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

Jensen, J.D., K.R. Thornton and P. Andolfatto. (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. Epub 2008 Sep 14 [link].

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

Jeong, S., M. Rebeiz, P. Andolfatto, T. Werner, J. True and S.B. Carroll. (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, K.R., J.D. Jensen, C. Becquet, and P. Andolfatto. (2007) Progress and prospects in mapping recent selection in the genome. Heredity 98(6):340-8 (Thornton_etal.pdf).

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

Huelsenbeck, J.P. and P. Andolfatto. (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, and 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, and 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, and 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).