Cui R, Schumer M, Kruesi K, Walter R,  Andolfatto P, Rosenthal G.  2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution, in press.

Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI. 2013 . The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet. 45:831-5. http://www.ncbi.nlm.nih.gov/pubmed/23749190

Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P.  2013. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution,67:1155-68. [Epub ahead of print Dec 2012] http://www.ncbi.nlm.nih.gov/pubmed/23550763.

Hu TT, Eisen MB, Thornton KR, Andolfatto P. 2013. A second generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Research, 23:89-98. [Epub ahead of print Aug 2012] http://www.ncbi.nlm.nih.gov/pubmed/22936249.


Zhen Y, Aardema ML, Medina EM, Schumer M, Andolfatto P. 2012. Parallel molecular evolution in an herbivore community. Science. 337:1634-7. http://www.ncbi.nlm.nih.gov/pubmed/23019645.

Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M.  2012. Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? PLoS Biol. 10:e1001388. http://www.ncbi.nlm.nih.gov/pubmed/22984349

Cande J, Andolfatto P, Prud'homme B, Stern DL, Gompel N. 2012. Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS ONE 7: e43888. doi:10.1371/journal.pone.0043888

Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark AG, Thornton KR, Presgraves DC. 2012. Genome sequencing reveals complex speciation in the Drosophila simulans clade.  Genome Research. Jun 6. [Epub ahead of print] [http://genome.cshlp.org/content/early/2012/04/13/gr.130922.111.abstract]

Slotte T, Hazzouri KM, Stern D, Andolfatto P, Wright SI. 2012. Interspecific QTL mapping reveals the genetic basis of the selfing syndrome in Capsella rubella. Evolution. 66:1360-74 [http://www.ncbi.nlm.nih.gov/pubmed/22519777]

Aardema, M, Zhen Y, Andolfatto P. 2012 The evolution of cardenolide-resistant forms of Na+,K+-ATPase in Danainae butterflies. Molecular Ecology. 21:340-9. Epub 2011 Nov 29. [http://www.ncbi.nlm.nih.gov/pubmed/22126595]

Zhen Y, Andolfatto P. 2012. Methods to detect selection on non-coding DNA. Methods Mol Biol. 856:141-59. [http://www.ncbi.nlm.nih.gov/pubmed/22399458 or request a pdf]


Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M, 2011.  A Population Genetics-Phylogenetic Approach to Inferring Natural Selection in Coding Sequences. PLoS Genetics. 7:e1002395. [http://www.ncbi.nlm.nih.gov/pubmed/22144911]

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET. 2011 Structurama: Bayesian Inference of Population Structure.  Evolutionary Bioinformatics, 7:1-5. [http://www.ncbi.nlm.nih.gov/pubmed/21698091]

Callahan B, Neher RA, Bachtrog D, Andolfatto P, Shraiman BI.  2011.  Correlated evolution of nearby residues in Drosophilid proteins.  PLoS Genetics, 7(2): e1001315. [link].

Andolfatto P., Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. 2011. Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.  Genome Research, 21: 610-7. [link].


Andolfatto P, Wong KM, Bachtrog D. 2010. Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species. Genome Biol Evol. 3:114-28. Epub 2010. [link].

Parsch J, Novozhilov S, Saminadin-Peter SS, Wong KM and Andolfatto P. 2010. On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol Biol Evol. 27:1226-34. [link].


Rebeiz M, Ramos-Womack M, Jeong S, Andolfatto P, Werner T, True J, Stern DL, Carroll SB. 2009. Evolution of the tan locus contributed to pigment loss in Drosophila santomea: A response to Matute et al. Cell. 139:1189-96 [link].

Sella G., Petrov DA, Przeworski M Andolfatto P. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet. Jun;5(6):e1000495. [link]


Jensen JD, Thornton KR, Andolfatto P. 2008. An approximate Bayesian estimator suggests strong recurrent selective sweeps in Drosophila. PLoS Genetics,4:e1000198 [link].

Andolfatto P. 2008. Controlling type-I error of the McDonald-Kreitman test in genome wide scans for selection on noncoding DNA. Genetics, 180:1767-71. [link].

Wright SI, Andolfatto P. 2008. The impact of natural selection on the genome: Emerging patterns in Drosophila and Arabidopsis. Annual Review of Ecology, Evolution and Systematics, 39:193-213 [link].

Haddrill PR, Bachtrog D, Andolfatto P. 2008. Positive and negative selection on noncoding DNA in Drosophila simulans. MBE 25:1825-1834 (Haddrill_etal2008.pdf).

Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB. 2008. The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell 132:783-793 (Jeong_etal2008.pdf).


Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in Drosophila melanogaster. Genome Research 17:1755-62 (Andolfatto_GenRes2007.pdf, suppmat.pdf, erratum.pdf).

Thornton KR, Jensen JD, Becquet C, Andolfatto P. 2007. Progress and prospects in mapping recent selection in the genome. Heredity 98(6):340-8 (Thornton_etal.pdf).

Putnam AS, Scriber JM, Andolfatto P. 2007. Discordant divergence times among Z chromosome regions between two ecologically distinct swallowtail butterfly species. Evolution 61(4):912-927 (putnam_2007.pdf).

Huelsenbeck JP, Andolfatto P. 2007. Inference of population structure under a Dirichlet process model. Genetics. 175: 1787-1802 (Huelsenbeck_Andolfatto.pdf).


Bachtrog D, Andolfatto P. 2006. Selection, recombination and demographic history in Drosophila miranda.  Genetics. 174:2045-2059 (Bachtrog_Andolfatto.pdf).

Bachtrog D, Thornton KR, Clark AC, Andolfatto P. 2006. Extensive introgression of mitochondrial DNA in the absence of nuclear gene flow in the Drosophila yakuba subgroup. Evolution, 60(2): 292-302 (Bachtrog_etal2006.pdf).

Thornton KR, Bachtrog D, Andolfatto P. 2006. X-chromosomes and autosomes evolve at similar rates in Drosophila - no evidence for faster-X protein evolution. Genome Research, 16:498-504 (Thornton_etal2006.pdf).

Thornton KR, Andolfatto P. 2006. Approximate bayesian inference reveals evidence for a recent, severe, bottleneck in a Netherlands population of Drosophila melanogaster. Genetics, 172:1607-1619 (Thornton_Andolfatto_2006.pdf).


Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437(7062): 1149-1153 (Andolfatto_Nature.pdf).

Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. 2005.  Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 6(8):R67 (Haddrill_etal_GenomeBiol2005.pdf).

Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P. 2005.  Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15(6):790-799 (Haddrill_etal2005.pdf).


Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD. 2004.  Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res 14(2):273-279 (Halligan_etal2004.pdf).


Andolfatto P, Wall JD. 2003. Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster. Genetics 165(3):1289-1305 (Andolfatto_Wall.pdf).

Andolfatto P, Scriber JM, Charlesworth B. 2003. No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus. Evolution 57(2):305-316 (Andolfatto_etal2003.pdf).


Wall JD, Andolfatto P, Przeworski M. 2002. Testing models of selection and demography in Drosophila simulans. Genetics 162(1):203-216 (Wall_etal2002.pdf).


Andolfatto P. 2001. Adaptive hitchhiking effects on genome variability. Curr Opin Genet Dev 11(6):635-641 (Andolfatto_2001.pdf).

Andolfatto P, Przeworski M. 2001. Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158(2):657-665 (Andolfatto_Przeworski2001.pdf).

Andolfatto P, Depaulis F, Navarro A. 2001. Inversion polymorphisms and nucleotide variability in Drosophila. Genet Res 77(1):1-8 (Andolfatto_etal2001.pdf).

Wu Q, Andolfatto P, Haunerland NH. 2001. Cloning and sequence of the gene encoding the muscle fatty acid binding protein from the desert locust, Schistocerca gregaria. Insect Biochem Mol Biol 31(6-7):553-562 (Wu_etal2001.pdf).

Przeworski M, Wall JD, Andolfatto P. 2001. Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 18(3):291-298 (Przeworski_etal2001.pdf).

Andolfatto P. 2001. Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol Biol Evol 18(3):279-290 (Andolfatto_MBE_2001.pdf).


Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156(4):1913-1931 (Kliman_etal2000.pdf).

Andolfatto P, Przeworski M. 2000. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156(1):257-268 (Andolfatto_Przeworski2000.pdf).

Andolfatto P, Kreitman M. 2000. Molecular variation at the In(2L)t proximal breakpoint site in natural populations of Drosophila melanogaster and D. simulans. Genetics 154(4):1681-1691 (Andolfatto_Kreitman2000.pdf).


Andolfatto P, Wall JD, Kreitman M. 1999. Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153(3):1297-1311 (Andolfatto_etal1999.pdf).


Andolfatto P, Nordborg M. 1998. The effect of gene conversion on intralocus associations. Genetics 148(3):1397-1399 (Andolfatto_Nordborg1998.pdf).