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SPRING 2012

Chen, B., and A. Wagner, 2012. Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations. BMC Evolutionary Biology 12: 25.

Cheng, C., B.J. White, C. Kamdem, K. Mockaitis, C. Constantini, M.W. Hahn, and N.J. Besansky, 2012. Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics 190: 1417-1432.

Collaborative Cross Consortium, 2012. The genomic architecture of the collaborative cross mouse genetic reference population. Genetics 190: 389-401.

Degner, J.F., A.A. Pai, R. Pique-Regi, J.-B. Veyrieras, D.J. Gaffney, J.K. Pickrell, S. De Leon, K. Michellini, N. Lewellen, G.E. Crawford, M. Stephens, Y. Gilad, and J.K. Pritchard, 2012. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.

DeVeale, B., D. van der Kooy, and T. Babak, 2012. Critical evaluation of imprinted gene expression by RNA-Seq: A new perspective. PLoS Genetics 8(3): e1002600.

Dorshorst, B., A.-M. Molin, C.-J. Rubin, A.M. Johansson, L. Stromstedt, M.-H. Pham, C.-F. Chen, F. Hallbook, C. Ashwell, and L. Andersson, 2011. A complex genomic rearrangement involving the Endothelian 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genetics 7(12): e1002412.

Gerard, P.R. and D.C. Presgraves, 2012. Abundant genetic variability in Drosophila simulans for hybrid female lethality in interspecific crosses to Drosophila melanogaster. Genetics Research 94: 1-7.

Gruber, J.D., K. Vogel, G. Kalay, and P.J. Wittkopp, 2012. Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects and dominance. PLoS Genetics 8(2): e1002497.

Hopkins, R., and M.D. Rausher, in press. Pollinator-mediated selection on flower color allele drives reinforcement. Science Express, February 2, doi: 10.1126/science.1215198.

Jones, F.C., M.G. grabherr, Y.F. Chan, P. Russell, E.Mauceli, J. Johnson, R. Swofford, et al., 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61.

Keightley, P.D., 2012. Rates and fitness consequences of new mutations in humans. Genetics 190: 295-304.

Keller, I and O. Seehausen, 2012. Thermal adaptation and ecological speciation. Molecular Ecology 21: 785-799.

Kolbe, J.J., M. Leal, T.W. Schoener, D.A. Spiller, and J.B. Losos, in press. Founder effects persist despite adaptive differentiation: A field experiement with lizards. Science Express, February 2, doi: 10.1126/science.1209566.

Lindblad-Toh, K., M. Garber, O. Zuk, M.F. Lin, B.J. Parker, S. Washietl, P. Kheradpour, et al., 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.

MacArthur, D.G., S. Balasubramanian, A. Frankish, N. Huang, J. Morris, K. Walter, L. Jostins, et al., 2012. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335: 823-828.

Mackay, T.F.C., S. Richards, E.A. Stone, A. Barbadilla, J.F. Ayroles, et al., 2012. The Drosphila melangaster genetic reference panel. Nature 482: 173-178.

Rockman, M.V., 2011. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution 66-1: 1-17.

Sackton, T.B., H. Montenegro, D.L. Hartl, and B. Lemos, 2011. Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila. PNAS 108 (41): 17046-17051.

Shapiro, B.J., J. Friedman, O.X. Cordero, S.P. Preheim, S.C. Timberlake, G. Szabo, M.F. Polz, and E.J. Alm, 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336: 48-51.

Stadler, T., A.M. Florez-Rueda, and M. Paris, 2012. Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates. Molecular Biology and Evolution 29(1): 31-34.

Storz, J.F., C. Natarajan, Z.A. Cheviron, F.G. Hoffmann, and J.K. Kelly, 2012. Altitudinal variation at duplicated beta-globin genes in deer mice: effects of selection, recombination, and gene conversion. Genetics 190: 203-216.

FALL 2011

Aylor, D.L., W. Valdar, W. Foulds-Mathes, R.J. Buus, R.A. Verdugo, R.S. Baric, M.T. Ferris, J.A. Frelinger, et al., 2011. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Research 21: 1213-1222.

Barbash, D.A., 2011. Comment on "A test of the snowball theory for the rate of evolution of hybrid incompatibilities." Science 333:1576-b.

