Haddrill, Penelope R, Brian Charlesworth, Daniel L Halligan, and Peter Andolfatto. 2005. “Patterns of Intron Sequence Evolution in Drosophila Are Dependent Upon Length and GC Content.”. Genome Biol 6 (8): R67.

Rebeiz, Mark, Margarita Ramos-Womack, Sangyun Jeong, Peter Andolfatto, Thomas Werner, John True, David L Stern, and Sean B Carroll. (2009) 2009. “Evolution of the Tan Locus Contributed to Pigment Loss in Drosophila Santomea: A Response to Matute Et Al.”. Cell 139 (6): 1189-96.

Halligan, Daniel L, Adam Eyre-Walker, Peter Andolfatto, and Peter D Keightley. (2004) 2004. “Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila.”. Genome Res 14 (2): 273-9.

Cande, Jessica Doran, Peter Andolfatto, Benjamin Prud’homme, David L Stern, and Nicolas Gompel. 2012. “Evolution of Multiple Additive Loci Caused Divergence Between Drosophila Yakuba and D. Santomea in Wing Rowing During Male Courtship.”. PLoS One 7 (8): e43888.

Zhen, Ying, Matthew L Aardema, Edgar M Medina, Molly Schumer, and Peter Andolfatto. (2012) 2012. “Parallel Molecular Evolution in an Herbivore Community.”. Science 337 (6102): 1634-7.

Jeong, Sangyun, Mark Rebeiz, Peter Andolfatto, Thomas Werner, John True, and Sean B Carroll. (2008) 2008. “The Evolution of Gene Regulation Underlies a Morphological Difference Between Two Drosophila Sister Species.”. Cell 132 (5): 783-93.

Andolfatto, Peter, Mark Scriber, and Brian Charlesworth. (2003) 2003. “No Association Between Mitochondrial DNA Haplotypes and a Female-Limited Mimicry Phenotype in Papilio Glaucus.”. Evolution 57 (2): 305-16.

Aardema, Matthew L, Ying Zhen, and Peter Andolfatto. (2012) 2012. “The Evolution of Cardenolide-Resistant Forms of Na⁺,K⁺ -ATPase in Danainae Butterflies.”. Mol Ecol 21 (2): 340-9.

Thornton, Kevin, Doris Bachtrog, and Peter Andolfatto. (2006) 2006. “X Chromosomes and Autosomes Evolve at Similar Rates in Drosophila: No Evidence for Faster-X Protein Evolution.”. Genome Res 16 (4): 498-504.

Andolfatto, Peter, Dan Davison, Deniz Erezyilmaz, Tina T Hu, Joshua Mast, Tomoko Sunayama-Morita, and David L Stern. (2011) 2011. “Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.”. Genome Res 21 (4): 610-7.

Schumer, Molly, Rongfeng Cui, Bastien Boussau, Ronald Walter, Gil Rosenthal, and Peter Andolfatto. (2013) 2013. “An Evaluation of the Hybrid Speciation Hypothesis for Xiphophorus Clemenciae Based on Whole Genome Sequences.”. Evolution 67 (4): 1155-68.

Parsch, John, Sergey Novozhilov, Sarah S Saminadin-Peter, Karen M Wong, and Peter Andolfatto. (2010) 2010. “On the Utility of Short Intron Sequences As a Reference for the Detection of Positive and Negative Selection in Drosophila.”. Mol Biol Evol 27 (6): 1226-34.

Haddrill, Penelope R, Kevin R Thornton, Brian Charlesworth, and Peter Andolfatto. (2005) 2005. “Multilocus Patterns of Nucleotide Variability and the Demographic and Selection History of Drosophila Melanogaster Populations.”. Genome Res 15 (6): 790-9.

Andolfatto, Peter, Karen M Wong, and Doris Bachtrog. 2011. “Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species.”. Genome Biol Evol 3: 114-28.

Wall, Jeffrey D, Peter Andolfatto, and Molly Przeworski. (2002) 2002. “Testing Models of Selection and Demography in Drosophila Simulans.”. Genetics 162 (1): 203-16.

Zhen, Ying, and Peter Andolfatto. 2012. “Methods to Detect Selection on Noncoding DNA.”. Methods Mol Biol 856: 141-59.

Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.

Huelsenbeck, John P, Peter Andolfatto, and Edna T Huelsenbeck. 2011. “Structurama: Bayesian Inference of Population Structure.”. Evol Bioinform Online 7: 55-9.

Andolfatto, Peter, and Jeffrey D Wall. (2003) 2003. “Linkage Disequilibrium Patterns across a Recombination Gradient in African Drosophila Melanogaster.”. Genetics 165 (3): 1289-305.

Callahan, Benjamin, Richard A Neher, Doris Bachtrog, Peter Andolfatto, and Boris I Shraiman. (2011) 2011. “Correlated Evolution of Nearby Residues in Drosophilid Proteins.”. PLoS Genet 7 (2): e1001315.

Bachtrog, Doris, and Peter Andolfatto. (2006) 2006. “Selection, Recombination and Demographic History in Drosophila Miranda.”. Genetics 174 (4): 2045-59.

