
             problems of combining disparate data sources with
             appropriate character weighting and algorithm
             choice.},
   Doi = {10.3389/fevo.2016.00005},
   Key = {fds342449}
}

@article{fds324078,
   Author = {Janies, DA and Witter, Z and Linchangco, GV and Foltz, DW and Miller,
             AK and Kerr, AM and Jay, J and Reid, RW and Wray, GA},
   Title = {EchinoDB, an application for comparative transcriptomics of
             deeply-sampled clades of echinoderms.},
   Journal = {Bmc Bioinformatics},
   Volume = {17},
   Pages = {48},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1186/s12859-016-0883-2},
   Abstract = {One of our goals for the echinoderm tree of life project
             (http://echinotol.org) is to identify orthologs suitable for
             phylogenetic analysis from next-generation transcriptome
             data. The current dataset is the largest assembled for
             echinoderm phylogeny and transcriptomics. We used RNA-Seq to
             profile adult tissues from 42 echinoderm specimens from 24
             orders and 37 families. In order to achieve sampling members
             of clades that span key evolutionary divergence, many of our
             exemplars were collected from deep and polar seas.A small
             fraction of the transcriptome data we produced is being used
             for phylogenetic reconstruction. Thus to make a larger
             dataset available to researchers with a wide variety of
             interests, we made a web-based application, EchinoDB
             (http://echinodb.uncc.edu). EchinoDB is a repository of
             orthologous transcripts from echinoderms that is searchable
             via keywords and sequence similarity.From transcripts we
             identified 749,397 clusters of orthologous loci. We have
             developed the information technology to manage and search
             the loci their annotations with respect to the Sea Urchin
             (Strongylocentrotus purpuratus) genome. Several users have
             already taken advantage of these data for spin-off projects
             in developmental biology, gene family studies, and
             neuroscience. We hope others will search EchinoDB to
             discover datasets relevant to a variety of additional
             questions in comparative biology.},
   Doi = {10.1186/s12859-016-0883-2},
   Key = {fds324078}
}

@article{fds323818,
   Author = {Dutta, V and Altermann, E and Olson, J and Wray, GA and Siletzky, RM and Kathariou, S},
   Title = {Whole-Genome Sequences of Agricultural, Host-Associated
             Campylobacter coli and Campylobacter jejuni
             Strains.},
   Journal = {Genome Announcements},
   Volume = {4},
   Number = {4},
   Year = {2016},
   Month = {January},
   url = {http://dx.doi.org/10.1128/genomeA.00833-16},
   Abstract = {We report here the genome sequences of four agricultural,
             multidrug-resistant Campylobacter spp.: C. coli 11601 and
             C. jejuni 11601MD, isolated from turkey cecum and jejunum,
             respectively, and C. coli 6067 and C. coli 6461, isolated
             from turkey-house water and swine feces, respectively. The
             genomes provide insights on Campylobacter antimicrobial
             resistance and host adaptations.},
   Doi = {10.1128/genomeA.00833-16},
   Key = {fds323818}
}

@article{fds231458,
   Author = {Byrne, M and Koop, D and Cisternas, P and Strbenac, D and Yang, JYH and Wray, GA},
   Title = {Transcriptomic analysis of Nodal- and BMP-associated genes
             during juvenile development of the sea urchin Heliocidaris
             erythrogramma.},
   Journal = {Marine Genomics},
   Volume = {24 Pt 1},
   Pages = {41-45},
   Year = {2015},
   Month = {December},
   ISSN = {1874-7787},
   url = {http://dx.doi.org/10.1016/j.margen.2015.05.019},
   Abstract = {Understanding the unusual radial body plan of echinoderms
             and its relationship to the bilateral plan of other
             deuterostomes remains a challenge. The molecular processes
             of embryonic and early larval development in sea urchins are
             well characterised, but those giving rise to the adult and
             its radial body remain poorly studied. We used the
             developmental transcriptome generated for Heliocidaris
             erythrogramma, a species that forms the juvenile soon after
             gastrulation, to investigate changes in gene expression
             underlying radial body development. As coelomogenesis is key
             to the development of pentamery and juvenile formation on
             the left side of the larva, we focussed on genes associated
             with the nodal and BMP2/4 network that pattern this
             asymmetry. We identified 46 genes associated with this Nodal
             and BMP2/4 signalling network, and determined their
             expression profiles from the gastrula, through to rudiment
             development, metamorphosis and the fully formed juvenile.
             Genes associated with Nodal signalling shared similar
             expression profiles, indicating that they may have a
             regulatory relationship in patterning morphogenesis of the
             juvenile sea urchin. Similarly, many genes associated with
             BMP2/4 signalling had similar expression profiles through
             juvenile development. Further examination of the roles of
             Nodal- and BMP2/4-associated genes is required to determine
             function and whether the gene expression profiles seen in H.
             erythrogramma are due to ongoing activity of gene networks
             established during early development, or to redeployment of
             regulatory cassettes to pattern the adult radial body
             plan.},
   Doi = {10.1016/j.margen.2015.05.019},
   Key = {fds231458}
}

@article{fds323974,
   Author = {PsychENCODE Consortium, and Akbarian, S and Liu, C and Knowles, JA and Vaccarino, FM and Farnham, PJ and Crawford, GE and Jaffe, AE and Pinto,
             D and Dracheva, S and Geschwind, DH and Mill, J and Nairn, AC and Abyzov,
             A and Pochareddy, S and Prabhakar, S and Weissman, S and Sullivan, PF and State, MW and Weng, Z and Peters, MA and White, KP and Gerstein, MB and Amiri, A and Armoskus, C and Ashley-Koch, AE and Bae, T and Beckel-Mitchener, A and Berman, BP and Coetzee, GA and Coppola, G and Francoeur, N and Fromer, M and Gao, R and Grennan, K and Herstein, J and Kavanagh, DH and Ivanov, NA and Jiang, Y and Kitchen, RR and Kozlenkov,
             A and Kundakovic, M and Li, M and Li, Z and Liu, S and Mangravite, LM and Mattei, E and Markenscoff-Papadimitriou, E and Navarro, FCP and North, N and Omberg, L and Panchision, D and Parikshak, N and Poschmann,
             J and Price, AJ and Purcaro, M and Reddy, TE and Roussos, P and Schreiner,
             S and Scuderi, S and Sebra, R and Shibata, M and Shieh, AW and Skarica, M and Sun, W and Swarup, V and Thomas, A and Tsuji, J and van Bakel, H and Wang,
             D and Wang, Y and Wang, K and Werling, DM and Willsey, AJ and Witt, H and Won,
             H and Wong, CCY and Wray, GA and Wu, EY and Xu, X and Yao, L and Senthil, G and Lehner, T and Sklar, P and Sestan, N},
   Title = {The PsychENCODE project.},
   Journal = {Nat Neurosci},
   Volume = {18},
   Number = {12},
   Pages = {1707-1712},
   Year = {2015},
   Month = {December},
   url = {http://dx.doi.org/10.1038/nn.4156},
   Doi = {10.1038/nn.4156},
   Key = {fds323974}
}

@article{fds322331,
   Author = {Wray, GA},
   Title = {Molecular clocks and the early evolution of metazoan nervous
             systems.},
   Journal = {Philosophical Transactions of the Royal Society of London.
             Series B, Biological Sciences},
   Volume = {370},
   Number = {1684},
   Year = {2015},
   Month = {December},
   url = {http://dx.doi.org/10.1098/rstb.2015.0046},
   Abstract = {The timing of early animal evolution remains poorly
             resolved, yet remains critical for understanding nervous
             system evolution. Methods for estimating divergence times
             from sequence data have improved considerably, providing a
             more refined understanding of key divergences. The best
             molecular estimates point to the origin of metazoans and
             bilaterians tens to hundreds of millions of years earlier
             than their first appearances in the fossil record. Both the
             molecular and fossil records are compatible, however, with
             the possibility of tiny, unskeletonized, low energy budget
             animals during the Proterozoic that had planktonic, benthic,
             or meiofaunal lifestyles. Such animals would likely have had
             relatively simple nervous systems equipped primarily to
             detect food, avoid inhospitable environments and locate
             mates. The appearance of the first macropredators during the
             Cambrian would have changed the selective landscape
             dramatically, likely driving the evolution of complex sense
             organs, sophisticated sensory processing systems, and
             diverse effector systems involved in capturing prey and
             avoiding predation.},
   Doi = {10.1098/rstb.2015.0046},
   Key = {fds322331}
}

@article{fds231457,
   Author = {Bauernfeind, AL and Reyzer, ML and Caprioli, RM and Ely, JJ and Babbitt,
             CC and Wray, GA and Hof, PR and Sherwood, CC},
   Title = {High spatial resolution proteomic comparison of the brain in
             humans and chimpanzees.},
   Journal = {The Journal of Comparative Neurology},
   Volume = {523},
   Number = {14},
   Pages = {2043-2061},
   Year = {2015},
   Month = {October},
   ISSN = {0021-9967},
   url = {http://dx.doi.org/10.1002/cne.23777},
   Abstract = {We performed high-throughput mass spectrometry at high
             spatial resolution from individual regions (anterior
             cingulate and primary motor, somatosensory, and visual
             cortices) and layers of the neocortex (layers III, IV, and
             V) and cerebellum (granule cell layer), as well as the
             caudate nucleus in humans and chimpanzees. A total of 39
             mass spectrometry peaks were matched with probable protein
             identifications in both species, allowing for comparison in
             expression. We explored how the pattern of protein
             expression varies across regions and cortical layers to
             provide insights into the differences in molecular phenotype
             of these neural structures between species. The expression
             of proteins differed principally in a region- and
             layer-specific pattern, with more subtle differences between
             species. Specifically, human and chimpanzee brains were
             similar in their distribution of proteins related to the
             regulation of transcription and enzyme activity but differed
             in their expression of proteins supporting aerobic
             metabolism. Whereas most work assessing molecular expression
             differences in the brains of primates has been performed on
             gene transcripts, this dataset extends current understanding
             of the differential molecular expression that may underlie
             human cognitive specializations.},
   Doi = {10.1002/cne.23777},
   Key = {fds231457}
}

@article{fds323975,
   Author = {Bauernfeind, AL and Soderblom, EJ and Turner, ME and Moseley, MA and Ely, JJ and Hof, PR and Sherwood, CC and Wray, GA and Babbitt,
             CC},
   Title = {Evolutionary Divergence of Gene and Protein Expression in
             the Brains of Humans and Chimpanzees.},
   Journal = {Genome Biology and Evolution},
   Volume = {7},
   Number = {8},
   Pages = {2276-2288},
   Year = {2015},
   Month = {July},
   url = {http://dx.doi.org/10.1093/gbe/evv132},
   Abstract = {Although transcriptomic profiling has become the standard
             approach for exploring molecular differences in the primate
             brain, very little is known about how the expression levels
             of gene transcripts relate to downstream protein abundance.
             Moreover, it is unknown whether the relationship changes
             depending on the brain region or species under
             investigation. We performed high-throughput transcriptomic
             (RNA-Seq) and proteomic (liquid chromatography coupled with
             tandem mass spectrometry) analyses on two regions of the
             human and chimpanzee brain: The anterior cingulate cortex
             and caudate nucleus. In both brain regions, we found a lower
             correlation between mRNA and protein expression levels in
             humans and chimpanzees than has been reported for other
             tissues and cell types, suggesting that the brain may engage
             extensive tissue-specific regulation affecting protein
             abundance. In both species, only a few categories of
             biological function exhibited strong correlations between
             mRNA and protein expression levels. These categories
             included oxidative metabolism and protein synthesis and
             modification, indicating that the expression levels of mRNA
             transcripts supporting these biological functions are more
             predictive of protein expression compared with other
             functional categories. More generally, however, the two
             measures of molecular expression provided strikingly
             divergent perspectives into differential expression between
             human and chimpanzee brains: mRNA comparisons revealed
             significant differences in neuronal communication, ion
             transport, and regulatory processes, whereas protein
             comparisons indicated differences in perception and
             cognition, metabolic processes, and organization of the
             cytoskeleton. Our results highlight the importance of
             examining protein expression in evolutionary analyses and
             call for a more thorough understanding of tissue-specific
             protein expression levels.},
   Doi = {10.1093/gbe/evv132},
   Key = {fds323975}
}

@article{fds231459,
   Author = {Muntané, G and Horvath, JE and Hof, PR and Ely, JJ and Hopkins, WD and Raghanti, MA and Lewandowski, AH and Wray, GA and Sherwood,
             CC},
   Title = {Analysis of synaptic gene expression in the neocortex of
             primates reveals evolutionary changes in glutamatergic
             neurotransmission.},
   Journal = {Cerebral Cortex (New York, N.Y. : 1991)},
   Volume = {25},
   Number = {6},
   Pages = {1596-1607},
   Year = {2015},
   Month = {June},
   ISSN = {1047-3211},
   url = {http://dx.doi.org/10.1093/cercor/bht354},
   Abstract = {Increased relative brain size characterizes the evolution of
             primates, suggesting that enhanced cognition plays an
             important part in the behavioral adaptations of this
             mammalian order. In addition to changes in brain anatomy,
             cognition can also be regulated by molecular changes that
             alter synaptic function, but little is known about
             modifications of synapses in primate brain evolution. The
             aim of the current study was to investigate the expression
             patterns and evolution of 20 synaptic genes from the
             prefrontal cortex of 12 primate species. The genes
             investigated included glutamate receptors, scaffolding
             proteins, synaptic vesicle components, as well as factors
             involved in synaptic vesicle release and structural
             components of the nervous system. Our analyses revealed that
             there have been significant changes during primate brain
             evolution in the components of the glutamatergic signaling
             pathway in terms of gene expression, protein expression, and
             promoter sequence changes. These results could entail
             functional modifications in the regulation of specific genes
             related to processes underlying learning and
             memory.},
   Doi = {10.1093/cercor/bht354},
   Key = {fds231459}
}

@article{fds324079,
   Author = {Babbitt, CC and Pfefferle, LW and Crawford, GE and Wray,
             GA},
   Title = {Evolution of gene expression network underlying a disease
             state},
   Journal = {Integrative and Comparative Biology},
   Volume = {55},
   Pages = {E7-E7},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2015},
   Month = {April},
   Key = {fds324079}
}

@article{fds231461,
   Author = {Boyd, JL and Skove, SL and Rouanet, JP and Pilaz, L-J and Bepler, T and Gordân, R and Wray, GA and Silver, DL},
   Title = {Human-chimpanzee differences in a FZD8 enhancer alter
             cell-cycle dynamics in the developing neocortex.},
   Journal = {Curr Biol},
   Volume = {25},
   Number = {6},
   Pages = {772-779},
   Year = {2015},
   Month = {March},
   ISSN = {0960-9822},
   url = {http://hdl.handle.net/10161/9492 Duke open
             access},
   Abstract = {The human neocortex differs from that of other great apes in
             several notable regards, including altered cell cycle,
             prolonged corticogenesis, and increased size [1-5]. Although
             these evolutionary changes most likely contributed to the
             origin of distinctively human cognitive faculties, their
             genetic basis remains almost entirely unknown. Highly
             conserved non-coding regions showing rapid sequence changes
             along the human lineage are candidate loci for the
             development and evolution of uniquely human traits. Several
             studies have identified human-accelerated enhancers [6-14],
             but none have linked an expression difference to a specific
             organismal trait. Here we report the discovery of a
             human-accelerated regulatory enhancer (HARE5) of FZD8, a
             receptor of the Wnt pathway implicated in brain development
             and size [15, 16]. Using transgenic mice, we demonstrate
             dramatic differences in human and chimpanzee HARE5 activity,
             with human HARE5 driving early and robust expression at the
             onset of corticogenesis. Similar to HARE5 activity, FZD8 is
             expressed in neural progenitors of the developing neocortex
             [17-19]. Chromosome conformation capture assays reveal that
             HARE5 physically and specifically contacts the core Fzd8
             promoter in the mouse embryonic neocortex. To assess the
             phenotypic consequences of HARE5 activity, we generated
             transgenic mice in which Fzd8 expression is under control of
             orthologous enhancers (Pt-HARE5::Fzd8 and Hs-HARE5::Fzd8).
             In comparison to Pt-HARE5::Fzd8, Hs-HARE5::Fzd8 mice showed
             marked acceleration of neural progenitor cell cycle and
             increased brain size. Changes in HARE5 function unique to
             humans thus alter the cell-cycle dynamics of a critical
             population of stem cells during corticogenesis and may
             underlie some distinctive anatomical features of the human
             brain.},
   Doi = {10.1016/j.cub.2015.01.041},
   Key = {fds231461}
}

@article{fds324080,
   Author = {Bauernfeind, AL and Reyzer, ML and Caprioli, RM and Ely, JJ and Babbitt,
             CC and Wray, GA and Hof, PR and Sherwood, CC},
   Title = {Differences in energy metabolism in the brains of humans and
             chimpanzees: a study of protein expression},
   Journal = {American Journal of Physical Anthropology},
   Volume = {156},
   Pages = {80-80},
   Publisher = {WILEY-BLACKWELL},
   Year = {2015},
   Month = {March},
   Key = {fds324080}
}

@article{fds324081,
   Author = {Babbitt, CC and Wray, GA},
   Title = {Evolution of gene expression network underlying a disease
             state in humans and non-human primates},
   Journal = {American Journal of Physical Anthropology},
   Volume = {156},
   Pages = {74-74},
   Publisher = {WILEY-BLACKWELL},
   Year = {2015},
   Month = {March},
   Key = {fds324081}
}

@article{fds231460,
   Author = {Laland, K and Uller, T and Feldman, M and Sterelny, K and Müller, GB and Moczek, A and Jablonka, E and Odling-Smee, J and Wray, GA and Hoekstra,
             HE and Futuyma, DJ and Lenski, RE and Mackay, TFC and Schluter, D and Strassmann, JE},
   Title = {Does evolutionary theory need a rethink?},
   Journal = {Nature},
   Volume = {514},
   Number = {7521},
   Pages = {161-164},
   Publisher = {NATURE PUBLISHING GROUP},
   Year = {2014},
   Month = {October},
   ISSN = {0028-0836},
   url = {http://dx.doi.org/10.1038/514161a},
   Doi = {10.1038/514161a},
   Key = {fds231460}
}

@article{fds231463,
   Author = {Horvath, JE and Ramachandran, GL and Fedrigo, O and Nielsen, WJ and Babbitt, CC and St Clair and EM and Pfefferle, LW and Jernvall, J and Wray,
             GA and Wall, CE},
   Title = {Genetic comparisons yield insight into the evolution of
             enamel thickness during human evolution.},
   Journal = {Journal of Human Evolution},
   Volume = {73},
   Pages = {75-87},
   Year = {2014},
   Month = {August},
   ISSN = {0047-2484},
   url = {http://dx.doi.org/10.1016/j.jhevol.2014.01.005},
   Abstract = {Enamel thickness varies substantially among extant hominoids
             and is a key trait with significance for interpreting
             dietary adaptation, life history trajectory, and
             phylogenetic relationships. There is a strong link in humans
             between enamel formation and mutations in the exons of the
             four genes that code for the enamel matrix proteins and the
             associated protease. The evolution of thick enamel in humans
             may have included changes in the regulation of these genes
             during tooth development. The cis-regulatory region in the
             5' flank (upstream non-coding region) of MMP20, which codes
             for enamelysin, the predominant protease active during
             enamel secretion, has previously been shown to be under
             strong positive selection in the lineages leading to both
             humans and chimpanzees. Here we examine evidence for
             positive selection in the 5' flank and 3' flank of AMELX,
             AMBN, ENAM, and MMP20. We contrast the human sequence
             changes with other hominoids (chimpanzees, gorillas,
             orangutans, gibbons) and rhesus macaques (outgroup), a
             sample comprising a range of enamel thickness. We find no
             evidence for positive selection in the protein-coding
             regions of any of these genes. In contrast, we find strong
             evidence for positive selection in the 5' flank region of
             MMP20 and ENAM along the lineage leading to humans, and in
             both the 5' flank and 3' flank regions of MMP20 along the
             lineage leading to chimpanzees. We also identify putative
             transcription factor binding sites overlapping some of the
             species-specific nucleotide sites and we refine which
             sections of the up- and downstream putative regulatory
             regions are most likely to harbor important changes. These
             non-coding changes and their potential for differential
             regulation by transcription factors known to regulate tooth
             development may offer insight into the mechanisms that allow
             for rapid evolutionary changes in enamel thickness across
             closely-related species, and contribute to our understanding
             of the enamel phenotype in hominoids.},
   Doi = {10.1016/j.jhevol.2014.01.005},
   Key = {fds231463}
}

@article{fds231456,
   Author = {Liu, S and Lorenzen, ED and Fumagalli, M and Li, B and Harris, K and Xiong,
             Z and Zhou, L and Korneliussen, TS and Somel, M and Babbitt, C and Wray, G and Li, J and He, W and Wang, Z and Fu, W and Xiang, X and Morgan, CC and Doherty,
             A and O'Connell, MJ and McInerney, JO and Born, EW and Dalén, L and Dietz,
             R and Orlando, L and Sonne, C and Zhang, G and Nielsen, R and Willerslev,
             E and Wang, J},
   Title = {Population genomics reveal recent speciation and rapid
             evolutionary adaptation in polar bears.},
   Journal = {Cell},
   Volume = {157},
   Number = {4},
   Pages = {785-794},
   Year = {2014},
   Month = {May},
   ISSN = {0092-8674},
   url = {http://dx.doi.org/10.1016/j.cell.2014.03.054},
   Abstract = {Polar bears are uniquely adapted to life in the High Arctic
             and have undergone drastic physiological changes in response
             to Arctic climates and a hyper-lipid diet of primarily
             marine mammal prey. We analyzed 89 complete genomes of polar
             bear and brown bear using population genomic modeling and
             show that the species diverged only 479-343 thousand years
             BP. We find that genes on the polar bear lineage have been
             under stronger positive selection than in brown bears; nine
             of the top 16 genes under strong positive selection are
             associated with cardiomyopathy and vascular disease,
             implying important reorganization of the cardiovascular
             system. One of the genes showing the strongest evidence of
             selection, APOB, encodes the primary lipoprotein component
             of low-density lipoprotein (LDL); functional mutations in
             APOB may explain how polar bears are able to cope with
             life-long elevated LDL levels that are associated with high
             risk of heart disease in humans.},
   Doi = {10.1016/j.cell.2014.03.054},
   Key = {fds231456}
}

@article{fds231465,
   Author = {Wygoda, JA and Yang, Y and Byrne, M and Wray, GA},
   Title = {Transcriptomic analysis of the highly derived radial body
             plan of a sea urchin.},
   Journal = {Genome Biology and Evolution},
   Volume = {6},
   Number = {4},
   Pages = {964-973},
   Year = {2014},
   Month = {April},
   url = {http://dx.doi.org/10.1093/gbe/evu070},
   Abstract = {With their complex life cycle and highly derived body plan,
             echinoderms are unique among bilaterians. Although early
             development has been intensively studied, the molecular
             mechanisms underlying development of the adult echinoderm
             and its unusual radial body plan are largely unknown. To
             investigate the evolution of developmental changes in gene
             expression underlying radial body plan development and
             metamorphosis, we assembled a reference transcriptome de
             novo and used RNA-seq to measure gene expression profiles
             across larval, metamorphic, and postmetamorphic life cycle
             phases in the sea urchin Heliocidaris erythrogramma. Our
             results present a high-resolution view of gene expression
             dynamics during the complex transition from pre- to
             postmetamorphic development and suggest that distinct sets
             of regulatory and effector proteins are used during
             different life history phases. These analyses provide an
             important foundation for more detailed analyses of the
             evolution of the radial adult body of echinoderms.},
   Doi = {10.1093/gbe/evu070},
   Key = {fds231465}
}

@article{fds231464,
   Author = {Bauernfeind, AL and Soderblom, EJ and Turner, ME and Moseley, AM and Ely, JJ and Hof, PR and Sherwood, CC and Wray, GA and Babbitt,
             CC},
   Title = {Differential gene and protein expression in the human and
             chimpanzee brain: A comparison using high-throughput
             techniques},
   Journal = {American Journal of Physical Anthropology},
   Volume = {153},
   Pages = {73-73},
   Publisher = {WILEY-BLACKWELL},
   Year = {2014},
   Month = {March},
   ISSN = {0002-9483},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000331225100043&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231464}
}

@article{fds324082,
   Author = {Wygoda, JA and Byrne, M and Mcclay, DR and Wray, GA},
   Title = {Shifts in the Expression of Developmental Regulatory Genes
             Involved in the Evolution of a Novel Life History
             Difference},
   Journal = {Integrative and Comparative Biology},
   Volume = {54},
   Pages = {E230-E230},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2014},
   Month = {January},
   Key = {fds324082}
}

@article{fds324083,
   Author = {Wygoda, JA and Koop, D and Yang, J and Wray, GA and Byrne,
             M},
   Title = {Developmental Transcriptome of Heliociaris erythrogramma -
             from bilateral larva to radial juvenile},
   Journal = {Integrative and Comparative Biology},
   Volume = {54},
   Pages = {E372-E372},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2014},
   Month = {January},
   Key = {fds324083}
}

@article{fds322169,
   Author = {Ganapathy, G and Howard, JT and Ward, JM and Li, J and Li, B and Li, Y and Xiong, Y and Zhang, Y and Zhou, S and Schwartz, DC and Schatz, M and Aboukhalil, R and Fedrigo, O and Bukovnik, L and Wang, T and Wray, G and Rasolonjatovo, I and Winer, R and Knight, JR and Koren, S and Warren,
             WC and Zhang, G and Phillippy, AM and Jarvis, ED},
   Title = {High-coverage sequencing and annotated assemblies of the
             budgerigar genome.},
   Journal = {Gigascience},
   Volume = {3},
   Pages = {11},
   Year = {2014},
   url = {http://dx.doi.org/10.1186/2047-217X-3-11},
   Abstract = {BACKGROUND: Parrots belong to a group of behaviorally
             advanced vertebrates and have an advanced ability of vocal
             learning relative to other vocal-learning birds. They can
             imitate human speech, synchronize their body movements to a
             rhythmic beat, and understand complex concepts of
             referential meaning to sounds. However, little is known
             about the genetics of these traits. Elucidating the genetic
             bases would require whole genome sequencing and a robust
             assembly of a parrot genome. FINDINGS: We present a genomic
             resource for the budgerigar, an Australian Parakeet
             (Melopsittacus undulatus) -- the most widely studied parrot
             species in neuroscience and behavior. We present genomic
             sequence data that includes over 300× raw read coverage
             from multiple sequencing technologies and chromosome optical
             maps from a single male animal. The reads and optical maps
             were used to create three hybrid assemblies representing
             some of the largest genomic scaffolds to date for a bird;
             two of which were annotated based on similarities to
             reference sets of non-redundant human, zebra finch and
             chicken proteins, and budgerigar transcriptome sequence
             assemblies. The sequence reads for this project were in part
             generated and used for both the Assemblathon 2 competition
             and the first de novo assembly of a giga-scale vertebrate
             genome utilizing PacBio single-molecule sequencing.
             CONCLUSIONS: Across several quality metrics, these
             budgerigar assemblies are comparable to or better than the
             chicken and zebra finch genome assemblies built from
             traditional Sanger sequencing reads, and are sufficient to
             analyze regions that are difficult to sequence and assemble,
             including those not yet assembled in prior bird genomes, and
             promoter regions of genes differentially regulated in vocal
             learning brain regions. This work provides valuable data and
             material for genome technology development and for
             investigating the genomics of complex behavioral
             traits.},
   Doi = {10.1186/2047-217X-3-11},
   Key = {fds322169}
}