Brawand, D., M. Soumillon, A. Necsulea, P. Julien, G. Csardi, P. Harrigan, M. Weier, A. Liechti, et al., 2011. The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.

Chandler, J.A., J.M. Lang, S. Bhatnagar, J.A. Eisen, and A. Kopp, 2011. Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genetics 7(9): e1002272.

Devitt, T.J., S.J.E. Baird, and C. Moritz, 2011. Asymmetric reproductive isolation between terminal forms of the salamander ring species Ensatina eschscholtzii revealed by fine-scale genetic analysis of a hybrid zone. BMC Evolutionary Biology, in press.

Dumont, B.L. and B.A. Payseur, 2011. Genetic analysis of genome-scale recombination rate evolution in house mice. PLoS Genetics 7(6): e10021116.

Duvaux, L., K. Belkhir, M. Boulesteix, and P. Boursot, 2011. Isolation and gene flow: inferring the speciation history of European house mice. Molecular Ecology 20: 5248-5264.

Ellis, P.J.I., J. Bacon, and N.A. Affara, 2011. Association of Sly with sex-linked gene amplification during mouse evolution: a side effect of genomic conflict in spermatids? Human Molecular Genetics 20(15): 3010-3021.

Ellison, C.E, C. Hall, D. Kowbel, J. Welch, R.B. Brem, N.L. Glass, and J.W. Taylor, 2011. Population genomics and local adaptation in wild isolates of a model microbial eukaryote. PNAS 108(7): 2831-2836.

Firman, R.C. and L.W. Simmons, 2011. Male house mice evolving with post-copulatory sexual selection sire embryos with increased viability. Ecology Letters, doi: 10.1111/j.1461-0248.2011.01706.x

Fumagalli, M., M. Sironi, U. Pozzoli, A. Ferrer-Admettla, L. Pattini, R. Nielsen, 2011. Signature of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genetics 7(11): e1002355.

Ghaderi, D., S.A. Springer, F. Ma, M. Cohen, P. Secrest, R.E. Taylor, A. Varki, and P. Gagneux, 2011. Sexual selection by female immunity against paternal antigens can fix loss of function alleles. PNAS, doi:10.1073/pnas.1102302108.

Gossmann, T.I., M. Woolfit, and A. Eyre-Walker, 2011. Quantifying the variation in the effective population size within a genome. Genetics, ahead of print, doi: 10.1534/genetics.111.132654.

Hancock, A.M., B. Brachi, N. Faure, M.W. Horton, L.B. Jarymowycz, F.G. Sperone, C. Toomajian, F. Roux, and J. Bergelson, 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.

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.

Joron, M., L. Frezal, R.T. Jones, N.L. Chamberlain, S.F. Lee, C.R. Haag, A. Whibley, M. Becuwe, S.W. Baxter, L. Ferguson, et al., 2011. Chromosomal arrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature, doi:10.1038/nature10341.

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.

Lienert, F., C. Wirbelauer, I. Som, A. Dean, F. Mohn, and D. Schubeler, 2011. Identification of genetic elements that autonomously determine DNA methylation states. Nature Genetics 43(11): 1091-1097.

Lohmueller, K.E., A. Albrechtsen, Y. Li, S.Y. Kim, T. Korneliussen, N.Vinckenbosch, G. Tian, et al., 2011. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genetics 7(10): e1002326.

Marie Curie Speciation Network, 2011. What do we need to know about speciation? TREE, in press.

Matute, D.R., D.A. Turissini, and J.A. Coyne, 2011. Response to comment on "A test of the snowball theory for the rate of evolution of hybrid incompatibilities." Science 333 1576-c.

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.

Payseur, B.A., 2010. Using differential introgression in hybrid hybrid zones to identify genomic regions involved in speciation. Molecular Ecology Resources 10: 806-820.

Phadnis, N., 2011. Genetic architechture of male sterility and segregation distortion in Drosophila pseudoobscura Bogota-USA hybrids. Genetics, ahead of print: 10.1534/genetics.111.132324.

Schmitz, R.J., M.D. Schultz, M.G. Lewsey, R.C. O'Malley, M.A. Urich, O. Libiger, N.J. Schork, and J.R. Ecker, 2011. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334: 369-373.

