WrayLab publications

Selected Publications

Haygood, R.H., Fedrigo, O., Hanson, B., Yokoyama, K-D., and G.A. Wray. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics 39 (9): 1140-1144. pdf

Wray, G.A. 2007. The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics 8:206-216.pdf

Tishkoff, S.A., Reed, F.A., Ranciaro, A., Voight, B.F., Babbitt, C.C., Silverman, J.S., Powell, K., Mortensen, H.M., Hirbo, J.B., Osman, M., Ibrahim, M., Omar, S.A., Lema, G., Nyambo, T.B., Ghori, J., Bumpstead, S., Pritchard, J.K., Wray, G.A., and P. Deloukas. 2007. Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39 (1):31-40.pdf

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 Stongylocentrotus purpuratus. Science 314:914-952.pdf

Nyberg, K.G., C.N. Ciampaglio, and G.A. Wray. 2006. Tracing the ancestry of the great white shark, Carcharadon carcharias, using morphometric analysis of fossil teeth. Journal of Vertebrate Paleontology 26(4):806-814. pdf

Balhoff, J.P. and G.A. Wray. 2005. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. PNAS 102:8591-8596.pdf

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.pdf

Rockman, M.V., M.W. Hahn, N. Soranzo, D.A. Loisel, D.B. Goldstein, and G.A. Wray. 2004. Positive selection on MMP3 regulation has shaped heart disease risk. Current Biology 14:1531-1539.pdf

Romano, L.A. 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.pdf

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.pdf

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.pdf

Rockman, M. V. and G. A. Wray. 2002. Abundant raw material for cis-regulatory evolution in humans. Molecular Biology & Evolution 19:1991-2004.pdf

Abouheif, E. and G. A. Wray. 2002. Evolutionary lability of the regulatory gene network underlying the wing polyphenism in ants. Science 297:249-252.pdf

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

All Publications

Journal articles

Horvath, J. E., Weisrock, D. W., Embry, S. L., Fiorentino, I., Balhoff, J. P., Kappeler, P., Wray, G. A., Willard, H. F., and A. D. Yoder. 2008. Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs. Genome Research 18:489-499. pdf

Babbit, C.C., Haygood, R., and G.A. Wray. 2007. When two is better than one. Cell 131:225-227.pdf

Wray, G.A. 2007. The evolutionary significance of cis-regulatory mutations. Nature Reviews Genetics 8:206-216.pdf

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(1):149-163.pdf

Wray, G.A. 2006. The evolution of embryonic gene expression in sea urchins. Integrative and Comparative Biology 46:233-242.pdf

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.pdf

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 (USA) 103:16331-16336.pdf

Wray, G.A. 2006. Evolution: Spot on (and off). Nature 440:1001-1002.pdf

Rudd, M. K., G. A. Wray, and H. F. Willard. 2006. The evolutionary dynamics of Alpha satellite. Genome Research 16:88-96.pdf

Balhoff, J.P. and G.A. Wray. 2005. Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites. PNAS 102:8591-8596.pdf

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.pdf

Rockman, M.V., M.W. Hahn, N. Soranzo, D.A. Loisel, D.B. Goldstein, and G.A. Wray. 2004. Positive selection on MMP3 regulation has shaped heart disease risk. Current Biology 14:1531-1539.pdf

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 in humans. Genetics 167:867-877.pdf

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.pdf

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.pdf

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

Bely, A.E. and G.A. Wray. 2003. Molecular phylogeny of naidid worms (Annelida: Clitellata) based on cytochrome oxidase I. Molecular Phylogenetics and Evolution 30:50-63.pdf

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.pdf

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.pdf

Abouheif, E. and G. A. Wray. 2002. Evolutionary lability of the regulatory gene network underlying the wing polyphenism in ants. Science 297:249-252.pdf

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

Rockman, M. V. and G. A. Wray. 2002. Abundant raw material for cis-regulatory evolution in humans. Molecular Biology & Evolution 19:1991-2004.pdf

Stone, J. & G. A. Wray. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Molecular Biology & Evolution 18: 1764-1770.pdf

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.pdf

Wray, G. A. 2001. Resolving the Hox paradox. Science 292: 2256-2257.

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

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

Knott, K. E., and G. A. Wray. 2000. Controversy and consensus in asteroid systematics: new insights into ordinal and familial relationships. Amer. Zool. 40: 382-392.

Cameron, R. A., G. Mahairas, J. P. Rast, P. Martinez, T. R. Biondi, S. Swartzell, J. C. Wallace, A. J. Poustka, 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.

Wray, G. A. 2000. Peering ahead (cautiously). Evolution & Development 2:1-2.

Wray, G. A. 1998. Promoter logic. Science 279: 1871-1872.

Wray, G. A. and E. Abouheif. 1998. When is homology not homology? Current Opinion in Genetics and Development 8: 675-680.

