Paper Archive

Home

People

Research

Publications

Courses

Photos

Lab meetings

Links

Contact

 

Fall 2011

Bomblies, K., J. Lempe, P. Epple, N. Warthmann, C. Lanz, J.L. Dangl, and D. Weigel, 2007. Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biology 5(9): 1962-1972.

Fournier-Level, A., A. Korte, M.D. Cooper, M. Nordborg, J. Schmitt, and A.M. Wilczek, 2011. A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.

Hall, M.C., D.B. Lowry, and J.H. Willis, 2010. Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci? Molecular Ecology 19: 2739-2753.

Isogai, Y., S. Si, L. Pont-Lezica, T. Tan, V. Kapoor, V.N. Murthy, and C. Dulac, 2011. Molecular organization of vomeronasal chemoreception. Nature 478: 241-245.

Keane, T.M., L. Goodstadt, P. Danecek, M.W. White, K. Wong, B. Yalcin, et al., 2011. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.

Meiklejohn, C.D., E.L. Landeen, J.M. Cook, S.B. Kingan, and D.C. Presgraves, 2011. Sex chromosome-specific regulation in the Drosophila male germline but little evidence for chromosomal dosage compensation or meiotic inactivation. PLoS Biology 9(8): e1001126.

Phadnis, N., 2011. Genetic architechture of male sterility and segregation distortion in Drosophila pseudoobscura Bogota-USA hybrids. Genetics 189(3): 1001-1009.

Stevison, L.S., K.B. Hoehn, and M.A.F. Noor, 2011. Effects of inversions on within- and between-species recombination and divergence. Genome Biology and Evolution 3: 830-841.

Tennessen, J.A. and J.M. Akey, 2011. Parallel adaptive divergence among geographically diverse human populations. PLoS Genetics 7(6): e1002127.

Turner, L.M. Schwahn, D.J. and B. Harr, 2011. Reduced male fertility is common but highly variable in form and severity in a natural house mouse hybrid zone. Evolution, doi:10.1111/j.1558-5646.2011.01445.x

White, M.A., B. Steffy, T. Wiltshire, and B.A. Payseur, 2011. Genetic dissection of a key reproductive barrier between nascent species of house mice. Genetics 189: 289-304.

Spring 2011

Boyko, A.R., P. Quignon, L. Li, J.J. Schoenebeck, J.D. Degenhardt, K.E. Lohmueller, K. Zhao, A. Brishbin, H.G. Parker, B.M. vonHoldt, M. Cargill, A. Auton, A. Reynolds, A.G. Elkahloun, M. Castelhano, D.S. Mosher, N.B. Sutter, G.S. Johnson, J. Novembre, M.J. Hubisz, A. Siepel, R.K. Wayne, C.D. Bustamante, and E.A. Ostrander, 2010. A simple genetic architecture underlies morphological variation in dogs. PLoS Biology 8(8): e1000451.

Clark, M.E., F.P. O'Hara, A. Chawla, and J.H. Werren, 2010. Behavioral and spermatogenic hybrid male breakdown in Nasonia. Heredity 104: 289-301.

Fraser, H.B., T. Babak, J. Tsang, Y. Zhou, B. Zhang, M. Mehrabian, and E.E. Schadt, 2011. Systematic detection of polygenic cis-regulatory evolution. PLoS Genetics 7(3): e1002023.

Hancock, A.M., D.B. Witonsky, E. Ehler, G. Alkorta-Aranburu, C. Beall, A. Gebremedhin, R. Sukernik, G. Utermann, J. Pritchard, G. Coop, and A. Di Rienzo, 2010. Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. PNAS 107: 8924-8930.

Hernandez, R.D., J.L. Kelley, E. Elyashiv, S. C. Melton, A. Auton, G. McVean, 1000 Genomes Project, G. Sella, and M. Przeworski, 2011. Classic selective sweeps were rare in recent human evolution. Science 331: 920-924.

Hopkins, R. and M.D. Rausher, 2011. Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. Nature 469: 411-414.

Lowry, D.B. and J.H. Willis, 2010. A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biology 8(9): e1000500.

Lynch, M., 2010. Rate, molecular spectrum, and consequences of human mutation. PNAS 107(3): 961-968.

