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Genome sequencing reveals complex speciation in the Drosophila simulans clade

The 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 tim...

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Autores principales: Garrigan, Daniel, Kingan, Sarah B., Geneva, Anthony J., Andolfatto, Peter, Clark, Andrew G., Thornton, Kevin R., Presgraves, Daven C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409263/
https://www.ncbi.nlm.nih.gov/pubmed/22534282
http://dx.doi.org/10.1101/gr.130922.111
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author Garrigan, Daniel
Kingan, Sarah B.
Geneva, Anthony J.
Andolfatto, Peter
Clark, Andrew G.
Thornton, Kevin R.
Presgraves, Daven C.
author_facet Garrigan, Daniel
Kingan, Sarah B.
Geneva, Anthony J.
Andolfatto, Peter
Clark, Andrew G.
Thornton, Kevin R.
Presgraves, Daven C.
author_sort Garrigan, Daniel
collection PubMed
description The 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.
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spelling pubmed-34092632013-02-01 Genome sequencing reveals complex speciation in the Drosophila simulans clade Garrigan, Daniel Kingan, Sarah B. Geneva, Anthony J. Andolfatto, Peter Clark, Andrew G. Thornton, Kevin R. Presgraves, Daven C. Genome Res Research The 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. Cold Spring Harbor Laboratory Press 2012-08 /pmc/articles/PMC3409263/ /pubmed/22534282 http://dx.doi.org/10.1101/gr.130922.111 Text en © 2012, Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Research
Garrigan, Daniel
Kingan, Sarah B.
Geneva, Anthony J.
Andolfatto, Peter
Clark, Andrew G.
Thornton, Kevin R.
Presgraves, Daven C.
Genome sequencing reveals complex speciation in the Drosophila simulans clade
title Genome sequencing reveals complex speciation in the Drosophila simulans clade
title_full Genome sequencing reveals complex speciation in the Drosophila simulans clade
title_fullStr Genome sequencing reveals complex speciation in the Drosophila simulans clade
title_full_unstemmed Genome sequencing reveals complex speciation in the Drosophila simulans clade
title_short Genome sequencing reveals complex speciation in the Drosophila simulans clade
title_sort genome sequencing reveals complex speciation in the drosophila simulans clade
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409263/
https://www.ncbi.nlm.nih.gov/pubmed/22534282
http://dx.doi.org/10.1101/gr.130922.111
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