Research Topics
Species | G A WraySummaryAffiliation: Duke University Medical Center Country: USA Publications
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Detail Information
Publications
The evolution of transcriptional regulation in eukaryotesGregory A Wray
Department of Biology, Duke University, USA
Mol Biol Evol 20:1377-419. 2003..Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating...
Comparative embryology without a microscope: using genomic approaches to understand the evolution of developmentDavid A Garfield
Biology Department and Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA
J Biol 8:65. 2009..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...- Genetics. Enhancing gene regulationGregory A Wray
Department of Biology and Institute for Genome Science and Policy, Duke University, Box 90338, Durham, NC 27708, USA
Science 321:1300-1. 2008 - Do convergent developmental mechanisms underlie convergent phenotypes?Gregory A Wray
Department of Biology, Duke University, Durham, NC 27708, USA
Brain Behav Evol 59:327-36. 2002..Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons... - Developmental regulatory genes and echinoderm evolutionG A Wray
Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794 5245, USA
Syst Biol 49:28-51. 2000..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... - Transcriptional regulation and the evolution of developmentGregory A Wray
Department of Biology, Duke University, Durham, North Carolina 27708 0338, USA
Int J Dev Biol 47:675-84. 2003..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... - Dating branches on the tree of life using DNAGregory A Wray
Department of Biology, Duke University, Durham, NC 27708 0338, USA
Genome Biol 3:REVIEWS0001. 2002.... - The evolutionary significance of cis-regulatory mutationsGregory A Wray
Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
Nat Rev Genet 8:206-16. 2007..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... - The evolution of embryonic patterning mechanisms in animalsG A Wray
Department of Biology, Duke University, Durham, NC 27708 0325, USA
Semin Cell Dev Biol 11:385-93. 2000..These differences show surprisingly little correlation with phylogenetic relationships; instead, many are correlated with ecological factors, such as changes in life histories... - Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sitesJames P Balhoff
Department of Biology, Duke University, Durham, NC 27708, USA
Proc Natl Acad Sci U S A 102:8591-6. 2005.... - Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humansMatthew W Hahn
Department of Biology, Duke University, Durham, North Carolina 27708, USA
Genetics 167:867-77. 2004..Our results thus further support the hypothesis that regulatory mutations have been important in human evolution... - Ancient and recent positive selection transformed opioid cis-regulation in humansMatthew V Rockman
Department of Biology, Duke University, Durham, North Carolina, USA
PLoS Biol 3:e387. 2005.... - Abundant raw material for cis-regulatory evolution in humansMatthew V Rockman
Department of Biology, Duke University, Durham, NC 27708, USA
Mol Biol Evol 19:1991-2004. 2002..Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation... - Rapid evolution of cis-regulatory sequences via local point mutationsJ R Stone
Department of Ecology and Evolution, State University of New York at Stony Brook, USA
Mol Biol Evol 18:1764-70. 2001..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... 
Allele-specific gene expression in a wild nonhuman primate populationJ Tung
Department of Biology, Duke University, PO Box 90338, Durham, NC 27708, USA Institute for Genome Sciences and Policy, Durham, NC 27708, USA
Mol Ecol 20:725-39. 2011..They also highlight the potential importance of early life environmental variation in shaping the genetic architecture of complex traits in wild mammals...- Evolution of regeneration and fission in annelids: insights from engrailed- and orthodenticle-class gene expressionA E Bely
Department of Ecology and Evolution, State University of New York at Stony Brook, 11794 5245, USA
Development 128:2781-91. 2001..Furthermore, by comparing our data to existing data from leech embryos, we find evidence that embryonic processes are re-deployed during regeneration and fission... - Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory regionDagan A Loisel
Department of Biology, Duke University, Durham, NC 27705, USA
Proc Natl Acad Sci U S A 103:16331-6. 2006.... - Generation-biased gene expression in a bryophyte model systemPéter Szövényi
Department of Biology and Institute for Genome Sciences and Policy, Duke University, USA
Mol Biol Evol 28:803-12. 2011.... - Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolutionRalph Haygood
Biology Department, Duke University, Durham, North Carolina 27708, USA
Nat Genet 39:1140-4. 2007.... - Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitroLisa R Warner
Institute for Genome Sciences and Policy, Duke University, Durham 27708, USA Department of Biology, Duke University, Durham 27708, USA
Brain Res 1288:1-8. 2009..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... - Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemursJulie E Horvath
Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
Genome Res 18:489-99. 2008..Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve... - Evolution of a malaria resistance gene in wild primatesJenny Tung
Department of Biology, Duke University, North Carolina 27708, USA
Nature 460:388-91. 2009..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... - Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variationJenny Tung
