Abstract:
:The serial coalescent extends traditional coalescent theory to include genealogies in which not all individuals were sampled at the same time. Inference in this framework is powerful because population size and evolutionary rate may be estimated independently. However, when the sequences in question are affected by selection acting at many sites, the genealogies may differ significantly from their neutral expectation, and inference of demographic parameters may become inaccurate. I demonstrate that this inaccuracy is severe when the mutation rate and strength of selection are jointly large, and I develop a new likelihood calculation that, while approximate, improves the accuracy of population size estimates. When used in a Bayesian parameter estimation context, the new calculation allows for estimation of the shape of the pairwise coalescent rate function and can be used to detect the presence of selection acting at many sites in a sequence. Using the new method, I investigate two sets of dengue virus sequences from Puerto Rico and Thailand, and show that both genealogies are likely to have been distorted by selection.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
O'Fallon BDdoi
10.1093/molbev/msr153subject
Has Abstractpub_date
2011-11-01 00:00:00pages
3171-81issue
11eissn
0737-4038issn
1537-1719pii
msr153journal_volume
28pub_type
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss191
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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pub_type: 杂志文章
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pub_type: 杂志文章
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pub_type: 信件
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040096
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pub_type: 杂志文章
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026061
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pub_type: 杂志文章
doi:10.1093/molbev/msu196
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pub_type: 杂志文章
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更新日期:2008-11-01 00:00:00
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pub_type: 杂志文章
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pub_type: 杂志文章
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pub_type: 杂志文章
doi:10.1093/molbev/msh074
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pub_type: 杂志文章
doi:10.1093/molbev/msw293
更新日期:2017-04-01 00:00:00
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journal_title:Molecular biology and evolution
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journal_title:Molecular biology and evolution
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv273
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003935
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pub_type: 杂志文章
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更新日期:2019-12-01 00:00:00