@article{fds231470,
   Author = {Garfield, DA and Runcie, DE and Babbitt, CC and Haygood, R and Nielsen,
             WJ and Wray, GA},
   Title = {The impact of gene expression variation on the robustness
             and evolvability of a developmental gene regulatory
             network.},
   Journal = {Plos Biology},
   Volume = {11},
   Number = {10},
   Pages = {e1001696},
   Year = {2013},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24204211},
   Abstract = {Regulatory interactions buffer development against genetic
             and environmental perturbations, but adaptation requires
             phenotypes to change. We investigated the relationship
             between robustness and evolvability within the gene
             regulatory network underlying development of the larval
             skeleton in the sea urchin Strongylocentrotus purpuratus. We
             find extensive variation in gene expression in this network
             throughout development in a natural population, some of
             which has a heritable genetic basis. Switch-like regulatory
             interactions predominate during early development, buffer
             expression variation, and may promote the accumulation of
             cryptic genetic variation affecting early stages. Regulatory
             interactions during later development are typically more
             sensitive (linear), allowing variation in expression to
             affect downstream target genes. Variation in skeletal
             morphology is associated primarily with expression variation
             of a few, primarily structural, genes at terminal positions
             within the network. These results indicate that the position
             and properties of gene interactions within a network can
             have important evolutionary consequences independent of
             their immediate regulatory role.},
   Doi = {10.1371/journal.pbio.1001696},
   Key = {fds231470}
}

@article{fds231473,
   Author = {Runcie, DE and Wiedmann, RT and Archie, EA and Altmann, J and Wray, GA and Alberts, SC and Tung, J},
   Title = {Social environment influences the relationship between
             genotype and gene expression in wild baboons.},
   Journal = {Philosophical Transactions of the Royal Society of London.
             Series B, Biological Sciences},
   Volume = {368},
   Number = {1618},
   Pages = {20120345},
   Year = {2013},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23569293},
   Abstract = {Variation in the social environment can have profound
             effects on survival and reproduction in wild social mammals.
             However, we know little about the degree to which these
             effects are influenced by genetic differences among
             individuals, and conversely, the degree to which social
             environmental variation mediates genetic reaction norms. To
             better understand these relationships, we investigated the
             potential for dominance rank, social connectedness and group
             size to modify the effects of genetic variation on gene
             expression in the wild baboons of the Amboseli basin. We
             found evidence for a number of gene-environment interactions
             (GEIs) associated with variation in the social environment,
             encompassing social environments experienced in adulthood as
             well as persistent effects of early life social environment.
             Social connectedness, maternal dominance rank and group size
             all interacted with genotype to influence gene expression in
             at least one sex, and either in early life or in adulthood.
             These results suggest that social and behavioural variation,
             akin to other factors such as age and sex, can impact the
             genotype-phenotype relationship. We conclude that GEIs
             mediated by the social environment are important in the
             evolution and maintenance of individual differences in wild
             social mammals, including individual differences in
             responses to social stressors.},
   Doi = {10.1098/rstb.2012.0345},
   Key = {fds231473}
}

@article{fds231466,
   Author = {Runcie, DE and Garfield, DA and Babbitt, CC and Pfefferle, A and Nielsen, WJ and Wray, GA},
   Title = {Phenotypic plasticity and the developmental regulatory
             network in the purple sea urchin},
   Journal = {Echinoderms in a Changing World},
   Pages = {300-301},
   Publisher = {CRC PRESS-TAYLOR & FRANCIS GROUP},
   Editor = {Johnson, C},
   Year = {2013},
   Month = {January},
   ISBN = {978-1-138-00010-0},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000328334100125&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231466}
}

@article{fds231467,
   Author = {Wray, GA and Garfield, D and Runcie, D},
   Title = {Evolution of an embryonic gene regulatory network in the sea
             urchin Strongylocentrotus purpuratus},
   Journal = {Echinoderms in a Changing World},
   Pages = {276-276},
   Publisher = {CRC PRESS-TAYLOR & FRANCIS GROUP},
   Editor = {Johnson, C},
   Year = {2013},
   Month = {January},
   ISBN = {978-1-138-00010-0},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000328334100087&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231467}
}

@article{fds231468,
   Author = {Wray, GA},
   Title = {Genomics and the evolution of phenotypic
             traits},
   Journal = {Annual Review of Ecology, Evolution, and
             Systematics},
   Volume = {44},
   Number = {1},
   Pages = {51-72},
   Publisher = {ANNUAL REVIEWS},
   Year = {2013},
   Month = {January},
   ISSN = {1543-592X},
   url = {http://dx.doi.org/10.1146/annurev-ecolsys-110512-135828},
   Abstract = {Evolutionary genetics has entered an unprecedented era of
             discovery, catalyzed in large part by the development of
             technologies that provide information about genome sequence
             and function. An important benefit is the ability to move
             beyond a handful of model organisms in lab settings to
             identify the genetic basis for evolutionarily interesting
             traits in many organisms in natural settings. Other benefits
             are the abilities to identify causal mutations and validate
             their phenotypic consequences more readily and in many more
             species. Genomic technologies have reinvigorated interest in
             some of the most fundamental and persistent questions in
             evolutionary genetics, revealed previously unsuspected
             evolutionary phenomena, and opened the door to a wide range
             of new questions. © Copyright ©2013 by Annual Reviews. All
             rights reserved.},
   Doi = {10.1146/annurev-ecolsys-110512-135828},
   Key = {fds231468}
}

@article{fds231471,
   Author = {Pfefferle, LW and Wray, GA},
   Title = {Insights from a chimpanzee adipose stromal cell population:
             opportunities for adult stem cells to expand primate
             functional genomics.},
   Journal = {Genome Biology and Evolution},
   Volume = {5},
   Number = {10},
   Pages = {1995-2005},
   Year = {2013},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24092797},
   Abstract = {Comparisons between humans and chimpanzees are essential for
             understanding traits unique to each species. However,
             linking important phenotypic differences to underlying
             molecular changes is often challenging. The ability to
             generate, differentiate, and profile adult stem cells
             provides a powerful but underutilized opportunity to
             investigate the molecular basis for trait differences
             between species within specific cell types and in a
             controlled environment. Here, we characterize adipose
             stromal cells (ASCs) from Clint, the chimpanzee whose genome
             was first sequenced. Using imaging and RNA-Seq, we compare
             the chimpanzee ASCs with three comparable human cell lines.
             Consistent with previous studies on ASCs in humans, the
             chimpanzee cells have fibroblast-like morphology and express
             genes encoding components of the extracellular matrix at
             high levels. Differentially expressed genes are enriched for
             distinct functional classes between species: immunity and
             protein processing are higher in chimpanzees, whereas cell
             cycle and DNA processing are higher in humans. Although
             hesitant to draw definitive conclusions from these data
             given the limited sample size, we wish to stress the
             opportunities that adult stem cells offer for studying
             primate evolution. In particular, adult stem cells provide a
             powerful means to investigate the profound disease
             susceptibilities unique to humans and a promising tool for
             conservation efforts with nonhuman primates. By allowing for
             experimental perturbations in relevant cell types, adult
             stem cells promise to complement classic comparative primate
             genomics based on in vivo sampling.},
   Doi = {10.1093/gbe/evt148},
   Key = {fds231471}
}

@article{fds219910,
   Author = {L.W. Pfefferle and G.A. Wray},
   Title = {Insights from a chimpanzee adipose stromal cells population:
             opportunities for adult stem cells to expand primate
             functional genomics},
   Journal = {Genome Biology and Evolution},
   Volume = {5},
   Pages = {1995-2005},
   Year = {2013},
   Key = {fds219910}
}

@article{fds231558,
   Author = {Runcie, DE and Garfield, DA and Babbitt, CC and Wygoda, JA and Mukherjee, S and Wray, GA},
   Title = {Genetics of gene expression responses to temperature stress
             in a sea urchin gene network.},
   Journal = {Molecular Ecology},
   Volume = {21},
   Number = {18},
   Pages = {4547-4562},
   Year = {2012},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22856327},
   Abstract = {Stress responses play an important role in shaping species
             distributions and robustness to climate change. We
             investigated how stress responses alter the contribution of
             additive genetic variation to gene expression during
             development of the purple sea urchin, Strongylocentrotus
             purpuratus, under increased temperatures that model
             realistic climate change scenarios. We first measured gene
             expression responses in the embryos by RNA-seq to
             characterize molecular signatures of mild, chronic
             temperature stress in an unbiased manner. We found that an
             increase from 12 to 18 °C caused widespread alterations in
             gene expression including in genes involved in protein
             folding, RNA processing and development. To understand the
             quantitative genetic architecture of this response, we then
             focused on a well-characterized gene network involved in
             endomesoderm and ectoderm specification. Using a breeding
             design with wild-caught individuals, we measured genetic and
             gene-environment interaction effects on 72 genes within this
             network. We found genetic or maternal effects in 33 of these
             genes and that the genetic effects were correlated in the
             network. Fourteen network genes also responded to higher
             temperatures, but we found no significant
             genotype-environment interactions in any of the genes. This
             absence may be owing to an effective buffering of the
             temperature perturbations within the network. In support of
             this hypothesis, perturbations to regulatory genes did not
             affect the expression of the genes that they regulate.
             Together, these results provide novel insights into the
             relationship between environmental change and developmental
             evolution and suggest that climate change may not expose
             large amounts of cryptic genetic variation to selection in
             this species.},
   Doi = {10.1111/j.1365-294X.2012.05717.x},
   Key = {fds231558}
}

@article{fds231557,
   Author = {Shibata, Y and Sheffield, NC and Fedrigo, O and Babbitt, CC and Wortham,
             M and Tewari, AK and London, D and Song, L and Lee, B-K and Iyer, VR and Parker, SCJ and Margulies, EH and Wray, GA and Furey, TS and Crawford,
             GE},
   Title = {Extensive evolutionary changes in regulatory element
             activity during human origins are associated with altered
             gene expression and positive selection.},
   Journal = {Plos Genet},
   Volume = {8},
   Number = {6},
   Pages = {e1002789},
   Year = {2012},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22761590},
   Abstract = {Understanding the molecular basis for phenotypic differences
             between humans and other primates remains an outstanding
             challenge. Mutations in non-coding regulatory DNA that alter
             gene expression have been hypothesized as a key driver of
             these phenotypic differences. This has been supported by
             differential gene expression analyses in general, but not by
             the identification of specific regulatory elements
             responsible for changes in transcription and phenotype. To
             identify the genetic source of regulatory differences, we
             mapped DNaseI hypersensitive (DHS) sites, which mark all
             types of active gene regulatory elements, genome-wide in the
             same cell type isolated from human, chimpanzee, and macaque.
             Most DHS sites were conserved among all three species, as
             expected based on their central role in regulating
             transcription. However, we found evidence that several
             hundred DHS sites were gained or lost on the lineages
             leading to modern human and chimpanzee. Species-specific DHS
             site gains are enriched near differentially expressed genes,
             are positively correlated with increased transcription, show
             evidence of branch-specific positive selection, and overlap
             with active chromatin marks. Species-specific sequence
             differences in transcription factor motifs found within
             these DHS sites are linked with species-specific changes in
             chromatin accessibility. Together, these indicate that the
             regulatory elements identified here are genetic contributors
             to transcriptional and phenotypic differences among primate
             species.},
   Doi = {10.1371/journal.pgen.1002789},
   Key = {fds231557}
}

@article{fds231483,
   Author = {Babbitt, CC and Pfefferle, LW and Fedrigo, O and Wray,
             GA},
   Title = {Conservation and function of noncoding RNAs in primate
             evolution},
   Journal = {Integrative and Comparative Biology},
   Volume = {52},
   Pages = {E8-E8},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2012},
   Month = {April},
   ISSN = {1540-7063},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000303165000031&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231483}
}

@article{fds231556,
   Author = {Garfield, D and Haygood, R and Nielsen, WJ and Wray,
             GA},
   Title = {Population genetics of cis-regulatory sequences that operate
             during embryonic development in the sea urchin
             Strongylocentrotus purpuratus.},
   Journal = {Evolution & Development},
   Volume = {14},
   Number = {2},
   Pages = {152-167},
   Year = {2012},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23017024},
   Abstract = {Despite the fact that noncoding sequences comprise a
             substantial fraction of functional sites within all genomes,
             the evolutionary mechanisms that operate on genetic
             variation within regulatory elements remain poorly
             understood. In this study, we examine the population
             genetics of the core, upstream cis-regulatory regions of
             eight genes (AN, CyIIa, CyIIIa, Endo16, FoxB, HE, SM30 a,
             and SM50) that function during the early development of the
             purple sea urchin, Strongylocentrotus purpuratus.
             Quantitative and qualitative measures of segregating
             variation are not conspicuously different between
             cis-regulatory and closely linked "proxy neutral" noncoding
             regions containing no known functional sites. Length and
             compound mutations are common in noncoding sequences;
             conventional descriptive statistics ignore such mutations,
             under-representing true genetic variation by approximately
             28% for these loci in this population. Patterns of variation
             in the cis-regulatory regions of six of the genes examined
             (CyIIa, CyIIIa, Endo16, FoxB, AN, and HE) are consistent
             with directional selection. Genetic variation within
             annotated transcription factor binding sites is comparable
             to, and frequently greater than, that of surrounding
             sequences. Comparisons of two paralog pairs (CyIIa/CyIIIa
             and AN/HE) suggest that distinct evolutionary processes have
             operated on their cis-regulatory regions following gene
             duplication. Together, these analyses provide a detailed
             view of the evolutionary mechanisms operating on noncoding
             sequences within a natural population, and underscore how
             little is known about how these processes operate on
             cis-regulatory sequences.},
   Doi = {10.1111/j.1525-142x.2012.00532.x},
   Key = {fds231556}
}

@article{fds231486,
   Author = {Horvath, JE and Wu, C and Toler, M and Fedrigo, O and Pfefferle, LW and Moore, A and Ramachandran, GL and Babbitt, CC and Jernvall, J and Wray,
             GA and Wall, CE},
   Title = {Enamel thickness in Microcebus murinus and Macaca mulana and
             the evolutionary genetics of enamel matrix proteins in
             hominoids.},
   Journal = {American Journal of Physical Anthropology},
   Volume = {147},
   Pages = {168-168},
   Publisher = {WILEY-BLACKWELL},
   Year = {2012},
   Month = {January},
   ISSN = {0002-9483},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000300498700392&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231486}
}

@article{fds231560,
   Author = {Babbitt, CC and Tung, J and Wray, GA and Alberts,
             SC},
   Title = {Changes in gene expression associated with reproductive
             maturation in wild female baboons.},
   Journal = {Genome Biology and Evolution},
   Volume = {4},
   Number = {2},
   Pages = {102-109},
   Year = {2012},
   Month = {January},
   ISSN = {1759-6653},
   url = {http://dx.doi.org/10.1093/gbe/evr134},
   Abstract = {Changes in gene expression during development play an
             important role in shaping morphological and behavioral
             differences, including between humans and nonhuman primates.
             Although many of the most striking developmental changes
             occur during early development, reproductive maturation
             represents another critical window in primate life history.
             However, this process is difficult to study at the molecular
             level in natural primate populations. Here, we took
             advantage of ovarian samples made available through an
             unusual episode of human-wildlife conflict to identify genes
             that are important in this process. Specifically, we used
             RNA sequencing (RNA-Seq) to compare genome-wide gene
             expression patterns in the ovarian tissue of juvenile and
             adult female baboons from Amboseli National Park, Kenya. We
             combined this information with prior evidence of selection
             occurring on two primate lineages (human and chimpanzee). We
             found that in cases in which genes were both differentially
             expressed over the course of ovarian maturation and also
             linked to lineage-specific selection this selective
             signature was much more likely to occur in regulatory
             regions than in coding regions. These results suggest that
             adaptive change in the development of the primate ovary may
             be largely driven at the mechanistic level by selection on
             gene regulation, potentially in relationship to the
             physiology or timing of female reproductive
             maturation.},
   Doi = {10.1093/gbe/evr134},
   Key = {fds231560}
}

@article{fds231555,
   Author = {Smith, MS and Wray, GA and Raff, RA},
   Title = {Revisiting cell lineage and cell fate in light of the
             evolution of axis formation in Heliocidaris
             erythrogramma},
   Journal = {Evolution & Development},
   Year = {2012},
   Key = {fds231555}
}

@article{fds231564,
   Author = {Bilbo, SD and Wray, GA and Perkins, SE and Parker,
             W},
   Title = {Reconstitution of the human biome as the most reasonable
             solution for epidemics of allergic and autoimmune
             diseases.},
   Journal = {Med Hypotheses},
   Volume = {77},
   Number = {4},
   Pages = {494-504},
   Year = {2011},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21741180},
   Abstract = {A wide range of hyperimmune-associated diseases plague
             post-industrial society, with a prevalence and impact that
             is staggering. Strong evidence points towards a loss of
             helminths from the ecosystem of the human body (the human
             biome) as the most important factor in this epidemic.
             Helminths, intestinal worms which are largely eradicated by
             elements of post-industrial culture including toilets and
             water treatment facilities, have an otherwise ubiquitous
             presence in vertebrates, and have co-evolved with the immune
             system. Not only do helminths discourage allergic and
             autoimmune reactions by diverting the immune system away
             from these pathologic processes and stimulating host
             regulatory networks, helminths release a variety of factors
             which down-modulate the immune system. A comprehensive view
             of hyperimmune-related disease based on studies in
             immunology, parasitology, evolutionary biology,
             epidemiology, and neurobiology indicates that the effects of
             biome depletion may not yet be fully realized, and may have
             an unexpectedly broad impact on many areas of human biology,
             including cognition. Fortunately, colonization with
             helminths results in a cure of numerous autoimmune and
             allergic diseases in laboratory rodents, and clinical
             studies in humans have indicated their utility for treatment
             of both multiple sclerosis and inflammatory bowel disease.
             Based on these considerations, commitment of considerable
             resources toward understanding the effects of "biome
             depletion" and systematically evaluating the most effective
             approach toward biome reconstitution is strongly
             encouraged.},
   Doi = {10.1016/j.mehy.2011.06.019},
   Key = {fds231564}
}

@article{fds231563,
   Author = {Wray, GA},
   Title = {Evolution. CNCing is believing.},
   Journal = {Science (New York, N.Y.)},
   Volume = {333},
   Number = {6045},
   Pages = {946-947},
   Year = {2011},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21852480},
   Doi = {10.1126/science.1210771},
   Key = {fds231563}
}

@article{fds231539,
   Author = {Babbitt, CC and Warner, LR and Fedrigo, O and Wall, CE and Wray,
             GA},
   Title = {Genomic signatures of diet-related shifts during human
             origins.},
   Journal = {Proceedings of the Royal Society B: Biological
             Sciences},
   Volume = {278},
   Number = {1708},
   Pages = {961-969},
   Year = {2011},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21177690},
   Abstract = {There are numerous anthropological analyses concerning the
             importance of diet during human evolution. Diet is thought
             to have had a profound influence on the human phenotype, and
             dietary differences have been hypothesized to contribute to
             the dramatic morphological changes seen in modern humans as
             compared with non-human primates. Here, we attempt to
             integrate the results of new genomic studies within this
             well-developed anthropological context. We then review the
             current evidence for adaptation related to diet, both at the
             level of sequence changes and gene expression. Finally, we
             propose some ways in which new technologies can help
             identify specific genomic adaptations that have resulted in
             metabolic and morphological differences between humans and
             non-human primates.},
   Doi = {10.1098/rspb.2010.2433},
   Key = {fds231539}
}

@article{fds231538,
   Author = {Pfefferle, AD and Warner, LR and Wang, CW and Nielsen, WJ and Babbitt,
             CC and Fedrigo, O and Wray, GA},
   Title = {Comparative expression analysis of the phosphocreatine
             circuit in extant primates: Implications for human brain
             evolution.},
   Journal = {Journal of Human Evolution},
   Volume = {60},
   Number = {2},
   Pages = {205-212},
   Year = {2011},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21190724},
   Abstract = {While the hominid fossil record clearly shows that brain
             size has rapidly expanded over the last ~2.5 M.yr. the
             forces driving this change remain unclear. One popular
             hypothesis proposes that metabolic adaptations in response
             to dietary shifts supported greater encephalization in
             humans. An increase in meat consumption distinguishes the
             human diet from that of other great apes. Creatine, an
             essential metabolite for energy homeostasis in muscle and
             brain tissue, is abundant in meat and was likely ingested in
             higher quantities during human origins. Five phosphocreatine
             circuit proteins help regulate creatine utilization within
             energy demanding cells. We compared the expression of all
             five phosphocreatine circuit genes in cerebral cortex,
             cerebellum, and skeletal muscle tissue for humans,
             chimpanzees, and rhesus macaques. Strikingly, SLC6A8 and CKB
             transcript levels are higher in the human brain, which
             should increase energy availability and turnover compared to
             non-human primates. Combined with other well-documented
             differences between humans and non-human primates, this
             allocation of energy to the cerebral cortex and cerebellum
             may be important in supporting the increased metabolic
             demands of the human brain.},
   Doi = {10.1016/j.jhevol.2010.10.004},
   Key = {fds231538}
}

@article{fds231567,
   Author = {Tung, J and Akinyi, MY and Mutura, S and Altmann, J and Wray, GA and Alberts, SC},
   Title = {Allele-specific gene expression in a wild nonhuman primate
             population.},
   Journal = {Molecular Ecology},
   Volume = {20},
   Number = {4},
   Pages = {725-739},
   Year = {2011},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21226779},
   Abstract = {Natural populations hold enormous potential for evolutionary
             genetic studies, especially when phenotypic, genetic and
             environmental data are all available on the same
             individuals. However, untangling the genotype-phenotype
             relationship in natural populations remains a major
             challenge. Here, we describe results of an investigation of
             one class of phenotype, allele-specific gene expression
             (ASGE), in the well-studied natural population of baboons of
             the Amboseli basin, Kenya. ASGE measurements identify cases
             in which one allele of a gene is overexpressed relative to
             the alternative allele of the same gene, within individuals,
             thus providing a control for background genetic and
             environmental effects. Here, we characterize the incidence
             of ASGE in the Amboseli baboon population, focusing on the
             genetic and environmental contributions to ASGE in a set of
             eleven genes involved in immunity and defence. Within this
             set, we identify evidence for common ASGE in four genes. We
             also present examples of two relationships between
             cis-regulatory genetic variants and the ASGE phenotype.
             Finally, we identify one case in which this relationship is
             influenced by a novel gene-environment interaction.
             Specifically, the dominance rank of an individual's mother
             during its early life (an aspect of that individual's social
             environment) influences the expression of the gene CCL5 via
             an interaction with cis-regulatory genetic variation. These
             results illustrate how environmental and ecological data can
             be integrated into evolutionary genetic studies of
             functional variation in natural populations. They also
             highlight the potential importance of early life
             environmental variation in shaping the genetic architecture
             of complex traits in wild mammals.},
   Doi = {10.1111/j.1365-294X.2010.04970.x},
   Key = {fds231567}
}

@article{fds231540,
   Author = {Fedrigo, O and Pfefferle, AD and Babbitt, CC and Haygood, R and Wall,
             CE and Wray, GA},
   Title = {A potential role for glucose transporters in the evolution
             of human brain size.},
   Journal = {Brain, Behavior and Evolution},
   Volume = {78},
   Number = {4},
   Pages = {315-326},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21986508},
   Abstract = {Differences in cognitive abilities and the relatively large
             brain are among the most striking differences between humans
             and their closest primate relatives. The energy trade-off
             hypothesis predicts that a major shift in energy allocation
             among tissues occurred during human origins in order to
             support the remarkable expansion of a metabolically
             expensive brain. However, the molecular basis of this
             adaptive scenario is unknown. Two glucose transporters
             (SLC2A1 and SLC2A4) are promising candidates and present
             intriguing mutations in humans, resulting, respectively, in
             microcephaly and disruptions in whole-body glucose
             homeostasis. We compared SLC2A1 and SLC2A4 expression
             between humans, chimpanzees and macaques, and found
             compensatory and biologically significant expression changes
             on the human lineage within cerebral cortex and skeletal
             muscle, consistent with mediating an energy trade-off. We
             also show that these two genes are likely to have undergone
             adaptation and participated in the development and
             maintenance of a larger brain in the human lineage by
             modulating brain and skeletal muscle energy allocation. We
             found that these two genes show human-specific signatures of
             positive selection on known regulatory elements within their
             5'-untranslated region, suggesting an adaptation of their
             regulation during human origins. This study represents the
             first case where adaptive, functional and genetic lines of
             evidence implicate specific genes in the evolution of human
             brain size.},
   Doi = {10.1159/000329852},
   Key = {fds231540}
}

@article{fds231559,
   Author = {Szövényi, P and Rensing, SA and Lang, D and Wray, GA and Shaw,
             AJ},
   Title = {Generation-biased gene expression in a bryophyte model
             system.},
   Journal = {Molecular Biology and Evolution},
   Volume = {28},
   Number = {1},
   Pages = {803-812},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20855429},
   Abstract = {The evolution of land plants is tightly linked to the
             evolution of the alternation of generations. Because
             alternating ploidal generations share their genomes,
             investigating generation-biased gene expression can give
             insight into the evolution of life cycles in land plants.
             Toward this end, we describe gene expression differences
             associated with the alternation of isogenic sporophyte and
             gametophyte generations in bryophytes, extant
             representatives of early diverging land plants, using a moss
             model system (Funaria hygrometrica). We found that
             differentiation in gene expression between the sporophyte
             and gametophyte generations is weaker in the bryophyte model
             system than in Arabidopsis thaliana. This is in line with
             the basal phylogenetic position of bryophytes and with the
             origin of alternating generations from a purely haplontic
             life cycle. Comparative analysis of F. hygrometrica and A.
             thaliana gene expression data shows that there is limited
             conservation of generation-biased gene expression across
             land plants. However, genes showing shared sporophyte-biased
             expression in both F. hygrometrica and A. thaliana appear to
             be enriched for biological pathways representing critical
             molecular adaptations to terrestrial life. Comparative
             analyses of the expression of F. hygrometrica and A.
             thaliana regulatory genes suggest that conserved regulatory
             networks may be involved in growth and reproductive tissue
             development of the angiosperm and bryophyte sporophyte
             generations despite their morphological divergence. This
             study represents the first attempt to describe
             generation-biased gene expression in a plant with a
             well-developed sporophyte and gametophyte generations, and
             as such it lays the foundation for future targeted research
             on the developmental mechanisms underlying evolutionary
             diversification of plant sporophytes.},
   Doi = {10.1093/molbev/msq254},
   Key = {fds231559}
}

