THE WRAY LAB

RECENT PUBLICATIONS


click here for publications prior to 2000

2013

Muntane, J, J E Horvath, P Hof, J Ely, W D Hopkins, M A Raghanti, A H Lewandowski, G A Wray, and C Sherwood (2013) Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission. Cerebral Cortex, in press.

Horvath, J E, G L Ramachandran, O Fedrigo, W J Nielsen, C C Babbitt, E M St. Clair, L W Pfefferle, J Jernvall, G A Wray, and C E Wall (2013) Genetic comparisons yield insight into the evolution of enamel thickness during human evolution. Journal of Human Evolution, in press.

Pfefferle, L W and G A Wray (2013) Insights from a chimpanzee adipose stromal cells population: opportunities for adult stem cells to expand primate functional genomics. Genome Biology and Evolution 5: 1995-2005. P

Garfield, D A, D E Runcie, C C Babbitt, R Haygood, W J Nielsen, and G A Wray (2013) The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biology 11: e1001696. P

Wray, G A (2013) Genomics and the evolution of phenotypic traits. Annual Review of Ecology, Evolution, and Systematics 44: 51-72. P

Runcie, D E, R T Wiedmann, E A Archie, J Altmann, G A Wray, S C Alberts, and J Tung (2013) Social environment influences the relationship between genotype and gene expression in wild baboons. Phil. Trans. R. Soc. B. 368: 20120345. P

2012

Garfield, D, R Haygood, W J Nielsen, and G A Wray (2012) Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus. Evolution & Development 14: 152-167. P

Shibata, Y, N C Sheffield, O Fedrigo, C C Babbitt, M Wortham, A K Tewari, D London, L Song, B-K Lee, V R Iyer, S C Parker, E H Margulies, G A Wray, T S Furey, and G E Crawford (2012) Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genetics 8: e1002789. P

Runcie, D E, D A Garfield, C C Babbitt, J A Wygoda, S Mukherjee, and G A Wray (2012) Genetics of gene expression responses to temperature stress in a sea urchin gene network. Molecular Ecology 21: 4547-4562. P

Babbitt, C C, J Tung, G A Wray, and S C Alberts (2012) Changes in gene expression associated with reproductive maturation in wild female baboons. Genome Biology and Evolution 4(2): 102-109. P

2011

Tung, J, M Y Akinyi, S Matura, J Altmann, G A Wray, and S C Alberts (2011) Allele-specific gene expression in wild nonhuman primates. Molecular Ecology 20: 725-739. P

Fedrigo, O, A D Pfefferle, C C Babbitt, R Haygood, C E Wall, and G A Wray (2011) Molecular evidence that a metabolic trade-off contributed to brain size evolution. Brain, Behavior and Evolution 78: 315-326. P

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. P

Pfefferle, A D*, L R Warner*, C W Wang, W J Nielsen, C C Babbitt, O Fedrigo, and G A Wray (2011) 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) P

Bilbo, S D, G A Wray, S E Perkins, and W Parker (2011) Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune disease. Medical Hypotheses 77: 494-504. P

Yokoyama, K D, J L Thorne, and G A Wray (2011) Coordinated genome-wide modification within proximal promoter cis-regulatory elements during vertebrate evolution. Genome Biology and Evolution 3: 66-74. P

Wray, G A (2011) CNCing is believing. Science 333: 946-947. P

2010

Szovenyi, P, S A Rensing, D Lang, G A Wray, and A J Shaw (2010) Generation-biased gene expression in a bryophyte model system. Molecular Biology and Evolution 28: 803-812. P

Tung, J, S C Alberts, and G A Wray (2010) Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends in Genetics 26: 353-362. P

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. P

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. P

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. P

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. P

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. P

Wray, G A (2010) Embryos and evolution: 150 years of reciprocal illumination. In Evolution Since Darwin. Sinauer Associates. Pp. 215-239.

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. P

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

Wray, G A (2009) Evolution and Development. In Evolution: The First Four Billion Years (M Ruse and J Travis, eds.), Belknap Press. Pp. 208-236.

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) P

Smith, M S, 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 Fiorentino, 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) P

Babbitt, C C and G A Wray (2007) Evolution of human gene expression control. In Encyclopedia of Life Sciences. Nature Publishing Group.

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

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). P

2004

Ettensohn, C A, G M Wessell, and G A Wray (eds) (2004) Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches. Academic Press, San Diego CA.

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. P

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. P

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. P

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. P

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. P

Wray, G A (2003) Transcriptional regulation and the evolution of development. International Journal of Developmental Biology 47: 675-684. P

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. P

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. P

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) P

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. P

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. P Supplement

Abouheif, E and G A Wray (2002) Evolution of the gene network underlying wing polyphenism in ants. Science 297: 249-252. P

Lowe, C J, L Issel-Tarver, and G A Wray (2002) Gene expression an larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae. Evolution & Development 4: 111-123. P

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. P

Hahn, M W and G A Wray (2002) The G-value paradox. Evolution & Development 4: 73-75. P

2001

Wray, G A (2001) Dating branches on the tree of life using DNA.Genome Biology 3: 0001.1-0001.7. P

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) P

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. P

2000

Wray, G A (2000) The evolution of embryonic patterning mechanisms in animals. Seminars in Cell & Developmental Biology 11: 353-393. P

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. P

Wray, G A and C J Lowe (2000) Developmental regulatory genes and echinoderm evolution. Systematic Biology 49: 151-174. P

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. P


WRAY LABDEPARTMENT OF BIOLOGYDEPARTMENT OF EVOLUTIONARY ANTHROPOLOGY • INSTITUTE FOR GENOME SCIENCES & POLICY
4115 FRENCH FAMILY SCIENCES CENTERDUKE UNIVERSITY • DURHAM, NC 27708, USA • 919-668-6249