THE WRAY LAB
PUBLICATIONS
FEATURED PAPERS: Tung et al. (2009), Yokoyama et al. (2009)
Under construction: Publications from years prior to 2000 will be added soon, as will links to pdfs, supplemental materials, datasets, etc.
2011
Fedrigo, F, A D Pfefferle, C C Babbitt, R Haygood, C E Wall, and G A Wray (in press) A potential role for glucose transporters in the evolution of human brain size. Brain, Behavior and Evolution.
Babbitt, C C, L R Warner, O Fedrigo, C E Wall, and G A Wray (2011) Genomic signatures of diet-related shifts in primate evolution. Proceedings of the Royal Society B 278: 961-969.
Pfefferle, A D*, L R Warner*, C W Wang, W J Nielsen, C C Babbitt, O Fedrigo, and G A Wray (2011) Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution. Journal for Human Evolution 60: 205-212. (*These authors contributed equally)
2010
Yokoyama, K D, Thorne, J L, and G A Wray (accepted) Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. Genome Biology and Evolution.
Szovenyi, P, S A Rensing, D Lang, G A Wray, and A J Shaw (in press) Generation-biased gene expression in a bryophyte model system. Molecular Biology and Evolution.
Tung, J, S C Alberts, and G A Wray (in press) Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends in Genetics.
Oliver, T A*, D A Garfield*, M K Manier, R Haygood, G A Wray, and S R Palumbi (2010) Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin. Genome Biology and Evolution 2: 800-814.(*These authors contributed equally) P
Cruz-Gordillo, P, O Fedrigo, G A Wray, and C C Babbitt (2010) Extensive Changes in the Expression of the Opioid Genes between Humans and Chimpanzees. Brain Behavior and Evolution 76: 154-162.
Haygood, R, C C Babbitt, O Fedrigo, and G A Wray (2010) Contrasts between adaptive coding and noncoding changes during human evolution. Proceedings of the National Academy of Sciences, U.S.A. 107: 7853-7857.
Babbitt, C C, O Fedrigo, A D Pfefferle, A P Boyle, J E Horvath, T S Furey, and G A Wray (2010) Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain. Genome Biology and Evolution 2: 67-69. P
Babbitt, C C, J S Silverman, R Haygood, J M Reininga, M V Rockman, and G A Wray (2010) Multiple functional variants in cis modulate PDYN expression. Molecular Biology and Evolution 27: 465-479.
Garfield, D A and G A Wray (2010) The evolution of gene regulatory interactions. BioScience 60: 15-23. (review) P
Fedrigo, O and G A Wray (2010) Developmental evolution: How beetles evolved their shields. Current Biology 20: R64-R66.
Fedrigo, O, L R Warner, A D Pfefferle, P Cruz-Gordillo, C C Babbitt, and G A Wray (2010) A pipeline to determine RT-PCR control genes for evolutionary studies: application to primate gene expression across multiple tissues. PLoS One 5: e12545.
2009
Yokoyama, K D, U Ohler, and G A Wray (2009) Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Research 37: e92. P
Tung, J, A E Primus, A Bouley, T F Severson, S Alberts, and G A Wray (2009) Evolution of a malaria resistance gene in wild primates. Nature 460: 388-391.
Warner, L R, C C Babbitt, A E Primus, T F Severson, R Haygood, and G A Wray (2009) Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitro. Brain Research 1288: 1-8. P
Tung, J, O Fedrigo, R Haygood, S Mukerjee, and G A Wray (2009) Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Molecular Biology and Evolution 26: 2047-2059. P
Garfield, DA and G A Wray (2009) Comparative embryology without a microscope: using genomic approaches to understand the evolution of development. Journal of Biology 8: 65. (minireview)
Smith, MS, G A Wray, and R A Raff (2009) Revisiting cell lineage and cell fate in light of the evolution of axis formation of Heliocidaris erythrogramma. Evolution & Development, in press.