@article{fds231565,
   Author = {Yokoyama, KD and Thorne, JL and Wray, GA},
   Title = {Coordinated genome-wide modifications within proximal
             promoter cis-regulatory elements during vertebrate
             evolution.},
   Journal = {Genome Biology and Evolution},
   Volume = {3},
   Pages = {66-74},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21118975},
   Abstract = {There often exists a "one-to-many" relationship between a
             transcription factor and a multitude of binding sites
             throughout the genome. It is commonly assumed that
             transcription factor binding motifs remain largely static
             over the course of evolution because changes in binding
             specificity can alter the interactions with potentially
             hundreds of sites across the genome. Focusing on regulatory
             motifs overrepresented at specific locations within or near
             the promoter, we find that a surprisingly large number of
             cis-regulatory elements have been subject to coordinated
             genome-wide modifications during vertebrate evolution, such
             that the motif frequency changes on a single branch of
             vertebrate phylogeny. This was found to be the case even
             between closely related mammal species, with nearly a third
             of all location-specific consensus motifs exhibiting
             significant modifications within the human or mouse lineage
             since their divergence. Many of these modifications are
             likely to be compensatory changes throughout the genome
             following changes in protein factor binding affinities,
             whereas others may be due to changes in mutation rates or
             effective population size. The likelihood that this happened
             many times during vertebrate evolution highlights the need
             to examine additional taxa and to understand the
             evolutionary and molecular mechanisms underlying the
             evolution of protein-DNA interactions.},
   Doi = {10.1093/gbe/evq078},
   Key = {fds231565}
}

@article{fds203307,
   Author = {P. Szovenyi and S.A. Rensing and D. Lang and G.A. Wray and A.J.
             Shaw},
   Title = {Generation-biased gene expression in a bryophyte model
             systems},
   Journal = {Molecular Biology and Evolution},
   Volume = {28},
   Pages = {803-812},
   Year = {2011},
   Key = {fds203307}
}

@article{fds231561,
   Author = {Babbitt, CC and Warner, LR and Fedrigo, O and Wall, CE and Wray,
             GA},
   Title = {Genomic signatures of diet-related shifts in primate
             evolution},
   Journal = {Proceedings of the Royal Society of London
             B},
   Volume = {278},
   Pages = {961-969},
   Year = {2011},
   Key = {fds231561}
}

@article{fds231562,
   Author = {Fedrigo, O and Pfefferele, AD and Babbitt, CC and Haygood, R and Wall,
             CE and Wray, GA},
   Title = {Molecular evidence that a metabolic trade-off contributed to
             human brain size evolution},
   Journal = {Brain, Behavior, and Evolution},
   Volume = {78},
   Pages = {315-326},
   Year = {2011},
   Key = {fds231562}
}

@article{fds231566,
   Author = {Pfefferle, AD and Warner, LR and Wang, CW and Nielsen, WJ and Babbitt,
             CC and Fedrigo, O and Wray, GA},
   Title = {Expression analysis of the phosphocreatine circuit in extant
             primates: Implications for human brain evolution},
   Journal = {Journal for Human Evolution},
   Volume = {60},
   Pages = {205-211},
   Year = {2011},
   Key = {fds231566}
}

@article{fds231568,
   Author = {Tung, J and Alberts, SC and Wray, GA},
   Title = {Evolutionary genetics in wild primates: combining genetic
             approaches with field studies of natural
             populations.},
   Journal = {Trends in Genetics : Tig},
   Volume = {26},
   Number = {8},
   Pages = {353-362},
   Year = {2010},
   Month = {August},
   ISSN = {0168-9525},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20580115},
   Abstract = {Ecological and evolutionary studies of wild primates hold
             important keys to understanding both the shared
             characteristics of primate biology and the genetic and
             phenotypic differences that make specific lineages,
             including our own, unique. Although complementary genetic
             research on nonhuman primates has long been of interest,
             recent technological and methodological advances now enable
             functional and population genetic studies in an
             unprecedented manner. In the past several years, novel
             genetic data sets have revealed new information about the
             demographic history of primate populations and the genetics
             of adaptively important traits. In combination with the rich
             history of behavioral, ecological, and physiological work on
             natural primate populations, genetic approaches promise to
             provide a compelling picture of primate evolution in the
             past and in the present day.},
   Doi = {10.1016/j.tig.2010.05.005},
   Key = {fds231568}
}

@article{fds231571,
   Author = {Haygood, R and Babbitt, CC and Fedrigo, O and Wray,
             GA},
   Title = {Contrasts between adaptive coding and noncoding changes
             during human evolution.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {107},
   Number = {17},
   Pages = {7853-7857},
   Year = {2010},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20385805},
   Abstract = {Changes in non-protein-coding regulatory DNA sequences have
             been proposed to play distinctive roles in adaptive
             evolution. We analyzed correlations between gene functions
             and evidence for positive selection in a common statistical
             framework across several large surveys of coding and
             noncoding sequences throughout the human genome. Strong
             correlations with both classifications in gene ontologies
             and measurements of gene expression indicate that neural
             development and function have adapted mainly through
             noncoding changes. In contrast, adaptation via coding
             changes is dominated by immunity, olfaction, and male
             reproduction. Genes with highly tissue-specific expression
             have undergone more adaptive coding changes, suggesting that
             pleiotropic constraints inhibit such changes in broadly
             expressed genes. In contrast, adaptive noncoding changes do
             not exhibit this pattern. Our findings underscore the
             probable importance of noncoding changes in the evolution of
             human traits, particularly cognitive traits.},
   Doi = {10.1073/pnas.0911249107},
   Key = {fds231571}
}

@article{fds231576,
   Author = {Babbitt, CC and Silverman, JS and Haygood, R and Reininga, JM and Rockman, MV and Wray, GA},
   Title = {Multiple Functional Variants in cis Modulate PDYN
             Expression.},
   Journal = {Molecular Biology and Evolution},
   Volume = {27},
   Number = {2},
   Pages = {465-479},
   Year = {2010},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19910384},
   Abstract = {Understanding genetic variation and its functional
             consequences within cis-regulatory regions remains an
             important challenge in human genetics and evolution. Here,
             we present a fine-scale functional analysis of segregating
             variation within the cis-regulatory region of prodynorphin,
             a gene that encodes an endogenous opioid precursor with
             roles in cognition and disease. In order to characterize the
             functional consequences of segregating variation in cis in a
             region under balancing selection in different human
             populations, we examined associations between specific
             polymorphisms and gene expression in vivo and in vitro. We
             identified five polymorphisms within the 5' flanking region
             that affect transcript abundance: a 68-bp repeat recognized
             in prior studies, as well as two microsatellites and two
             single nucleotide polymorphisms not previously implicated as
             functional variants. The impact of these variants on
             transcription differs by brain region, sex, and cell type,
             implying interactions between cis genotype and the
             differentiated state of cells. The effects of individual
             variants on expression level are not additive in some
             combinations, implying epistatic interactions between nearby
             variants. These data reveal an unexpectedly complex
             relationship between segregating genetic variation and its
             expression-trait consequences and highlights the importance
             of close functional scrutiny of natural genetic variation
             within even relatively well-studied cis-regulatory
             regions.},
   Doi = {10.1093/molbev/msp276},
   Key = {fds231576}
}

@article{fds231573,
   Author = {Babbitt, CC and Fedrigo, O and Pfefferle, AD and Boyle, AP and Horvath,
             JE and Furey, TS and Wray, GA},
   Title = {Both noncoding and protein-coding RNAs contribute to gene
             expression evolution in the primate brain.},
   Journal = {Genome Biology and Evolution},
   Volume = {2},
   Pages = {67-79},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20333225},
   Abstract = {Despite striking differences in cognition and behavior
             between humans and our closest primate relatives, several
             studies have found little evidence for adaptive change in
             protein-coding regions of genes expressed primarily in the
             brain. Instead, changes in gene expression may underlie many
             cognitive and behavioral differences. Here, we used digital
             gene expression: tag profiling (here called Tag-Seq, also
             called DGE:tag profiling) to assess changes in global
             transcript abundance in the frontal cortex of the brains of
             3 humans, 3 chimpanzees, and 3 rhesus macaques. A
             substantial fraction of transcripts we identified as
             differentially transcribed among species were not assayed in
             previous studies based on microarrays. Differentially
             expressed tags within coding regions are enriched for gene
             functions involved in synaptic transmission, transport,
             oxidative phosphorylation, and lipid metabolism.
             Importantly, because Tag-Seq technology provides
             strand-specific information about all polyadenlyated
             transcripts, we were able to assay expression in noncoding
             intragenic regions, including both sense and antisense
             noncoding transcripts (relative to nearby genes). We find
             that many noncoding transcripts are conserved in both
             location and expression level between species, suggesting a
             possible functional role. Lastly, we examined the overlap
             between differential gene expression and signatures of
             positive selection within putative promoter regions, a sign
             that these differences represent adaptations during human
             evolution. Comparative approaches may provide important
             insights into genes responsible for differences in cognitive
             functions between humans and nonhuman primates, as well as
             highlighting new candidate genes for studies investigating
             neurological disorders.},
   Doi = {10.1093/gbe/evq002},
   Key = {fds231573}
}

@article{fds231474,
   Author = {Tung, J and Alberts, SC and Wray, GA},
   Title = {Evolution of functional genetic variation at immune loci in
             wild baboons.},
   Journal = {American Journal of Physical Anthropology},
   Pages = {231-231},
   Publisher = {WILEY-LISS},
   Year = {2010},
   Month = {January},
   ISSN = {0002-9483},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000275295200793&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231474}
}

@article{fds231569,
   Author = {Oliver, TA and Garfield, DA and Manier, MK and Haygood, R and Wray, GA and Palumbi, SR},
   Title = {Whole-genome positive selection and habitat-driven evolution
             in a shallow and a deep-sea urchin.},
   Journal = {Genome Biology and Evolution},
   Volume = {2},
   Pages = {800-814},
   Year = {2010},
   Month = {January},
   ISSN = {1759-6653},
   url = {http://dx.doi.org/10.1093/gbe/evq063},
   Abstract = {Comparisons of genomic sequence between divergent species
             can provide insight into the action of natural selection
             across many distinct classes of proteins. Here, we examine
             the extent of positive selection as a function of
             tissue-specific and stage-specific gene expression in two
             closely-related sea urchins, the shallow-water
             Strongylocentrotus purpuratus and the deep-sea Allocentrotus
             fragilis, which have diverged greatly in their adult but not
             larval habitats. Genes that are expressed specifically in
             adult somatic tissue have significantly higher dN/dS ratios
             than the genome-wide average, whereas those in larvae are
             indistinguishable from the genome-wide average.
             Testis-specific genes have the highest dN/dS values, whereas
             ovary-specific have the lowest. Branch-site models involving
             the outgroup S. franciscanus indicate greater selection
             (ω(FG)) along the A. fragilis branch than along the S.
             purpuratus branch. The A. fragilis branch also shows a
             higher proportion of genes under positive selection,
             including those involved in skeletal development,
             endocytosis, and sulfur metabolism. Both lineages are
             approximately equal in enrichment for positive selection of
             genes involved in immunity, development, and cell-cell
             communication. The branch-site models further suggest that
             adult-specific genes have experienced greater positive
             selection than those expressed in larvae and that
             ovary-specific genes are more conserved (i.e., experienced
             greater negative selection) than those expressed
             specifically in adult somatic tissues and testis. Our
             results chart the patterns of protein change that have
             occurred after habitat divergence in these two species and
             show that the developmental or functional context in which a
             gene acts can play an important role in how divergent
             species adapt to new environments.},
   Doi = {10.1093/gbe/evq063},
   Key = {fds231569}
}

@article{fds231570,
   Author = {Cruz-Gordillo, P and Fedrigo, O and Wray, GA and Babbitt,
             CC},
   Title = {Extensive changes in the expression of the opioid genes
             between humans and chimpanzees.},
   Journal = {Brain, Behavior and Evolution},
   Volume = {76},
   Number = {2},
   Pages = {154-162},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21079395},
   Abstract = {The various means by which the body perceives, transmits,
             and resolves the experiences of pain and nociception are
             mediated by a host of molecules, including neuropeptides
             within the opioid gene signaling pathway. The peptide
             ligands and receptors encoded by this group of genes have
             been linked to behavioral disorders as well as a number of
             psychiatric affective disorders. Our aim was to explore the
             recent evolutionary history of these two gene families by
             taking a comparative genomics approach, specifically through
             a comparison between humans and chimpanzees. Our analyses
             indicate differential expression of these genes between the
             two species, more than expected based on genome-wide
             comparisons, indicating that differential expression is
             pervasive among the opioid genes. Of the 8 family members,
             three genes showed significant expression differences (PENK,
             PNOC, and OPRL1), with two others marginally significant
             (OPRM1 and OPRD1). Accelerated substitution rates along
             human and chimpanzee lineages within the putative regulatory
             regions of OPRM1, POMC, and PDYN between the human and
             chimpanzee branches are consistent with positive selection.
             Collectively, these results suggest that there may have been
             a selective advantage to modulating the expression of the
             opioid genes in humans compared with our closest living
             relatives. Information about the cognitive roles mediated by
             these genes in humans may help to elucidate the trait
             consequences of these putatively adaptive expression
             changes.},
   Doi = {10.1159/000320968},
   Key = {fds231570}
}

@article{fds231572,
   Author = {Fedrigo, O and Warner, LR and Pfefferle, AD and Babbitt, CC and Cruz-Gordillo, P and Wray, GA},
   Title = {A pipeline to determine RT-QPCR control genes for
             evolutionary studies: application to primate gene expression
             across multiple tissues.},
   Journal = {Plos One},
   Volume = {5},
   Number = {9},
   Pages = {e12489},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20824057},
   Abstract = {Because many species-specific phenotypic differences are
             assumed to be caused by differential regulation of gene
             expression, many recent investigations have focused on
             measuring transcript abundance. Despite the availability of
             high-throughput platforms, quantitative real-time polymerase
             chain reaction (RT-QPCR) is often the method of choice
             because of its low cost and wider dynamic range. However,
             the accuracy of this technique heavily relies on the use of
             multiple valid control genes for normalization. We created a
             pipeline for choosing genes potentially useful as RT-QPCR
             control genes for measuring expression between human and
             chimpanzee samples across multiple tissues, using published
             microarrays and a measure of tissue-specificity. We
             identified 13 genes from the pipeline and from commonly used
             control genes: ACTB, USP49, ARGHGEF2, GSK3A, TBP, SDHA,
             EIF2B2, GPDH, YWHAZ, HPTR1, RPL13A, HMBS, and EEF2. We then
             tested these candidate genes and validated their expression
             stability across species. We established the rank order of
             the most preferable set of genes for single and combined
             tissues. Our results suggest that for at least three tissues
             (cerebral cortex, liver, and skeletal muscle), EIF2B2, EEF2,
             HMBS, and SDHA are useful genes for normalizing human and
             chimpanzee expression using RT-QPCR. Interestingly, other
             commonly used control genes, including TBP, GAPDH, and,
             especially ACTB do not perform as well. This pipeline could
             be easily adapted to other species for which expression data
             exist, providing taxonomically appropriate control genes for
             comparisons of gene expression among species.},
   Doi = {10.1371/journal.pone.0012545},
   Key = {fds231572}
}

@article{fds231574,
   Author = {Garfield, DA and Wray, GA},
   Title = {The evolution of gene regulatory interactions},
   Journal = {Bioscience},
   Volume = {60},
   Number = {1},
   Pages = {15-23},
   Publisher = {Oxford University Press (OUP)},
   Year = {2010},
   Month = {January},
   ISSN = {0006-3568},
   url = {http://dx.doi.org/10.1525/bio.2010.60.1.6},
   Abstract = {Changes in the timing and level at which genes are expressed
             are known to play an important role in evolution, but the
             mechanisms underlying changes in gene expression remain
             relatively obscure. Until quite recently, evolutionary
             biologists, like most biologists, tended to study single
             genes as isolated entities. These studies have added
             enormously to our understanding of biological evolution. But
             because gene regulation by its very nature involves
             interactions between two (or more) genes, researchers have
             missed a range of evolutionary phenomena that can be
             observed only at the level of networks of interacting genes.
             In this article, we consider the change in perspective that
             genomic technologiesparticularly the advent of large-scale
             platforms for DNA sequencing, genotyping, and measuring gene
             expressionare bringing to evolutionary biology. We focus
             specifically on how these technologies can and are being
             used to increase our understanding of how and why gene
             expression evolves. © 2010 by American Institute of
             Biological Sciences. All rights reserved.},
   Doi = {10.1525/bio.2010.60.1.6},
   Key = {fds231574}
}

@article{fds231575,
   Author = {Fédrigo, O and Wray, GA},
   Title = {Developmental evolution: how beetles evolved their
             shields.},
   Journal = {Current Biology : Cb},
   Volume = {20},
   Number = {2},
   Pages = {R64-R66},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20129042},
   Abstract = {Beetle forewings are modified into hardened structures
             called elytra. A recent study indicates that the evolution
             of elytra involved co-opting genes for exoskeleton formation
             into the wing development gene network of beetles on at
             least three separate occasions.},
   Doi = {10.1016/j.cub.2009.12.012},
   Key = {fds231575}
}

@article{fds231537,
   Author = {Fedrigo, O and Warner, LR and Pfefferle, AD and Babbitt, CC and Cruz-Gordillo, P and Wray, GA},
   Title = {A pipeline to determine RT-QPCR control genes for
             evolutionary studies: Application to primate gene expression
             across multiple tissues},
   Journal = {Plos One},
   Volume = {5},
   Number = {9},
   Pages = {1-7},
   Year = {2010},
   ISSN = {1932-6203},
   url = {http://hdl.handle.net/10161/4570 Duke open
             access},
   Abstract = {Because many species-specific phenotypic differences are
             assumed to be caused by differential regulation of gene
             expression, many recent investigations have focused on
             measuring transcript abundance. Despite the availability of
             high throughput platforms, quantitative real-time polymerase
             chain reaction (RT-QPCR) is often the method of choice
             because of its low cost and wider dynamic range. However,
             the accuracy of this technique heavily relies on the use of
             multiple valid control genes for normalization. We created a
             pipeline for choosing genes potentially useful as RT-QPCR
             control genes for measuring expression between human and
             chimpanzee samples across multiple tissues, using published
             microarrays and a measure of tissue-specificity. We
             identified 13 genes from the pipeline and from commonly used
             control genes: ACTB, USP49, ARGHGEF2, GSK3A, TBP, SDHA,
             EIF2B2, GPDH, YWHAZ, HPTR1, RPL13A, HMBS, and EEF2. We then
             tested these candidate genes and validated their expression
             stability across species. We established the rank order of
             the most preferable set of genes for single and combined
             tissues. Our results suggest that for at least three tissues
             (cerebral cortex, liver, and skeletal muscle), EIF2B2, EEF2,
             HMBS, and SDHA are useful genes for normalizing human and
             chimpanzee expression using RT-QPCR. Interestingly, other
             commonly used control genes, including TBP, GAPDH, and,
             especially ACTB do not perform as well. This pipeline could
             be easily adapted to other species for which expression data
             exist, providing taxonomically appropriate control genes for
             comparisons of gene expression among species. © 2010
             Fedrigo et al.},
   Doi = {10.1371/journal.pone.0012545},
   Key = {fds231537}
}

@article{fds231578,
   Author = {Tung, J and Fédrigo, O and Haygood, R and Mukherjee, S and Wray,
             GA},
   Title = {Genomic features that predict allelic imbalance in humans
             suggest patterns of constraint on gene expression
             variation.},
   Journal = {Molecular Biology and Evolution},
   Volume = {26},
   Number = {9},
   Pages = {2047-2059},
   Year = {2009},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19506001},
   Abstract = {Variation in gene expression is an important contributor to
             phenotypic diversity within and between species. Although
             this variation often has a genetic component, identification
             of the genetic variants driving this relationship remains
             challenging. In particular, measurements of gene expression
             usually do not reveal whether the genetic basis for any
             observed variation lies in cis or in trans to the gene, a
             distinction that has direct relevance to the physical
             location of the underlying genetic variant, and which may
             also impact its evolutionary trajectory. Allelic imbalance
             measurements identify cis-acting genetic effects by assaying
             the relative contribution of the two alleles of a
             cis-regulatory region to gene expression within individuals.
             Identification of patterns that predict commonly imbalanced
             genes could therefore serve as a useful tool and also shed
             light on the evolution of cis-regulatory variation itself.
             Here, we show that sequence motifs, polymorphism levels, and
             divergence levels around a gene can be used to predict
             commonly imbalanced genes in a human data set. Reduction of
             this feature set to four factors revealed that only one
             factor significantly differentiated between commonly
             imbalanced and nonimbalanced genes. We demonstrate that
             these results are consistent between the original data set
             and a second published data set in humans obtained using
             different technical and statistical methods. Finally, we
             show that variation in the single allelic
             imbalance-associated factor is partially explained by the
             density of genes in the region of a target gene (allelic
             imbalance is less probable for genes in gene-dense regions),
             and, to a lesser extent, the evenness of expression of the
             gene across tissues and the magnitude of negative selection
             on putative regulatory regions of the gene. These results
             suggest that the genomic distribution of functional
             cis-regulatory variants in the human genome is nonrandom,
             perhaps due to local differences in evolutionary
             constraint.},
   Doi = {10.1093/molbev/msp113},
   Key = {fds231578}
}

@article{fds231580,
   Author = {Warner, LR and Babbitt, CC and Primus, AE and Severson, TF and Haygood,
             R and Wray, GA},
   Title = {Functional consequences of genetic variation in primates on
             tyrosine hydroxylase (TH) expression in vitro.},
   Journal = {Brain Research},
   Volume = {1288},
   Pages = {1-8},
   Year = {2009},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19591812},
   Abstract = {Tyrosine hydroxylase, the rate-limiting enzyme in
             catecholamine synthesis, is known to contain naturally
             occurring genetic variation in it's promoter region that
             associates with a number of neuropsychological disorders. As
             such, examining non-coding regions is important for
             understanding tyrosine hydroxylase function in human health
             and disease. We examined approximately 2 kb upstream of the
             translation start site within humans and non-human primates
             to obtain a fine resolution map of evolutionarily and
             functionally relevant cis-regulatory differences. Our study
             investigated Macaca mulatta, Pan troglodytes, Gorilla
             gorilla, and Homo sapiens haplotypes using transient
             dual-luciferase transfection in three neuroblastoma cell
             lines to assay the impact of naturally occurring sequence
             variation on expression level. In addition to trans effects
             between cell lines, there are several significant expression
             differences between primate species, but the most striking
             difference was seen between human haplotypes in one cell
             line. Underlying this variation are numerous sequence
             polymorphisms, two of which influence expression within
             humans in a non-additive and cell line-specific manner. This
             study highlights functional consequences of tyrosine
             hydroxylase genetic variation in primates. Additionally, the
             results emphasize the importance of examining more than one
             cell line, the existence of multiple functional variants in
             a given promoter region and the presence of non-additive
             cis-interactions.},
   Doi = {10.1016/j.brainres.2009.06.086},
   Key = {fds231580}
}

@article{fds231581,
   Author = {Tung, J and Primus, A and Bouley, AJ and Severson, TF and Alberts, SC and Wray, GA},
   Title = {Evolution of a malaria resistance gene in wild
             primates.},
   Journal = {Nature},
   Volume = {460},
   Number = {7253},
   Pages = {388-391},
   Year = {2009},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19553936},
   Abstract = {The ecology, behaviour and genetics of our closest living
             relatives, the nonhuman primates, should help us to
             understand the evolution of our own lineage. Although a
             large amount of data has been amassed on primate ecology and
             behaviour, much less is known about the functional and
             evolutionary genetic aspects of primate biology, especially
             in wild primates. As a result, even in well-studied
             populations in which nongenetic factors that influence
             adaptively important characteristics have been identified,
             we have almost no understanding of the underlying genetic
             basis for such traits. Here, we report on the functional
             consequences of genetic variation at the malaria-related FY
             (DARC) gene in a well-studied population of yellow baboons
             (Papio cynocephalus) living in Amboseli National Park in
             Kenya. FY codes for a chemokine receptor normally expressed
             on the erythrocyte surface that is the known entry point for
             the malarial parasite Plasmodium vivax. We identified
             variation in the cis-regulatory region of the baboon FY gene
             that was associated with phenotypic variation in
             susceptibility to Hepatocystis, a malaria-like pathogen that
             is common in baboons. Genetic variation in this region also
             influenced gene expression in vivo in wild individuals, a
             result we confirmed using in vitro reporter gene assays. The
             patterns of genetic variation in and around this locus were
             also suggestive of non-neutral evolution, raising the
             possibility that the evolution of the FY cis-regulatory
             region in baboons has exhibited both mechanistic and
             selective parallels with the homologous region in humans.
             Together, our results represent the first reported
             association and functional characterization linking genetic
             variation and a complex trait in a natural population of
             nonhuman primates.},
   Doi = {10.1038/nature08149},
   Key = {fds231581}
}

@article{fds304345,
   Author = {Yokoyama, KD and Ohler, U and Wray, GA},
   Title = {Measuring spatial preferences at fine-scale resolution
             identifies known and novel cis-regulatory element candidates
             and functional motif-pair relationships.},
   Journal = {Nucleic Acids Res},
   Volume = {37},
   Number = {13},
   Pages = {e92},
   Year = {2009},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19483094},
   Abstract = {Transcriptional regulation is mediated by the collective
             binding of proteins called transcription factors to
             cis-regulatory elements. A handful of factors are known to
             function at particular distances from the transcription
             start site, although the extent to which this occurs is not
             well understood. Spatial dependencies can also exist between
             pairs of binding motifs, facilitating factor-pair
             interactions. We sought to determine to what extent spatial
             preferences measured at high-scale resolution could be
             utilized to predict cis-regulatory elements as well as
             motif-pairs binding interacting proteins. We introduce the
             'motif positional function' model which predicts spatial
             biases using regression analysis, differentiating noise from
             true position-specific overrepresentation at
             single-nucleotide resolution. Our method predicts 48
             consensus motifs exhibiting positional enrichment within
             human promoters, including fourteen motifs without known
             binding partners. We then extend the model to analyze
             distance preferences between pairs of motifs. We find that
             motif-pairs binding interacting factors often co-occur
             preferentially at multiple distances, with intervals between
             preferred distances often corresponding to the turn of the
             DNA double-helix. This offers a novel means by which to
             predict sequence elements with a collective role in gene
             regulation.},
   Doi = {10.1093/nar/gkp423},
   Key = {fds304345}
}

@article{fds231577,
   Author = {Garfield, DA and Wray, GA},
   Title = {Comparative embryology without a microscope: using genomic
             approaches to understand the evolution of
             development.},
   Journal = {Journal of Biology},
   Volume = {8},
   Number = {7},
   Pages = {65},
   Year = {2009},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19664180},
   Abstract = {Until recently, understanding developmental conservation and
             change has relied on embryological comparisons and analyses
             of single genes. Several studies, including one recently
             published in BMC Biology, have now taken a genomic approach
             to this classical problem, providing insights into how
             selection operates differentially across the life
             cycle.},
   Doi = {10.1186/jbiol161},
   Key = {fds231577}
}