Department of Biology, Duke University, Durham, NC, USA
Mol Biol Evol 26:2047-59. 2009..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... - Multiple Functional Variants in cis Modulate PDYN ExpressionCourtney C Babbitt
Institute for Genome Sciences and Policy, Duke University, USA
Mol Biol Evol 27:465-79. 2010.... - Positive selection on a human-specific transcription factor binding site regulating IL4 expressionMatthew V Rockman
Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
Curr Biol 13:2118-23. 2003..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... - Evolution of the gene network underlying wing polyphenism in antsEhab Abouheif
Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
Science 297:249-52. 2002.... - The g-value paradoxMatthew W Hahn
Department of Biology, Duke University, Durham, North Carolina 27708, USA
Evol Dev 4:73-5. 2002 - Positive selection on MMP3 regulation has shaped heart disease riskMatthew V Rockman
Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
Curr Biol 14:1531-9. 2004..The polymorphism contributes to variation in arterial traits and to the risk of coronary heart disease and its progression... - Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvaeChristopher J Lowe
Department of Ecology and Evolution, State University of New York at Stony Brook, 11732, USA
Evol Dev 4:111-23. 2002..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... - Convergent adaptation of human lactase persistence in Africa and EuropeSarah A Tishkoff
Department of Biology, University of Maryland, College Park, Maryland 20742, USA
Nat Genet 39:31-40. 2007..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... - Contrasts between adaptive coding and noncoding changes during human evolutionRalph Haygood
Biology Department and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Proc Natl Acad Sci U S A 107:7853-7. 2010..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... - Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populationsJenny Tung
Department of Biology, Duke University, P O Box 90338, Durham NC 27708, USA
Trends Genet 26:353-62. 2010..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... - Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationshipsKen Daigoro Yokoyama
Biology Department, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Nucleic Acids Res 37:e92. 2009..This offers a novel means by which to predict sequence elements with a collective role in gene regulation... - The evolutionary dynamics of alpha-satelliteM Katharine Rudd
Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
Genome Res 16:88-96. 2006..However, higher-order alpha-satellite is less conserved, suggesting different evolutionary rates for the two types of alpha-satellite... - Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invictaJulia H Bowsher
Department of Biology, Duke University, Durham, North Carolina, USA
J Exp Zool B Mol Dev Evol 308:769-76. 2007..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... - When is homology not homology?G A Wray
Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794 5245, USA
Curr Opin Genet Dev 8:675-80. 1998..These dissociations have interesting and important implications for understanding the genetic basis for evolutionary change in morphology... - Identification of asteroid genera with species capable of larval cloningK Emily Knott
Department of Ecology and Evolution, State University of New York, Stony Brook 11794 5245, USA
Biol Bull 204:246-55. 2003..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... - Developmental evolution: how beetles evolved their shieldsOlivier Fedrigo
Department of Biology, Duke University, Durham NC 27708 0338, USA
Curr Biol 20:R64-6. 2010..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... - The effects of selection against spurious transcription factor binding sitesMatthew W Hahn
Department of Biology, Duke University, USA
Mol Biol Evol 20:901-6. 2003..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... - When two is better than oneCourtney C Babbitt
Institute for Genome Science and Policy, Duke University, Box 90338, Durham, NC 27708 0338, USA
Cell 131:225-7. 2007..This combination of evolutionary changes appears to have resolved an adaptive conflict, leading to increased organismal fitness... - Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase IAlexandra E Bely
Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794 5245, USA
Mol Phylogenet Evol 30:50-63. 2004..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... - Endo16 is required for gastrulation in the sea urchin Lytechinus variegatusLaura A Romano
Department of Biology, Duke University, Durham, North Carolina 27708, USA
Dev Growth Differ 48:487-97. 2006..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... - Evolution: spot on (and off)Gregory A Wray
Nature 440:1001-2. 2006 - The invertebrate deuterostomes: an introduction to their phylogeny, reproduction, development, and genomicsCharles A Ettensohn
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
Methods Cell Biol 74:1-13. 2004 - Arrays in rays: terminal addition in echinoderms and its correlation with gene expressionRich Mooi
Department of Invertebrate Zoology and Geology, California Academy of Sciences, 875 Howard Street, San Francisco, CA 94103 3009, USA
Evol Dev 7:542-55. 2005..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... - Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulationLaura A Romano
Duke U, Durham, NC
Development 130:4187-99. 2003..purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation...