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  Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum

Tellier, A., Pfaffelhuber, P., Haubold, B., Naduvilezhath, L., Rose, L. E., Städler, T., et al. (2011). Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS ONE, 6(5): e18155. doi:10.1371/journal.pone.0018155.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-D3C0-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-D3C1-1
Genre: Journal Article

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 Creators:
Tellier, Aurélien, Author
Pfaffelhuber, Peter, Author
Haubold, Bernhard1, Author              
Naduvilezhath, Lisha, Author
Rose, Laura E., Author
Städler, Thomas, Author
Stephan, Wolfgang, Author
Metzler, Dirk, Author
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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 Abstract: Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches.

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Language(s): eng - English
 Dates: 2011-05-26
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 572149
DOI: 10.1371/journal.pone.0018155
Other: 2861/S 39204
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Title: PLoS ONE
Source Genre: Journal
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Pages: - Volume / Issue: 6 (5) Sequence Number: e18155 Start / End Page: - Identifier: ISSN: 1932-6203 (online)