@article{fds231579,
   Author = {Yokoyama, KD and Ohler, U and Wray, GA},
   Title = {Spatial preferences identify known and novel cis-regulatory
             element candidates and functional motif-pair
             relationships},
   Journal = {Nucleic Acids Research},
   Volume = {37},
   Number = {13},
   Pages = {e92},
   Year = {2009},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19483094},
   Abstract = {Transcriptional regulation is mediated by the collective
             binding of proteins called transcription factors to
             cis-regulatory elements. A handful of factors are known to
             function at particular distances from the transcription
             start site, although the extent to which this occurs is not
             well understood. Spatial dependencies can also exist between
             pairs of binding motifs, facilitating factor-pair
             interactions. We sought to determine to what extent spatial
             preferences measured at high-scale resolution could be
             utilized to predict cis-regulatory elements as well as
             motif-pairs binding interacting proteins. We introduce the
             'motif positional function' model which predicts spatial
             biases using regression analysis, differentiating noise from
             true position-specific overrepresentation at
             single-nucleotide resolution. Our method predicts 48
             consensus motifs exhibiting positional enrichment within
             human promoters, including fourteen motifs without known
             binding partners. We then extend the model to analyze
             distance preferences between pairs of motifs. We find that
             motif-pairs binding interacting factors often co-occur
             preferentially at multiple distances, with intervals between
             preferred distances often corresponding to the turn of the
             DNA double-helix. This offers a novel means by which to
             predict sequence elements with a collective role in gene
             regulation.},
   Doi = {10.1093/nar/gkp423},
   Key = {fds231579}
}

@article{fds231536,
   Author = {Haygood, R and Fedrigo, O and Wray, GA},
   Title = {Reply to "Rapidly evolving human promoter
             regions"},
   Journal = {Nature Genetics},
   Volume = {40},
   Number = {11},
   Pages = {1263-1264},
   Publisher = {Springer Nature},
   Year = {2008},
   Month = {November},
   ISSN = {1061-4036},
   url = {http://dx.doi.org/10.1038/ng1108-1263},
   Doi = {10.1038/ng1108-1263},
   Key = {fds231536}
}

@article{fds304344,
   Author = {Wray, GA and Babbitt, CC},
   Title = {Genetics. Enhancing gene regulation.},
   Journal = {Science (New York, N.Y.)},
   Volume = {321},
   Number = {5894},
   Pages = {1300-1301},
   Year = {2008},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18772422},
   Doi = {10.1126/science.1163568},
   Key = {fds304344}
}

@article{fds231582,
   Author = {Horvath, JE and Weisrock, DW and Embry, SL and Fiorentino, I and Balhoff, JP and Kappeler, P and Wray, GA and Willard, HF and Yoder,
             AD},
   Title = {Development and application of a phylogenomic toolkit:
             resolving the evolutionary history of Madagascar's
             lemurs.},
   Journal = {Genome Research},
   Volume = {18},
   Number = {3},
   Pages = {489-499},
   Year = {2008},
   Month = {March},
   ISSN = {1088-9051},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18245770},
   Abstract = {Lemurs and the other strepsirrhine primates are of great
             interest to the primate genomics community due to their
             phylogenetic placement as the sister lineage to all other
             primates. Previous attempts to resolve the phylogeny of
             lemurs employed limited mitochondrial or small nuclear data
             sets, with many relationships poorly supported or entirely
             unresolved. We used genomic resources to develop 11 novel
             markers from nine chromosomes, representing approximately 9
             kb of nuclear sequence data. In combination with previously
             published nuclear and mitochondrial loci, this yields a data
             set of more than 16 kb and adds approximately 275 kb of DNA
             sequence to current databases. Our phylogenetic analyses
             confirm hypotheses of lemuriform monophyly and provide
             robust resolution of the phylogenetic relationships among
             the five lemuriform families. We verify that the genus
             Daubentonia is the sister lineage to all other lemurs. The
             Cheirogaleidae and Lepilemuridae are sister taxa and
             together form the sister lineage to the Indriidae; this
             clade is the sister lineage to the Lemuridae. Divergence
             time estimates indicate that lemurs are an ancient group,
             with their initial diversification occurring around the
             Cretaceous-Tertiary boundary. Given the power of this data
             set to resolve branches in a notoriously problematic area of
             primate phylogeny, we anticipate that our phylogenomic
             toolkit will be of value to other studies of primate
             phylogeny and diversification. Moreover, the methods applied
             will be broadly applicable to other taxonomic groups where
             phylogenetic relationships have been notoriously difficult
             to resolve.},
   Doi = {10.1101/gr.7265208},
   Key = {fds231582}
}

@article{fds231543,
   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 = {fds231543}
}

@article{fds231583,
   Author = {Wray, GA and Babbitt, CC},
   Title = {Enhancing gene regulation},
   Journal = {Science},
   Volume = {321},
   Number = {5894},
   Pages = {1300-1301},
   Year = {2008},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18772422},
   Doi = {10.1126/science.1163568},
   Key = {fds231583}
}

@article{fds324084,
   Author = {Wray, GA},
   Title = {Developmental Genes and the Evolution of
             Morphology},
   Pages = {147-152},
   Booktitle = {Palaeobiology II},
   Year = {2007},
   Month = {December},
   ISBN = {0632051477},
   url = {http://dx.doi.org/10.1002/9780470999295ch.31},
   Doi = {10.1002/9780470999295ch.31},
   Key = {fds324084}
}

@article{fds231534,
   Author = {Sumrall, CD and Wray, GA},
   Title = {Ontogeny in the fossil record: Diversification of body plans
             and the evolution of "aberrant" symmetry in Paleozoic
             echinoderms},
   Journal = {Paleobiology},
   Volume = {33},
   Number = {1},
   Pages = {149-163},
   Publisher = {Cambridge University Press (CUP)},
   Year = {2007},
   Month = {December},
   ISSN = {0094-8373},
   url = {http://dx.doi.org/10.1666/06053.1},
   Abstract = {Echinoderms have long been characterized by the presence of
             ambulacra that exhibit pentaradiate symmetry and define five
             primary body axes. In reality, truly pentaradial ambulacral
             symmetry is a condition derived only once in the
             evolutionary history of echinoderms and is restricted to
             eleutherozoans, the clade that contains most living
             echinoderm species. In contrast, early echinoderms have a
             bilaterally symmetrical 2-1-2 arrangement, with three
             ambulacra radiating from the mouth. Branching of the two
             side ambulacra during ontogeny produces the five adult rays.
             During the Cambrian Explosion and Ordovician Radiation, some
             30 clades of echinoderms evolved, many of which have
             aberrant ambulacral systems with one to four rays.
             Unfortunately, no underlying model has emerged that explains
             ambulacral homologies among disparate forms. Here we show
             that most Paleozoic echinoderms are characterized by
             uniquely identifiable ambulacra that develop in three
             distinct postlarval stages. Nearly all "aberrant" echinoderm
             morphologies can be explained by the paedomorphic ambulacra
             reduction (PAR) model through the loss of some combination
             of these growth stages during ontogeny. Superficially
             similar patterns of ambulacral reduction in distantly
             related clades have resulted from the parallel loss of
             homologous ambulacra during ontogeny. Pseudo-fivefold
             symmetry seen in Blastoidea and the true fivefold symmetry
             seen in Eleutherozoa result from great reduction and total
             loss, respectively, of the 2-1-2 symmetry early in ontogeny.
             These ambulacral variations suggest that both developmental
             and ecological constraints affect the evolution of novel
             echinoderm body plans. © 2007 The Paleontological Society.
             All rights reserved.},
   Doi = {10.1666/06053.1},
   Key = {fds231534}
}

@article{fds231584,
   Author = {Bowsher, JH and Wray, GA and Abouheif, E},
   Title = {Growth and patterning are evolutionarily dissociated in the
             vestigial wing discs of workers of the red imported fire
             ant, Solenopsis invicta.},
   Journal = {Journal of Experimental Zoology. Part B, Molecular and
             Developmental Evolution},
   Volume = {308},
   Number = {6},
   Pages = {769-776},
   Year = {2007},
   Month = {December},
   ISSN = {1552-5007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17894383},
   Abstract = {Over the last decade, it has become clear that organismal
             form is largely determined by developmental and evolutionary
             changes in the growth and pattern formation of tissues. Yet,
             there is little known about how these two integrated
             processes respond to environmental cues or how they evolve
             relative to one another. Here, we present the discovery of
             vestigial wing imaginal discs in worker larvae of the red
             imported fire ant, Solenopsis invicta. These vestigial wing
             discs are present in all worker larvae, which is uncommon
             for a species with a large worker size distribution.
             Furthermore, the growth trajectory of these vestigial discs
             is distinct from all of the ant species examined to date
             because they grow at a rate slower than the leg discs. We
             predicted that the growth trajectory of the vestigial wing
             discs would be mirrored by evolutionary changes in their
             patterning. We tested this prediction by examining the
             expression of three patterning genes, extradenticle,
             ultrabithorax, and engrailed, known to underlie the wing
             polyphenism in ants. Surprisingly, the expression patterns
             of these three genes in the vestigial wing discs was the
             same as those found in ant species with different worker
             size distributions and wing disc growth than fire ants. We
             conclude that growth and patterning are evolutionarily
             dissociated in the vestigial wing discs of S. invicta
             because patterning in these discs is conserved, whereas
             their growth trajectories are not. The evolutionary
             dissociation of growth and patterning may be an important
             feature of gene networks that underlie polyphenic
             traits.},
   Doi = {10.1002/jez.b.21200},
   Key = {fds231584}
}

@article{fds304343,
   Author = {Babbitt, CC and Haygood, R and Wray, GA},
   Title = {When two is better than one.},
   Journal = {Cell},
   Volume = {131},
   Number = {2},
   Pages = {225-227},
   Year = {2007},
   Month = {October},
   ISSN = {0092-8674},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17956721},
   Abstract = {Gene duplication and divergence has long been considered an
             important route to adaptation and phenotypic evolution.
             Reporting in Nature, Hittinger and Carroll (2007) provide
             the first clear example of adaptations in both regulatory
             regions and protein-coding regions after gene duplication.
             This combination of evolutionary changes appears to have
             resolved an adaptive conflict, leading to increased
             organismal fitness.},
   Doi = {10.1016/j.cell.2007.10.001},
   Key = {fds304343}
}

@article{fds231587,
   Author = {Haygood, R and Fedrigo, O and Hanson, B and Yokoyama, K-D and Wray,
             GA},
   Title = {Promoter regions of many neural- and nutrition-related genes
             have experienced positive selection during human
             evolution.},
   Journal = {Nature Genetics},
   Volume = {39},
   Number = {9},
   Pages = {1140-1144},
   Year = {2007},
   Month = {September},
   ISSN = {1061-4036},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17694055},
   Abstract = {Surveys of protein-coding sequences for evidence of positive
             selection in humans or chimpanzees have flagged only a few
             genes known to function in neural or nutritional processes,
             despite pronounced differences between humans and
             chimpanzees in behavior, cognition and diet. It may be that
             most such differences are due to changes in gene regulation
             rather than protein structure. Here, we present the first
             survey of promoter (5'-flanking) regions, which are rich in
             cis-regulatory sequences, for evidence of positive selection
             in humans. Our results indicate that positive selection has
             targeted the regulation of many genes known to be involved
             in neural development and function, both in the brain and
             elsewhere in the nervous system, and in nutrition,
             particularly in glucose metabolism.},
   Doi = {10.1038/ng2104},
   Key = {fds231587}
}

@article{fds231585,
   Author = {Wray, GA},
   Title = {The evolutionary significance of cis-regulatory
             mutations.},
   Journal = {Nature Reviews. Genetics},
   Volume = {8},
   Number = {3},
   Pages = {206-216},
   Year = {2007},
   Month = {March},
   ISSN = {1471-0056},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17304246},
   Abstract = {For decades, evolutionary biologists have argued that
             changes in cis-regulatory sequences constitute an important
             part of the genetic basis for adaptation. Although
             originally based on first principles, this claim is now
             empirically well supported: numerous studies have identified
             cis-regulatory mutations with functionally significant
             consequences for morphology, physiology and behaviour. The
             focus has now shifted to considering whether cis-regulatory
             and coding mutations make qualitatively different
             contributions to phenotypic evolution. Cases in which
             parallel mutations have produced parallel trait
             modifications in particular suggest that some phenotypic
             changes are more likely to result from cis-regulatory
             mutations than from coding mutations.},
   Doi = {10.1038/nrg2063},
   Key = {fds231585}
}

@article{fds304342,
   Author = {Tishkoff, SA and Reed, FA and Ranciaro, A and Voight, BF and Babbitt,
             CC and Silverman, JS and Powell, K and Mortensen, HM and Hirbo, JB and Osman, M and Ibrahim, M and Omar, SA and Lema, G and Nyambo, TB and Ghori,
             J and Bumpstead, S and Pritchard, JK and Wray, GA and Deloukas,
             P},
   Title = {Convergent adaptation of human lactase persistence in Africa
             and Europe.},
   Journal = {Nature Genetics},
   Volume = {39},
   Number = {1},
   Pages = {31-40},
   Year = {2007},
   Month = {January},
   ISSN = {1061-4036},
   url = {http://dx.doi.org/10.1038/ng1946},
   Abstract = {A SNP in the gene encoding lactase (LCT) (C/T-13910) is
             associated with the ability to digest milk as adults
             (lactase persistence) in Europeans, but the genetic basis of
             lactase persistence in Africans was previously unknown. We
             conducted a genotype-phenotype association study in 470
             Tanzanians, Kenyans and Sudanese and identified three SNPs
             (G/C-14010, T/G-13915 and C/G-13907) that are associated
             with lactase persistence and that have derived alleles that
             significantly enhance transcription from the LCT promoter in
             vitro. These SNPs originated on different haplotype
             backgrounds from the European C/T-13910 SNP and from each
             other. Genotyping across a 3-Mb region demonstrated
             haplotype homozygosity extending >2.0 Mb on chromosomes
             carrying C-14010, consistent with a selective sweep over the
             past approximately 7,000 years. These data provide a marked
             example of convergent evolution due to strong selective
             pressure resulting from shared cultural traits-animal
             domestication and adult milk consumption.},
   Doi = {10.1038/ng1946},
   Key = {fds304342}
}

@article{fds231586,
   Author = {Babbitt, and CC, and Haygood, R and Wray, GA},
   Title = {When two is better than one},
   Journal = {Cell},
   Volume = {19},
   Number = {2},
   Pages = {3-4},
   Year = {2007},
   ISSN = {0092-8674},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17956721},
   Abstract = {Gene duplication and divergence has long been considered an
             important route to adaptation and phenotypic evolution.
             Reporting in Nature, Hittinger and Carroll (2007) provide
             the first clear example of adaptations in both regulatory
             regions and protein-coding regions after gene duplication.
             This combination of evolutionary changes appears to have
             resolved an adaptive conflict, leading to increased
             organismal fitness.},
   Doi = {10.1016/j.cell.2007.10.001},
   Key = {fds231586}
}

@article{fds231594,
   Author = {Tishkoff, and A, S and Reed, FA and Ranciaro, A and Voight, BF and Babbitt, CC and Silverman, JS and Powell, K and Mortensen, H and Hirbo,
             JB and Osman, M and Ibrahim, M and Omar, SA and Lema, G and N, TB and Ghori,
             J and Bumpstead, S and Pritchard, JK and Wray, GA and Deloukas,
             P},
   Title = {Convergent adaptation in humans: the genetic basis of
             lactase persistence in Africa},
   Journal = {Nature Genetics},
   Volume = {39},
   Number = {1},
   Pages = {31-40},
   Year = {2007},
   ISSN = {1061-4036},
   url = {http://dx.doi.org/10.1038/ng1946},
   Abstract = {A SNP in the gene encoding lactase (LCT) (C/T-13910) is
             associated with the ability to digest milk as adults
             (lactase persistence) in Europeans, but the genetic basis of
             lactase persistence in Africans was previously unknown. We
             conducted a genotype-phenotype association study in 470
             Tanzanians, Kenyans and Sudanese and identified three SNPs
             (G/C-14010, T/G-13915 and C/G-13907) that are associated
             with lactase persistence and that have derived alleles that
             significantly enhance transcription from the LCT promoter in
             vitro. These SNPs originated on different haplotype
             backgrounds from the European C/T-13910 SNP and from each
             other. Genotyping across a 3-Mb region demonstrated
             haplotype homozygosity extending >2.0 Mb on chromosomes
             carrying C-14010, consistent with a selective sweep over the
             past ∼7,000 years. These data provide a marked example of
             convergent evolution due to strong selective pressure
             resulting from shared cultural traits - animal domestication
             and adult milk consumption. © 2006 Nature Publishing
             Group.},
   Doi = {10.1038/ng1946},
   Key = {fds231594}
}

@article{fds231588,
   Author = {Nyberg, KG and Ciampaglio, CN and Wray, GA},
   Title = {Tracing the ancestry of the great white shark, Carcharodon
             carcharias, using morphometric analyses of fossil
             teeth},
   Journal = {Journal of Vertebrate Paleontology},
   Volume = {26},
   Number = {4},
   Pages = {806-814},
   Publisher = {Informa UK Limited},
   Year = {2006},
   Month = {December},
   ISSN = {0272-4634},
   url = {http://dx.doi.org/10.1671/0272-4634(2006)26[806:TTAOTG]2.0.CO;2},
   Abstract = {The evolutionary origin of the great white shark
             (Carcharodon carcharias) is unclear, with debate centering
             around two principal hypotheses. The first, based on
             similarity in tooth shape, claims that C. carcharias
             originated from a group of extinct mako sharks that includes
             Isurus hastalis. The second hypothesis, based mostly on
             cladistic evidence, claims that C. carcharias originated
             from the same lineage as the giant megatoothed sharks,
             sharing a close evolutionary ancestor with the extinct
             Carcharodon megalodon. To distinguish between the two
             hypotheses we performed several morphometric analyses. In
             the first analysis, we used Procrustes method and principal
             components analysis to quantify variation between C.
             carcharias, I. hastalis, and C. megalodon in four different
             positions within the dentition. The results indicate no
             significant difference in tooth shape between C. carcharias
             and I. hastalis. In the second analysis, correlating tooth
             size with age, we analyzed teeth from upper anterior and
             lower anterior positions. For both tooth positions, we show
             that the growth rate of C. carcharias is more congruent with
             the growth rate of I. hastalis than that of C. megalodon.
             Finally, we used scanning electron microscopy to show that
             the tooth serrations of C. carcharias are distinct from
             those of the megatooths and more similar in size to those of
             slightly serrated mako teeth. Taken together, these results
             indicate that C. carcharias originated from an extinct group
             of mako sharks and not from the megatoothed sharks. © 2006
             by the Society of Vertebrate Paleontology.},
   Doi = {10.1671/0272-4634(2006)26[806:TTAOTG]2.0.CO;2},
   Key = {fds231588}
}

@article{fds231485,
   Author = {Babbitt, CC and Wray, GA},
   Title = {Functional analysis of cis-regulatory evolution in humans
             and other primates},
   Journal = {Integrative and Comparative Biology},
   Volume = {46},
   Pages = {E6-E6},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2006},
   Month = {December},
   ISSN = {1540-7063},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000202970100024&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231485}
}

@article{fds231591,
   Author = {Sea Urchin Genome Sequencing Consortium, and Sodergren, E and Weinstock, GM and Davidson, EH and Cameron, RA and Gibbs, RA and Angerer, RC and Angerer, LM and Arnone, MI and Burgess, DR and Burke,
             RD and Coffman, JA and Dean, M and Elphick, MR and Ettensohn, CA and Foltz,
             KR and Hamdoun, A and Hynes, RO and Klein, WH and Marzluff, W and McClay,
             DR and Morris, RL and Mushegian, A and Rast, JP and Smith, LC and Thorndyke, MC and Vacquier, VD and Wessel, GM and Wray, G and Zhang, L and Elsik, CG and Ermolaeva, O and Hlavina, W and Hofmann, G and Kitts, P and Landrum, MJ and Mackey, AJ and Maglott, D and Panopoulou, G and Poustka,
             AJ and Pruitt, K and Sapojnikov, V and Song, X and Souvorov, A and Solovyev, V and Wei, Z and Whittaker, CA and Worley, K and Durbin, KJ and Shen, Y and Fedrigo, O and Garfield, D and Haygood, R and Primus, A and Satija, R and Severson, T and Gonzalez-Garay, ML and Jackson, AR and Milosavljevic, A and Tong, M and Killian, CE and Livingston, BT and Wilt, FH and Adams, N and Bellé, R and Carbonneau, S and Cheung, R and Cormier, P and Cosson, B and Croce, J and Fernandez-Guerra, A and Genevière, A-M and Goel, M and Kelkar, H and Morales, J and Mulner-Lorillon, O and Robertson, AJ and Goldstone, JV and Cole, B and Epel, D and Gold, B and Hahn, ME and Howard-Ashby, M and Scally, M and Stegeman, JJ and Allgood, EL and Cool, J and Judkins, KM and McCafferty,
             SS and Musante, AM and Obar, RA and Rawson, AP and Rossetti, BJ and Gibbons, IR and Hoffman, MP and Leone, A and Istrail, S and Materna, SC and Samanta, MP and Stolc, V and Tongprasit, W and Tu, Q and Bergeron, K-F and Brandhorst, BP and Whittle, J and Berney, K and Bottjer, DJ and Calestani, C and Peterson, K and Chow, E and Yuan, QA and Elhaik, E and Graur, D and Reese, JT and Bosdet, I and Heesun, S and Marra, MA and Schein, J and Anderson, MK and Brockton, V and Buckley, KM and Cohen,
             AH and Fugmann, SD and Hibino, T and Loza-Coll, M and Majeske, AJ and Messier, C and Nair, SV and Pancer, Z and Terwilliger, DP and Agca, C and Arboleda, E and Chen, N and Churcher, AM and Hallböök, F and Humphrey,
             GW and Idris, MM and Kiyama, T and Liang, S and Mellott, D and Mu, X and Murray, G and Olinski, RP and Raible, F and Rowe, M and Taylor, JS and Tessmar-Raible, K and Wang, D and Wilson, KH and Yaguchi, S and Gaasterland, T and Galindo, BE and Gunaratne, HJ and Juliano, C and Kinukawa, M and Moy, GW and Neill, AT and Nomura, M and Raisch, M and Reade, A and Roux, MM and Song, JL and Su, Y-H and Townley, IK and Voronina, E and Wong, JL and Amore, G and Branno, M and Brown, ER and Cavalieri, V and Duboc, V and Duloquin, L and Flytzanis, C and Gache, C and Lapraz, F and Lepage, T and Locascio, A and Martinez, P and Matassi, G and Matranga, V and Range, R and Rizzo, F and Röttinger, E and Beane, W and Bradham, C and Byrum, C and Glenn, T and Hussain, S and Manning, G and Miranda, E and Thomason, R and Walton, K and Wikramanayke, A and Wu,
             S-Y and Xu, R and Brown, CT and Chen, L and Gray, RF and Lee, PY and Nam, J and Oliveri, P and Smith, J and Muzny, D and Bell, S and Chacko, J and Cree, A and Curry, S and Davis, C and Dinh, H and Dugan-Rocha, S and Fowler, J and Gill, R and Hamilton, C and Hernandez, J and Hines, S and Hume, J and Jackson, L and Jolivet, A and Kovar, C and Lee, S and Lewis, L and Miner,
             G and Morgan, M and Nazareth, LV and Okwuonu, G and Parker, D and Pu, L-L and Thorn, R and Wright, R},
   Title = {The genome of the sea urchin Strongylocentrotus
             purpuratus.},
   Journal = {Science (New York, N.Y.)},
   Volume = {314},
   Number = {5801},
   Pages = {941-952},
   Year = {2006},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17095691},
   Abstract = {We report the sequence and analysis of the 814-megabase
             genome of the sea urchin Strongylocentrotus purpuratus, a
             model for developmental and systems biology. The sequencing
             strategy combined whole-genome shotgun and bacterial
             artificial chromosome (BAC) sequences. This use of BAC
             clones, aided by a pooling strategy, overcame difficulties
             associated with high heterozygosity of the genome. The
             genome encodes about 23,300 genes, including many previously
             thought to be vertebrate innovations or known only outside
             the deuterostomes. This echinoderm genome provides an
             evolutionary outgroup for the chordates and yields insights
             into the evolution of deuterostomes.},
   Doi = {10.1126/science.1133609},
   Key = {fds231591}
}

@article{fds231589,
   Author = {Loisel, DA and Rockman, MV and Wray, GA and Altmann, J and Alberts,
             SC},
   Title = {Ancient polymorphism and functional variation in the primate
             MHC-DQA1 5' cis-regulatory region.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {103},
   Number = {44},
   Pages = {16331-16336},
   Year = {2006},
   Month = {October},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17053068},
   Abstract = {Precise regulation of MHC gene expression is critical to
             vertebrate immune surveillance and response. Polymorphisms
             in the 5' proximal promoter region of the human class II
             gene HLA-DQA1 have been shown to influence its
             transcriptional regulation and may contribute to the
             pathogenesis of autoimmune diseases. We investigated the
             evolutionary history of this cis-regulatory region by
             sequencing the DQA1 5' proximal promoter region in eight
             nonhuman primate species. We observed unexpectedly high
             levels of sequence variation and multiple strong signatures
             of balancing selection in this region. Specifically, the
             considerable DQA1 promoter region diversity was
             characterized by abundant shared (or trans-species)
             polymorphism and a pronounced lack of fixed differences
             between species. The majority of transcription factor
             binding sites in the DQA1 promoter region were polymorphic
             within species, and these binding site polymorphisms were
             commonly shared among multiple species despite evidence for
             negative selection eliminating a significant fraction of
             binding site mutations. We assessed the functional
             consequences of intraspecific promoter region diversity
             using a cell line-based reporter assay and detected
             significant differences among baboon DQA1 promoter
             haplotypes in their ability to drive transcription in vitro.
             The functional differentiation of baboon promoter
             haplotypes, together with the significant deviations from
             neutral sequence evolution, suggests a role for balancing
             selection in the evolution of DQA1 transcriptional
             regulation in primates.},
   Doi = {10.1073/pnas.0607662103},
   Key = {fds231589}
}

@article{fds231592,
   Author = {Romano, LA and Wray, GA},
   Title = {Endo16 is required for gastrulation in the sea urchin
             Lytechinus variegatus.},
   Journal = {Development, Growth & Differentiation},
   Volume = {48},
   Number = {8},
   Pages = {487-497},
   Year = {2006},
   Month = {October},
   ISSN = {0012-1592},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17026713},
   Abstract = {The Endo16 gene encodes a large extracellular protein with
             several functional domains that provide some insight into
             the role of this protein during embryonic development. We
             isolated the full-length cDNA sequence from Lytechinus
             variegatus and utilized morpholinos to further investigate
             the role of Endo16 during embryonic development in this
             species. Endo16-deficient embryos failed to undergo
             gastrulation and the blastocoele became filled with
             dissociated cells after 24 h of incubation. Moreover, there
             was a delay in endoderm differentiation as assayed by
             staining with an antibody that recognizes Endo1. The
             differentiation of other cell types including oral ectoderm,
             primary mesenchymal cells (PMC) and secondary mesenchymal
             cells (SMC) appeared to be normal, although the patterns of
             protein expression did not resemble control embryos due to
             the gross morphological abnormalities elicited by the
             LvEndo16 morpholino. Microinjection of full-length EGFP mRNA
             with the LvEndo16 morpholino-targeted sequence confirmed
             that this phenotype can be attributed specifically to the
             loss of Endo16 protein. Taken together, our data suggest
             that Endo16 may be required for the cell-extracellular
             matrix (ECM) interactions that are required for endoderm
             differentiation in the sea urchin embryo.},
   Doi = {10.1111/j.1440-169x.2006.00884.x},
   Key = {fds231592}
}