Manceau, M., V.S. Domingues, R. Mallarino, and H.E. Hoekstra, 2011. The developmental role of Agouti in color pattern evolution. Science 331: 1062-1065.

McBride, C.S. and M.C. Singer, 2010. Field studies reveal strong postmating isolation between ecologically divergent butterfly populations. PLoS Biology 8(10): e1000529.

McLean, C.Y., P.L. Reno, A.A. Pollen, A.I. Bassan, T.D. Capellini, C. Guenther, V.B. Indjeian, X.Lim, D.B. Menke, B.T. Scharr, A.M. Wenger, G. Bejerano, and D.M. Kingsley, 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216-219.

Nasonia Genome Working Group, 2010. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327: 343-348.

Pai, A.A., J.T. Bell, J.C. Marioni, J.K. Pritchard, and Y. Gilad, 2011. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genetics 7(2): e1001316.

Fall 2010

Akey, J.M., A.L. Ruhe, D.T. Akey, A.K. Wong, C.F. Connelly, J. Madeoy, T.J. Nicholas, and M.W. Neff, 2010. Tracking footprints of artificial selection in the dog genome. PNAS 10.1073/pnas.0909918107.

Bellott, D.W., H. Skaletsky, T. Pyntikova, E.R. Mardis, T. Graves, C. Kremitzki, L.G. Brown, S. Rozen, W.C. Warren, R.K. Wilson, and D.C. Page, 2010. Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature Letters 466: 612-616.

Burke, M.K., J.P. Dunham, P. Shahrestani, K.R. Thorton, M.R. Rose and A.D. Long, 2010. Genome-wide anaylsis of long-term evolution experiement with Drosophila. Nature doi:10.1038/nature09352.

Cizkova, D., J. Gouy de Bellocq, S.J.E. Baird, J. Pialek and J. Bryja, 2010. Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations. Heredity, doi: 10.1038/hdy.2010.112.

Gregg, C., J. Zhang, J.E. Butler, D. Haig, and C. Dulac, 2010. Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329: 682-685.

Gregg, C., J. Zhang, B. Weissbourd, S. Luo, G.P. Schroth, D. Haig, and C. Dulac, 2010. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329: 643-648.

Jiang, P., D.L. Hartl, and B. Lemos. Y not a dead end: epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression in Drosophila melanogaster. Genetics 186: 109-118.

Lawniczak, M.K.N., S.J. Emrich, A.K. Holloway, A.P. Regier, M. Olson, B. White, et al., 2010. Widespread divergence between incipient Anopheles gambiae species revealved by whole genome sequences. Science 330: 512-514.

Matute, D.R., I.A. Butler, D.A. Turissini, and J.A. Coyne, 2010. A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science 329: 1518-1521.

Merrill, R.M., B. Van Schooten, J.A. Scott, and C.D. Jiggins, 2010. Pervasive genetic associations between traits causing reproductive isolation in Heliconius butterflies. Proceedings of the Royal Society B, doi: 10.1098/rspb.2010.1493.

Moyle, L.C., C.D. Muir, M.V. Han, and M.W. Hahn, 2010. The contribution of gene movement to the "two rules of speciation." Evolution 64(6): 1541-1557.

Moyle, L.C. and T. Nakazato, 2010. Hybrid incompatibility "snowballs" between Solanum species. Science 329: 1521.

Moyle, L.C. and T. Nakazato, 2009. Complex epistasis for Dobzhansky-Muller hybrid incompatibility in Solanum. Genetics 181: 347-351.

Muir, C.D. and L.C. Moyle, 2009. Antagonistic epistasis for ecophysiological trait differences between Solanum species. New Phytologist 183: 789-802.

Neafsey, D.E., M.K.N. Lawniczack, D.J. Park, S.N. Redmond, M.B. Coulibaly, S.F. Traore, et al., 2010. SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes. Science 330: 514-517.

Oka, A., A. Mita, Y. Takada, H. Koseki, and T. Shiroiski, 2010. Reproductive isolation in hybrid mice due to spermatogenesis defects at three meiotic stages. Genetics 186: 339-351.