2008
Horvath, J E, D W Weisrock, S L Embry, I Fiorention, J P Balhoff, P Kappeler, G A Wray, H F Willard, and A D Yoder (2008) Development and application of a phylogenomic toolkit: resolving the history of Madagascar's lemurs. Genome Research 18: 489-499. P
Wray, G A and C C Babbitt (2008) Enhancing gene regulation. Science 321: 1300-1301. (minireview) P
Haygood, R, O Fedrigo, and G A Wray (2008) Reply to "Rapidly evolving human promoter regions." Nature Genetics 40: 1263-1264.
2007
Haygood, R H*, O Fedrigo*, B Hanson, K D Yokoyama, and G A Wray (2007) Promoter regions of many neural- and nutrition-related genes experienced positive selection during human evolution. Nature Genetics 39: 1140-1144. (these authors contributed equally to this research) P
Wray, G A (2007) The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics 8: 206-216. (review)
Bowsher, J H, G A Wray, and E Abouheif (2007) Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invicta. Journal of Experimental Zoology 308: 769-776. P
Tishkoff, S A, F A Reed, A Ranciaro, B F Voight, C C Babbitt, J S Silverman, K Powell, H M Mortensen, J B Hirbo, M Osman, M Ibrahim, S A Omar, G Lema, T B Nyambo, J Ghori, S Bumpstead, J K Pritchard, G A Wray, and P Deloukas (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39: 31-40. P
Babbitt, C C, R Haygood, and G A Wray (2007) When two is better than one. Cell 19: 225-227. (minireview) P
Sumrall, C D and G A Wray (2007) Ontogeny in the fossil record: diversification of body plans and the evolution of "aberrant" symmetry in Paleozoic echinoderms. Paleobiology 33: 149-163. P
2006
Sodergren, E, G M Weinstock, E H Davidson, R A Cameron, and the Sea Urchin Genome Sequencing Consortium (includes G A Wray and 6 members of the Wray lab group) (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314: 941-952. P
Loisel, D A, M V Rockman, G A Wray, J Altmann, and S C Alberts (2006) Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region. Proceedings of the National Academy of Sciences, U.S.A. 103: 16331-16336. P
Wray, G A (2006) Spot on (and off). Nature 440: 1001-1002. (minireview) P
Nyberg, K G, C N Ciampaglio, and G A Wray (2006) Tracing the ancestry of the great white shark,Carcharadon carcharias, using morphological analysis of fossil teeth. Journal of Vertebrate Paleontology 26: 806-814. P
Wray, G A (2006) The evolution of embryonic gene expression in sea urchins. Integrative and Comparative Biology 46: 233-242. (review) P
Romano, L and G A Wray (2006) Endo16 is required for gastrulation in the sea urchin Lytechinus variegatus. Development, Growth, and Differentiation 48: 487-497. P
Rudd, M K, G A Wray, and H F Willard (2006) The evolutionary dynamics of alpha satellite. Genome Research 16: 88-96. P
2005
Balhoff, J P and G A Wray (2005) Evolutionary analysis of the well-characterized endo16 promoter reveals substantial variation within functional sites. Proceedings of the National Academy of Sciences, U.S.A. 102: 8591-8596. P
Rockman, M V, M W Hahn, N Soranzo, F Zimprich, D B Goldstein, and G A Wray (2005) Ancient and recent positive selection transformed opioid cis-regulation in humans. PLoS Biology 3: e387. P
Mooi, R, B David, and G A Wray (2005) Arrays in rays: terminal addition in echinoderms and its correlation with gene expression. Evolution & Development 7: 542-555. (review) P
Ciampaglio, C, G A Wray, and B H Corliss (2005) A toothy tale of evolution: Convergence in tooth morphology among marine Mesozoic-Cenozoic sharke, reptiles, and mammals. The Sedimentary Record 3: 4-8 (cover).
2004
Rockman, M V, M W Hahn, N Soranzo, D Loisel, D B Goldstein, and G A Wray (2004) Positive selection on MMP3 regulation has shaped heart disease risk. Current Biology 14: 1531-1539.
Hahn, M W, M V Rockman, N Soranzo, D B Goldstein, and G A Wray (2004) Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the Factor VII locus. Genetics 167: 867-877.
Bely, A E and G A Wray (2004) Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrom oxidase I. Molecular Phylogeny and Evolution 30: 50-63.
Levinton, J S, L Dubb, and G A Wray (2004) Simulations of evolutionary radiations and their application to understanding the probability of a Cambrian explosion. Journal of Paleontology 78: 31-38.
2003
Rockman, M V, M W Hahn, N Soranzo, D B Goldstein, and G A Wray (2003) Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Current Biology 13: 2118-2123.
Wray, G A (2003) Transcriptional regulation and the evolution of development. International Journal of Developmental Biology 47: 675-684.
Romano, L and G A Wray (2003) Conservation of Endo16 expression in sea urchins despite divergence in both cis and trans-acting elements of transcriptional regulation. Development 130: 4187-4199.
Wray, G A, M W Hahn, E Abouheif, J P Balhoff, M Pizer, M V Rockman, and L Romano (2003) The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20: 1377-1419.
Knott, K E, E J Balser, W B Jaeckle, and G A Wray (2003) Identification of asteroid genera with species capable of larval cloning. Biological Bulletin 204: 246-255. (cover)
Hahn, M W, J Stajich, and G A Wray (2003) The effects of selection against spurious transcription factor binding sites. Molecular Biology and Evolution 20: 901-906.
2002
Rockman, M V and G A Wray (2002) Abundant raw material for cis-regulatory evolution in humans. Molecular Biology and Evolution 19: 1991-2004.
Abouheif, E and G A Wray (2002) Evolution of the gene network underlying wing polyphenism in ants. Science 297: 249-252.
Lowe, C J, L Issel-Tarver, and G A Wray (2002) Evolution of new developmental roles for orthodenticle and distal-less in the larvae of echinoderms. Evolution & Development 4: 111-123.
Wray, G A and R R Strathmann (2002) Stasis, change, and functional constraint in the evolution of animal body plans, whatever they may be. Vie et Milieu 52: 189-199.
Wray G A (2002) Do convergent developmental mechanisms underlie convergent phenotypes? Brain, Behavior, and Evolution 59: 327-336.
Hahn, M W and G A Wray (2002) The G-value paradox. Evolution & Development 4: 73-75.
2001
Wray, G A (2001) Dating branches on the tree of life using DNA.Genome Biology 3: 0001.1-0001.7.
Bely, A E and G A Wray (2001) Evolution of regeneration and fission in an annelid: insights from engrailed- and orthodenticle-class gene expression. Development 128: 2781-2791. (cover)
Stone, J R and G A Wray (2001) Rapid appearance of new transcription factor binding sites by local point mutation. Molecular Biology and Evolution 18: 1764-1770.
2000
Wray, G A (2000) The evolution of embryonic patterning mechanisms in animals. Seminars in Cell & Developmental Biology 11: 353-393.
Knott, K E and G A Wray (2000) Controversy and consensus in asteroid systematics: new insights into ordinal and familial relationships. American Zoologist 40: 382-392.
Wray, G A and C J Lowe (2000) Developmental regulatory genes and echinoderm evolution. Systematic Biology 49: 151-174.
Wray, G A (2000) Peering ahead (cautiously). Evolution & Development 2: 1-2.
Cameron, R A, G Mahairas, J P Rast, T R Biondi, S Schwartzell, J Wallace, B T Livingston, G A Wray, C A Ettensohn, H Lehrach, R J Britten, E H Davidson, and L Hood (2000) A sea urchin genome project: sequence scan, virtual map, and additional resources. Proceedings of the National Academy of Sciences (USA) 97: 9514-9518.