@article{fds231590,
   Author = {Wray, GA},
   Title = {The evolution of embryonic gene expression in sea
             urchins.},
   Journal = {Integrative and Comparative Biology},
   Volume = {46},
   Number = {3},
   Pages = {233-242},
   Year = {2006},
   Month = {June},
   ISSN = {1540-7063},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21672738},
   Abstract = {Many evolutionary modifications in development and life
             history derive from changes in embryonic gene expression.
             However, the genetic variation affecting gene expression in
             natural populations is not well understood, nor are the
             evolutionary mechanisms that operate on that variation. The
             early embryonic gene network of the purple sea urchin
             (Strongylocentrotus purpuratus) has been studied in
             considerable detail, providing an informative basis for
             analyzing the developmental and evolutionary mechanisms that
             alter gene expression. Comparative functional analyses have
             been carried out for several genes. These case studies
             indicate a complex relationship between sequence divergence
             and gene expression: in some cases, gene expression is
             conserved despite extensive divergence in cis-regulatory
             sequences, while in others the basis for a change in gene
             expression does not reside locally but rather in the
             expression or activity of transcription factors that
             regulate its expression. Diverse evolutionary mechanisms
             apparently operate on cis-regulatory regions, including
             negative, balancing, and stabilizing selection.},
   Doi = {10.1093/icb/icj030},
   Key = {fds231590}
}

@article{fds304341,
   Author = {Wray, GA},
   Title = {Evolution: spot on (and off).},
   Journal = {Nature},
   Volume = {440},
   Number = {7087},
   Pages = {1001-1002},
   Year = {2006},
   Month = {April},
   ISSN = {0028-0836},
   url = {http://dx.doi.org/10.1038/4401001a},
   Doi = {10.1038/4401001a},
   Key = {fds304341}
}

@article{fds231595,
   Author = {Rudd, MK and Wray, GA and Willard, HF},
   Title = {The evolutionary dynamics of alpha-satellite.},
   Journal = {Genome Research},
   Volume = {16},
   Number = {1},
   Pages = {88-96},
   Year = {2006},
   Month = {January},
   ISSN = {1088-9051},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16344556},
   Abstract = {Alpha-satellite is a family of tandemly repeated sequences
             found at all normal human centromeres. In addition to its
             significance for understanding centromere function,
             alpha-satellite is also a model for concerted evolution, as
             alpha-satellite repeats are more similar within a species
             than between species. There are two types of alpha-satellite
             in the human genome; while both are made up of approximately
             171-bp monomers, they can be distinguished by whether
             monomers are arranged in extremely homogeneous higher-order,
             multimeric repeat units or exist as more divergent monomeric
             alpha-satellite that lacks any multimeric periodicity. In
             this study, as a model to examine the genomic and
             evolutionary relationships between these two types, we have
             focused on the chromosome 17 centromeric region that has
             reached both higher-order and monomeric alpha-satellite in
             the human genome assembly. Monomeric and higher-order
             alpha-satellites on chromosome 17 are phylogenetically
             distinct, consistent with a model in which higher-order
             evolved independently of monomeric alpha-satellite.
             Comparative analysis between human chromosome 17 and the
             orthologous chimpanzee chromosome indicates that monomeric
             alpha-satellite is evolving at approximately the same rate
             as the adjacent non-alpha-satellite DNA. However,
             higher-order alpha-satellite is less conserved, suggesting
             different evolutionary rates for the two types of
             alpha-satellite.},
   Doi = {10.1101/gr.3810906},
   Key = {fds231595}
}

@article{fds231593,
   Author = {Sumrall, CD and Wray, GA},
   Title = {Developmental control of ambulacral reduction in fossil
             echinoderms},
   Journal = {Paleobiology},
   Volume = {33},
   Pages = {149-163},
   Year = {2006},
   Key = {fds231593}
}

@article{fds231596,
   Author = {Wray, GA},
   Title = {Spot on (and off)},
   Journal = {Nature},
   Volume = {440},
   Number = {7087},
   Pages = {1001-1002},
   Year = {2006},
   ISSN = {0028-0836},
   url = {http://dx.doi.org/10.1038/4401001a},
   Doi = {10.1038/4401001a},
   Key = {fds231596}
}

@article{fds231546,
   Author = {Rockman, MV and Hahn, MW and Soranzo, N and Zimprich, F and Goldstein,
             DB and Wray, GA},
   Title = {Ancient and recent positive selection transformed opioid
             cis-regulation in humans.},
   Journal = {Plos Biology},
   Volume = {3},
   Number = {12},
   Pages = {e387},
   Year = {2005},
   Month = {December},
   ISSN = {1545-7885},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16274263},
   Abstract = {Changes in the cis-regulation of neural genes likely
             contributed to the evolution of our species' unique
             attributes, but evidence of a role for natural selection has
             been lacking. We found that positive natural selection
             altered the cis-regulation of human prodynorphin, the
             precursor molecule for a suite of endogenous opioids and
             neuropeptides with critical roles in regulating perception,
             behavior, and memory. Independent lines of phylogenetic and
             population genetic evidence support a history of selective
             sweeps driving the evolution of the human prodynorphin
             promoter. In experimental assays of chimpanzee-human hybrid
             promoters, the selected sequence increases transcriptional
             inducibility. The evidence for a change in the response of
             the brain's natural opioids to inductive stimuli points to
             potential human-specific characteristics favored during
             evolution. In addition, the pattern of linked nucleotide and
             microsatellite variation among and within modern human
             populations suggests that recent selection, subsequent to
             the fixation of the human-specific mutations and the
             peopling of the globe, has favored different prodynorphin
             cis-regulatory alleles in different parts of the
             world.},
   Doi = {10.1371/journal.pbio.0030387},
   Key = {fds231546}
}

@article{fds231597,
   Author = {Mooi, R and David, B and Wray, GA},
   Title = {Arrays in rays: terminal addition in echinoderms and its
             correlation with gene expression.},
   Journal = {Evolution & Development},
   Volume = {7},
   Number = {6},
   Pages = {542-555},
   Year = {2005},
   Month = {November},
   ISSN = {1520-541X},
   url = {http://dx.doi.org/10.1111/j.1525-142x.2005.05058.x},
   Abstract = {The echinoderms are deuterostomes that superimpose radial
             symmetry upon bilateral larval morphology. Consequently,
             they are not the first animals that come to mind when the
             concepts of segmentation and terminal addition are being
             discussed. However, it has long been recognized that
             echinoderms have serial elements along their radii formed in
             accordance with the ocular plate rule (OPR). The OPR is a
             special case of terminal growth, forming elements of the
             ambulacra that define the rays in echinoderms. New elements
             are added at the terminus of the ray, which may or may not
             be marked by a calcified element called the terminal plate
             (the "ocular" of sea urchins). The OPR operates in every
             echinoderm, from the occasionally bizarre fossils of the
             Cambrian to the most familiar extant taxa. Using the OPR and
             other criteria of recognition, echinoderm body wall can be
             divided into two main regions: extraxial components are
             associated with the somatocoels, axial components (formed in
             accordance with the OPR) with the hydrocoel. We compare
             patterns of development in axial regions of echinoderms with
             those found in the anterior-posterior axes of the earliest
             echinoderms as well as other invertebrates. Although axial
             and extraxial skeletons appear to be composed of the same
             biomineral matrix, the genes involved in patterning these
             two skeletal components are likely distinct. During
             development of the axial skeleton, for instance, the genes
             engrailed and orthodenticle are expressed in spatial and
             temporal patterns consistent with the OPR. Other genes such
             as distal-less seem to demarcate early ontogenetic
             boundaries between the axial rudiment and the extraxial
             larval body. There is a complex and pervasive reorganization
             of gene expression domains to produce the highly divergent
             morphologies seen in the Echinodermata. We integrate
             morphological and genetic information, particularly with
             respect to the origins of radial symmetry in the rudiment,
             and the concomitant development of the rays.},
   Doi = {10.1111/j.1525-142x.2005.05058.x},
   Key = {fds231597}
}

@article{fds231530,
   Author = {Balhoff, JP and Wray, GA},
   Title = {Evolutionary analysis of the well characterized endo16
             promoter reveals substantial variation within functional
             sites.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {102},
   Number = {24},
   Pages = {8591-8596},
   Year = {2005},
   Month = {June},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15937122},
   Abstract = {The evolutionary mechanisms that operate on genetic
             variation within transcriptional regulatory sequences are
             not well understood. We present here an evolutionary
             analysis of an exceptionally well characterized
             cis-regulatory region, the endo16 promoter of the purple sea
             urchin. Segregating variation reveals striking differences
             in the intensity of negative selection among regulatory
             modules, reflecting their distinct functional roles.
             Surprisingly, transcription-factor-binding sites are as
             polymorphic and as likely to contain fixed differences as
             flanking nucleotides. Whereas nucleotides in protein-binding
             sites in the most proximal regulatory module exhibit reduced
             variation, those in other modules tend to be more
             polymorphic than putatively nonfunctional nucleotides. Two
             unrelated large insertions at the same position within the
             promoter are segregating at low frequencies; one is a strong
             ectodermal repressor that contains 16 verified
             transcription-factor-binding sites. These results
             demonstrate that a simple relationship between conservation
             and function does not exist within this cis-regulatory
             region and highlight significant population heterogeneity in
             the fine structure of a well understood promoter.},
   Doi = {10.1073/pnas.0409638102},
   Key = {fds231530}
}

@article{fds231484,
   Author = {Wray, GA},
   Title = {Evolutionary mechanisms that operate on embryonic gene
             expression in purple sea urchin Strongylocentrotus
             purpuratus},
   Journal = {Integrative and Comparative Biology},
   Volume = {44},
   Number = {6},
   Pages = {668-668},
   Publisher = {OXFORD UNIV PRESS INC},
   Year = {2004},
   Month = {December},
   ISSN = {1540-7063},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000226721401176&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231484}
}

@article{fds231605,
   Author = {Rockman, MV and Hahn, MW and Soranzo, N and Loisel, DA and Goldstein,
             DB and Wray, GA},
   Title = {Positive selection on MMP3 regulation has shaped heart
             disease risk.},
   Journal = {Current Biology : Cb},
   Volume = {14},
   Number = {17},
   Pages = {1531-1539},
   Year = {2004},
   Month = {September},
   ISSN = {0960-9822},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15341739},
   Abstract = {The evolutionary forces of mutation, natural selection, and
             genetic drift shape the pattern of phenotypic variation in
             nature, but the roles of these forces in defining the
             distributions of particular traits have been hard to
             disentangle. To better understand the mechanisms
             contributing to common variation in humans, we investigated
             the evolutionary history of a functional polymorphism in the
             upstream regulatory region of the MMP3 gene. This single
             base pair insertion/deletion variant, which results in a run
             of either 5 or 6 thymidines 1608 bp from the transcription
             start site, alters transcription factor binding and
             influences levels of MMP3 mRNA and protein. The polymorphism
             contributes to variation in arterial traits and to the risk
             of coronary heart disease and its progression.Phylogenetic
             and population genetic analysis of primate sequences
             indicate that the binding site region is rapidly evolving
             and has been a hot spot for mutation for tens of millions of
             years. We also find evidence for the action of positive
             selection, beginning approximately 24,000 years ago,
             increasing the frequency of the high-expression allele in
             Europe but not elsewhere. Positive selection is evident in
             statistical tests of differentiation among populations and
             haplotype diversity within populations. Europeans have
             greater arterial elasticity and suffer dramatically fewer
             coronary heart disease events than they would have had this
             selection not occurred.Locally elevated mutation rates and
             strong positive selection on a cis-regulatory variant have
             shaped contemporary phenotypic variation and public
             health.},
   Doi = {10.1016/j.cub.2004.08.051},
   Key = {fds231605}
}

@article{fds231608,
   Author = {Hahn, MW and Rockman, MV and Soranzo, N and Goldstein, DB and Wray,
             GA},
   Title = {Population genetic and phylogenetic evidence for positive
             selection on regulatory mutations at the factor VII locus in
             humans.},
   Journal = {Genetics},
   Volume = {167},
   Number = {2},
   Pages = {867-877},
   Year = {2004},
   Month = {June},
   ISSN = {0016-6731},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15238535},
   Abstract = {The abundance of cis-regulatory polymorphisms in humans
             suggests that many may have been important in human
             evolution, but evidence for their role is relatively rare.
             Four common polymorphisms in the 5' promoter region of
             factor VII (F7), a coagulation factor, have been shown to
             affect its transcription and protein abundance both in vitro
             and in vivo. Three of these polymorphisms have low-frequency
             alleles that decrease expression of F7 and may provide
             protection against myocardial infarction (heart attacks).
             The fourth polymorphism has a minor allele that increases
             the level of transcription. To look for evidence of natural
             selection on the cis-regulatory variants flanking F7, we
             genotyped three of the polymorphisms in six Old World
             populations for which we also have data from a group of
             putatively neutral SNPs. Our population genetic analysis
             shows evidence for selection within humans; surprisingly,
             the strongest evidence is due to a large increase in
             frequency of the high-expression variant in Singaporean
             Chinese. Further characterization of a Japanese population
             shows that at least part of the increase in frequency of the
             high-expression allele is found in other East Asian
             populations. In addition, to examine interspecific patterns
             of selection we sequenced the homologous 5' noncoding region
             in chimpanzees, bonobos, a gorilla, an orangutan, and a
             baboon. Analysis of these data reveals an excess of fixed
             differences within transcription factor binding sites along
             the human lineage. Our results thus further support the
             hypothesis that regulatory mutations have been important in
             human evolution.},
   Doi = {10.1534/genetics.103.025726},
   Key = {fds231608}
}

@article{fds231526,
   Author = {Levinton, J and Dubb, L and Wray, GA},
   Title = {Simulations of evolutionary radiations and their application
             to understanding the probability of a Cambrian
             explosion},
   Journal = {Journal of Paleontology},
   Volume = {78},
   Number = {1},
   Pages = {31-38},
   Publisher = {Cambridge University Press (CUP)},
   Year = {2004},
   Month = {January},
   url = {http://dx.doi.org/10.1666/0022-3360(2004)078<0031:SOERAT>2.0.CO;2},
   Abstract = {A molecular survey of animal phylogeny (Wray et al., 1996)
             recovered the presumed correct temporal order of the
             phylogenetic splits Protostomata- Deuterostomata,
             Echinodermata-Chordata, and Agnatha-Gnathostomata in studies
             of six of seven gene sequences. This result raised the
             question of how this order could be recovered if all of the
             phyla had appeared in a Cambrian "explosion" of less than 10
             m.y., given the expected erratic nature of the molecular
             "clock." We simulated trees, and molecular sequence
             evolution along the trees, under different evolutionary
             radiation scenarios, with different periods of radiation,
             relative to times of subsequent evolution. Simulations and
             phylogenetic analyses of sequences derived from a simulated
             "Cambrian explosion" of 10-35 million years did not allow
             the successful recovery of the correct tree, using
             neighbor-joining, maximum likelihood, or parsimony methods.
             Success in recovering phylogenies under a Cambrian
             divergence scenario (520 million years ago) did not exceed
             80 percent without an extended divergence time interval of
             at least 100 m.y. An increased substitution rate during the
             initial radiation improved the ability to recover correct
             phylogenies, especially when the rate was 8-10 times the
             rate following the radiation. Our results militate against
             the likelihood of an Early Cambrian or slightly longer
             explosion of the animal phyla, as apparently supported by
             the fossil record. Some limitations to these conclusions are
             discussed.},
   Doi = {10.1666/0022-3360(2004)078<0031:SOERAT>2.0.CO;2},
   Key = {fds231526}
}

@article{fds231527,
   Author = {Bely, AE and Wray, GA},
   Title = {Molecular phylogeny of naidid worms (Annelida: Clitellata)
             based on cytochrome oxidase I.},
   Journal = {Molecular Phylogenetics and Evolution},
   Volume = {30},
   Number = {1},
   Pages = {50-63},
   Year = {2004},
   Month = {January},
   ISSN = {1055-7903},
   url = {http://dx.doi.org/10.1016/s1055-7903(03)00180-5},
   Abstract = {Naidids are tiny, primarily freshwater oligochaete annelids
             which reproduce asexually by fission. We investigated the
             phylogenetic relationships within this group by sequencing
             1224 bp of the mitochondrial gene cytochrome oxidase I (COI)
             from 26 species of naidids (representing 13 of the 23 genera
             currently recognized), as well as from four tubificids,
             their closest allies. Although not completely concordant,
             maximum parsimony and Bayesian inference analyses agreed in
             several important respects, with no well-supported
             conflicts. Our study, the first detailed molecular
             investigation of naidid relationships, suggests that naidids
             fall into two groups, one comprised of the genus Pristina,
             and another comprised of all other genera sampled. The clear
             division of naidids into these two groups best matches an
             early, simple classification of the group by Lastockin
             (1924); the more recent classifications proposed by Sperber
             (1948) and Nemec and Brinkhurst (1987) are not as consistent
             with our results. We note that our study suggests the genus
             Stylaria is comprised of two distinct species, Stylaria
             lacustris and Stylaria fossularis, rather than merely two
             morphotypes of a single species. Based on our phylogenetic
             results, we suggest that pigmented eyes evolved only once
             among naidids but must have been lost multiple times, and
             that the elongation of the prostomium into a proboscis
             evolved at least twice independently. The simplest form of
             fission, architomy (fragmentation), occurs in two of the
             most basally branching naidid genera, and may represent the
             plesiomorphic condition for naidids.},
   Doi = {10.1016/s1055-7903(03)00180-5},
   Key = {fds231527}
}

@article{fds231528,
   Author = {Ettensohn, CA and Wessel, GM and Wray, GA},
   Title = {The invertebrate deuterostomes: an introduction to their
             phylogeny, reproduction, development, and
             genomics.},
   Journal = {Methods in Cell Biology},
   Volume = {74},
   Pages = {1-13},
   Year = {2004},
   Month = {January},
   ISSN = {0091-679X},
   url = {http://dx.doi.org/10.1016/s0091-679x(04)74001-7},
   Doi = {10.1016/s0091-679x(04)74001-7},
   Key = {fds231528}
}

@article{fds231529,
   Author = {Wray, GA and Kitazawa, C and Miner, B},
   Title = {Culture of echinoderm larvae through metamorphosis.},
   Journal = {Methods in Cell Biology},
   Volume = {74},
   Pages = {75-86},
   Year = {2004},
   Month = {January},
   ISSN = {0091-679X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15575603},
   Doi = {10.1016/s0091-679x(04)74004-2},
   Key = {fds231529}
}

@article{fds29612,
   Author = {Wray, G. A. and C. Kitazawa and B. Miner},
   Title = {Culture of echinoderm larvae though metamorphosis},
   Pages = {75-86},
   Booktitle = {Development of Sea Urchins, Ascidians, and Other
             Invertebrate Deuterostomes: Experimental
             Approaches},
   Publisher = {Academic Press, San Diego CA},
   Year = {2004},
   Key = {fds29612}
}

@article{fds231607,
   Author = {Bely, AE and Wray, GA},
   Title = {Molecular phylogeny of naidid worms (Annelida:
             Clitellata)},
   Journal = {Molecular Phylogeny and Evolution},
   Volume = {30},
   Pages = {50-63},
   Year = {2004},
   Key = {fds231607}
}

@article{fds231609,
   Author = {Rockman, MV and Hahn, MW and Soranzo, N and Goldstein, DB and Wray,
             GA},
   Title = {Positive selection on a human-specific transcription factor
             binding site regulating IL4 expression.},
   Journal = {Current Biology : Cb},
   Volume = {13},
   Number = {23},
   Pages = {2118-2123},
   Year = {2003},
   Month = {December},
   ISSN = {0960-9822},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14654003},
   Abstract = {A single nucleotide polymorphism in the promoter of the
             multifunctional cytokine Interleukin 4 (IL4) affects the
             binding of NFAT, a key transcriptional activator of IL4 in T
             cells. This regulatory polymorphism influences the balance
             of cytokine signaling in the immune system, with important
             consequences-positive and negative-for human health. We
             determined that the NFAT binding site is unique to humans;
             it arose by point mutation along the lineage separating
             humans from other great apes. We show that its frequency
             distribution among human subpopulations has been shaped by
             the balance of selective forces on IL4's diverse roles. New
             statistical approaches, based on parametric and
             nonparametric comparisons to neutral variants typed in the
             same individuals, indicate that differentiation among
             subpopulations at the IL4 promoter polymorphism is too great
             to be attributed to neutral drift. The allele frequencies of
             this binding site represent local adaptation to diverse
             pathogenic challenges; disease states associated with the
             common derived allele are side-effects of positive selection
             on other IL4 functions.},
   Doi = {10.1016/j.cub.2003.11.025},
   Key = {fds231609}
}

@article{fds231611,
   Author = {Romano, LA and Wray, GA},
   Title = {Conservation of Endo16 expression in sea urchins despite
             evolutionary divergence in both cis and trans-acting
             components of transcriptional regulation.},
   Journal = {Development (Cambridge, England)},
   Volume = {130},
   Number = {17},
   Pages = {4187-4199},
   Year = {2003},
   Month = {September},
   ISSN = {0950-1991},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12874137},
   Abstract = {Evolutionary changes in transcriptional regulation
             undoubtedly play an important role in creating morphological
             diversity. However, there is little information about the
             evolutionary dynamics of cis-regulatory sequences. This
             study examines the functional consequence of evolutionary
             changes in the Endo16 promoter of sea urchins. The Endo16
             gene encodes a large extracellular protein that is expressed
             in the endoderm and may play a role in cell adhesion. Its
             promoter has been characterized in exceptional detail in the
             purple sea urchin, Strongylocentrotus purpuratus. We have
             characterized the structure and function of the Endo16
             promoter from a second sea urchin species, Lytechinus
             variegatus. The Endo16 promoter sequences have evolved in a
             strongly mosaic manner since these species diverged
             approximately 35 million years ago: the most proximal region
             (module A) is conserved, but the remaining modules (B-G) are
             unalignable. Despite extensive divergence in promoter
             sequences, the pattern of Endo16 transcription is largely
             conserved during embryonic and larval development. Transient
             expression assays demonstrate that 2.2 kb of upstream
             sequence in either species is sufficient to drive GFP
             reporter expression that correctly mimics this pattern of
             Endo16 transcription. Reciprocal cross-species transient
             expression assays imply that changes have also evolved in
             the set of transcription factors that interact with the
             Endo16 promoter. Taken together, these results suggest that
             stabilizing selection on the transcriptional output may have
             operated to maintain a similar pattern of Endo16 expression
             in S. purpuratus and L. variegatus, despite dramatic
             divergence in promoter sequence and mechanisms of
             transcriptional regulation.},
   Doi = {10.1242/dev.00611},
   Key = {fds231611}
}

@article{fds231612,
   Author = {Wray, GA and Hahn, MW and Abouheif, E and Balhoff, JP and Pizer, M and Rockman, MV and Romano, LA},
   Title = {The evolution of transcriptional regulation in
             eukaryotes.},
   Journal = {Molecular Biology and Evolution},
   Volume = {20},
   Number = {9},
   Pages = {1377-1419},
   Year = {2003},
   Month = {September},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12777501},
   Abstract = {Gene expression is central to the genotype-phenotype
             relationship in all organisms, and it is an important
             component of the genetic basis for evolutionary change in
             diverse aspects of phenotype. However, the evolution of
             transcriptional regulation remains understudied and poorly
             understood. Here we review the evolutionary dynamics of
             promoter, or cis-regulatory, sequences and the evolutionary
             mechanisms that shape them. Existing evidence indicates that
             populations harbor extensive genetic variation in promoter
             sequences, that a substantial fraction of this variation has
             consequences for both biochemical and organismal phenotype,
             and that some of this functional variation is sorted by
             selection. As with protein-coding sequences, rates and
             patterns of promoter sequence evolution differ considerably
             among loci and among clades for reasons that are not well
             understood. Studying the evolution of transcriptional
             regulation poses empirical and conceptual challenges beyond
             those typically encountered in analyses of coding sequence
             evolution: promoter organization is much less regular than
             that of coding sequences, and sequences required for the
             transcription of each locus reside at multiple other loci in
             the genome. Because of the strong context-dependence of
             transcriptional regulation, sequence inspection alone
             provides limited information about promoter function.
             Understanding the functional consequences of sequence
             differences among promoters generally requires biochemical
             and in vivo functional assays. Despite these challenges,
             important insights have already been gained into the
             evolution of transcriptional regulation, and the pace of
             discovery is accelerating.},
   Doi = {10.1093/molbev/msg140},
   Key = {fds231612}
}

@article{fds231610,
   Author = {Knott, KE and Balser, EJ and Jaeckle, WB and Wray,
             GA},
   Title = {Identification of asteroid genera with species capable of
             larval cloning.},
   Journal = {The Biological Bulletin},
   Volume = {204},
   Number = {3},
   Pages = {246-255},
   Year = {2003},
   Month = {June},
   url = {http://dx.doi.org/10.2307/1543596},
   Abstract = {Asexual reproduction in larvae, larval cloning, is a
             recently recognized component of the complex life histories
             of asteroids. We compare DNA sequences of mitochondrial tRNA
             genes (Ala, Leu, Asn, Pro, and Gln) from larvae in the
             process of cloning collected in the field with sequences
             from adults of known species in order to identify asteroid
             taxa capable of cloning. Neighbor-joining analysis
             identified four distinct groups of larvae, each having no,
             or very little, sequence divergence (p distances ranging
             from 0.00000 to 0.02589); thus, we conclude that each larval
             group most likely represents a single species. These
             field-collected larvae cannot be identified to species with
             certainty, but the close assemblage of known taxa with the
             four larval groups indicates generic or familial identity.
             We can assign two of the larval groups discerned here to the
             genera Luidia and Oreaster and another two to the family
             Ophidiasteridae. This study is the first to identify
             field-collected cloning asteroid larvae, and provides
             evidence that larval cloning is phylogenetically widespread
             within the Asteroidea. Additionally, we note that cloning
             occurs regularly and in multiple ways within species that
             are capable of cloning, emphasizing the need for further
             investigation of the role of larval cloning in the ecology
             and evolution of asteroids.},
   Doi = {10.2307/1543596},
   Key = {fds231610}
}

@article{fds231613,
   Author = {Hahn, MW and Stajich, JE and Wray, GA},
   Title = {The effects of selection against spurious transcription
             factor binding sites.},
   Journal = {Molecular Biology and Evolution},
   Volume = {20},
   Number = {6},
   Pages = {901-906},
   Year = {2003},
   Month = {June},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12716998},
   Abstract = {Most genomes contain nucleotide sequences with no known
             function; such sequences are assumed to be free of
             constraints, evolving only according to the vagaries of
             mutation. Here we show that selection acts to remove
             spurious transcription factor binding site motifs throughout
             52 fully sequenced genomes of Eubacteria and Archaea.
             Examining the sequences necessary for polymerase binding, we
             find that spurious binding sites are underrepresented in
             both coding and noncoding regions. The average proportion of
             spurious binding sites found relative to the expected is 80%
             in eubacterial genomes and 89% in archaeal genomes. We also
             estimate the strength of selection against spurious binding
             sites in the face of the constant creation of new binding
             sites via mutation. Under conservative assumptions, we
             estimate that selection is weak, with the average efficacy
             of selection against spurious binding sites, Nes, of -0.12
             for eubacterial genomes and -0.06 for archaeal genomes,
             similar to that of codon bias. Our results suggest that both
             coding and noncoding sequences are constrained by selection
             to avoid specific regions of sequence space.},
   Doi = {10.1093/molbev/msg096},
   Key = {fds231613}
}