Schneider, A., B. Charlesworth, A. Eyre-Walker, and P.D. Keightley, 2011. A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics, ahead of print, doi: 10.1534/genetics.111.131730.

Sheehan, M.J. and E.A. Tibbetts, 2011. Specialized face learning is associated with individual recognition in paper wasps. Science 334: 1272-1275.

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: online ahead of print.

Yalcin, B., K. Wong, A. Agam, M. Goodson, T.M. Keane, X. Gan, et al., 2011. Sequence-based characterization of structural variation in the mouse genome. Nature 477: 326-329.

Zwarts, L., M.M. Magwire, M.A. Carbone, M. Versteven, L. Herteleer, R.R.H. Anholt, P. Callaerts, and T.F.C. Mackay, 2011. Complex genetic architecture of Drosophila aggressive behavior. PNAS, ahead of print, doi: 10.1073/pnas.1113877108.

SPRING 2011

Abbott, P., J. Abe, J. Alcock, S. Alizon, J.A.C. Alpedrinha, M. Andersson, et al., 2011. Inclusive fitness theory and eusociality. Nature 471(7339): E1-E10.

Beisel, C. and R. Paro, 2011. Silencing chromatin: comparing modes and mechanisms. Nature Reviews Genetics 12: 123-135.

Bergelson, J. and F. Roux, 2010. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nature Reviews Genetics 11: 867-879.

Colbourne, J.K., M.E. Pfrender, D. Gilbert, W.K. Thomas, A. Tucker, T.H. Oakley, et al., 2011. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.

He, B.Z., A.K. Holloway, S.J. Maerkl, and M. Kreitman, 2011. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genetics 7(4): e1002053.

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: 920-923.

Hopkins, R. and M.D. Rausher, 2011. Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. Nature Letter, doi:10.1038/nature09641.

Hoso, M., Y. Kameda, S. Wu, T. Asami, M. Kato, and M. Hori, 2010. A speciation gene for left-right reversal in snails results in anti-predator adapation. Nature Communications, doi: 10.1038/ncomms1133.

Hubbard, J.K., J.A.C. Uy, M.E. Hauber, H.E. Hoekstra, and R.J. Safran, 2010. Vertebrate pigmentation: from underlying genes to adaptive function. Trends in Genetics 26(5): 231-239.

Kauppi, L., M. Barchi, F. Baudat, P.J. Romanienko, S. Keeney, and M. Jasin, 2011. Distinct properties of XY pseudoautosomal region crucial for male meiosis. Science 331: 916-920.

Kolaczkowski, B., A.D. Kern, A.K. Holloway, and D.J. Begun, 2011. Genomic differentiation between temperate and tropical Australian popluations of Drosophila melanogaster. Genetics 187: 245-260.

Larsen, P.A., M.R. Marchan-Rivadeneira, and R.J. Baker, 2010. Natural hybridization generates mammalian lineage with species characterisitics. PNAS 107 (25): 11447-11452.

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.

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. Schaar, 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.

Mills, R.E., K. Walter, C. Stewart, R.E. Handsaker, K. Chen, C. Alkan, et al., 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65.

Moorjani, P., N. Patterson, J.N. Hirschhorn, A. Keinan, L. Hao, G. Atzmon, E. Burns, H. Ostrer, A.L. Price, and D. Reich, 2011. The history of African gene flow into southern Europeans, Levantines, and Jews. PLoS Genetics 7(4): e1001373.

Rosenblum, E.B. and L.J. Harmon, 2011. "Same same but different": Replicated ecological speciation at white sands. Evolution 65(4): 946-960.

Royo, H., G. Polikiewicz, S.K. Mahadevaiah, H. Prosser, M. Mitchell, A. Bradley, D.G. de Rooij, P.S. Burgoyne, and J.M.A. Turner, 2010. Evidence that meiotic sex chromosome inactivation is essential for male fertility. Current Biology 20: 2117-2123.

FALL 2010

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.

Etges, W.J., C. Cardoso de Oliveira, M.A.F. Noor, and M.G. Ritchie, 2010. Genetics of incipient speciation in Drosophila mojavensis. III. Life-history divergence in allopatry and reproductive isolation. Evolution 64(12): 3549-3569.