Lowe, C. J. and G. A. Wray. 1997. Radical alterations in the roles of homeobox genes during echinoderm evolution. Nature 389: 718-721.

Abouheif, E, M. Akam, W. J. Dickinson, P. W. H. Holland, A. Meyer, N. H. Patel., R. A. Raff, V. L. Roth, and G. A. Wray. 1997. Homology and developmental genetics. Trends in Genetics 11: 432-433.

Benink, H., G. A. Wray, and J. Hardin. 1997. Endodermal precursors can organize secondary axial structures in the sea urchin embryo. Development 124: 3461-3470.

Panganiban, G., S. M. Irvine, C. Lowe, H. Roehl, L. S. Corley, B. Sherbon, J. K. Grenier, J. F. Fallon, J. Kimble, M. Walker, G. A. Wray, B. J. Swalla, M. Q. Martindale, and S. B. Carroll. 1997. The origin and evolution of animal appendages. Proceedings of the National Academy of Sciences (USA) 94: 5162-5166.

Craig, S., L. Slobodkin, G. A. Wray, and C. Biermann. 1997. The “paradox” of polyembryony: a review of the cases and an explanation for it’s evolution. Evolutionary Ecology 11: 127-143.

Wray, G. A., J. S. Levinton, and L. Shapiro. 1996. Molecular evidence for deep pre-Cambrian divergences among the metazoan phyla. Science 274: 568-573.

Wray, G. A. 1996. Parallel evolution of non-feeding larvae in echinoids. Systematic Biology 45: 308-322.

Wray, G. A. 1995. Punctuated evolution of embryos. Science 267: 1115-1116.

Smith, A. B., D. T. J. Littlewood, and G. A. Wray. 1995. Comparing patterns of evolution: larval and adult life history stages and small subunit ribosomal RNA of post-Palaeozoic echinoids. Philosophical Transactions of the Royal Society, London, 349: 11-18.

Wray, G. A., and A. E. Bely. 1994. The evolution of echinoderm development is driven by several distinct factors. Development, 1994 supplement, 97-106.

Wray, G. A. 1994. The evolution of cell lineage in echinoderms. American Zoologist 34: 353-363.

Wray, G. A. 1994. Developmental evolution: new paradigms and paradoxes. Developmental Genetics 15: 1-6.

Wray, G.A. 1992. The evolution of larval morphology during the post-Paleozoic radiation of echinoids. Paleobiology 18: 258-287.

Wray, G.A. 1992. Rates of evolution in developmental processes. American Zoologist 32: 123-134.

Wray, G.A., and R.A. Raff. 1991. Rapid evolution of gastrulation mechanisms in a sea urchin with lecithotrophic larvae. Evolution 45: 1741-1750.pdf

Wray, G.A., and R.A. Raff. 1991. The evolution of developmental strategy in marine invertebrates. Trends in Ecology & Evolution 6: 45-50.

Henry, J.J., G.A. Wray, and R.A. Raff. 1991. Mechanism of an alternate type of blastula formation: the wrinkled blastula of the sea urchin Heliocidaris erythrogramma. Development, Growth & Differentiation 33: 317-328.

Wray, G.A., and R.A. Raff. 1990. Novel origins of lineage founder cells in the direct-developing sea urchin Heliocidaris erythrogramma. Developmental Biology 141: 41-54.

Henry, J.J., G.A. Wray, and R.A. Raff. 1990. The dorsoventral axis is specified prior to first cleavage in the direct developing sea urchin Heliocidaris erythrogramma. Development 110: 875-884.

Wray, G.A., and R.A. Raff. 1990. Pattern and process heterochronies in the early development of sea urchins. Seminars in Developmental Biology 1: 245-251.

Scott, L.B., W.J. Lennarz, R.A. Raff, and G.A. Wray. 1990. The ‘lecithotrophic’ sea urchin Heliocidaris erythrogramma lacks typical yolk platelets and yolk glycoproteins. Developmental Biology 138: 188-193.

Nijhout, H.F., G.A. Wray, and L.A. Gilbert. 1990. An analysis of the phenotypic effects of certain color pattern genes in Heliconius (Lepidoptera: Nymphalidae). Biological Journal of the Linnean Society 40: 357-372.

Wray, G.A., and R.A. Raff. 1989. Evolutionary modification of cell lineage in the direct-developing sea urchin Heliocidaris erythrogramma. Developmental Biology 132: 458-470.

Raff, R.A., and G.A. Wray. 1989. Heterochrony: developmental processes and evolutionary results. Journal of Evolutionary Biology 2: 409-434.

Henry, J.J., S. Amemiya, G.A. Wray, and R.A. Raff. 1989. Early inductive interactions are involved in restricting cell fates of mesomeres in sea urchin embryos. Developmental Biology 136: 140-153.