Pelak, K., K.V. Shianna, D. Ge, J.M. Maia, M. Zhu, J.P. Smith, et al., 2010. The characterization of twenty sequenced human genomes. PLoS Genetics 6(9): e1001111.

Sun, C., C. Southard, D.B. Witonsky, R. Kittler, and A. Di Rienzo, 2010. Allele-specific down-regulation of RPTOR expression induced by retinoids contributes to climate adaptations. PLoS Genetics 6(10): e10011178.

Turner, T.L., M.W. Hahn, and S.V. Nuzhdin, 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biology 3:e285.

Wiley, C. and K.L. Shaw, 2010. Multiple genetic linkages between female preference and male signal in rapidly speciating Hawaiian crickets. Evolution 64(8): 2238-2245.

Zhang, Y.E., M.D. Vibranovski, P. Landback, G.A.B. Marais, and M. Long, 2010. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biology 8(10): e1000494.

 

Spring 2010

Baudat, F., J. Buard, C. Grey, A. Fledel-Alon, C. Ober, M.Przeworski, G. Coop, and B. de Massy, 2010. PRMD9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327(5967): 826-840.

Chapman, T., 2009. Finding the right plugin: Mosquitoes have the answer. PLoS Biology 7(12): e1000273.

Derome, N., P. Duchesne and L. Bernatchez, 2006. Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchell) ecotypes. Molecular Ecology 15: 1239-1249.

Ellison, C.K. and R.S. Burton, 2006. Distruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60(7): 1382-1391.

Ellison, C.K. and R.S. Burton, 2010. Cytonuclear conflict in interpopulation hybrids: the role of RNA polymerase in mtDNA transcription and replication. J. Evol. Biol. 23: 528-538.

Halligan, D.L., F. Oliver, A. Eyre-Walker, B. Harr, and P.D. Keightley, 2010. Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genetics 6(1): e1000825.

Hancock, A.M., D.B. Witonsky, A.S. Gordon, G. Eshel, J.K. Pritchard, G. Coop, and A. Di Rienzo, 2008. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genetics 4(2): e32.

Jeukens, J., D. Bittner, R. Knudsen, and L. Bernatchez, 2009. Candidate genes and adaptive radiation: insight from transcriptional adaptation to the limnetic niche among coregonine fishes (Coregonus spp., Salmonidae). Molecular Biology and Evolution 26(1): 155-166.

Luca, F., S. Kashyap, C. Southward, M. Zou, D. Witonsky, A. Di Rienzo, and S.D. Conzen, 2009. Adaptive variation regulates the expression of the human SGK1 gene in response to stress. PLoS Genetics 5(5): e1000489.

Mair, W., 2010. Reinforcing reinforcement. PLoS Biology 8(3): e1000340.

Manier, M.K., J.M. Belote, K.S. Berben, D. Novikov, W.T. Stuart, and S. Pitnick, 2010. Resolving mechanisms of competitive fertilization success in Drosophila melanogaster. Science 328(5976): 354-357.

Mank, J.E., B. Vicoso, S. Berlin, and B. Charlesworth, 2009. Effective population size and the faster-x effect: empirial results and their interpretation. Evolution 64(3): 663-674.

Manolio, T.A., F.S. Collins, N.J. Cox, D.B. Goldstein, L.A. Hindorff, D.J. Hunter, M.I. McCarthy, E.M. Ramos, L.R. Cardon, A. Chakravarti, J.H. Cho, A.E. Guttmacher, A. Kong, L. Kruglyak, E. Mardis, C.N. Rotimi, M. Slatkin, D. Valle, A.S. Whittemore, M. Boehnke, A.G. Clark, E.E. Eichler, G. Gibson, J.L. Haines, T.F.C. Mackay, S.A. McCarroll, and P.M. Visscher, 2009. Finding the missing heritability of complex diseases. Nature Reviews 46(8): 747-753.

Matute, D.R., 2010. Reinforcement of gametic isolation in Drosophila. PLoS Biology 8(3): e1000341.

Moehring, A.J., A. Llopart, S. Elwyn, J.A. Coyne, and T.F.C. Mackay, 2006. The genetic basis of postzygotic reproduction isolation between Drosophila santomea and D. yakuba due to hybrid male sterility. Genetics 173: 225-233.