Galindo, J., J.W. Grahame and R.K. Butlin, 2010. An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis. Journal of Evolutionary Biology 23: 2004-2016.

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.

Kong, A., G. Thoreifsson, D.F. Gudbjartsson, G. Masson, A. Sigurdsson, A. Jonasdottir, et al., 2010. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467: 1099-1103.

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.

Li, Y., N. Vinckenbosch, G. Tian, E. Huerta-Sanchez, T. Jiang, H. Jiang, et al., 2010. Resequencing of 200 human exomes identifies an excess of low-frequency of non-synonymous coding variants. Nature Genetics, doi: 10.1038/ng.680.

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. Scaling expectations for the time to establishment of complex adaptations. PNAS, doi: 10.1073/pnas.1010836107.

Magwire, M.M., A. Yamamoto, M.A. Carbone, N.V. Roshina, A.V. Symonenko, E.G. Pasyukova, T.V. Morozova, and T.F.C. Mackay, 2010. Quantitative and molecular genetic analyses of mutations increasing Drosophila life span. PLoS Genetics 6(7): e1001037.

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

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.

Montooth, K.L., C.D. Meiklejohn, D.N. Abt, and D.M. Rand, 2010. Mitochondrial-nuclear epistasis affects fitness within species but does not contribute to fixed incompatibilities between species of Drosophila. Evolution 64(12): 3364-3379.

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.

Pritchard, J.K., J.K. Pickrell, and G. Coop, 2010. The genetics of human adapation: hard sweeps, soft sweeps, and polygenic adaptation. Current Biology 20: R208-R215.

Pryke, S.R., L.A. Rollins, and S.C. Griffith, 2010. Femals use multiple mating and genetically loaded sperm competition to target compatible genes. Science 329: 964-967.

Scavetta, R.J. and D. Tautz, 2010. Copy number changes of CNV regions in intersubspecific crosses of the house mouse. Molecular Biology and Evolution 27(8):1845-1856.

Sharon, G., D. Segal, J.M. Ringo, a. Hefetz, I. Zilber-Rosenberg, and E. Rosenberg, 2010. Commensal bacteria play a role in mating preference of Drosophila melangaster. PNAS 107 (46): 20051-20056.

Shin, J.D., M. Bossenz, Y. Chung, H. Ma, M.Byron, N. Taniguchi-Ishigaki, et al., 2010. Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice. Nature 467: 977-981.

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.

Xiong, Y., X. Chen, Z. Chen, X. Wang, S. Shi, X. Wang, J. Zhang, and X. He, 2010. RNA sequencing shows no dosage compensation of the active X-chromosome. Nature Genetics 42(12): 1043-1047.

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

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.

Baudat, F., J. Buard, C.Grey, A. Fledel-Alon, C. Ober, M. Przeworski, G. Coop, and B. de Massy, 2009. PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 10.1126/science.1183439.

Bradley, R.K., X.Y. Li, C. Trapnell, S. Davidson, L. Pachter, H.C. Chu, L.A. Tonkin, M.D. Biggin, and M.B. Eisen, 2010. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biology 8(3): e1000343.

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

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

Haygood, R., C.C. Babbitt, O. Fedrigo, and G.A. Wray, 2010. Contrasts between adaptive coding and noncoding changes during human evolution. PNAS 10.1073/pnas.0911249107.

Eizirik, E., V.A. David, V. Buckley-Beason, M.E. Roelke, A.A. Schaffer, S.S. Hannah, K. Narfstrom, S.J. O'Brien, M. Menotti-Raymond, 2010. Defining and mapping mammalian coat pattern genes: Multiple genomic regions implicated in domestic cat stripes an spots. Genetics 184: 267-275.

Ellison, C.K. and R.S. Burton, 2010. Cytonuclear conflict in interpopulation hybrids: the role of RNA polymerase in mtDNA transcription and replication. Journal of Evolutionary Biology 23(3): 528-538.

Fisher, H.S., and H.E. Hoekstra, 2010. Competition drives cooperation among closely related sperm of deer mice. Nature doi:10.1038/nature08736.

Hughes, J.F., H. Skalestsky, T. Pyntikova, T.A. Graves, S.K.M. van Daalen, P.J. Minx, R.S. Fulton, S.D. McGrath, D.P. Locke, C. Friedman, B.J. Trask, E.R. Mardis, W.C. Warren, S. Repping, S. Rozen, R.K. Wilson, and D.C. Page, 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature doi:10.1038/nature08700.

Keinan, A. and D. Reich, 2010. Human population differentiation is strongly correlated with local recombination rate. PLoS Genetics 6(3): e1000886.

Krause, J., Q. Fu, J.M. Good, B. Viola, M.V. Shunkov, A.P. Derevianko, and S. Paabo, 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 10.1038/nature08976

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 10.1126/science.1187096

Mank, J.E., B. Vicoso, S. Berlin, and B. Charlesworth, 2010. Effective population size and the faster X-effect: empirical results and their interpretation. Evolution 64(3): 663-674.

Myers, S., R. Bowden, A. Tumian, R.E. Bontrop, C. Freeman, T.S. MacFie, G. McVean, and P. Donnelly, 2009. Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 10.1126/science.1182363.

Nunome, M., C. Ishimori, K.P. Aplin, K. Tsuchiya, H. Yonekawa, K. Moriwaki, and H. Suzuki, 2010. Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice. Molecular Ecology 19: 2474-2489.

Parvanov, E.D., P.M. Petkov, and K. Paigen, 2009. Prdm9 controls activation of mammalian recombination hotspots. Science 10.1126/science.1181495.

Presgraves, D.C., 2010. The molecular evolutionary basis of species formation. Nature Reviews Genetics 10.1038/nrg2718.

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, 2009. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. PNAS 10.1073/pnas.0911042107.

Sackton, T.B., B.P. Lazzaro, and A.G. Clark, 2010. Genotype and gene expression associations with immune function in Drosophila. PLoS Genetics 6(1): e1000797.

Scascitelli, M., K.D. Whitney, R.A. Randell, M. King, C.A. Buerkle and L.H. Rieseberg, 2010. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Molecular Ecology 10.1111/j.1365-294X.2009.04504.x.

Sobel, J.M., G.F. Chen, L.R. Watt, and D.W. Schemske, 2010. The biology of speciation. Evolution 64(2): 295-315.

Stelkens, R.B., K.A. Young, and O. Seehausen, 2010. The accumulation of reproductive incompatibilities in African cichlid fish. Evolution 64(3): 617-633.

Storchova, R., J. Reif, and M.W. Nachman, 2010. Female heterogamety and speciation: reduced introgression of the Z chromosome between two species of nightingales. Evolution 64(2): 456-471.

Teeter, K.C., L.M. Thibodeau, Z. Gompert, C.A. Buerkle, M.W. Nachman, and P.K. Tucker, 2010. The variable genomic architecture of isolation between hybridizing species of house mice. Evolution 64(2): 472-485.

Vaquerizas, J.M., R. Suyama, J. Kind, K. Miura, N.M. Luscombe, and A. Akhtar, 2010. Nuclear pore proteins Nup153 and megator define transcriptionally actie regions in the Drosophila genome. PLoS Genetics 6(2): e1000846.

Vibranovski, M.D., H.F. Lopes, T.L. Karr, and M. Long, 2009. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genetics 5(11): e1000731.

Yang, Z. and B. Rannala, 2010. Bayesian species delimitation using multilocus sequence data. PNAS doi:10.1073/pnas.0913022107.

 

FALL 2009

Bridgham, J.T., E.A. Ortlund, and J.W. Thornton, 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.

Calsbeek, R., and C. Bonneaud, 2008. Postcopulatory fertilization bias as a form of cryptic sexual selection. Evolution 62(5): 1137-1148.

Chang, A.S., and M.A.F. Noor, 2009. Epistasis modifies the dominance of loci causing hybrid male sterility in the Drosophila pseudoobscura species group. Evolution: doi:10.111/j.1558-5646.2009.00823.x.

Church, D.M., L. Goodstadt, L.W. Hillier, M.C. Zody, S. Goldstein, et. al., 2009. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biology 7(5): e1000112.

