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Items: 1 to 50 of 76


Dichotomy of Dosage Compensation along the Neo Z Chromosome of the Monarch Butterfly.

Gu L, Reilly PF, Lewis JJ, Reed RD, Andolfatto P, Walters JR.

Curr Biol. 2019 Dec 2;29(23):4071-4077.e3. doi: 10.1016/j.cub.2019.09.056. Epub 2019 Nov 14.


Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo.

Taverner AM, Yang L, Barile ZJ, Lin B, Peng J, Pinharanda AP, Rao AS, Roland BP, Talsma AD, Wei D, Petschenka G, Palladino MJ, Andolfatto P.

Elife. 2019 Aug 27;8. pii: e48224. doi: 10.7554/eLife.48224.


Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.

Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M.

Curr Biol. 2019 Jul 8;29(13):2157-2166.e6. doi: 10.1016/j.cub.2019.05.074. Epub 2019 Jun 27.


Predictability in the evolution of Orthopteran cardenolide insensitivity.

Yang L, Ravikanthachari N, Mariño-Pérez R, Deshmukh R, Wu M, Rosenstein A, Kunte K, Song H, Andolfatto P.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 22;374(1777):20180246. doi: 10.1098/rstb.2018.0246. Epub 2019 Jun 3.


Natural selection interacts with recombination to shape the evolution of hybrid genomes.

Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M.

Science. 2018 May 11;360(6389):656-660. doi: 10.1126/science.aar3684. Epub 2018 Apr 19.


How the manakin got its crown: A novel trait that is unlikely to cause speciation.

Rosenthal GG, Schumer M, Andolfatto P.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4144-E4145. doi: 10.1073/pnas.1804061115. Epub 2018 Apr 18. No abstract available.


What do we mean when we talk about hybrid speciation?

Schumer M, Rosenthal GG, Andolfatto P.

Heredity (Edinb). 2018 Apr;120(4):379-382. doi: 10.1038/s41437-017-0036-z. Epub 2018 Jan 5. No abstract available.


Assortative mating and persistent reproductive isolation in hybrids.

Schumer M, Powell DL, Delclós PJ, Squire M, Cui R, Andolfatto P, Rosenthal GG.

Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):10936-10941. doi: 10.1073/pnas.1711238114. Epub 2017 Sep 25.


Correction to 'Population differences in olfaction accompany host shift in Drosophila mojavensis'.

Crowley-Gall A, Date P, Han C, Rhodes N, Andolfatto P, Layne JE, Rollmann SM.

Proc Biol Sci. 2017 Jul 12;284(1858). pii: 20171260. doi: 10.1098/rspb.2017.1260. No abstract available.


Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies.

McCulloch KJ, Yuan F, Zhen Y, Aardema ML, Smith G, Llorente-Bousquets J, Andolfatto P, Briscoe AD.

Mol Biol Evol. 2017 Sep 1;34(9):2271-2284. doi: 10.1093/molbev/msx163.


The within-host dynamics of infection in trans-generationally primed flour beetles.

Tate AT, Andolfatto P, Demuth JP, Graham AL.

Mol Ecol. 2017 Jul;26(14):3794-3807. doi: 10.1111/mec.14088. Epub 2017 Apr 4.


Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex.

Cleard F, Wolle D, Taverner AM, Aoki T, Deshpande G, Andolfatto P, Karch F, Schedl P.

Genetics. 2017 Feb;205(2):589-603. doi: 10.1534/genetics.116.195586. Epub 2016 Dec 22.


Population differences in olfaction accompany host shift in Drosophila mojavensis.

Crowley-Gall A, Date P, Han C, Rhodes N, Andolfatto P, Layne JE, Rollmann SM.

Proc Biol Sci. 2016 Aug 31;283(1837). pii: 20161562. doi: 10.1098/rspb.2016.1562. Erratum in: Proc Biol Sci. 2017 Jul 12;284(1858):.


A Genomic Map of the Effects of Linked Selection in Drosophila.

Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, Coop G, Sella G.

PLoS Genet. 2016 Aug 18;12(8):e1006130. doi: 10.1371/journal.pgen.1006130. eCollection 2016 Aug.


Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies.

Aardema ML, Andolfatto P.

Evolution. 2016 Aug;70(8):1913-21. doi: 10.1111/evo.12999. Epub 2016 Jul 27.


Ancient hybridization and genomic stabilization in a swordtail fish.

Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P.

Mol Ecol. 2016 Jun;25(11):2661-79. doi: 10.1111/mec.13602. Epub 2016 Apr 20.


Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans.

Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P, Thornton KR.

PLoS One. 2015 Jul 15;10(7):e0132184. doi: 10.1371/journal.pone.0132184. eCollection 2015.


Genetics of Intraspecies Variation in Avoidance Behavior Induced by a Thermal Stimulus in Caenorhabditis elegans.

Ghosh R, Bloom JS, Mohammadi A, Schumer ME, Andolfatto P, Ryu W, Kruglyak L.

Genetics. 2015 Aug;200(4):1327-39. doi: 10.1534/genetics.115.178491. Epub 2015 Jun 19.


simMSG: an experimental design tool for high-throughput genotyping of hybrids.

Schumer M, Cui R, Rosenthal GG, Andolfatto P.

Mol Ecol Resour. 2016 Jan;16(1):183-92. doi: 10.1111/1755-0998.12434. Epub 2015 Jul 3.


Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes.

Smith HA, White BJ, Kundert P, Cheng C, Romero-Severson J, Andolfatto P, Besansky NJ.

Heredity (Edinb). 2015 Nov;115(5):471-9. doi: 10.1038/hdy.2015.39. Epub 2015 Apr 29.


Reproductive isolation of hybrid populations driven by genetic incompatibilities.

Schumer M, Cui R, Rosenthal GG, Andolfatto P.

PLoS Genet. 2015 Mar 13;11(3):e1005041. doi: 10.1371/journal.pgen.1005041. eCollection 2015 Mar.


Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR.

G3 (Bethesda). 2014 Oct 1;4(12):2345-51. doi: 10.1534/g3.114.013532.


High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.

Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P.

Elife. 2014 Jun 4;3. doi: 10.7554/eLife.02535.


Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.

Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P, Thornton KR.

Mol Biol Evol. 2014 Jul;31(7):1750-66. doi: 10.1093/molbev/msu124. Epub 2014 Apr 7.


How common is homoploid hybrid speciation?

Schumer M, Rosenthal GG, Andolfatto P.

Evolution. 2014 Jun;68(6):1553-60. doi: 10.1111/evo.12399. Epub 2014 Apr 13.


Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.

Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal GG.

Evolution. 2013 Aug;67(8):2166-79. doi: 10.1111/evo.12099. Epub 2013 Apr 4.


The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Slotte T, Hazzouri KM, Ågren 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.

Nat Genet. 2013 Jul;45(7):831-5. doi: 10.1038/ng.2669. Epub 2013 Jun 9.


An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.

Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P.

Evolution. 2013 Apr;67(4):1155-68. doi: 10.1111/evo.12009. Epub 2012 Dec 20.


Parallel molecular evolution in an herbivore community.

Zhen Y, Aardema ML, Medina EM, Schumer M, Andolfatto P.

Science. 2012 Sep 28;337(6102):1634-7.


Revisiting an old riddle: what determines genetic diversity levels within species?

Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M.

PLoS Biol. 2012;10(9):e1001388. doi: 10.1371/journal.pbio.1001388. Epub 2012 Sep 11.


Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.

Cande J, Andolfatto P, Prud'homme B, Stern DL, Gompel N.

PLoS One. 2012;7(8):e43888. doi: 10.1371/journal.pone.0043888. Epub 2012 Aug 30.


A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.

Hu TT, Eisen MB, Thornton KR, Andolfatto P.

Genome Res. 2013 Jan;23(1):89-98. doi: 10.1101/gr.141689.112. Epub 2012 Aug 30.


Genome sequencing reveals complex speciation in the Drosophila simulans clade.

Garrigan D, Kingan SB, Geneva AJ, Andolfatto P, Clark AG, Thornton KR, Presgraves DC.