@article{fds231606,
   Author = {Wray, GA},
   Title = {Transcriptional regulation and the evolution of
             development.},
   Journal = {The International Journal of Developmental
             Biology},
   Volume = {47},
   Number = {7-8},
   Pages = {675-684},
   Year = {2003},
   Month = {January},
   ISSN = {0214-6282},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14756343},
   Abstract = {A growing body of evidence suggests that changes in
             transcriptional regulation form an important part of the
             genetic basis for the evolution of development. At a
             microevolutionary level, all the necessary conditions are
             present: populations harbor abundant genetic variation for
             differences in transcription profiles, a substantial
             fraction of these variants can influence organismal
             phenotype, and some variants have fitness consequences and
             are subject to natural selection. At a macroevolutionary
             level, the evidence is less direct but strongly suggestive:
             specific differences in anatomy and gene expression are
             often correlated, while comparisons of transcription
             profiles among distantly related taxa point to extensive
             evolutionary changes in regulatory gene networks.
             Understanding how transcriptional regulatory systems evolve,
             and what contributions these changes have made to the
             evolution of phenotype, represents a major challenge for
             Evo-Devo.},
   Key = {fds231606}
}

@article{fds5030,
   Author = {Wray, G.A.},
   Title = {Transcriptional regulation: evolution},
   Booktitle = {Encyclopedia of the Human Genome},
   Publisher = {Nature Publishing Group},
   Editor = {D. Cooper},
   Year = {2003},
   Key = {fds5030}
}

@article{fds231525,
   Author = {Wray, GA and Strathmann, RR},
   Title = {Stasis, change, and functional constraint in the evolution
             of animal body plans, whatever they may be},
   Journal = {Vie Et Milieu},
   Volume = {52},
   Number = {4},
   Pages = {189-199},
   Year = {2002},
   Month = {December},
   Abstract = {The phrase "body plan" or "bauplan" has been used to mean
             (1) the characteristic features of a phylum or other taxon
             of high rank, (2) architectural features of animals (such as
             symmetry; modular units; types of body walls, body cavities,
             body openings, and body subdivisions; types of supporting
             structures; position and structure of organ systems), (3)
             traits characteristic of an especially invariant stage in a
             life history (phylotypic stage), or (4) patterns of gene
             expression that first indicate the development of regions of
             the body. Multiple meanings of bodyplan within one argument
             can be misleading, but under all four meanings, body plans
             of animals have changed after stasis for long periods and
             after stasis during divergence of other traits. Change in
             body plans is often associated with an identifiable change
             in a functional constraint. Examples include decreases in
             body size and changes in requirements for feeding or
             locomotion. These observations support the hypothesis that
             functional constraints contribute to stasis in body plans.
             There is evidence that ancestral developmental processes
             constrain directions of evolutionary changes in body plans.
             There is little evidence that developmental processes
             prevent changes in body plans, but evidence for
             developmental constraint is more difficult to obtain than
             evidence for functional constraint.},
   Key = {fds231525}
}

@article{fds231617,
   Author = {Rockman, MV and Wray, GA},
   Title = {Abundant raw material for cis-regulatory evolution in
             humans.},
   Journal = {Molecular Biology and Evolution},
   Volume = {19},
   Number = {11},
   Pages = {1991-2004},
   Year = {2002},
   Month = {November},
   ISSN = {0737-4038},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12411608},
   Abstract = {Changes in gene expression and regulation--due in particular
             to the evolution of cis-regulatory DNA sequences--may
             underlie many evolutionary changes in phenotypes, yet little
             is known about the distribution of such variation in
             populations. We present in this study the first survey of
             experimentally validated functional cis-regulatory
             polymorphism. These data are derived from more than 140
             polymorphisms involved in the regulation of 107 genes in
             Homo sapiens, the eukaryote species with the most available
             data. We find that functional cis-regulatory variation is
             widespread in the human genome and that the consequent
             variation in gene expression is twofold or greater for 63%
             of the genes surveyed. Transcription factor-DNA interactions
             are highly polymorphic, and regulatory interactions have
             been gained and lost within human populations. On average,
             humans are heterozygous at more functional cis-regulatory
             sites (>16,000) than at amino acid positions (<13,000), in
             part because of an overrepresentation among the former in
             multiallelic tandem repeat variation, especially (AC)(n)
             dinucleotide microsatellites. The role of microsatellites in
             gene expression variation may provide a larger store of
             heritable phenotypic variation, and a more rapid mutational
             input of such variation, than has been realized. Finally, we
             outline the distinctive consequences of cis-regulatory
             variation for the genotype-phenotype relationship, including
             ubiquitous epistasis and genotype-by-environment
             interactions, as well as underappreciated modes of
             pleiotropy and overdominance. Ordinary small-scale mutations
             contribute to pervasive variation in transcription rates and
             consequently to patterns of human phenotypic
             variation.},
   Doi = {10.1093/oxfordjournals.molbev.a004023},
   Key = {fds231617}
}

@article{fds231614,
   Author = {Bely, AE and Wray, GA},
   Title = {Getting a head in the world},
   Journal = {Natural History},
   Volume = {10/02},
   Pages = {30-32},
   Year = {2002},
   Month = {October},
   Key = {fds231614}
}

@article{fds231476,
   Author = {Wray, GA},
   Title = {Evolution of a well-characterized embryonic promoter: the
             Endo16 cis-regulatory system of sea urchins.},
   Journal = {Developmental Biology},
   Volume = {247},
   Number = {2},
   Pages = {519-519},
   Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
   Year = {2002},
   Month = {July},
   ISSN = {0012-1606},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000176830700339&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231476}
}

@article{fds231618,
   Author = {Abouheif, E and Wray, GA},
   Title = {Evolution of the gene network underlying wing polyphenism in
             ants.},
   Journal = {Science (New York, N.Y.)},
   Volume = {297},
   Number = {5579},
   Pages = {249-252},
   Year = {2002},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12114626},
   Abstract = {Wing polyphenism in ants evolved once, 125 million years
             ago, and has been a key to their amazing evolutionary
             success. We characterized the expression of several genes
             within the network underlying the wing primordia of
             reproductive (winged) and sterile (wingless) ant castes. We
             show that the expression of several genes within the network
             is conserved in the winged castes of four ant species,
             whereas points of interruption within the network in the
             wingless castes are evolutionarily labile. The simultaneous
             evolutionary lability and conservation of the network
             underlying wing development in ants may have played an
             important role in the morphological diversification of this
             group and may be a general feature of polyphenic development
             and evolution in plants and animals.},
   Doi = {10.1126/science.1071468},
   Key = {fds231618}
}

@article{fds231522,
   Author = {Lowe, CJ and Issel-Tarver, L and Wray, GA},
   Title = {Gene expression and larval evolution: changing roles of
             distal-less and orthodenticle in echinoderm
             larvae.},
   Journal = {Evolution & Development},
   Volume = {4},
   Number = {2},
   Pages = {111-123},
   Year = {2002},
   Month = {March},
   ISSN = {1520-541X},
   url = {http://dx.doi.org/10.1046/j.1525-142x.2002.01066.x},
   Abstract = {We describe the expression of the homeobox genes
             orthodenticle (Otx) and distal-less (Dlx) during the larval
             development of seven species representing three classes of
             echinoderms: Holothuroidea, Asteroidea, and Echinoidea.
             Several expression domains are conserved between species
             within a single class, including Dlx expression within the
             brachiolar arms of asteroid larvae and Otx expression within
             the ciliated bands of holothuroid larvae. Some expression
             domains are apparently conserved between classes, such as
             the expression of Dlx within the hydrocoel (left mesocoel)
             in all three classes. However, several substantial
             differences in expression domains among taxa were also
             evident for both genes. Some autapomorphic (unique derived)
             features of gene expression are phylogenetically associated
             with autapomorphic structures, such as Dlx expression within
             the invaginating rudiment of euechinoids. Other
             autapomorphic gene expression domains are associated with
             evolutionary shifts in life history from feeding to
             nonfeeding larval development, such as Otx expression within
             the ciliated bands of a nonfeeding holothuroid larva.
             Similar associations between evolutionary changes in
             morphology and life history mode with changes in regulatory
             gene expression have also been observed in arthropods,
             urochordates, and chordates. We predict that recruitment of
             regulatory genes to a new developmental role is commonly
             associated with evolutionary changes in morphology and may
             be particularly common in clades with complex life cycles
             and diversity of life history modes. Caution should be used
             when making generalizations about gene expression and
             function based on a single species, which may not accurately
             reflect developmental processes and life histories of the
             phyla to which it belongs.},
   Doi = {10.1046/j.1525-142x.2002.01066.x},
   Key = {fds231522}
}

@article{fds231615,
   Author = {Hahn, MW and Wray, GA},
   Title = {The g-value paradox.},
   Journal = {Evolution & Development},
   Volume = {4},
   Number = {2},
   Pages = {73-75},
   Year = {2002},
   Month = {March},
   ISSN = {1520-541X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12004964},
   Doi = {10.1046/j.1525-142x.2002.01069.x},
   Key = {fds231615}
}

@article{fds231616,
   Author = {Lowe, CJ and Issel Tarver and L and Wray, GA},
   Title = {Evolution of new developmental roles for orthodenticle and
             distal-less in the larvae of echinoderms},
   Journal = {Evolution & Development},
   Volume = {4},
   Pages = {111-123},
   Year = {2002},
   Month = {February},
   Key = {fds231616}
}

@article{fds231523,
   Author = {Wray, GA},
   Title = {Dating branches on the tree of life using
             DNA.},
   Journal = {Genome Biology},
   Volume = {3},
   Number = {1},
   Pages = {REVIEWS0001},
   Year = {2002},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11806830},
   Abstract = {The use of DNA sequences to estimate the timing of
             evolutionary events is increasingly popular, although it is
             fraught with practical difficulties. But the exponential
             growth of relevant information and improved methods of
             analysis are providing increasingly reliable
             sequence-derived dates, and it may become possible to
             reconcile fossil-derived and molecular estimates of
             divergence times within the next few years.},
   Doi = {10.1186/gb-2001-3-1-reviews0001},
   Key = {fds231523}
}

@article{fds231524,
   Author = {Wray, GA},
   Title = {Do convergent developmental mechanisms underlie convergent
             phenotypes?},
   Journal = {Brain, Behavior and Evolution},
   Volume = {59},
   Number = {5-6},
   Pages = {327-336},
   Year = {2002},
   Month = {January},
   ISSN = {0006-8977},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12207087},
   Abstract = {Convergence is a pervasive evolutionary process, affecting
             many aspects of phenotype and even genotype. Relatively
             little is known about convergence in developmental
             processes, however, nor about the degree to which
             convergence in development underlies convergence in anatomy.
             A switch in the ecology of sea urchins from feeding to
             nonfeeding larvae illustrates how convergence in development
             can be associated with convergence in anatomy. Comparisons
             to more distantly related taxa, however, suggest that this
             association may be limited to relatively close phylogenetic
             comparisons. Similarities in gene expression during
             development provide another window into the association
             between convergence in developmental processes and
             convergence in anatomy. Several well-studied transcription
             factors exhibit likely cases of convergent gene expression
             in distantly related animal phyla. Convergence in regulatory
             gene expression domains is probably more common than
             generally acknowledged, and can arise for several different
             reasons.},
   Doi = {10.1159/000063566},
   Key = {fds231524}
}

@article{fds304340,
   Author = {Stone, JR and Wray, GA},
   Title = {Rapid evolution of cis-regulatory sequences via local point
             mutations.},
   Journal = {Molecular Biology and Evolution},
   Volume = {18},
   Number = {9},
   Pages = {1764-1770},
   Year = {2001},
   Month = {September},
   ISSN = {0737-4038},
   url = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a003964},
   Abstract = {Although the evolution of protein-coding sequences within
             genomes is well understood, the same cannot be said of the
             cis-regulatory regions that control transcription. Yet,
             changes in gene expression are likely to constitute an
             important component of phenotypic evolution. We simulated
             the evolution of new transcription factor binding sites via
             local point mutations. The results indicate that new binding
             sites appear and become fixed within populations on
             microevolutionary timescales under an assumption of neutral
             evolution. Even combinations of two new binding sites evolve
             very quickly. We predict that local point mutations
             continually generate considerable genetic variation that is
             capable of altering gene expression.},
   Doi = {10.1093/oxfordjournals.molbev.a003964},
   Key = {fds304340}
}

@article{fds231604,
   Author = {Bely, AE and Wray, GA},
   Title = {Evolution of regeneration and fission in annelids: insights
             from engrailed- and orthodenticle-class gene
             expression.},
   Journal = {Development (Cambridge, England)},
   Volume = {128},
   Number = {14},
   Pages = {2781-2791},
   Year = {2001},
   Month = {July},
   Abstract = {The recent explosion of information on the role of
             regulatory genes in embryogenesis provides an excellent
             opportunity to study how these genes participate in
             post-embryonic developmental processes. We present a
             detailed comparison of regulatory gene expression during
             regeneration and asexual reproduction (by fission) in the
             segmented worm Pristina leidyi (Annelida: Oligochaeta). We
             isolated three genes from Pristina, one homolog of engrailed
             and two homologs of orthodenticle, and characterized their
             expression in different developmental contexts. In situ
             hybridization studies on worms undergoing normal growth,
             regeneration and fission demonstrate that in all three
             processes, Pl-en is expressed primarily in the developing
             nervous system, and Pl-Otx1 and Pl-Otx2 are expressed
             primarily in the anterior body wall, foregut and developing
             nervous system. Our data reveal extensive similarities
             between expression during regeneration and fission,
             consistent with the idea that similar developmental
             processes underlie these two types of development. Thus, we
             argue that in these annelids fission may have evolved by
             recruitment of regenerative processes. Furthermore, by
             comparing our data to existing data from leech embryos, we
             find evidence that embryonic processes are re-deployed
             during regeneration and fission.},
   Key = {fds231604}
}

@article{fds231480,
   Author = {Wray, GA},
   Title = {DEVELOPMENT: Resolving the Hox Paradox},
   Journal = {Science (New York, N.Y.)},
   Volume = {292},
   Number = {5525},
   Pages = {2256-2257},
   Publisher = {American Association for the Advancement of Science
             (AAAS)},
   Year = {2001},
   Month = {June},
   ISSN = {0036-8075},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000169455900031&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1126/science.1060305},
   Key = {fds231480}
}

@article{fds231478,
   Author = {Wray, GA},
   Title = {A world apart - The larval lifestyle may seem alien to us
             terrestrial bipeds, but it comes quite naturally to most
             creatures - especially inhabitants of the world's
             oceans.},
   Journal = {Natural History},
   Volume = {110},
   Number = {2},
   Pages = {52-+},
   Publisher = {AMER MUSEUM NAT HISTORY},
   Year = {2001},
   Month = {March},
   ISSN = {0028-0712},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000167053900013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231478}
}

@article{fds231603,
   Author = {Stone, JR and Wray, GA},
   Title = {Rapid appearance of new transcription factor binding sites
             by local point mutation},
   Journal = {Molecular Biology and Evolution},
   Volume = {18},
   Number = {9},
   Pages = {1764-1770},
   Year = {2001},
   ISSN = {0737-4038},
   Abstract = {Although the evolution of protein-coding sequences within
             genomes is well understood, the same cannot be said of the
             cis-regulatory regions that control transcription. Yet,
             changes in gene expression are likely to constitute an
             important component of phenotypic evolution. We simulated
             the evolution of new transcription factor binding sites via
             local point mutations. The results indicate that new binding
             sites appear and become fixed within populations on
             microevolutionary timescales under an assumption of neutral
             evolution. Even combinations of two new binding sites evolve
             very quickly. We predict that local point mutations
             continually generate considerable genetic variation that is
             capable of altering gene expression.},
   Key = {fds231603}
}

@article{fds231482,
   Author = {Pizer, M and Wray, GA},
   Title = {The evolution and development of left-right asymmetry in
             echinoderms.},
   Journal = {American Zoologist},
   Volume = {40},
   Number = {6},
   Pages = {1173-1173},
   Publisher = {AMER SOC ZOOLOGISTS},
   Year = {2000},
   Month = {December},
   ISSN = {0003-1569},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000168132000638&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231482}
}

@article{fds231601,
   Author = {Emily, K and Wray, GA},
   Title = {Controversy and consensus in asteroid systernatics: New
             insights to ordinal and familial relationships},
   Journal = {American Zoologist},
   Volume = {40},
   Number = {3},
   Pages = {382-392},
   Publisher = {Society for Integrative and Comparative Biology},
   Year = {2000},
   Month = {December},
   ISSN = {0003-1569},
   url = {http://dx.doi.org/10.1668/0003-1569(2000)040[0382:cacias]2.0.co;2},
   Abstract = {SYNOPSIS. Phylogenetic approaches have sparked controversy
             in asteroid systematics since 1987. Despite recent attempts
             at resolving these differences and evidence of some
             consensus, our understanding of relationships among asteroid
             taxa remains unsatisfactory. This paper presents results'of
             an investigation into asteroid evolutionary history using
             DNA sequence data from mitochondria! transfer RNA and the
             cytochrome oxidase c subunit I genes analyzed with and
             without previously published ribosomal gene sequences.
             Analysis of these genes provides an assessment of familial
             relationships but does little to elucidate ordinal
             relationships. A basal position for the Paxillosida is not
             supported. However, close relationships of some vlatid and
             valvatid taxa are upheld. The resulting phytogenies are not
             a definitive answer to controversies in asteroid systematic.
             However, with new insights to some asteroid relationships,
             they highlight the need for a redirection of future
             systematic studies so a consensus can be
             made.},
   Doi = {10.1668/0003-1569(2000)040[0382:cacias]2.0.co;2},
   Key = {fds231601}
}

@article{fds303170,
   Author = {Wray, GA},
   Title = {The evolution of embryonic patterning mechanisms in
             animals.},
   Journal = {Seminars in Cell & Developmental Biology},
   Volume = {11},
   Number = {6},
   Pages = {385-393},
   Year = {2000},
   Month = {December},
   ISSN = {1084-9521},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11145866},
   Abstract = {Animals exhibit an enormous diversity of life cycles and
             larval morphologies. The developmental basis for this
             diversity is not well understood. It is clear, however, that
             mechanisms of pattern formation in early embryos differ
             significantly among and within groups of animals. These
             differences show surprisingly little correlation with
             phylogenetic relationships; instead, many are correlated
             with ecological factors, such as changes in life
             histories.},
   Doi = {10.1006/scdb.2000.0191},
   Key = {fds303170}
}

@article{fds231598,
   Author = {Cameron, RA and Mahairas, G and Rast, JP and Martinez, P and Biondi, TR and Swartzell, S and Wallace, JC and Poustka, AJ and Livingston, BT and Wray, GA and Ettensohn, CA and Lehrach, H and Britten, RJ and Davidson,
             EH and Hood, L},
   Title = {A sea urchin genome project: sequence scan, virtual map, and
             additional resources.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {97},
   Number = {17},
   Pages = {9514-9518},
   Year = {2000},
   Month = {August},
   url = {http://dx.doi.org/10.1073/pnas.160261897},
   Abstract = {Results of a first-stage Sea Urchin Genome Project are
             summarized here. The species chosen was Strongylocentrotus
             purpuratus, a research model of major importance in
             developmental and molecular biology. A virtual map of the
             genome was constructed by sequencing the ends of 76,020
             bacterial artificial chromosome (BAC) recombinants (average
             length, 125 kb). The BAC-end sequence tag connectors (STCs)
             occur an average of 10 kb apart, and, together with
             restriction digest patterns recorded for the same BAC
             clones, they provide immediate access to contigs of several
             hundred kilobases surrounding any gene of interest. The STCs
             survey >5% of the genome and provide the estimate that this
             genome contains approximately 27,350 protein-coding genes.
             The frequency distribution and canonical sequences of all
             middle and highly repetitive sequence families in the genome
             were obtained from the STCs as well. The 500-kb Hox gene
             complex of this species is being sequenced in its entirety.
             In addition, arrayed cDNA libraries of >10(5) clones each
             were constructed from every major stage of embryogenesis,
             several individual cell types, and adult tissues and are
             available to the community. The accumulated STC data and an
             expanding expressed sequence tag database (at present
             including >12, 000 sequences) have been reported to GenBank
             and are accessible on public web sites.},
   Doi = {10.1073/pnas.160261897},
   Key = {fds231598}
}

@article{fds304339,
   Author = {Wray, GA},
   Title = {Peering ahead (cautiously).},
   Journal = {Evolution & Development},
   Volume = {2},
   Number = {3},
   Pages = {125-126},
   Year = {2000},
   Month = {May},
   url = {http://dx.doi.org/10.1046/j.1525-142x.2000.00001.x},
   Doi = {10.1046/j.1525-142x.2000.00001.x},
   Key = {fds304339}
}

@article{fds303169,
   Author = {Wray, GA and Lowe, CJ},
   Title = {Developmental regulatory genes and echinoderm
             evolution.},
   Journal = {Systematic Biology},
   Volume = {49},
   Number = {1},
   Pages = {28-51},
   Year = {2000},
   Month = {March},
   ISSN = {1063-5157},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12116481},
   Abstract = {Modified interactions among developmental regulatory genes
             and changes in their expression domains are likely to be an
             important part of the developmental basis for evolutionary
             changes in morphology. Although developmental regulatory
             genes are now being studied in an increasing number of taxa,
             there has been little attempt to analyze the resulting data
             within an explicit phylogenetic context. Here we present
             comparative analyses of expression data from regulatory
             genes in the phylum Echinodermata, considering the
             implications for understanding both echinoderm evolution as
             well as the evolution of regulatory genes in general.
             Reconstructing the independent evolutionary histories of
             regulatory genes, their expression domains, their
             developmental roles, and the structures in which they are
             expressed reveals a number of distinct evolutionary
             patterns. A few of these patterns correspond to
             interpretations common in the literature, whereas others
             have received little prior mention. Together, the analyses
             indicate that the evolution of echinoderms involved: (1) the
             appearance of many apomorphic developmental roles and
             expression domains, some of which have plesiomorphic
             bilateral symmetry and others of which have apomorphic
             radial symmetry or left-right asymmetry; (2) the loss of
             some developmental roles and expression domains thought to
             be plesiomorphic for Bilateria; and (3) the retention of
             some developmental roles thought to be plesiomorphic for
             Bilateria, although with modification in expression domains.
             Some of the modifications within the Echinodermata concern
             adult structures; others, transient larval structures. Some
             changes apparently appeared early in echinoderm evolution (>
             450 Ma), whereas others probably happened more recently (<
             50 Ma). Cases of likely convergence in expression domains
             suggest caution when using developmental regulatory genes to
             make inferences about homology among morphological
             structures of distantly related taxa.},
   Doi = {10.1080/10635150050207375},
   Key = {fds303169}
}

@article{fds231475,
   Author = {Wray, GA},
   Title = {The evolution of sea urchin development},
   Journal = {Regulatory Processes in Development},
   Volume = {76},
   Pages = {49-60},
   Booktitle = {Regulatory Processes in Development},
   Publisher = {PORTLAND PRESS LTD},
   Editor = {Olsson, L and Jacobson, CO},
   Year = {2000},
   Month = {January},
   ISBN = {1-85578-136-0},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000176557000004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231475}
}

@article{fds231515,
   Author = {Wray, GA},
   Title = {Gene expression during echinoderm metamorphosis.},
   Journal = {Zygote (Cambridge, England)},
   Volume = {8 Suppl 1},
   Pages = {S48-S49},
   Year = {2000},
   Month = {January},
   ISSN = {0967-1994},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11191307},
   Key = {fds231515}
}

@article{fds231517,
   Author = {Lowe, CJ and Wray, GA},
   Title = {Rearing larvae of sea urchins and sea stars for
             developmental studies.},
   Journal = {Methods in Molecular Biology (Clifton, N.J.)},
   Volume = {135},
   Pages = {9-15},
   Booktitle = {Methods in Molecular Biology, Vol. 135: Developmental
             Biology Protocols},
   Publisher = {Totowa NJ: Humana Press},
   Editor = {R. Tuan and C. Lo},
   Year = {2000},
   Month = {January},
   url = {http://dx.doi.org/10.1385/1-59259-685-1:9},
   Doi = {10.1385/1-59259-685-1:9},
   Key = {fds231517}
}

@article{fds231599,
   Author = {Wray, GA},
   Title = {Peering ahead (cautiously)},
   Journal = {Evolution and Development},
   Volume = {2},
   Number = {3},
   Pages = {1-2},
   Year = {2000},
   url = {http://dx.doi.org/10.1046/j.1525-142X.2000.00001.x},
   Doi = {10.1046/j.1525-142X.2000.00001.x},
   Key = {fds231599}
}

@article{fds231600,
   Author = {Wray, GA and Lowe, CJ},
   Title = {Developmental regulatory genes and echinoderm
             evolution},
   Journal = {Systematic Biology},
   Volume = {49},
   Number = {1},
   Pages = {151-174},
   Year = {2000},
   ISSN = {1063-5157},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12116481},
   Abstract = {Modified interactions among developmental regulatory genes
             and changes in their expression domains are likely to be an
             important part of the developmental basis for evolutionary
             changes in morphology. Although developmental regulatory
             genes are now being studied in an increasing number of taxa,
             there has been little attempt to analyze the resulting data
             within an explicit phylogenetic context. Here we present
             comparative analyses of expression data from regulatory
             genes in the phylum Echinodermata, considering the
             implications for understanding both echinoderm evolution as
             well as the evolution of regulatory genes in general.
             Reconstructing the independent evolutionary histories of
             regulatory genes, their expression domains, their
             developmental roles, and the structures in which they are
             expressed reveals a number of distinct evolutionary
             patterns. A few of these patterns correspond to
             interpretations common in the literature, whereas others
             have received little prior mention. Together, the analyses
             indicate that the evolution of echinoderms involved: (1) the
             appearance of many apomorphic developmental roles and
             expression domains, some of which have plesiomorphic
             bilateral symmetry and others of which have apomorphic
             radial symmetry or left-right asymmetry; (2) the loss of
             some developmental roles and expression domains thought to
             be plesiomorphic for Bilateria; and (3) the retention of
             some developmental roles thought to be plesiomorphic for
             Bilateria, although with modification in expression domains.
             Some of the modifications within the Echinodermata concern
             adult structures; others, transient larval structures. Some
             changes apparently appeared early in echinoderm evolution (>
             450 Ma), whereas others probably happened more recently (<
             50 Ma). Cases of likely convergence in expression domains
             suggest caution when using developmental regulatory genes to
             make inferences about homology among morphological
             structures of distantly related taxa.},
   Key = {fds231600}
}