Moehring, A.J., A. Llopart, S. Elwyn, J.A. Coyne, and T.F.C. Mackay, 2006. The genetic basis of prezyotic reproduction isolation between Drosophila santomea and D. yakuba due to mating preference. Genetics 173: 215-223.

Myers, S., R. Bowden, A. Tumian, R.E. Bontrop, C. Freeman, T.S. MacFie, G. McVean, and P. Donnelly, 2010. Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327(5967): 876-879.

Parvanov, E.D., P.M. Petkov, and K. Paigen, 2010. Prdm9 controls activation of mammalian recombination hotspots. Science 327(5967): 835.

Presgraves, D.C., 2005. Recombination enhances protein adaptation in Drosophila melanogaster. Current Biology 15: 1651-1656.

Presgraves, D.C., 2010. The molecular evolutionary basis of species formation. Nature Reviews 11: 175-180.

Renaut, S., A.W. Nolte, and L. Bernatchez, 2010. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology 19(suppl. 1): 115-131.

Rogers, D.W., F. Baldini, F. Battaglia, M. Panico, A. Dell, H.R. Morris, and F. Catteruccia, 2009. Transglutaminase-mediated semen coagulation controls sperm storage in the malaria mosquito. PLoS Biology 7(12): e1000272.

Rosenblum, E.B., H. Rompler, T. Schoneberg, and H.E. Hoekstra, 2010. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. PNAS 107(5): 2113-2117.

Rosenblum, E.B., H.E. Hoekstra, and M.W. Nachman, 2004. Adaptive reptile color variation and the evolution of the MC1R gene. Evolution 58(8): 1794-1808.

Tang, S. and D.C. Presgraves, 2009. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323(5915): 779-782.

FALL 2009

Coyne, J.A., 1985. The genetic basis of Haldane's Rule. Nature 314(25): 736-738.

Denver, D.R., P.C. Dolan, L.J. Wilhelm, W. Sung, J.I. Lucas-Lledo, D.K. Howe, S.C. Lewis, K. Okamoto, W.K. Thomas, M. Lynch, and C.F. Baer, 2009. A genome-wide view of Caenorhabditis elegans base-substitution mutation process. PNAS 106(38): 16310-16314.

Henikoff, S., K. Ahmad, and H.S. Malik, 2001. The centromere paradox: Stable inheritance with rapidly evolving DNA. Science: 293(5532): 1098-1102.

Lynch, M., and J.S. Conery, 2003. The origins of genome complexity. Science 302(5649): 1401-1404.

Masly, J.P., and D.C. Presgraves, 2007. High-resolution genome-wide dissection of the two rules of speciation in Drosophila. PLoS Biol 5(9): 1890-1898.

Orr, H.A., 1993. Haldane's rule has multiple genetic causes. Nature 361(11): 532-533.

Presgraves, D.C., and H.A. Orr, 1998. Haldane's rule in taxa lacking a hemizygous X. Science 282(5390): 952-954.

 

SPRING 2009

Boursot, P., and K. Belkhir, 2006. Mouse SNPs for evolutionary biology: Beware of ascertainment biases. Genome Reserarch 16: 1191-1192.

Harr, B., 2006. Genomic islands of differentiation between house mouse subspecies. Genome Research 16: 730-737.

Harr, B., 2006. Regions of high differentiation - Worth a check. Genome Research 16: 1193-1194.

Martin-Coelle, J., J. Benavent-Corai, E.R.S. Roldan, and M. Gomendio, 2009. Sperm competition promotes asymmetries in reproductive barriers between closely related species. Evolution 63(3): 613-623.

Yngvadottir, B., Y. Xue, S. Searle, S. Hunt, M. Delgado, J. Morrison, P. Whittaker, P. Deloukas, and C. Tyler-Smith, 2009. A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs. American Journal of Human Genetics 84: 224-234.

 

FALL 2008

Ferguson, W., S. Dvora, J. Gallo, A. Orth, and S. Boissinot, 2008. Long-term balancing selection at the West Nile virus resistance gene Oas1b maintains transspecific polymorphisms in the house mouse. Mol. Biol. Evol. 25(8): 1609-1618.

