Publications

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* trainees

2018
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. https://www.ncbi.nlm.nih.gov/pubmed/29674434.

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. https://www.ncbi.nlm.nih.gov/pubmed/29669913.

Schumer M*, Rosenthal GG, Andolfatto P. 2018. What do we mean when we talk about hybrid speciation? Heredity. 120:379-382. https://www.ncbi.nlm.nih.gov/pubmed/29302049

2017
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. https://www.ncbi.nlm.nih.gov/pubmed/28973863

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. https://www.ncbi.nlm.nih.gov/pubmed/28505307

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. https://www.ncbi.nlm.nih.gov/pubmed/28277618

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289839/

2016
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. https://www.ncbi.nlm.nih.gov/pubmed/27581882

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. arXiv doi: http://arxiv.org/abs/1408.5461. PLoS Genetics, 12:e1006130. https://www.ncbi.nlm.nih.gov/pubmed/27536991

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. https://www.ncbi.nlm.nih.gov/pubmed/27405795

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. https://www.ncbi.nlm.nih.gov/pubmed/26937625

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. https://www.ncbi.nlm.nih.gov/pubmed/26176952

2015
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. https://www.ncbi.nlm.nih.gov/pubmed/26032857

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. https://www.ncbi.nlm.nih.gov/pubmed/26092720

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. https://www.ncbi.nlm.nih.gov/pubmed/25920668

Schumer M*, Cui R, Rosenthal GG, Andolfatto P. 2015. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genetics, 11(3):e1005041.  http://www.ncbi.nlm.nih.gov/pubmed/25768654.

2014
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. http://www.ncbi.nlm.nih.gov/pubmed/25273863

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. http://dx.doi.org/10.7554/eLife.02535. (Podcast interview with Molly Schumer http://elife.elifesciences.org/podcast/episode13)

Schumer M*, Rosenthal GG, Andolfatto P. 2014. How common is homoploid hybrid speciation? Evolution. Mar 12. http://www.ncbi.nlm.nih.gov/pubmed/24620775

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. http://www.ncbi.nlm.nih.gov/pubmed/24710518.

2013
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. http://www.ncbi.nlm.nih.gov/pubmed/23888843

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. 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. http://www.ncbi.nlm.nih.gov/pubmed/22936249.

2012
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. https://www.ncbi.nlm.nih.gov/pubmed/22952802

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.http://www.ncbi.nlm.nih.gov/pubmed/22534282

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

2011
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: 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. [link].

2010
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. [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].

2009
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. 5:e1000495. [link]

2008
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.

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.

2007
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.

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.

2006
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.

2005
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.

2004
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.

2003
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.

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

2001
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 Res 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.

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.

2000
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.

1999
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.

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

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