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Genome sequencing reveals complex speciation in the Drosophila simulans clade

Author(s): Garrigan, Daniel; Kingan, Sarah B.; Geneva, Anthony J.; Andolfatto, Peter; Clark, Andrew G.; et al

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dc.contributor.authorGarrigan, Daniel-
dc.contributor.authorKingan, Sarah B.-
dc.contributor.authorGeneva, Anthony J.-
dc.contributor.authorAndolfatto, Peter-
dc.contributor.authorClark, Andrew G.-
dc.contributor.authorThornton, Kevin R.-
dc.contributor.authorPresgraves, Daven C.-
dc.date.accessioned2019-04-23T16:10:26Z-
dc.date.available2019-04-23T16:10:26Z-
dc.date.issued2012-08-01en_US
dc.identifier.citationGarrigan, 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 - 1511. doi:10.1101/gr.130922.111en_US
dc.identifier.issn1088-9051-
dc.identifier.urihttp://arks.princeton.edu/ark:/88435/pr1v418-
dc.description.abstractThe three species of the Drosophila simulans clade—the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia—are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. The order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. Here we report on the analysis of a whole-genome four-species sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster reference sequence. The alignment comprises novel, paired short-read sequence data from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia. We are unable to reject a species phylogeny with a basal polytomy; the estimated age of the polytomy is 242,000 yr before the present. However, we also find that up to 4.6% of autosomal and 2.2% of X-linked regions have evolutionary histories consistent with recent gene flow between the mainland species (D. simulans) and the two island endemic species (D. mauritiana and D. sechellia). Our findings thus show that gene flow has occurred throughout the genomes of the D. simulans clade species despite considerable geographic, ecological, and intrinsic reproductive isolation. Last, our analysis of lineage-specific changes confirms that the D. sechellia genome has experienced a significant excess of slightly deleterious changes and a dearth of presumed favorable changes. The relatively reduced efficacy of natural selection in D. sechellia is consistent with its derived, persistently reduced historical effective population size.en_US
dc.format.extent1499 - 1511en_US
dc.language.isoen_USen_US
dc.relation.ispartofGenome Researchen_US
dc.rightsFinal published version. Article is made available in OAR by the publisher's permission or policy.en_US
dc.titleGenome sequencing reveals complex speciation in the Drosophila simulans cladeen_US
dc.typeJournal Articleen_US
dc.identifier.doidoi:10.1101/gr.130922.111-
dc.date.eissued2012-04-13en_US
pu.type.symplectichttp://www.symplectic.co.uk/publications/atom-terms/1.0/journal-articleen_US

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