Cocquet, J., P.J.I. Ellis, Y. Yamauchi, S.K. Mahadevaiah, N.A. Affara, et. al., 2009. The multicopy gene sly represses the sex chromosomes in the male mouse germline after meiosis. PLoS Biology 7(11):
e1000244.

Ferree, P.M., and D.A. Barbash, 2009. Species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in
Drosophila. PLoS Biology 7(10): e1000234.

Forster, D.W., I. Gunduz, A.C. Nunes, S. Gabriel, M.G. Ramalhinho, M.L. Mathias, J. Britton-Davidian, and J.B. Searle, 2009. Molecular insights into the colonization and chromosomal diversification of Madeiran house mice. Molecular Ecology 18: 4477-4494.

Hughes, A.L., 2007. Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364-373.

Kelleher, E.S., T.D. Watts, B.A. LaFlamme, P.A. Haynes, and T.A. Markow, 2009. Proteomic analysis of Drosophila mojavensis male accessory glands suggest novel classes of seminal fluid proteins. Insect Biochemistry and Molecular Biology 39: 366-371.

Moyle, L.C., and B.A. Payseur, 2009. Reproductive isolation grows on trees. Trends in Ecology and Evolution 1140: 1-8.

Parker, H.G., B.M. VonHoldt, P., Quignon, E.H. Margulies, S. Shao, D.S. Mosher, T.C. Spady, A. Elkahloun, M. Cargill, P.G. Jones, C.L. Maslen, G.M. Acland, N.B. Sutter, K. Kuroki, C.D. Bustamante, R.K. Wayne, and E.A. Ostrander, 2009. An expressed Fgf4 retrogene is associated with breed-defining Chondrodyspasia in domestic dogs. Science 325: 995-998.

Petit, R.J., and L. Excoffier, 2009. Gene flow and species delimitation. Trend in Ecology and Evolution 24(7): 386-393.

Phadnis, N., and H.A. Orr, 2009. A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323: 376-379.

Sella, G., D.A. Petrov, M. Przeworski, and P. Andolfatto, 2009. Pervasive natural selection in the Drosophila genome? PLoS Genetics 5(6): e1000495.

Torgerson, D.G., A.R. Boyko, R.D. Hernandez, A. Indap, X. Hu, T.J. White, J.J. Sninsky, M. Cargill, M.D. Adams, C.D. Bustamante, and A.G. Clark, 2009. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genetics 5(8): e1000592.

White, M.A., C. Ane, C.N. Dewey, B.R. Larget, and B.A. Payseur, 2009. Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genetics 5(11): e1000729.

SPRING 2009

Akey, J.M., 2009. Constructing genomic maps of positive selection in humans: Where do we go from here? Genome Research 19: 711-722.

Galtier, N., L. Duret, S. Glemin, and V. Ranwez, 2008. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends in Genetics 25(1): 1-5.

Gross, J.B., R. Borowsky, and C.J. Tabin, 2009. A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. PLoS Genetics 5(1): e1000326.

Pool, J.E. and R. Nielsen, 2008. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 10.1534/genetics.108.098095.

Wang, Z and J. Zhang, 2009. Why is the correlation between gene importance and gene evolutionary rate so weak? PLoS Genetics 5(1): e1000329.

FALL 2008

Des Marais, D.L. and M.D. Rausher, 2008. Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765.

Fernandez, A.A. and M.R. Morris, 2008. Mate choice for more melanin as a mechanism to maintain a functional oncogene. PNAS 105(36): 13503-13507.

Findlay, G.D. Y. Xianhua, M.J. MacCross, and W.J. Swanson, 2008. Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biology 6(7): 1417-1426.

Hammer, M.F., F.L. Mendez, M.P. Cox, A.E. Woerner, and J.D. Wall, 2008. Sex-biased evolutionary forces shape genomic patterns of human diversity. PLoS Genetics 4(9): e1000202.

Long, Y., L. Zhao, B. Niu, J. Su, H. Wu, Y. Chen, Q. Zhang, J. Guo, C. Zhuang, M. Mei, J. Xia, L. Wang, H. Wu, and Y-G. Liu, 2008. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. PNAS 105(48): 18871-18876.