Rogers, Rebekah L, Julie Cridland, Ling Shao, Tina T Hu, Peter Andolfatto, and Kevin R Thornton. (2014) 2014. “Landscape of Standing Variation for Tandem Duplications in Drosophila Yakuba and Drosophila Simulans.”. Mol Biol Evol 31 (7): 1750-66.

Andolfatto, Peter. (2008) 2008. “Controlling Type-I Error of the McDonald-Kreitman Test in Genomewide Scans for Selection on Noncoding DNA.”. Genetics 180 (3): 1767-71.

Hu, Tina T, Michael B Eisen, Kevin R Thornton, and Peter Andolfatto. (2013) 2013. “A Second-Generation Assembly of the Drosophila Simulans Genome Provides New Insights into Patterns of Lineage-Specific Divergence.”. Genome Res 23 (1): 89-98.

Huelsenbeck, John P, and Peter Andolfatto. (2007) 2007. “Inference of Population Structure under a Dirichlet Process Model.”. Genetics 175 (4): 1787-802.

Slotte, Tanja, Khaled M Hazzouri, Arvid Ågren, Daniel Koenig, Florian Maumus, Ya-Long Guo, Kim Steige, et al. (2013) 2013. “The Capsella Rubella Genome and the Genomic Consequences of Rapid Mating System Evolution.”. Nat Genet 45 (7): 831-5.

Leffler, Ellen M, Kevin Bullaughey, Daniel R Matute, Wynn K Meyer, Laure Ségurel, Aarti Venkat, Peter Andolfatto, and Molly Przeworski. 2012. “Revisiting an Old Riddle: What Determines Genetic Diversity Levels Within Species?”. PLoS Biol 10 (9): e1001388.

Schumer, Molly, Gil G Rosenthal, and Peter Andolfatto. (2014) 2014. “How Common Is Homoploid Hybrid Speciation?”. Evolution 68 (6): 1553-60.

Thornton, Kevin, and Peter Andolfatto. (2006) 2006. “Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila Melanogaster.”. Genetics 172 (3): 1607-19.

Rogers, Rebekah L, Ling Shao, Jaleal S Sanjak, Peter Andolfatto, and Kevin R Thornton. 2014. “Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila Melanogaster Group.”. G3 (Bethesda) 4 (12): 2345-51.

Andolfatto, Peter. (2007) 2007. “Hitchhiking Effects of Recurrent Beneficial Amino Acid Substitutions in the Drosophila Melanogaster Genome.”. Genome Res 17 (12): 1755-62.

Jensen, Jeffrey D, Kevin R Thornton, and Peter Andolfatto. 2008. “An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila.”. PLoS Genet 4 (9): e1000198.

Haddrill, Penelope R, Doris Bachtrog, and Peter Andolfatto. (2008) 2008. “Positive and Negative Selection on Noncoding DNA in Drosophila Simulans.”. Mol Biol Evol 25 (9): 1825-34.

Schumer, Molly, Rongfeng Cui, Daniel L Powell, Rebecca Dresner, Gil G Rosenthal, and Peter Andolfatto. 2014. “High-Resolution Mapping Reveals Hundreds of Genetic Incompatibilities in Hybridizing Fish Species.”. Elife 3.

Andolfatto, Peter. (2005) 2005. “Adaptive Evolution of Non-Coding DNA in Drosophila.”. Nature 437 (7062): 1149-52.

Wilson, Daniel J, Ryan D Hernandez, Peter Andolfatto, and Molly Przeworski. (2011) 2011. “A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences.”. PLoS Genet 7 (12): e1002395.

Garrigan, Daniel, Sarah B Kingan, Anthony J Geneva, Peter Andolfatto, Andrew Clark, Kevin R Thornton, and Daven C Presgraves. (2012) 2012. “Genome Sequencing Reveals Complex Speciation in the Drosophila Simulans Clade.”. Genome Res 22 (8): 1499-511.

Cui, Rongfeng, Molly Schumer, Karla Kruesi, Ronald Walter, Peter Andolfatto, and Gil G Rosenthal. (2013) 2013. “Phylogenomics Reveals Extensive Reticulate Evolution in Xiphophorus Fishes.”. Evolution 67 (8): 2166-79.

Slotte, Tanja, Khaled M Hazzouri, David Stern, Peter Andolfatto, and Stephen I Wright. (2012) 2012. “Genetic Architecture and Adaptive Significance of the Selfing Syndrome in Capsella.”. Evolution 66 (5): 1360-74.

Sella, Guy, Dmitri A Petrov, Molly Przeworski, and Peter Andolfatto. (2009) 2009. “Pervasive Natural Selection in the Drosophila Genome?”. PLoS Genet 5 (6): e1000495.

Bachtrog, Doris, Kevin Thornton, Andrew Clark, and Peter Andolfatto. (2006) 2006. “Extensive Introgression of Mitochondrial DNA Relative to Nuclear Genes in the Drosophila Yakuba Species Group.”. Evolution 60 (2): 292-302.