Gonzalez, J., K. Lenkov, M. Lipatov, J.M. Macpherson, and D.A. Petrov, 2008. High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biology 6(10): 2109-2129.

Liao, B-Y. and J. Zhang, 2008. Null mutations in human and mouse orthologs frequently result in different phenotypes. PNAS 105(19): 6987-6992.

Paigen, K., J.P. Szatkiewicz, K. Sawyer, N. Leahy, E.D. Parvanov, S.H.S. Ng, J.H. Graber, K.W. Broman, and P.M. Petkov, 2008. The recombinational anatomy of a mouse chromosome. PLoS Genetics 4(7): e1000119.

Seehausen, O., Y. Terai, I.S. Magalhaes, K.L. Carleton, H.D.J. Mrosso, R. Miyagi, I. van der Sluijs, M.V. Schneider, M.E. Maan, H. Tachida, H. Imai, and N. Okada, 2008. Speciation through sensory drive in cichlid fish. Nature 455: 620-626.

Via, S. and J. West, 2008. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Molecular Ecology 17: 4334-4345.

Yokoyama, S., T. Tada, H. Zhang, and L. Britt, 2008. Elucidation of phenotypic adaptations: Molecular analysis of dim-light vision proteins in vertebrates. PNAS 195(36): 13480-13485.

 

SPRING 2008

Begun, D.J., A.K. Holloway, K. Stevens, L.W. Hillier, Y-P. Poh, M.W. Hahn, P.M. Nistra, C.D. Jones, A.D. Kern, C.N. Dewey, L. Pachter, E. Myers, and C.L. Langley, 2007. Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology 5(11): e310.

Ellison, C.K., and R.S. Burton, 2008. Interpopulation hybrid breakdown maps to the mitochondrial genome. Evolution 62(3): 631-638.

Holloway, A.K., M.K.N. Lawniczak, J.G. Mezey, D.J. Begun, and C.D. Jones, 2007. Adaptive gene expression divergence inferred from population genomics. PLoS Genetics 3(10): e187.

Kruger, O., 2008. Engines of speciation: A comparative study in birds of prey. J. Evol. Biol. 21: 861-872.

Ramm, S.A., P.L. Oliver, C.P. Ponting, P. Stockley, and R.D. Emes, 2008. Sexual selection and the adaptive evolution of mammalian ejaculate proteins. Mol. Biol. Evol. 25(1): 207-219.

 

FALL 2007

Ahituv, N., Y. Zhu, A. Visel, A. Holt, V. Afzal, L.A. Pennacchio, and E.M. Rubin, 2007. Deletion of ultraconserved elements yields viable mice. PLoS Biology 5(9): e234.

Hahn, M.W., J.P. Demuth, and S.G. Han, 2007. Accelerated rate of gene gain and loss in primates. Genetics 177(3): 1941-1949.

Haygood, R., O. Fedrigo, B. Hanson, K-D. Yokoyama, 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.

Hoekstra, H.E., and J.A. Coyne, 2007. The locus of evolution: Evo Devo and the genetics of adaptation. Evolution 61(5): 995-1016.

Pfennig, K.S., 2007. Facultative mate choice drives adaptive evolution. Science 318: 965-967.

Saether, S.A., G-P. Saetre, T. Borge, C. Wiley, N. Svedin, G. Andersson, T. Veen, J. Haavie, M.R. Servedio, S. Bures, M. Kral, M.B. Hjernquist, L. Gustafsson, J. Traff, and A. Qvarnstrom, 2007. Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers. Science 318: 95-97.

Steiner, C.C., J.N. Weber, and H.E. Hoekstra, 2007. Adaptive variation in Beach Mice produced by two interacting pigmentation genes. PLoS Biology 5(9): e219.

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

 

SPRING 2007

Evans, P.D., N. Mekel-Bobrov, E.J. Vallender, R.R. Hudson, and B.T. Lahn, 2006. Evidence that the Adaptive Allele of the Brain Size Gene microcephalin Introgressed into Homo sapiens from an Archaic Homo Lineage. Proc. Nat. Acad. Sci. 103(48): 18178-18183.