Mancera, E., R. Bourgon, A. Brozzi, W. Huber, and L.M. Steinmetz, 2008. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454: 479-485.

Mihola, O., Z. Trachtulec, C. Vlcek, J.C. Schimenti, and J. Forejt, 2008. A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 10.1126/science.1163601.

Novembre, J., T. Johnson, K. Bryc, Z. Kutalik, A.R. Boyko, A. Auton, A. Indap, K.S. King, S. Bergmann, M.R. Nelson, M. Stephens, and C.D. Bustamante, 2008. Genes mirror geography within Europe. Nature doi: 10.1038/nature07331.

Palopoli, M.F., M.V. Rockman, A. TinMaung, C. Ramsay, S. Curwen, A. Aduna, J. Laurita, and L. Kruglyak, 2008. Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans. Nature 454: 1019-1022.

Phadnis, N. and H.A. Orr, 2008. A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 10.1126/science.1163934.

Price, T.A.R., D.J. Hodgson, Z. Lewis, G.D.D. Hurst, and N. Wedell, 2008. Selfish genetic elements promote polyandry in a fly. Science 322: 1241-1243.

Schmidt, P.S., C-T. Zhu, J. Das, M. Batavia, L. Yang, and W.F. Eanes, 2008. An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster. PNAS 105(42): 16207-16211.

Smadja, C. and G. Ganem, 2007. Divergence of odorant signals within and between the two European subspecies of the house mouse. Behavioral Ecology 19(1): 223-231.

Storz, J.F., M. Baze, J.L. Waite, F.G. Hoffmann, J.C. Opazo, and J.P. Hayes, 2007. Complex signatures of selection and gene conversion in the duplicated globin genes of house mice. Genetics 177: 481-500.

Sultan, M., M.H. Schultz, H. Richard, A. Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk, D. Schmidt, S. O'Keeffe, S. Haas, M. Vingron, H. Lehrach, and M-L. Yaspo, 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.

SPRING 2008

Bolnick, D.I., M. Turelli, H. Lopez-Fernandez, P.C. Wainwright, and T.J. Near, 2008. Accelerated Mitochondrial Evolution and "Darwin's Corollary": Asymmetric Viability of Reciprocal F1 Hybrids in Centrarchid Fishes. Genetics 178: 1037-1048.

Coyne, J.A., E.H. Kay, and S. Pruett-Jones, 2007. The Genetics Basis of Sexual Dimorphism in Birds. Evolution 62-1: 214-219.

Chaine, A.S. and B.E. Lyon, 2008. Adaptive Plasticity in Female Mate Choice Dampens Sexual Selection on Male Ornaments in the Lark Bunting. Science 319: 459-462.

Gratten, J., A.J., Wilson, A.F. McRae, D. Beraldi, P.M., Visscer, J.M. Pemberton, and J. Slate, 2008. A Localized Negative Genetic Correlation Constrains Microevolution of Coat Color in Wild Sheep. Science 319: 318-320.

Grim, T., 2008. A Possible Role of Social Activity to Explain Differences in Publication Output Among Ecologists. Oikos: doi: 10.1111/j.2008.0030-1299.16551.x.

Lohmueller, K.E., A.R. Indap, S. Schmidt, A.R. Boyko, R.D. Hernandez, M.J. Hubisz, J.J. Sninsky, T.J. White, S.R. Sunyaev, R. Nielsen, A.G. Clark, and C.D. Bustamante, 2008. Proportionally More Deleterious Genetic Variation in European than in African Populations. Nature 451: 994-998.

Hill, W.G., M.E. Goddard, and P.M. Visscher, 2008. Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits. PLoS Genetics doi:10.1371/journal.pgen.1000008.eor.

Malone, J.H. and P. Michalak, 2008. Physiological Sex Predicts Hybrid Sterility Regardless of Genotype. Science 319: 59.

FALL 2007

Chen, S-T., H-C. Cheng, D.A. Barbash, and H-P. Yang, 2007. Evolution of hydra, a Recently Evolved Testis-Expressed Gene with Nine Alternative First Exons in Drosophila melanogaster. PLoS Genetics 3(7): 1131-1143.