@article{fds231602,
   Author = {Wray, GA},
   Title = {The evolution of embryonic patterning mechanisms in
             animals},
   Journal = {Seminars in Cell and Developmental Biology},
   Volume = {11},
   Number = {6},
   Pages = {353-393},
   Year = {2000},
   ISSN = {1084-9521},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11145866},
   Abstract = {Animals exhibit an enormous diversity of life cycles and
             larval morphologies. The developmental basis for this
             diversity is not well understood. It is clear, however, that
             mechanisms of pattern formation in early embryos differ
             significantly among and within groups of animals. These
             differences show surprisingly little correlation with
             phylogenetic relationships; instead, many are correlated
             with ecological factors, such as changes in life
             histories.},
   Doi = {10.1006/scdb.2000.0191},
   Key = {fds231602}
}

@article{fds231516,
   Author = {Raff, RA and Arthur, W and Carroll, SB and Coates, MI and Wray,
             G},
   Title = {Chronicling the birth of a discipline.},
   Journal = {Evolution & Development},
   Volume = {1},
   Number = {1},
   Pages = {1-2},
   Year = {1999},
   Month = {July},
   url = {http://dx.doi.org/10.1046/j.1525-142x.1999.00110.x},
   Doi = {10.1046/j.1525-142x.1999.00110.x},
   Key = {fds231516}
}

@article{fds231479,
   Author = {Abouheif, E and Wray, GA},
   Title = {The evolutionary and developmental genetic basis of wing
             polymorphism in ants.},
   Journal = {American Zoologist},
   Volume = {39},
   Number = {5},
   Pages = {12A-12A},
   Publisher = {SOC INTEGRATIVE COMPARATIVE BIOLOGY},
   Year = {1999},
   Month = {January},
   ISSN = {0003-1569},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000085800400065&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231479}
}

@article{fds231481,
   Author = {Bely, AE and Wray, GA},
   Title = {Expression of homeobox genes during regeneration and asexual
             reproduction in an annelid.},
   Journal = {American Zoologist},
   Volume = {39},
   Number = {5},
   Pages = {12A-12A},
   Publisher = {SOC INTEGRATIVE COMPARATIVE BIOLOGY},
   Year = {1999},
   Month = {January},
   ISSN = {0003-1569},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000085800400066&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231481}
}

@article{fds231512,
   Author = {Wray, GA},
   Title = {Evolutionary dissociations between homologous genes and
             homologous structures.},
   Journal = {Novartis Foundation Symposium},
   Volume = {222},
   Pages = {189-203},
   Booktitle = {Homology},
   Publisher = {Chichester (Novartis Foundation Symposium 222):
             Wiley},
   Editor = {B. Hall},
   Year = {1999},
   Month = {January},
   url = {http://dx.doi.org/10.1002/9780470515655.ch13},
   Abstract = {Phenotype is encoded in the genome in an indirect manner:
             each morphological structure is the product of many
             interacting genes, and most regulatory genes have several
             distinct developmental roles and phenotypic consequences.
             The lack of a simple and consistent relationship between
             homologous genes and structures has important implications
             for understanding correlations between evolutionary changes
             at different levels of biological organization. Data from a
             variety of organisms are beginning to provide intriguing
             glimpses of the complex evolutionary relationship between
             genotype and phenotype. Much attention has been devoted to
             remarkably conserved relationships between homologous genes
             and structures. However, there is increasing evidence that
             several kinds of evolutionary dissociations can evolve
             between genotype and phenotype, some of which are quite
             unexpected. The existence of these dissocations limits the
             degree to which it is possible make inferences about the
             homology of structures based solely on the expression of
             homologous genes.},
   Doi = {10.1002/9780470515655.ch13},
   Key = {fds231512}
}

@article{fds231513,
   Author = {Wray, GA and Abouheif, E},
   Title = {When is homology not homology?},
   Journal = {Current Opinion in Genetics & Development},
   Volume = {8},
   Number = {6},
   Pages = {675-680},
   Year = {1998},
   Month = {December},
   ISSN = {0959-437X},
   url = {http://dx.doi.org/10.1016/s0959-437x(98)80036-1},
   Abstract = {Although genes have specific phenotypic consequences in a
             given species, this functional relationship can clearly
             change during the course of evolution. Many cases of
             evolutionary dissociations between homologous genes and
             homologous morphological features are now known. These
             dissociations have interesting and important implications
             for understanding the genetic basis for evolutionary change
             in morphology.},
   Doi = {10.1016/s0959-437x(98)80036-1},
   Key = {fds231513}
}

@article{fds231511,
   Author = {Lowe, CJ and Wray, GA},
   Title = {Erratum: Radical alterations in the roles of homeobox genes
             during echinoderm evolution (Nature (1997) 389
             (718-721))},
   Journal = {Nature},
   Volume = {392},
   Number = {6671},
   Pages = {105},
   Publisher = {Springer Nature},
   Year = {1998},
   Month = {March},
   url = {http://dx.doi.org/10.1038/32217},
   Doi = {10.1038/32217},
   Key = {fds231511}
}

@article{fds231514,
   Author = {Wray, GA},
   Title = {Promoter logic.},
   Journal = {Science (New York, N.Y.)},
   Volume = {279},
   Number = {5358},
   Pages = {1871-1872},
   Year = {1998},
   Month = {March},
   ISSN = {0036-8075},
   url = {http://dx.doi.org/10.1126/science.279.5358.1871},
   Doi = {10.1126/science.279.5358.1871},
   Key = {fds231514}
}

@article{fds231510,
   Author = {Passini, MA and Kurtzman, AL and Canger, AK and Asch, WS and Wray, GA and Raymond, PA and Schechter, N},
   Title = {Cloning of zebrafish vsx1: Expression of a paired-like
             homeobox gene during CNS development},
   Journal = {Developmental Genetics},
   Volume = {23},
   Number = {2},
   Pages = {128-141},
   Publisher = {WILEY},
   Year = {1998},
   ISSN = {0192-253X},
   url = {http://dx.doi.org/10.1002/(SICI)1520-6408(1998)23:2<128::AID-DVG5>3.0.CO;2-8},
   Abstract = {vsx1 is a homeobox gene encoding a paired-type homeodomain
             and a CVC domain that was originally cloned from an adult
             goldfish retinal library. We previously reported the
             spatiotemporal expression pattern of vsx1 in the adult and
             developing retina of zebrafish and goldfish, and we
             suggested that vsx1 plays a role in determining the cell
             fate and maintenance of retinal interneurons. Other related
             genes encoding a CVC domain, such as vsx2 (alx) and chx10,
             are expressed both within and outside the retina during
             development. In this study, we report the cloning of
             zebrafish vsx1 and its developmental expression in both
             retinal and nonretinal regions of the CNS in zebrafish
             embryos. vsx1 expression was detected in a subset of
             hindbrain and spinal card neurons before it was expressed in
             the retina. At about the same time that retinal expression
             began, the level of vsx1 was decreased in the spinal cord.
             The expression of vsx1 was progressively restricted, and
             eventually it was detected only in the inner nuclear layer
             (INL) of the developing retina. The combined expression
             patterns of teleost vsx1 and vsx2 (alx) during early
             zebrafish development encompasses the expression pattern
             observed for murine Chx10, and indicates a partitioning of
             function for CVC genes in lower vertebrates.},
   Doi = {10.1002/(SICI)1520-6408(1998)23:2<128::AID-DVG5>3.0.CO;2-8},
   Key = {fds231510}
}

@article{fds231487,
   Author = {Abouheif, E and Akam, M and Dickinson, WJ and Holland, PW and Meyer, A and Patel, NH and Raff, RA and Roth, VL and Wray, GA},
   Title = {Homology and developmental genes.},
   Journal = {Trends in Genetics : Tig},
   Volume = {13},
   Number = {11},
   Pages = {432-433},
   Year = {1997},
   Month = {November},
   ISSN = {0168-9525},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1997YF59200006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1016/s0168-9525(97)01271-7},
   Key = {fds231487}
}

@article{fds231506,
   Author = {Lowe, CJ and Wray, GA},
   Title = {Radical alterations in the roles of homeobox genes during
             echinoderm evolution.},
   Journal = {Nature},
   Volume = {389},
   Number = {6652},
   Pages = {718-721},
   Year = {1997},
   Month = {October},
   ISSN = {0028-0836},
   url = {http://dx.doi.org/10.1038/39580},
   Abstract = {Echinoderms possess one of the most highly derived body
             architectures of all metazoan phyla, with radial symmetry, a
             calcitic endoskeleton, and a water vascular system. How
             these dramatic morphological changes evolved has been the
             subject of extensive speculation and debate, but remains
             unresolved. Because echinoderms are closely related to
             chordates and postdate the protostome/deuterostome
             divergence, they must have evolved from bilaterally
             symmetrical ancestors. Here we report the expression domains
             in echinoderms of three important developmental regulatory
             genes (distal-less, engrailed and orthodenticle), all of
             which encode transcription factors that contain a
             homeodomain. Our findings show that the reorganization of
             body architecture involved extensive changes in the
             deployment and roles of homeobox genes. These changes
             include modifications in the symmetry of expression domains
             and the evolution of several new developmental roles, as
             well as the loss of roles conserved between arthropods and
             chordates. Some of these modifications seem to have evolved
             very early in the history of echinoderms, whereas others
             probably evolved during the subsequent diversification of
             adult and larval morphology. These results demonstrate the
             evolutionary lability of regulatory genes that are widely
             viewed as conservative.},
   Doi = {10.1038/39580},
   Key = {fds231506}
}

@article{fds231509,
   Author = {Benink, H and Wray, G and Hardin, J},
   Title = {Archenteron precursor cells can organize secondary axial
             structures in the sea urchin embryo.},
   Journal = {Development (Cambridge, England)},
   Volume = {124},
   Number = {18},
   Pages = {3461-3470},
   Year = {1997},
   Month = {September},
   ISSN = {0950-1991},
   Abstract = {Local cell-cell signals play a crucial role in establishing
             major tissue territories in early embryos. The sea urchin
             embryo is a useful model system for studying these
             interactions in deuterostomes. Previous studies showed that
             ectopically implanted micromeres from the 16-cell embryo can
             induce ectopic guts and additional skeletal elements in sea
             urchin embryos. Using a chimeric embryo approach, we show
             that implanted archenteron precursors differentiate
             autonomously to produce a correctly proportioned and
             patterned gut. In addition, the ectopically implanted
             presumptive archenteron tissue induces ectopic skeletal
             patterning sites within the ectoderm. The ectopic skeletal
             elements are bilaterally symmetric, and flank the ectopic
             archenteron, in some cases resulting in mirror-image,
             symmetric skeletal elements. Since the induced patterned
             ectoderm and supernumerary skeletal elements are derived
             from the host, the ectopic presumptive archenteron tissue
             can act to 'organize' ectopic axial structures in the sea
             urchin embryo.},
   Key = {fds231509}
}

@article{fds231508,
   Author = {Panganiban, G and Irvine, SM and Lowe, C and Roehl, H and Corley, LS and Sherbon, B and Grenier, JK and Fallon, JF and Kimble, J and Walker, M and Wray, GA and Swalla, BJ and Martindale, MQ and Carroll,
             SB},
   Title = {The origin and evolution of animal appendages.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {94},
   Number = {10},
   Pages = {5162-5166},
   Year = {1997},
   Month = {May},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.94.10.5162},
   Abstract = {Animals have evolved diverse appendages adapted for
             locomotion, feeding and other functions. The genetics
             underlying appendage formation are best understood in
             insects and vertebrates. The expression of the Distal-less
             (Dll) homeoprotein during arthropod limb outgrowth and of
             Dll orthologs (Dlx) in fish fin and tetrapod limb buds led
             us to examine whether expression of this regulatory gene may
             be a general feature of appendage formation in protostomes
             and deuterostomes. We find that Dll is expressed along the
             proximodistal axis of developing polychaete annelid
             parapodia, onychophoran lobopodia, ascidian ampullae, and
             even echinoderm tube feet. Dll/Dlx expression in such
             diverse appendages in these six coelomate phyla could be
             convergent, but this would have required the independent
             co-option of Dll/Dlx several times in evolution. It appears
             more likely that ectodermal Dll/Dlx expression along
             proximodistal axes originated once in a common ancestor and
             has been used subsequently to pattern body wall outgrowths
             in a variety of organisms. We suggest that this pre-Cambrian
             ancestor of most protostomes and the deuterostomes possessed
             elements of the genetic machinery for and may have even
             borne appendages.},
   Doi = {10.1073/pnas.94.10.5162},
   Key = {fds231508}
}

@article{fds231507,
   Author = {Craig, SF and Slobodkin, LB and Wray, GA and Biermann,
             CH},
   Title = {The 'paradox' of polyembryony: A review of the cases and a
             hypothesis for its evolution},
   Journal = {Evolutionary Ecology},
   Volume = {11},
   Number = {2},
   Pages = {127-143},
   Publisher = {Springer Nature},
   Year = {1997},
   Month = {January},
   url = {http://dx.doi.org/10.1023/A:1018443714917},
   Abstract = {Animal polyembryony appears to be paradoxical because it
             clones an unproven genotype at the expense of genetic
             diversity in a clutch. However, it is employed by at least
             18 taxa in six phyla (excluding instances of occasional
             twinning). Most polyembryony occurs in parasitic stages or
             in other environments whose quality is not predictable by
             the mother; in some instances, it compensates for a
             constraint on zygote number. We predict that polyembryony is
             likely to evolve when the offspring has more information
             regarding optimal clutch size than the parents.},
   Doi = {10.1023/A:1018443714917},
   Key = {fds231507}
}

@article{fds231504,
   Author = {Wray, GA and Levinton, JS and Shapiro, LH},
   Title = {Molecular evidence for deep Precambrian divergences among
             metazoan phyla},
   Journal = {Science (New York, N.Y.)},
   Volume = {274},
   Number = {5287},
   Pages = {568-581},
   Publisher = {American Association for the Advancement of Science
             (AAAS)},
   Year = {1996},
   Month = {January},
   url = {http://dx.doi.org/10.1126/science.274.5287.568},
   Abstract = {A literal reading of the fossil record suggests that the
             animal phyla diverged in an 'explosion' near the beginning
             of the Cambrian period. Calibrated rates of molecular
             sequence divergence were used to test this hypothesis. Seven
             independent data sets suggest that invertebrates diverged
             from chordates about a billion years ago, about twice as
             long ago as the Cambrian. Protostomes apparently diverged
             from chordates well before echinoderms, which suggests a
             prolonged radiation of animal phyla. These conclusions apply
             specifically to divergence times among phyla; the
             morphological features that characterize modern animal body
             plans, such as skeletons and coelams, may have evolved
             later.},
   Doi = {10.1126/science.274.5287.568},
   Key = {fds231504}
}

@article{fds231505,
   Author = {Wray, GA},
   Title = {Parallel evolution of nonfeeding larvae in
             echinoids},
   Journal = {Systematic Biology},
   Volume = {45},
   Number = {3},
   Pages = {308-322},
   Publisher = {Oxford University Press (OUP)},
   Year = {1996},
   Month = {January},
   url = {http://dx.doi.org/10.1093/sysbio/45.3.308},
   Abstract = {The switch from feeding to nonfeeding larvae is an
             ecologically important transformation that has evolved on
             several separate occasions within the echinoids. In each
             case, this life history transformation has been accompanied
             by extensive changes in larval morphology. A phylogenetic
             approach is used here to reconstruct these morphological
             changes, to begin asking why they have taken the particular
             forms observed, and to assess the degree of parallel
             transformation in separate cases. Both traditional character
             mapping and a less usual aggregate analysis indicate
             massively parallel transformations in larval morphology
             associated with, and only with, this particular life history
             transformation. Some of these parallel morphological
             transformations may be due to relaxed functional constraints
             associated with the ancestral life history mode, but many
             are probably the result of new functional constraints
             associated with the derived mode. The comparative data
             suggest a simple and testable model for the switch from
             feeding to nonfeeding larvae involving three sequential
             steps.},
   Doi = {10.1093/sysbio/45.3.308},
   Key = {fds231505}
}

@article{fds231501,
   Author = {Wray, GA},
   Title = {Punctuated evolution of embryos},
   Journal = {Science (New York, N.Y.)},
   Volume = {267},
   Number = {5201},
   Pages = {1115-1116},
   Publisher = {American Association for the Advancement of Science
             (AAAS)},
   Year = {1995},
   Month = {January},
   url = {http://dx.doi.org/10.1126/science.267.5201.1115},
   Doi = {10.1126/science.267.5201.1115},
   Key = {fds231501}
}

@article{fds231502,
   Author = {Smith, AB and Littlewood, DTJ and Wray, GA},
   Title = {Comparing patterns of evolution: larval and adult life
             history stages and ribosomal RNA of post-Palaeozoic
             echinoids},
   Journal = {Philosophical Transactions Royal Society of London,
             B},
   Volume = {349},
   Number = {1327},
   Pages = {11-18},
   Publisher = {The Royal Society},
   Year = {1995},
   Month = {January},
   url = {http://dx.doi.org/10.1098/rstb.1995.0085},
   Abstract = {A total-evidence approach to the phylogeny of 29 extant
             echinoids has been taken, combined data from larval
             morphology, adult morphology, small subunit rRNA complete
             gene sequence and large subunit rRNA partial gene sequence:
             a total of 176 morphological and 121 molecular
             phylogenetically informative characters. Also included are
             13 extinct taxa for which only adult morphology is known.
             Patterns of morphological evolution of larval and adult
             stages were compared by optimizing character sets onto the
             total evidence tree and assigning each character
             transformation to a branch. It is demonstrated that larval
             and adult morphological evolution has proceeded in a
             mosaic-like fashion over the last 250 Ma. -from
             Authors},
   Doi = {10.1098/rstb.1995.0085},
   Key = {fds231502}
}

@article{fds231503,
   Author = {Craig, SF and Slobodkin, LB and Wray, G},
   Title = {The 'paradox' of polyembryony},
   Journal = {Trends in Ecology and Evolution},
   Volume = {10},
   Number = {9},
   Pages = {371-372},
   Publisher = {Elsevier BV},
   Year = {1995},
   Month = {January},
   ISSN = {0169-5347},
   url = {http://dx.doi.org/10.1016/S0169-5347(00)89138-7},
   Doi = {10.1016/S0169-5347(00)89138-7},
   Key = {fds231503}
}

@article{fds231499,
   Author = {Wray, GA},
   Title = {The evolution of cell lineage in echinoderms},
   Journal = {Integrative and Comparative Biology},
   Volume = {34},
   Number = {3},
   Pages = {353-363},
   Publisher = {Oxford University Press (OUP)},
   Year = {1994},
   Month = {December},
   ISSN = {1540-7063},
   url = {http://dx.doi.org/10.1093/icb/34.3.353},
   Abstract = {SYNOPSIS. Metazoan embryos in various phyla and classes
             often utilize quite different processes to specify cell
             fates during embryogenesis. These differences have been
             interpreted either as constraints, necessary for fabricating
             distinct adult body plans, or as adaptations for particular
             life history strategies. This paper analyzes the evolution
             of echinoderm cell lineage within a phylogenetic context as
             a means of testing these hypotheses. Several features of
             echinoderm cell lineage are probably over 550 million years
             old, and have persisted despite extensive transformations in
             adult morphology. Other features are much more variable
             evolutionarily, and have changed on many separate occasions.
             Importantly, even some of the most ancient and conservative
             features of echinoderm cell lineage can still evolve. These
             transformations are correlated with a particular life
             history transformation, the switch from feeding to
             nonfeeding larvae. The results suggest that adaptation has
             played a significant role in the evolution of cell lineage
             in echinoderms: some ancient features have been maintained
             for functional reasons rather than because of constraints,
             and some derived features have evolved in response to
             particular environmental challenges. ©1994 by the American
             Society of Zoologists.},
   Doi = {10.1093/icb/34.3.353},
   Key = {fds231499}
}

@article{fds231500,
   Author = {Wray, GA and Bely, AE},
   Title = {The evolution of echinoderm development is driven by several
             distinct factors},
   Journal = {Development (Cambridge, England)},
   Volume = {120},
   Number = {SUPPL.},
   Pages = {97-106},
   Year = {1994},
   Month = {December},
   Abstract = {We analyzed a comparative data base of gene expression, cell
             fate specification, and morphogenetic movements from several
             echinoderms to determine why developmental processes do and
             do not evolve. Mapping this comparative data onto explicit
             phylogenetic frameworks revealed three distinct evolutionary
             patterns. First, some evolutionary differences in
             development correlate well with larval ecology but not with
             adult morphology. These associations are probably not
             coincidental because similar developmental changes accompany
             similar ecological transformations on separate occasions.
             This suggests that larval ecology has been a potent
             influence on the evolution of early development in
             echinoderms. Second, a few changes in early development
             correlate with transformations in adult morphology. Because
             most such changes have occurred only once, however, it is
             difficult to distinguish chance associations from causal
             relationships. And third, some changes in development have
             no apparent phenotypic consequences and do not correlate
             with obvious features of either life history or morphology.
             This suggests that some evolutionary changes in development
             may evolve in a neutral or nearly neutral mode. Importantly,
             these hypotheses make specific predictions that can be
             tested with further comparative data and by experimental
             manipulations. Together, our phylogenetic analyses of
             comparative data suggest that at least three distinct
             evolutionary mechanisms have shaped early development in
             echinoderms.},
   Key = {fds231500}
}

@article{fds231497,
   Author = {Wray, GA},
   Title = {Developmental evolution: new paradigms and
             paradoxes.},
   Journal = {Developmental Genetics},
   Volume = {15},
   Number = {1},
   Pages = {1-6},
   Year = {1994},
   Month = {January},
   url = {http://dx.doi.org/10.1002/dvg.1020150102},
   Doi = {10.1002/dvg.1020150102},
   Key = {fds231497}
}

@article{fds231498,
   Author = {Wray, GA and Bely, AE},
   Title = {The evolution of echinoderm development is driven by several
             distinct factors.},
   Journal = {Development (Cambridge, England). Supplement},
   Volume = {120},
   Number = {SUPPL.},
   Pages = {97-106},
   Year = {1994},
   Month = {January},
   Abstract = {We analyzed a comparative data base of gene expression, cell
             fate specification, and morphogenetic movements from several
             echinoderms to determine why developmental processes do and
             do not evolve. Mapping this comparative data onto explicit
             phylogenetic frameworks revealed three distinct evolutionary
             patterns. First, some evolutionary differences in
             development correlate well with larval ecology but not with
             adult morphology. These associations are probably not
             coincidental because similar developmental changes accompany
             similar ecological transformations on separate occasions.
             This suggests that larval ecology has been a potent
             influence on the evolution of early development in
             echinoderms. Second, a few changes in early development
             correlate with transformations in adult morphology. Because
             most such changes have occurred only once, however, it is
             difficult to distinguish chance associations from causal
             relationships. And third, some changes in development have
             no apparent phenotypic consequences and do not correlate
             with obvious features of either life history or morphology.
             This suggests that some evolutionary changes in development
             may evolve in a neutral or nearly neutral mode. Importantly,
             these hypotheses make specific predictions that can be
             tested with further comparative data and by experimental
             manipulations. Together, our phylogenetic analyses of
             comparative data suggest that at least three distinct
             evolutionary mechanisms have shaped early development in
             echinoderms.},
   Key = {fds231498}
}

@article{fds231496,
   Author = {Wray, GA},
   Title = {Rates of evolution in developmental processes},
   Journal = {Integrative and Comparative Biology},
   Volume = {32},
   Number = {1},
   Pages = {123-134},
   Publisher = {Oxford University Press (OUP)},
   Year = {1992},
   Month = {December},
   ISSN = {1540-7063},
   url = {http://dx.doi.org/10.1093/icb/32.1.123},
   Abstract = {The tempo and mode of morphological evolution are influenced
             by several factors, among which evolutionary transformations
             in developmental processes are likely to be important.
             Comparing the embryos of extant species in an explicit
             phylogenetic fram work allows the estimation of minimum
             average rates of evolution in quantitative developmental
             parameters. It also allows delineation of the maximum time
             that complex qualitative transformations in developmental
             mechanism take to evolve. This paper analyzes rates of
             quantitative and qualitative developmental evolution using
             examples drawn primarily from echinoderms. The results
             demonstrate that rates of developmental evolution can be
             comparable to rates of morphological evolution. There is no
             indication that rates of evolution in development are lower
             for earlier stages, contrary to the prediction of "tree"
             models of epigenetic interactions. In particular, rates of
             evolution in oogenesis can exceed rates of evolution in
             adult body size. Rates of developmental evolution can vary
             by up to two orders of magnitude within a clade. Whether
             such large scale variation in evolutionary rates of
             developmental processes is a general phenomenon can only be
             answered by further study. © 1992 by the American Society
             of Zoologists.},
   Doi = {10.1093/icb/32.1.123},
   Key = {fds231496}
}

@article{fds231494,
   Author = {Wray, GA},
   Title = {The evolution of larval morphology during the post-Paleozoic
             radiation of echinoids},
   Journal = {Paleobiology},
   Volume = {18},
   Number = {3},
   Pages = {258-287},
   Publisher = {Cambridge University Press (CUP)},
   Year = {1992},
   Month = {January},
   url = {http://dx.doi.org/10.1017/S0094837300010848},
   Abstract = {.—The post-Paleozoic radiation of echinoids entailed a
             rapid diversification not only of adult morphology, but also
             of larval morphology. The timing, order, and phylogenetic
             distribution of evolutionary transformations in
             echinopluteus larvae are reconstructed here under maximum
             parsimony assumptions from a large neontological data base.
             Many echinoid larval apomorphies apparently evolved within
             the Paleozoic stem lineage and were subsequently retained
             during much of the crown-group radiation. This suite of
             apomorphies includes most (and perhaps all) of the skeletal
             elements and some features of soft anatomy such as vibratile
             lobes. Other features apparently arose or were modified
             during the post-Paleozoic radiation. These include skeletal
             features such as arm-rod structure and length, and soft
             structures such as epaulettes and skeletal muscles.
             Transformational hypotheses of this kind can be supported or
             rejected with further neontological data, and many can
             potentially be tested from fossil evidence. Many
             post-Paleozoic transformations in echinopluteus structure
             may be adaptive. For example, increases in arm length and
             flattening of arm ectoderm may increase feeding rate and
             efficiency, and both types of transformation have occurred
             several times within the crown group. Relational hypotheses
             of this nature can be tested through comparative functional
             studies in extant echinoplutei. Parallel evolutionary losses
             of feeding in echinoplutei are accompanied by loss or
             modification of characteristic structures. This suggests
             that developmental constraints do not fully explain the
             conservation of these structures in plank-totrophic
             echinoplutei. Comparisons of larval and adult morphology
             over congruent time intervals demonstrate that the origin of
             many orders was accompanied by a suite of synapomorphies in
             larval morphology that was subsequently conserved. Many
             details of echinopluteus morphology are therefore of
             taxonomic significance. Intraordinal patterns of larval
             diversity, however, vary considerably. That larval
             morphology has diversified independently of adult morphology
             indicates that mosaic evolution has occurred within the life
             cycle and suggests that echinoid larvae and adults can and
             do respond to selection independently. Taken together, these
             findings underscore the complex ways in which complex life
             cycles can evolve. © 1992, Paleontological Society. All
             rights reserved.},
   Doi = {10.1017/S0094837300010848},
   Key = {fds231494}
}