Gojobori, J., H. Tang, J.M. Akey, and C-I. Wu, 2007. Adaptive Evolution in Humans Revealed by the Negative Correlation Between the Polymorphism and Fixation Phases of Evolution. Proc. Nat. Acad. Sci. 104(10): 3907-3912.

Pollinger, J.P., C.D. Bustamante, A. Fledel-Alon, S. Schmutz, M.M. Gray, and R.K. Wayne, 2005. Selective Sweep Mapping of Genes with Large Phenotypic Effects. Genome Research 15: 1809-1819.

Putnam, A.S., J.M. Scriber, and P. Andolfatto, 2007. Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterly Species. Evolution 61(4): 912-927.

Shifman, S., J.T. Bell, R.R. Copely, M.S. Taylor, R.W. Williams, R. Mott, and J. Flint, 2006. A High-Resolution Single Nucleotide Polymorphism Genetic Map of the Mouse Genome. PLoS Biology 4(12): 2227-2237.

Tishkoff, S.A., F.A. Reed, A. Ranciaro, B.F. Voight, C.C. Babbit, et. al., 2007. Convergent Adaptation of Human Lactase Persistence in Africa and Europe. Nature Genetics 39(1): 31-40.

 

FALL 2006

Clark, R.M., T.N. Wagler, P. Quijada, and J. Doebley, 2006. A distant upstream enhancer at the maize domestication gene tb1 has pleotropic effects on plant and inflorescent architecture. Nature Genetics 38(5): 594-597.

Conrad, D.F., M. Jakobsson, G. Coop, X. Wen, J.D. Wall, N.A. Rosenberg, and J.K. Pritchard, 2006. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38(11): 1251-1260.

Ellison, C.K. and R.S. Burton, 2006. Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60(7): 1382-1391.

Green, R.E., J. Krause, S.E. Ptak, A.W. Briggs, M.T. Ronan, J.F. Simons, L. Du, M. Egholm, J.M. Rothberg, M. Paunovic, and S. Paabo, 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330-336.

Hanski, I., and I. Saccheri, 2006. Molecular-level variation affects population growth in a butterfly metapopulation. PLoS Biology 4(5): 0719-0726.

Harr, B., C. Voolstra, T.J. Heinen, J.F. Baines, R. Rottscheidt, S. Ihle, W. Muller, F. Bonhomme, and D. Tautz, 2006. A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus. J. Evol. Biol. 19(5): 1486-1496.

Kronforst, M.R., L.G. Young, L.M. Blume, and L.E. Gilbert, 2006. Multilocus analyses of admixture and introgression among hybridizing Heliconicus butterflies. Evolution 60(6): 1254-1268.

Liao, B.-Y., N.M. Scott, and J. Zhang, 2006. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol. Biol. Evol. 23(11): 2072-2080.

Masly, J.P., C.D. Jones, M.A.F. Noor, J. Locke, and H.A. Orr, 2006. Gene transposition as a cause of hybrid sterility in Drosophila. Science 313: 1448-1450. (Supplemental information )

Noonan, J.P., G. Coop, S. Kudaravalli, D. Smith, J. Krause, J. Alessi, F. Chen, D. Platt, S. Paabo, J.K. Pritchard, and E.M. Rubin, 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-1118.

Spencer, C.C.A., P. Deloukas, S. Hunt, J. Mullikin, S. Myers, B. Silverman, P. Donnelly, D. Bentley, and G. McVean, 2006. The influence of recombination on human genetic diversity. PLoS Genetics 2(9): 1375-1385.

Voolstra, C., D. Tautz, P. Farbrother, L. Eichinger, and B. Harr, 2006. Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse. Genome Research 17: 42-49.

 

SPRING 2006

Wang, X., W.E. Grus, & J. Zhang. 2006. Gene losses during human origins. PLoS Biology 4(3): e52.

Wang, X., W.E. Grus, & J. Zhang. 2006. Gene losses during human origins. PLoS Biology 4(3): e76. (Accompanying article)

Stranger, B.E., M.S. Forest, A.G. Clark, M.J. Minichiello, S. Deutsch. , et al. 2005. Genome-wide associations of gene variation in humans . PLoS Genet 1(6): e78.

