List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Abdomen
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
Adaptation, Biological
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
Adaptation, Physiological
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Africa
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
Algorithms
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
Alleles
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
Amino Acid Sequence
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
Amino Acid Substitution
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
Animals
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
P. Andolfatto, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
Y. Zhen and Andolfatto, P., “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 2012.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
J. D. Wall, Andolfatto, P., and Przeworski, M., “Testing models of selection and demography in Drosophila simulans.”, Genetics, vol. 162, no. 1, pp. 203-16, 2002.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
P. Andolfatto and Wall, J. D., “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
Apocynaceae
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
Arabidopsis
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Base Composition
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
Base Pairing
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
Base Sequence
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
Bayes Theorem
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Biological Evolution
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
Butterflies
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Capsella
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Cardenolides
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
M. L. Aardema, Zhen, Y., and Andolfatto, P., “The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.”, Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
Chimera
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
Chromosomal Proteins, Non-Histone
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
Chromosome Breakpoints
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
Chromosome Mapping
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
Chromosomes
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Chromosomes, Insect
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
Codon
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
Computational Biology
Y. Zhen and Andolfatto, P., “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 2012.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
Computer Simulation
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
Conserved Sequence
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
Contig Mapping
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
Courtship
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
Cyprinodontiformes
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
Databases, Genetic
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
Demography
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
DNA
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
Y. Zhen and Andolfatto, P., “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 2012.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
DNA, Intergenic
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
P. Andolfatto, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
DNA, Mitochondrial
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
DNA, Plant
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
DNA-Binding Proteins
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
Drosophila
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. Andolfatto, “Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.”, Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
J. D. Wall, Andolfatto, P., and Przeworski, M., “Testing models of selection and demography in Drosophila simulans.”, Genetics, vol. 162, no. 1, pp. 203-16, 2002.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
Drosophila melanogaster
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
P. Andolfatto and Wall, J. D., “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
K. Thornton and Andolfatto, P., “Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.”, Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Drosophila Proteins
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
Ecosystem
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
Evolution, Molecular
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., “Correlated evolution of nearby residues in Drosophilid proteins.”, PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., “A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.”, Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., “Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.”, Genome Biol, vol. 6, no. 8, p. R67, 2005.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., “An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.”, PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., “Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.”, Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, “Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.”, Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Y. Zhen and Andolfatto, P., “Methods to detect selection on noncoding DNA.”, Methods Mol Biol, vol. 856, pp. 141-59, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., “Parallel molecular evolution in an herbivore community.”, Science, vol. 337, no. 6102, pp. 1634-7, 2012.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., “Positive and negative selection on noncoding DNA in Drosophila simulans.”, Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
D. Bachtrog and Andolfatto, P., “Selection, recombination and demographic history in Drosophila miranda.”, Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
Female
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
P. Andolfatto, J Scriber, M., and Charlesworth, B., “No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus.”, Evolution, vol. 57, no. 2, pp. 305-16, 2003.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., “Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.”, PLoS One, vol. 7, no. 8, p. e43888, 2012.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.”, Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., “Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.”, Evolution, vol. 60, no. 2, pp. 292-302, 2006.
Fertilization
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Flowers
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., “Genetic architecture and adaptive significance of the selfing syndrome in Capsella.”, Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
Gene Conversion
P. Andolfatto and Wall, J. D., “Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.”, Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
Gene Expression Regulation
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., “The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.”, Cell, vol. 132, no. 5, pp. 783-93, 2008.
Gene Flow
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., “An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.”, Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
Gene Frequency
J. P. Huelsenbeck and Andolfatto, P., “Inference of population structure under a Dirichlet process model.”, Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., “Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.”, Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
Genes, Dominant
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., “Multiplexed shotgun genotyping for rapid and efficient genetic mapping.”, Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
Genes, Insect
K. Thornton, Bachtrog, D., and Andolfatto, P., “X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.”, Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., “Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.”, Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
Genes, Plant
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., “The Capsella rubella genome and the genomic consequences of rapid mating system evolution.”, Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Genes, X-Linked
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
Genetic Drift
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
Genetic Fitness
P. Andolfatto, Wong, K. M., and Bachtrog, D., “Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.”, Genome Biol Evol, vol. 3, pp. 114-28, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.

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