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Mohammadi S, Özdemir HI, Ozbek P, Sumbul F, Stiller J, Deng Y, Crawford AJ, Rowland HM, Storz JF, Andolfatto P & Dobler S. 2022. Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na,K-ATPases. bioRXiv: Mol Biol Evol (in press).

Pallares LF#, Lea AJ#, Han C*, Filippova EV, Andolfatto P$, Ayroles JF$. 2022. Diet unmasks genetic variants that regulate lifespan in outbred Drosophila. #,$ == contributed equally. bioRXiv: 2020.10.19.346312v2. Nature Genetics (in press).

Mohammadi S, Herrera-Álvarez S, Yang L*, del Pilar Rodríguez-Ordoñez M, Zhang K*, Storz JF, Dobler S, Crawford AJ, Andolfatto P. 2022. Constraints on the evolution of toxin-resistant Na,K-ATPases have limited dependence on sequence divergence. bioRXiv:  PLoS Genetics

Tomihara K, Andolfatto P, Kiuchi T. 2022. Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval melanin pigmentation in the domesticated silkworm, Bombyx mori. bioRXiv: Insect Molecular Biology


Ng D, Pinharanda A*, Vogt MC, Litwin-Kumar A, Stearns K, Thopte U, Cannavo E, Enikolopov A, Fiederling F, Kosmidis S, Noro B, Rodrigues-Vaz I, Shayya H, Andolfatto P, Peterka DS, Tabachnik T, D’Armiento J, Goldklang M, Bendesky A 2021. WHotLAMP: A simple, inexpensive, and sensitive molecular test for the detection of SARS-CoV-2 in saliva. PLoS One. 16:e0257464.

Clark RD, Aardema ML*, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. 2021. Genomic signatures of spatially divergent selection at clownfish range margins. Proc. Royal Soc. B, 288: 20210407.

Mohammadi S, Yang L*, Harpak A, Herrera-Alvarez S, Rodríguez-Ordoñez MP, Peng J, Zhang K, Storz JF, Dobler S, Crawford AJ, Andolfatto P. 2021. Concerted evolution reveals co-adapted amino acid substitutions in Na+K+-ATPase of frogs that prey on toxic toads. bioRXiv:  Current Biology 31:1–9.

Korgaonkar A, Han C*, Lemire AL, Siwanowicz I, Bennouna D, Kopec R, Andolfatto P, Shigenobu S, Stern DL. 2021. A novel family of secreted insect proteins linked to plant gall development. Current Biology, in press. bioRXiv: Current Biology, 31:1836–1849

Powell, DL, Payne C; Keegan M,  Banerjee SM, Cui R, Andolfatto P, Schumer M, Rosenthal GG. 2021.  The genetic architecture of variation in the sexually selected sword ornament and its evolution in hybrid population.  bioRXiv Current Biology, 31: 923-935.e11.


Taverner A*, Blaine L*, Andolfatto P. 2020. Epistasis and physico-chemical constraints contribute to spatial clustering of amino acid substitutions in protein evolution. bioRXiv

Fuller Z, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L*, Peng J*, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. 2020. Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching. Science 369:eaba4674.  bioRXiv: 10.1101/867754v1

Powell DL, Garcia M, Keegan M, Reilly P*, Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal G, Schartl M, Schumer M. 2020. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 368: 731-736. bioRXiv: 2019.12.12.874586v1

Liuqi G, Reilly PF*, Lewis JL, Reed RD, Andolfatto P, Walters JR. 2019. Dichotomy of dosage compensation along the neo Z chromosome of the Monarch butterfly. Current Biology, 29:4071-7.

Taverner AM*, Yang L*, Barile ZJ, Lin B, Peng J, Pinharanda A*, Rao A*, Roland BP, Talsma AD, Wei D, Petschenka G, Palladino MJ, Andolfatto P. 2019. Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo. eLife, 8:e48224. bioRXiv:

Liu Y, Ramos-Womack M, Han C*, Reilly P*, LaRue-Brackett K, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M. 2019. Changes throughout a genetic network mask the contribution of Hox gene evolution. Current Biology, 29:2157-2166.e6. Read the accompanying dispatch by Prud’homme and Gompel.

Yang L*, Ravikanthachari N, Mariño-Pérez R, Deshmukh R, Wu M, Rosenstein A*, Kunte K, Song H, Andolfatto P. 2019. Predictability in the evolution of Orthopteran cardenolide insensitivity. Philosophical Transactions of the Royal Society of London Series B, 374:20180246.

Schumer M*, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M. 2018. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360:656-660.

Rosenthal GG, Schumer M*, Andolfatto P. 2018. How the manakin got its crown: A novel trait that is unlikely to cause speciation. Proc Natl Acad Sci U S A. 115:E4144-E4145.