Wray, G.A., and D.R. McClay. 1989. Molecular heterochronies and heterotopies in early echinoid development. Evolution 43: 803-813.pdf

Parks, A.L., B.W. Bisgrove, G.A. Wray, and R.A. Raff. 1989. Direct development in the sea urchin Phyllacanthus parvispinus (Cidaroidea): Phylogenetic history and functional modification. Biological Bulletin 177: 96-109.

Wray, G.A., and D.R. McClay. 1988. The origin of spicule-forming cells in a ‘primitive’ sea urchin (Eucidaris tribuloides) which appears to lack primary mesenchyme cells. Development 103: 305-315.

Nijhout, H.F., and G.A. Wray. 1988. Homologies in the color patterns of the genus Heliconius (Lepidoptera: Nymphalidae). Biological Journal of the Linnean Society 33: 345-365.

Nijhout, H.F., and G.A. Wray. 1986. Homologies in the color patterns of the genus Charaxes (Lepidoptera: Nymphalidae). Biological Journal of the Linnean Society 28: 387-410.

Nijhout, H.F., G.A. Wray, C. Kremen, and C.K. Teragawa. 1986. Ontogeny, phylogeny, and the evolution of form: an algorithmic approach. Systematic Zoology 35: 445-459.

Books

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.

Book chapters

Wray, G. A. 2000. The evolution of sea urchin development. In “Regulatory Processes in Development” (C.-O. Jacobson and L. Olsson, eds.). Portland Press, London. In press.

Wray, G. A. 2000. Developmental genes and the evolution of morphology. In “Palaeobiology II” (D. E. G. Briggs and R. Crowther, eds.). Blackwell Scientific, London. In press.

Lowe, C. J. and G. A. Wray. 1999. Rearing larvae of sea urchins and sea stars for developmental studies. In “Methods in Molecular Biology, Vol. 135: Developmental Biology Protocols, vol. 1” (R. Tuan and C. Lo, eds.), Humana Press, Totowa NJ. Pp. 9-15.

Wray, G. A. 1999. Evolutionary dissociations between homologous genes and homologous structures. In “Homology” (B. Hall, ed.). Wiley, Chichester (Novartis Foundation Symposium 222). Pp. 189-206.

Hart, M. W. and G. A. Wray. 1999. Heterochrony. In “Origin and Evolution of Larval Forms” (B. Hall and M. Wake, eds.), Academic Press. Pp. 159-165.

Wray, G. A. Introduction: sea urchins. 1998. In “Mechanisms of cell fate and cell lineage determination” (S. Moody, ed.), Academic Press. Pp. 3-9.

Wray, G. A. 1997. Echinoderms. In “Constructing the Organism: Comparative Embryology” (S. Gilbert and A. Raunio, eds.). Sinauer Assoc., Sunderland MA. Pp. 309-329.

Smith, A.B., D.T.J. Littlewood, and G.A. Wray. 1996. Comparative evolution of larval and adult life history stages and small subunit ribosomal RNA amongst post-Paleozoic echinoids. In “New uses for new phylogenies” (P. Harvey, ed.). Oxford Univ. Press, Oxford. Pp. 234-254.

Wray, G.A. 1995. Ecological and evolutionary consequences of heterochronies in early echinoderm development. In “Evolution through Heterochrony” (K. J. McNamara, ed.). Wiley-Liss, New York. Pp. 197-223.

Wray, G.A. 1995. Evolution of larvae and developmental patterns. In “Ecology of Marine Invertebrate Larvae” (L. R. McEdwards, ed.). Critical Reviews Series, C. R. C. Press, Boca Raton, FL. Pp. 413-447.

Raff, R.A., J.J. Henry, and G.A. Wray. 1993. Rapid evolution of early development: Reorganization of early morphogenetic processes in a direct-developing sea urchin. In “Gastrulation: Movements, Patterns and Molecules” (R. Keller, ed.). Plenum Press, New York.

Raff, R.A., G.A. Wray, and J.J. Henry. 1991. Implications of radical changes in early development for concepts of developmental constraint. In “New Perspectives on Evolution” (L. Warren and H. Koprowski, eds.). Wiley-Liss, New York. Pp. 189-207.

Raff, R.A., B.A. Parr, A.L. Parks, and G.A. Wray. 1990. Heterochrony and other mechanisms of radical evolutionary change. In “Evolutionary Innovations” (M.H. Nitecki, ed.). University of Chicago Press. Pp. 71-98.

McClay, D.R., G.A. Wray, M.C. Alliegro, and C.A. Ettensohn. 1990. Sequential changes in cell adhesion during morphogenesis. In “Morphoregulatory Molecules” (G.M. Edelman, B.A. Cunningham, and J.-P. Thiery, eds.). Wiley, New York. Pp. 533-546.

For the popular press

Wray, G. A. and R. A. Raff. 1998. Body-builders of the sea. Natural History, December 1998 issue, pp. 38-47.

The Wray Lab at Duke University