Frazer, K.A., E. Eskin, H.M. Kang, M.A. Brogue, D.A. Hinds, E.J. Beilharz, R.V. Gupta, J. Montgomery, M.M. Morenzoni, G.B. Nilsen, C.L. Pethiyagoda, L.L. Stuve, F.M. Johnson, M.J. Daly, C.M. Wade and D.R. Cox, 2007. A Sequence-Based Variation Map of 8.27 Million SNPs in Inbred Mouse Strains. Nature doi:10.1038/nature06067.

Levy, S., G. Sutton, P.C. Ng, L. Feuk, A.L. Halpern, et. al., 2007. The diploid genome sequence of an individual human. PLoS Biology 5(10): e254.

Qin, J., P. Calabrese, I. Tiemann-Boege, D. Narendra Shinde, S-R. Yoon, D. Gelfand, K. Bauer, and N. Arnheim, 2007. The molecular anatomy of spontaneous germline mutations in human testes. PLoS Biology 5(9): e224.

Yang, H., T.A. Bell, G.A. Churchill, and F. Pardo-Manuel de Villena, 2007. On the subspecific origin of the laboratory mouse. Nature Genetics doi:10.1038/np2087.

SPRING 2007

Anderson, W.W., Y-K. Kim, and P.A. Gowaty, 2007. Experimental Constraints on Mate Preferences in Drosophila pseudoobscura Decrease Offspring Viability and Fitness of Mated Pairs. PNAS 104(11): 4484-4488.

Armakolas, A., and A.J.S. Klar, 2007. Left-Right Dynein Motor Implicated in Selective Chromatid Segregation in Mouse Cells. Science 315: 100-101.

Bininda-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. MacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R.A. Vos, J.L. Gittleman, and A. Purvis, 2007. The Delayed Rise of Present-Day Mammals. Nature 446: 507-512.

Di Rienzo, A., and R.R. Hudson, 2006. An Evolutionary Framework for Common Diseases: the Ancestral-Susceptibility Model. Trends in Genetics 21(11): 596-601.

Greig, D., 2007. A Screen for Recessive Speciation Genes Expressed in the Gametes of F1 Hybrid Yeast. PLoS Genetics 3(2): 281-286.

Immler, S., H.D.M. Moore, W.G. Breed, and T.R. Birkhead, 2007. By Hook or by Crook? Morphometry, Competition, and Cooperation in Rodent Sperm. PLoS One 2(1): e170 doi:10.1371/journal.pone.0000170.

Libert, S., J. Zwiener, X. Chu, W. VanVoorhies, G. Roman, and S.D. Pletcher, 2007. Regulation of Drosophila Life Span by Olfaction and Food-Derived Odors. Science 315: 1133-1137.

Parera, M., G. Fernandez, B. Clotet, and M.A. Martinez, 2007. HIV-1 Protease Catalytic Efficiency Effects Caused by Random Single Amino Acid Substitutions. Mol. Biol. Evol. 24(2): 382-387.

Slotman, M.A., L.J. Reimer, T. Thiemann, G. Dolo, E. Fondjo, and G.C. Lanzaro, 2006. Reduced Recombination Rate and Genetic Differentiation Between the M and S Forms of Anopheles gambiae s.s. Genetics 174: 2081-2093.


FALL 2006

Brideau, N.J., H.A. Flores, J. Wang, S. Maheshwari, X. Wang, and D.A. Barbash, 2006. Two Dobzhansky-Muller Genes Interact to Cause Hybrid Lethality in Drosophila. Science 314: 1292 -1295.

Counterman, B.A., and M.A.F. Noor, 2006. Multilocus Test for Introgression between the Cactophilic Species Drosophila mojavensis and Drosophila arizonae. The American Naturalist 168 (5): 682-696.

Pattarini, J.M., W.T. Starmer, A. Bjork, and S. Pitnick, 2006. Mechanisms Underlying the Sperm Quality Advantage in Drosophila melanogaster. Evolution 60 (10): 2064-2080.

Tang, T., J. Lu, J. Huang, J. He, S.R. McCouch, Y. Shen, Z. Kai, M.D. Purugganan, S. Shi, and C-I. Wu, 2006. Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication. PLoS Genetics 2 (11): 1824 -1833.