Schumer M*, Rosenthal GG, Andolfatto P. 2018. What do we mean when we talk about hybrid speciation? Heredity. 120:379-382.  ** Editor’s choice: Best of Heredity 2018.

Schumer M*, Powell D, Delclos P, Squire M, Andolfatto P, Rosenthal GGR. 2017. Assortative mating and persistent reproductive isolation in hybrids. Proc. Nat. Acad. Sci., 114:10936-10941.

McCulloch KJ, Yuan F, Zhen Y*, Aardema ML*, Smith G, Llorente-Bousquets G, Andolfatto P, Briscoe AD. 2017. Sexual dimorphism and retinal mosaic diversification following the evolution of a violet receptor in butterflies. Molecular Biology and Evolution, 34:2271-2284.

Tate AT, Andolfatto P, Demuth JP, Graham AL. 2017. The within-host dynamics of infection in trans-generationally primed flour beetles. Molecular Ecology, 26:3794-3807.

Cleard F, Wolle D, Taverner AM*, Aoki T, Deshpande G, Andolfatto P, Karch F, Schedl P. 2016. Different evolutionary strategies to conserve chromatin boundary function in the Bithorax Complex. Genetics 205:589-603.

Crowley-Gall A, Date P, Han C*, Rhodes N, Andolfatto P, Layne J, Rollmann S. 2016. Population differences in olfaction accompany host shift in Drosophila mojavensis. Proc. Royal. Soc. Series B. 283(1837). pii: 20161562. doi: 10.1098/rspb.2016.1562.

Elyashiv E, Sattath S, Hu TT*, Strustovsky A, McVicker G, Andolfatto P, Coop G, Sella G. 2016. A genomic map of the effects of linked selection in Drosophila. PLoS Genetics, 12:e1006130., arXiv doi:

Aardema ML*, Andolfatto P. 2016. Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na+,K+-ATPase in Danaus butterflies. Evolution, 70:1913-21.

Schumer M*, Cui R, D Powell, Rosenthal GG, Andolfatto P. 2016. Ancient hybridization and genomic stabilization in a swordtail fish. Molecular Ecology, 25:2661-2679.

Rogers RL, Cridland JM, Shao L, Hu TT*, Andolfatto P, Thornton KR. 2015. Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans. PLoS One. 10:e0132184.

Schumer M*, Cui R, Rosenthal GG, Andolfatto P. 2015. simMSG: an experimental design tool for high-throughput genotyping of hybrids. Mol Ecol Resour. 16:183-92.

Ghosh R, Bloom JS, Mohammadi A, Schumer M*, Andolfatto P, Ryu W, Kruglyak L. 2015
Genetics of Intra-Species Variation in Avoidance Behavior Induced by a Thermal Stimulus in Caenorhabditis elegans. Genetics. 200:1327-39.

Smith HA, White BJ, Kundert P, Cheng C, Romero-Severson J, Andolfatto P, Besansky NJ. 2015. Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitos. Heredity, 115, 471–479.

Schumer M*, Cui R, Rosenthal GG, Andolfatto P. 2015. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genetics, 11(3):e1005041.

Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR. 2014. Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3, 4:2345-51.

Schumer M*, Cui R, Powell D, Dresner R, Rosenthal GG, Andolfatto P. 2014. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. Elife. Jun 4:e02535. (Podcast interview with Molly Schumer

Schumer M*, Rosenthal GG, Andolfatto P. 2014. How common is homoploid hybrid speciation? Evolution. Mar 12.

Rogers RL, Cridland JM, Shao L, Hu TT*, Andolfatto P, Thornton KR. 2014. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol. 31: 1750-66.

Cui R, Schumer M*, Kruesi K, Walter R, Andolfatto P, Rosenthal G. 2013. Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution, 67(8):2166-79.

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.

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.

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.

Zhen Y*, Aardema ML*, Medina EM, Schumer M*, Andolfatto P. 2012. Parallel molecular evolution in an herbivore community. Science. 337:1634-7.

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.

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.

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. 22(8):1499-511.

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.

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.

Zhen Y*, Andolfatto P. 2012. Methods to detect selection on non-coding DNA. Methods Mol Biol. 856:141-59. 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.

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET. 2011 Structurama: Bayesian Inference of Population Structure. Evolutionary Bioinformatics, 7:1-5.

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

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.

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.

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.

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.

Sella G., Petrov DA, Przeworski M, Andolfatto P. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet. 5:e1000495.

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

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.

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.

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

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.

Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in Drosophila melanogaster. Genome Research 17:1755-62. See Erratum.

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

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

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

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

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: 292-302.

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 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.

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

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 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.

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.

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

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.

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

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

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

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. WHotLA

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.

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.

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.

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