@article{fds318051,
   Author = {Wray, GA},
   Title = {Rates of evolution in developmental processes},
   Journal = {American Zoologist},
   Volume = {32},
   Number = {1},
   Pages = {123-134},
   Year = {1992},
   Abstract = {The tempo and mode of morphological evolution are influenced
             by several factors, among which evolutionary transformations
             in developmental processes are likely to be important.
             Comparing the embryos of extant species in an explicit
             phylogenetic framework allows estimation of minimum average
             rates of evolution in quantitative developmental parameters.
             It also allows delineation of the maximum time that complex
             qualitative trnasformations in developmental mechanism take
             to evolve. This paper analyzes rates of quantitative and
             qualitative developmental evolution using examples drawn
             primarily form echinoderms. Rates of developmental evolution
             can be comparable to rates of morphological evolution. There
             is no indication that rates of evolution in development are
             lower for earlier stages. In particular, rates of evolution
             in oogenesis can exceed rates of evolution in adult body
             size. Rates of developmental evolution can vary by up to two
             orders of magnitude within a clade. -from
             Author},
   Key = {fds318051}
}

@article{fds231492,
   Author = {Wray, GA and Raff, RA},
   Title = {The evolution of developmental strategy in marine
             invertebrates},
   Journal = {Trends in Ecology and Evolution},
   Volume = {6},
   Number = {2},
   Pages = {45-50},
   Publisher = {Elsevier BV},
   Year = {1991},
   Month = {January},
   url = {http://dx.doi.org/10.1016/0169-5347(91)90121-D},
   Abstract = {Developmental mode varies widely in most animal phyla. These
             differences in developmental strategy exert a profound
             influence on the ecology and evolution of closely related
             species. The mechanistic alterations in ontogeny that lead
             to switches in developmental mode are coming under
             increasing scrutiny. Echinoids are one of the
             best-understood groups in this regard. Parallel
             modifications in direct-developing echinoids point to some
             of the key changes in oogenesis and embryogenesis that
             produce switches in developmental mode. ©
             1991.},
   Doi = {10.1016/0169-5347(91)90121-D},
   Key = {fds231492}
}

@article{fds322332,
   Author = {Henry, JJ and Wray, GA and Raff, RA},
   Title = {Mechanism of an Alternate Type of Echinoderm Blastula
             Formation: The Wrinkled Blastula of the Sea Urchin
             Heliocidaris erythrogramma direct development/echinoderm
             development/morphogenesis/sea urchin embryos/wrinkled
             blastula},
   Journal = {Development, Growth & Differentiation},
   Volume = {33},
   Number = {4},
   Pages = {317-328},
   Publisher = {WILEY},
   Year = {1991},
   Month = {January},
   url = {http://dx.doi.org/10.1111/j.1440-169X.1991.00317.x},
   Abstract = {While most indirect‐developing echinoderms (possessing a
             feeding larval stage) form a hollow, smooth‐walled
             blastula, most direct‐developing species form a wrinkled
             blastula. The process of wrinkled blastula formation was
             examined in the direct‐developing sea urchin, Heliocidaris
             erythrogramma. Approximately 5 hrs after fertilization the
             blastula epithelium contains folds along one, two or three
             orthogonal planes, which superficially appear like 2‐,
             4‐ or 8‐cell stages, respectively. Microinjection of
             fluorescent dye into individual blastomeres of 2‐, 4‐
             and 8‐cell embryos revealed that the wrinkles correspond
             with the first, second and third cleavage planes. Two
             factors appear to generate the wrinkled blastula epithelium.
             First, blastomeres undergo a partial separation along the
             first, second and third cleavage planes during early
             cleavage. Subsequent cell divisions are oriented such that
             the blastula epithelium is constructed with deep creases
             along these planes of cell separation. Second, there is no
             room for the expansion of the developing blastoderm within
             the tightly fitting fertilization envelope. Prior to
             hatching from the fertilization envelope, wrinkles in the
             blastula epithelium disappear, due to an increased packing
             and elongation of the cells. In addition, a substantial
             volume of cellular material is removed as lipids are
             secreted into the blastocoel in an apocrine fashion.
             Copyright © 1991, Wiley Blackwell. All rights
             reserved},
   Doi = {10.1111/j.1440-169X.1991.00317.x},
   Key = {fds322332}
}

@article{fds231493,
   Author = {Hernry, JJ and Wray, GA and Raff, RA},
   Title = {Mechanism of an alternate type of echinoderm blastula
             formation: The wrinkled blastula of the sea urchin
             Heliocidaris erythrogramma},
   Journal = {Development, Growth & Differentiation},
   Volume = {33},
   Number = {4},
   Pages = {317-328},
   Year = {1991},
   ISSN = {0012-1592},
   Key = {fds231493}
}

@article{fds231550,
   Author = {Henry, JJ and Wray, GA and Raff, RA},
   Title = {The dorsoventral axis is specified prior to first cleavage
             in the direct developing sea urchin Heliocidaris
             erythrogramma.},
   Journal = {Development (Cambridge, England)},
   Volume = {110},
   Number = {3},
   Pages = {875-884},
   Year = {1990},
   Month = {November},
   ISSN = {0950-1991},
   Abstract = {Previous fate mapping studies as well as the culture of
             isolated blastomeres have revealed that the dorsoventral
             axis is specified as early as the 2-cell stage in the
             embryos of the direct developing echinoid, Heliocidaris
             erythrogramma. Normally, the first cleavage plane includes
             the animal-vegetal axis and bisects the embryo between
             future dorsal and ventral halves. Experiments were performed
             to establish whether the dorsoventral axis is set up prior
             to the first cleavage division in H. erythrogramma. Eggs
             were elongated and fertilized in silicone tubes of a small
             diameter in order to orient the cleavage spindle and thus
             the first plane of cell division. Following first cleavage,
             one of the two resulting blastomeres was then microinjected
             with a fluorescent cell lineage tracer dye. Fate maps were
             made after culturing these embryos to larval stages. The
             results indicate that the first cleavage division can be
             made to occur at virtually any angle relative to the
             animal-vegetal and dorsoventral axes. Therefore, the
             dorsoventral axis is specified prior to first cleavage. We
             argue that this axis resides in the unfertilized oocyte
             rather than being set up as a consequence of
             fertilization.},
   Key = {fds231550}
}

@article{fds231491,
   Author = {Wray, GA and Raff, RA},
   Title = {Novel origins of lineage founder cells in the
             direct-developing sea urchin Heliocidaris
             erythrogramma.},
   Journal = {Developmental Biology},
   Volume = {141},
   Number = {1},
   Pages = {41-54},
   Year = {1990},
   Month = {September},
   ISSN = {0012-1606},
   url = {http://dx.doi.org/10.1016/0012-1606(90)90100-w},
   Abstract = {The lineage and fate of each blastomere in the 32-cell
             embryo of the direct-developing sea urchin Heliocidaris
             erythrogramma have been traced by microinjection of
             tetramethylrhodamine-dextran. The results reveal substantive
             evolutionary modifications of the ancestral cell lineage
             pattern of indirect sea urchin development. Significant
             among these modifications are changes in the time and order
             of cell lineage segregation: vegetal ectodermal founder
             cells consistently arise earlier than during indirect
             development, while internal founder cells generally
             segregate later and in a different sequence. Modifications
             have also arisen in proportions of the embryo fated to
             become various cell types and larval structures. Ectodermal
             fates, particularly vestibular ectoderm, comprise a greater
             proportion of the total cellular volume in H. erythrogramma.
             Among internal cell types, coelom consumes more and endoderm
             less of the remaining cellular volume than during indirect
             sea urchin development. Evolutionary modifications are also
             apparent in the positional origin of larval cell types and
             structures in H. erythrogramma. These include an apparent
             tilt in the axis of prospective cell fate relative to the
             animal-vegetal axis as defined by cleavage planes. Together
             these evolutionary changes in the cell lineage of H.
             erythrogramma produce an accelerated loss of dorsoventral
             symmetry in cell fate relative to indirect development. The
             extent and diversity of rearrangements in its cell lineage
             indicate that the non-feeding larva of H. erythrogramma is a
             highly modified, novel form rather than a degenerate pluteus
             larva. These same modifications underscore the
             evolutionarily flexible relationship between cell lineage,
             gene expression, and larval morphology in sea urchin
             development.},
   Doi = {10.1016/0012-1606(90)90100-w},
   Key = {fds231491}
}

@article{fds231551,
   Author = {Scott, LB and Lennarz, WJ and Raff, RA and Wray, GA},
   Title = {The "lecithotrophic" sea urchin Heliocidaris erythrogramma
             lacks typical yolk platelets and yolk glycoproteins.},
   Journal = {Developmental Biology},
   Volume = {138},
   Number = {1},
   Pages = {188-193},
   Year = {1990},
   Month = {March},
   ISSN = {0012-1606},
   url = {http://dx.doi.org/10.1016/0012-1606(90)90188-o},
   Abstract = {The sea urchin Heliocidaris tuberculata undergoes typical
             development, forming an echinoid pluteus larva, whereas H.
             erythrogramma undergoes direct development via a highly
             modified, nonfeeding larva. Using a polyclonal antibody
             prepared against yolk glycoproteins from the typical
             developer Stronglyocentrotus purpuratus, we found that H.
             tuberculata contains cross-reactive proteins in abundance,
             but H. erythrogramma does not. In addition, we used
             immunoelectron microscopy to demonstrate that unfertilized
             eggs of H. tuberculata contain yolk platelets, but those of
             H. erythrogramma do not.},
   Doi = {10.1016/0012-1606(90)90188-o},
   Key = {fds231551}
}

@article{fds231542,
   Author = {NIJHOUT, HF and WRAY, GA and GILBERT, LE},
   Title = {An analysis of the phenotypic effects of certain colour
             pattern genes in Heliconius (Lepidoptera:
             Nymphalidae)},
   Journal = {Biological Journal of the Linnean Society},
   Volume = {40},
   Number = {4},
   Pages = {357-372},
   Publisher = {Oxford University Press (OUP)},
   Year = {1990},
   Month = {January},
   ISSN = {0024-4066},
   url = {http://dx.doi.org/10.1111/j.1095-8312.1990.tb00545.x},
   Abstract = {The colour patterns of Heliconius butterflies are built up
             from an array of serially homologous pattern elements known
             as the nymphalid groundplan. An analysis of the phenotypic
             effects of ten genetic loci from H. melpomene and H. cydno
             reveals that each alters the expression either of a single
             element of the groundplan or of an entire row of serially
             homologous elements. Five of the ten loci affect the size
             (or presence/absence) of specific pattern elements, two
             affect the colour in which a pattern element is expressed,
             two affect pattern‐inducing activity of the wing veins,
             and one appears to affect an overall threshold for pattern
             determination. Three of the ten loci have identical effects
             on homologues of the fore‐ and hindwing. We show that most
             of the apparently large and qualitative phenotypic effects
             of these genes can be readily explained by relatively small
             and quantitative changes in the dimensions or positions of
             specific pattern elements. Copyright © 1990, Wiley
             Blackwell. All rights reserved},
   Doi = {10.1111/j.1095-8312.1990.tb00545.x},
   Key = {fds231542}
}

@article{fds231552,
   Author = {Raff, RA and Parr, BA and Parks, AL and Wray, GA},
   Title = {Heterochrony and other mechanisms of radical evolutionary
             change in early development},
   Journal = {Evolutionary Innovations},
   Pages = {71-98},
   Year = {1990},
   Month = {January},
   Abstract = {Examines the view that developmental processes which happen
             together or sequentially in time are not necessarily tightly
             coupled mechanistically and may be shifted relative to each
             other in evolution without disrupting development.
             Heterochrony is the most familiar kind of dissociation in
             which relative timing of two developmental processes
             undergoes an evolutionary shift. -from Authors},
   Key = {fds231552}
}

@article{fds231547,
   Author = {Henry, JJ and Amemiya, S and Wray, GA and Raff, RA},
   Title = {Early inductive interactions are involved in restricting
             cell fates of mesomeres in sea urchin embryos.},
   Journal = {Developmental Biology},
   Volume = {136},
   Number = {1},
   Pages = {140-153},
   Year = {1989},
   Month = {November},
   ISSN = {0012-1606},
   url = {http://dx.doi.org/10.1016/0012-1606(89)90137-1},
   Abstract = {Isolated intact caps of animal blastomeres, obtained from
             either 8- or 16-cell embryos, differentiate as swollen
             ectodermal vesicles. These findings agree with earlier
             studies demonstrating that mesomeres contribute only to
             larval ectoderm during normal development. In contrast, we
             find that pairs of mesomeres isolated from 16-cell embryos
             can differentiate endodermal and mesenchymal cells in a
             substantial number of cases (23%). Thus, mesomeres have a
             greater developmental potential than is realized during
             normal development. Further results support hypotheses that
             graded distributions of morphogenetic determinants exist
             within these embryos, since the extent of differentiation of
             isolated mesomeres is related to the relative position of
             the third cleavage plane along the animal-vegetal axis. When
             the third cleavage plane is subequatorial and the resulting
             animal blastomeres inherit a fraction of the vegetal
             hemisphere, more cases (39%) differentiate endodermal and
             mesenchymal cell types. A significant number of mesomere
             pairs (9-14%), however, can still differentiate endodermal
             and mesenchymal cells when the mesomeres are formed within
             the animal hemisphere. Thus, putative vegetal morphogenetic
             determinants may extend into the animal hemisphere in some
             cases. Further results indicate a temporal restriction in
             the developmental potential of mesomeres or mesomere
             progenitor cells since their differentiative capability is
             greater if they are isolated earlier during development.
             Aggregates of isolated mesomere pairs also display a
             decreased developmental potential when compared to isolated
             mesomere pairs. These results suggest that associations with
             adjacent cells (vegetal cells as well as adjacent mesomeres)
             restrict the development of mesomeres between third and
             sixth cleavages.},
   Doi = {10.1016/0012-1606(89)90137-1},
   Key = {fds231547}
}

@article{fds231490,
   Author = {Wray, GA and McClay, DR},
   Title = {Molecular Heterochronies and Heterotopies in Early Echinoid
             Development},
   Journal = {Evolution; International Journal of Organic
             Evolution},
   Volume = {43},
   Number = {4},
   Pages = {803-803},
   Publisher = {JSTOR},
   Year = {1989},
   Month = {July},
   ISSN = {0014-3820},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1989AD55300008&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Abstract = {By comparing the spatial and temporal distribution of three
             proteins during early development in seven echinoid species,
             we demonstrate that both heterochronies and heterotopies in
             gene-product expression have accompanied the radiation of
             post-Paleozoic echinoids. All three proteins examined showed
             significant alterations in time of expression, site of
             expression, or both. These molecular heterochronies and
             heterotopies indicate that early development is not
             necessarily as evolutionarily conservative as morphology of
             embryos alone would suggest. Evolutionary alterations in
             early development may be more common than is generally
             assumed.},
   Doi = {10.2307/2409308},
   Key = {fds231490}
}

@article{fds231549,
   Author = {Wray, GA and Raff, RA},
   Title = {Evolutionary modification of cell lineage in the
             direct-developing sea urchin Heliocidaris
             erythrogramma.},
   Journal = {Developmental Biology},
   Volume = {132},
   Number = {2},
   Pages = {458-470},
   Year = {1989},
   Month = {April},
   ISSN = {0012-1606},
   url = {http://dx.doi.org/10.1016/0012-1606(89)90242-x},
   Abstract = {The sea urchin Heliocidaris erythrogramma undergoes direct
             development, bypassing the usual echinoid pluteus larva. We
             present an analysis of cell lineage in H. erythrogramma as
             part of a definition of the mechanistic basis for this
             evolutionary change in developmental mode. Microinjection of
             fluoresceinated tracer dye and surface marking with vital
             dye are used to follow larval fates of 2-cell, 8-cell, and
             16-cell blastomeres, and to examine axial specification. The
             animal-vegetal axis and adult dorsoventral axis are
             basically unmodified in H. erythrogramma. Animal cell fates
             are very similar to those of typically developing species;
             however, vegetal cell fates in H. erythrogramma are
             substantially altered. Radial differences exist among
             vegetal blastomere fates in the 8-cell embryo: dorsal
             vegetal blastomeres contribute proportionately more
             descendants to ectodermal and fewer to mesodermal fates,
             while ventral vegetal blastomeres have a complementary bias
             in fates. In addition, vegetal cell fates are more variable
             than in typical developers. There are no cells in H.
             erythrogramma with fates comparable to those of the
             micromeres and macromeres of typically developing echinoids.
             Instead, all vegetal cells in the 16-cell embryo can
             contribute progeny to ectoderm and gut. Alterations have
             thus arisen in cleavage patterns and timing of cell lineage
             partitioning during the evolution of direct development in
             H. erythrogramma.},
   Doi = {10.1016/0012-1606(89)90242-x},
   Key = {fds231549}
}

@article{fds231548,
   Author = {Raff, RA and Wray, GA},
   Title = {Heterochrony: Developmental mechanisms and evolutionary
             results},
   Journal = {Journal of Evolutionary Biology},
   Volume = {2},
   Number = {6},
   Pages = {409-434},
   Publisher = {WILEY},
   Year = {1989},
   Month = {January},
   ISSN = {1010-061X},
   url = {http://dx.doi.org/10.1046/j.1420-9101.1989.2060409.x},
   Abstract = {The concept of heterochrony, that the relative timing of
             ontogenetic events can shift during evolution, has been a
             major paradigm for understanding the role of developmental
             processes in evolution. In this paper we consider
             heterochrony from the perspective of developmental biology.
             Our objective is to redefine heterochrony more broadly so
             that the concept becomes readily applicable to the evolution
             of the full range of ontogenetic processes, from
             embryogenesis through the adult. Throughout, we stress the
             importance of considering heterochrony from a hierarchical
             perspective. Thus, we recognize that a heterochronic change
             at one level of organization may be the result of
             non‐heterochronic events at an underlying level. As such,
             heterochrony must be studied using a combination of genetic,
             molecular, cellular, and morphological approaches. Copyright
             © 1989, Wiley Blackwell. All rights reserved},
   Doi = {10.1046/j.1420-9101.1989.2060409.x},
   Key = {fds231548}
}

@article{fds231544,
   Author = {Wray, GA and McClay, DR},
   Title = {The origin of spicule-forming cells in a 'primitive' sea
             urchin (Eucidaris tribuloides) which appears to lack primary
             mesenchyme cells.},
   Journal = {Development (Cambridge, England)},
   Volume = {103},
   Number = {2},
   Pages = {305-315},
   Year = {1988},
   Month = {June},
   ISSN = {0950-1991},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/3066611},
   Abstract = {The calcareous larval skeleton of euechinoid sea urchins is
             synthesized by primary mesenchyme cells which ingress prior
             to gastrulation. In embryos of the cidaroid sea urchin
             Eucidaris tribuloides, no mesenchyme cells ingress before
             gastrulation, yet larvae later contain skeletons. This
             apparent paradox is resolved by immunochemical, cell lineage
             and morphological evidence showing that spicule-forming
             cells of Eucidaris are homologous to primary mesenchyme
             cells of euechinoids. In particular, these two cell types
             share expression of two cell lineage-specific gene products,
             are derived from the same cellular precursors, the
             micromeres, and undergo a similar migratory phase prior to
             skeletogenesis. Despite these similarities, there are far
             fewer spicule-forming cells in Eucidaris than in typical
             euechinoids and they assume a different pattern during
             spiculogenesis. The homology between Eucidaris
             spicule-forming cells and euechinoid primary mesenchyme
             cells indicates that a heterochrony in the time of
             spicule-forming cell ingression has occurred since the
             divergence of their respective lineages.},
   Key = {fds231544}
}

@article{fds231554,
   Author = {NIJHOUT, HF and WRAY, GA},
   Title = {Homologies in the colour patterns of the genus Heliconius
             (Lepidoptera: Nymphalidae)},
   Journal = {Biological Journal of the Linnean Society},
   Volume = {33},
   Number = {4},
   Pages = {345-365},
   Publisher = {Oxford University Press (OUP)},
   Year = {1988},
   Month = {January},
   ISSN = {0024-4066},
   url = {http://dx.doi.org/10.1111/j.1095-8312.1988.tb00449.x},
   Abstract = {The colour patterns of Heliconius butterflies are composed
             from a relatively simple set of pattern elements whose
             homologues are recognizable throughout the genus. Although
             Heliconius colour patterns look quite different from those
             of most nymphalids, these pattern elements are seen to
             derive from the generalized nymphalid groundplan. The
             differences arise primarily from the loss or positional
             shift of certain pattern elements, a high degree of fusion
             between individual pattern elements, and, in the forewing,
             asymmetries of the pattern elements relative to the
             wing‐cell midline. The scheme of homologies we present is
             consistent with what is currently known about the
             comparative morphology and developmental physiology of
             colour pattern formation in Lepidoptera, and provides a
             framework for the interpretation of developmental,
             evolutionary and genetic studies in Heliconius. Copyright ©
             1988, Wiley Blackwell. All rights reserved},
   Doi = {10.1111/j.1095-8312.1988.tb00449.x},
   Key = {fds231554}
}

@article{fds231489,
   Author = {WRAY, GA and MCCLAY, DR},
   Title = {THE EMBRYONIC MESENCHYME IN A PRIMITIVE SEA-URCHIN,
             EUCIDARIS-TRIBULOIDES},
   Journal = {The Journal of Cell Biology},
   Volume = {103},
   Number = {5},
   Pages = {A371-A371},
   Publisher = {ROCKEFELLER UNIV PRESS},
   Year = {1986},
   Month = {November},
   ISSN = {0021-9525},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1986E958901378&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds231489}
}

@article{fds231488,
   Author = {Frederik Nijhout and H and Wray, GA and Kremen, C and Teragawa,
             CK},
   Title = {Ontogeny, phylogeny and evolution of form: An algorithmic
             approach},
   Journal = {Systematic Zoology},
   Volume = {35},
   Number = {4},
   Pages = {445-457},
   Publisher = {Oxford University Press (OUP)},
   Year = {1986},
   Month = {January},
   ISSN = {0039-7989},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1986F931900001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Abstract = {A computer model that simulates general aspects of ontogeny
             is presented as a heuristic device for studying the
             relationship between ontogenetic changes and the evolution
             of morphologies. The model consists of a set of
             developmental rules limited to known cellular properties and
             activities of gene products; it assumes development to be an
             algorithmic and hierarchical process. Morphological patterns
             are generated through the interactions of developmental
             rules. Thus, by its very nature the model establishes
             pleiotropies and complex characters. To represent mutations,
             changes were introduced in the developmental rules.
             Phylogenetic analysis of mutant forms showed that morphology
             retained significant information about ancestry. Genetic
             parallelisms, as a rule, did not result in morphological
             parallelisms, because the effect of a given "genetic rule"
             is context-dependent. Morphological parallelisms that did
             arise were a consequence of different mutations that
             affected certain populations of cells in related ways. ©
             1986 Oxford University Press.},
   Doi = {10.2307/2413108},
   Key = {fds231488}
}

@article{fds231553,
   Author = {Nijhout, HF and Wray, GA},
   Title = {Homologies in the colour patterns of the genus Charaxes
             (Lepidoptera: Nymphalidae)},
   Journal = {Biological Journal of the Linnean Society},
   Volume = {28},
   Number = {4},
   Pages = {387-410},
   Publisher = {Oxford University Press (OUP)},
   Year = {1986},
   Month = {January},
   ISSN = {0024-4066},
   url = {http://dx.doi.org/10.1111/j.1095-8312.1986.tb01766.x},
   Abstract = {The phylogenetically and morphologically diverse patterns of
             Charaxes can be reduced to a simple set of pattern elements
             which can be homologized throughout the genus. At least five
             types of correspondence (homologies) exist among pattern
             elements: those between (1) species, (2) forewing and
             hindwing, (3) dorsal and ventral wing surface, (4) serial
             wing‐cells, and (5) individual pattern elements within a
             single wing‐cell. Differences in Charaxes colour patterns
             result from the distortion, elaboration, enlargement,
             reduction or loss of individual pattern elements. Further
             variation is often the result of dislocation of pattern
             elements from their serial homologues in neighbouring
             wing‐cells, and fusion of individual pattern elements to
             create larger areas of colour. The type of analysis
             presented in this paper should be broadly applicable within
             the Lepidoptera and may prove useful in studying the
             systematics of colour patterns and the evolution of the
             developmental system that gives rise to them. Copyright ©
             1986, Wiley Blackwell. All rights reserved},
   Doi = {10.1111/j.1095-8312.1986.tb01766.x},
   Key = {fds231553}
}


%% Papers Accepted   
@article{fds219912,
   Author = {J. Muntane and J.E. Horvath and P. Hof and J. Ely and W.D. Hopkins and M.A.
             Raghanti, A.H. Lewandowski and G.A. Wray and C.
             Sherwood},
   Title = {Analysis of synaptic gene expression in the neocortex of
             primates reveals evolutionary changes in glutamatergic
             neurotransmission},
   Journal = {Cerebral Cortex},
   Year = {2013},
   Key = {fds219912}
}


%% Papers Submitted   
@article{fds213393,
   Author = {L. Pinto and A. Ragunathan and P. Kapoor and M. McRae and D. Cantelmi and A. Heyland and G.A. Wray and J. Stone},
   Title = {Rudiment resorption observed serendipitously during sea
             urchin development},
   Year = {2012},
   Key = {fds213393}
}


%% Book Chapters   
@misc{fds183925,
   Author = {G.A. Wray},
   Title = {Embryos and evolution: 150 years of reciprical
             illumination},
   Pages = {215-239},
   Booktitle = {Evolution Since Darwin},
   Publisher = {Sinauer Associates},
   Editor = {M.A. Bell and D.J. Futuyma and W.F. Eanes and J.S.
             Levinton},
   Year = {2010},
   ISBN = {978-0878934133},
   Key = {fds183925}
}

@misc{fds166381,
   Author = {J. Tung and G.A. Wray},
   Title = {Evolution of traits deduced from genome comparisons},
   Booktitle = {Encyclopedia of Life Sciences},
   Editor = {Nature Publishing Group},
   Year = {2009},
   Key = {fds166381}
}

@misc{fds151739,
   Author = {G.A. Wray},
   Title = {Evolutionary synthesis in the genomic era},
   Booktitle = {Towards an Extended Evolutionary Synthesis},
   Publisher = {MIT Press},
   Year = {2009},
   Key = {fds151739}
}

@misc{fds152937,
   Author = {G.A. Wray},
   Title = {Evolution and Development},
   Pages = {208-236},
   Booktitle = {Evolution: The First Four Billion Years},
   Publisher = {Belknap Press},
   Editor = {M. Ruse and J. Travis},
   Year = {2009},
   Key = {fds152937}
}


%% Other   
@misc{fds140265,
   Author = {G.A. Wray},
   Title = {Guest in radio interview on evolutionary genomics for talk
             show "Radio in Vivo"},
   Year = {2007},
   Month = {February},
   Key = {fds140265}
}

@misc{fds2127,
   Author = {MW Hahn and GA Wray},
   Title = {the G-value paradox},
   Journal = {Evolution and Development},
   Year = {2001},
   Key = {fds2127}
}


%% Book Chapter   
@misc{fds140263,
   Author = {Babbitt, CC and GA Wray},
   Title = {Evolution of human gene expression control},
   Booktitle = {Encyclopedia of Life Sciences},
   Publisher = {Nature Publishing Group},
   Year = {2007},
   Key = {fds140263}
}


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