Drickamer, L.C., P.A. Gowaty, & C.M. Holmes. 2000. Free female mate choice in house mice affects reproductive success and offspring viability and performance. Animal Behaviour 59: 371-378.

Drickamer, L.C., P.A. Gowaty, & D.M. Wagner. 2003. Free mutual mate preferences in house mice affect reproductive success and offspring performance. Animal Behaviour 65: 105-114.

Gowaty, P.A., L.C. Drickamer, & S. Schmid-Holmes. 2003. Male house mice produce fewer offspring with lower viability and poorer performance when mated with females they do not prefer. Animal Behaviour 65: 95-103.

Voight, B.F., S. Kudaravalli, X. Wen, & K.J. Pritchard. 2006. A map of recent positive selection in the human genome. PLoS Biology 4(3): e72.

Vinckenbosch, N., I. Doupanloupe, & H. Kaessmann. 2006. Evolutionary fate of retroposed gene copies in the human genome. PNAS 103(9): 3220-3225.

Lu, J., T. Tang, H. Tang, J. Huang, S. Shi, & C.-I. Wu. 2006. The accumulation of delerterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends in Genetics 22(3): 126-131.

 

FALL 2005

Carroll, S.B., 2005. Evolution at two levels: On genes and form. PLoS Biology 3(7): e425.

Coyne, J.A., 2005. Switching on evolution. Nature 435: 1029-1030.

Llopart, A., D. Lachaise, J.A. Coyne, 2005. Multilocus analysis of introgression between two sympatric sister species of Drosophila: D. yakuba and D. santomea. Genetics 171: 197-210.

Mekel-Bobrov, N., et al., 2005. Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens. Science 309: 1720-1722.

Evans, P.D., et al. 2005. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309: 1717-1720.

Clark, N.L., and W.J. Swanson, 2005. Pervasive adaptive evolution in primate seminal proteins. PLoS Genetics 1(3): e35.

Johnston, D.S. et al., 2005. The Mouse Epididymal Transcriptome: Transcriptional profiling of segmental gene expression in the epididymis. Biology of Reproduction 73: 404-413.

Hughes, J.F., et al., 2005. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437: 101-104.

Turner, T.L., et al., 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biology 3(9): e285.

Andolfatto, P., 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.

Bustamante, C.D., et al., 2005. Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.

The International HapMap Consortium, 2005. A haplotype map of the human genome. Nature 437: 1299-1320.

Sabeti, P.C., et al., 2005. The case for selection at CCR5-∆32. PLoS Biology 3(11): 1963-1969.



SPRING 2005

Inoue, N., M. Ikawa, A. Isotani, M. Okabe. 2005. The immunoglobulin superfamily protein Izumo is required for sperm to fuse with eggs. Nature 434: 234-238.

Ptak, S.E., D.A. Hinds, K. Koehler, B. Nickel, N. Patil, D.G. Ballinger, M. Przeworski, K.A. Frazer, S. Paabo, 2005. Fine-scale recombination patterns differ between chimpanzees and humans. Nature Genetics 37: 429-434.

Roca, A.L., N. Georgiadis, S.J. O'Brien, 2005. Cytonuclear genomic dissociation in African elephant species. Nature Genetics 37: 96-100.

Singer, G.A.C., A.T. Lloyd, L.B. Huminiecki, K.H. Wolfe, 2005. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Molecular Biology and Evolution 22: 767-775.

Winckler, W., S.R. Myers, D.J. Richter, R.C. Onofrio, G.J. McDonald, R.E. Bontrop, G.A.T McVean, S.B. Gabriel, D. Reich, P. Donnelly, D. Altshuler, 2005. Comparison of fine-scale recombination rates inchimpanzees and humans. Science 308: 107-111.

Barbash, D.A., P. Awadalla, A.M. Tarone, 2004. Functional divergence caused by ancient positive selection of a Drosophila hybrid incompatibility locus. PLoS Biology 2: 0839-0848.

Ortiz-Barrientos, D., B.A. Counterman, M.A.F. Noor, 2004. The genetics of speciation by reinforcement. PLoS Biology 2: 2256-2263.