Genome Res. 2012 Aug;22(8):1499-511. doi: 10.1101/gr.130922.111. Epub 2012 Apr 13.


Genetic architecture and adaptive significance of the selfing syndrome in Capsella.

Slotte T, Hazzouri KM, Stern D, Andolfatto P, Wright SI.

Evolution. 2012 May;66(5):1360-74. doi: 10.1111/j.1558-5646.2011.01540.x. Epub 2012 Mar 3.


Methods to detect selection on noncoding DNA.

Zhen Y, Andolfatto P.

Methods Mol Biol. 2012;856:141-59. doi: 10.1007/978-1-61779-585-5_6. Review.


A population genetics-phylogenetics approach to inferring natural selection in coding sequences.

Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M.

PLoS Genet. 2011 Dec;7(12):e1002395. doi: 10.1371/journal.pgen.1002395. Epub 2011 Dec 1.


The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies.

Aardema ML, Zhen Y, Andolfatto P.

Mol Ecol. 2012 Jan;21(2):340-9. doi: 10.1111/j.1365-294X.2011.05379.x. Epub 2011 Nov 29.


Structurama: bayesian inference of population structure.

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET.

Evol Bioinform Online. 2011;7:55-9. doi: 10.4137/EBO.S6761. Epub 2011 Jun 2.


Correlated evolution of nearby residues in Drosophilid proteins.

Callahan B, Neher RA, Bachtrog D, Andolfatto P, Shraiman BI.

PLoS Genet. 2011 Feb;7(2):e1001315. doi: 10.1371/journal.pgen.1001315. Epub 2011 Feb 24.


Multiplexed shotgun genotyping for rapid and efficient genetic mapping.

Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL.

Genome Res. 2011 Apr;21(4):610-7. doi: 10.1101/gr.115402.110. Epub 2011 Jan 13.


Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species.

Andolfatto P, Wong KM, Bachtrog D.

Genome Biol Evol. 2011;3:114-28. doi: 10.1093/gbe/evq086. Epub 2010 Dec 20.


On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.

Parsch J, Novozhilov S, Saminadin-Peter SS, Wong KM, Andolfatto P.

Mol Biol Evol. 2010 Jun;27(6):1226-34. doi: 10.1093/molbev/msq046. Epub 2010 Feb 11.


Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al.

Rebeiz M, Ramos-Womack M, Jeong S, Andolfatto P, Werner T, True J, Stern DL, Carroll SB.

Cell. 2009 Dec 11;139(6):1189-96. doi: 10.1016/j.cell.2009.11.004.


Pervasive natural selection in the Drosophila genome?

Sella G, Petrov DA, Przeworski M, Andolfatto P.

PLoS Genet. 2009 Jun;5(6):e1000495. doi: 10.1371/journal.pgen.1000495. Epub 2009 Jun 5.


An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.

Jensen JD, Thornton KR, Andolfatto P.

PLoS Genet. 2008 Sep 19;4(9):e1000198. doi: 10.1371/journal.pgen.1000198.


Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.

Andolfatto P.

Genetics. 2008 Nov;180(3):1767-71. doi: 10.1534/genetics.108.091850. Epub 2008 Sep 14.


Positive and negative selection on noncoding DNA in Drosophila simulans.

Haddrill PR, Bachtrog D, Andolfatto P.

Mol Biol Evol. 2008 Sep;25(9):1825-34. doi: 10.1093/molbev/msn125. Epub 2008 May 29.


The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.

Jeong S, Rebeiz M, Andolfatto P, Werner T, True J, Carroll SB.

Cell. 2008 Mar 7;132(5):783-93. doi: 10.1016/j.cell.2008.01.014.


Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.

Andolfatto P.

Genome Res. 2007 Dec;17(12):1755-62. Epub 2007 Nov 7. Erratum in: Genome Res. 2008 Jan;18(1):197.


Progress and prospects in mapping recent selection in the genome.

Thornton KR, Jensen JD, Becquet C, Andolfatto P.

Heredity (Edinb). 2007 Jun;98(6):340-8. Epub 2007 May 2. Review.

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