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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.