Abstract:
:We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The prior distribution of gene tree topology and branch lengths at every locus is calculated using a Markov chain characterization of the genealogical process of coalescent and migration, which integrates over the histories of migration events analytically. The likelihood function is calculated by integrating over branch lengths in the gene trees (coalescent times) numerically. We analyze the model to study the gene tree-species tree mismatch probability and the time to the most recent common ancestor at a locus. The model is used to construct a likelihood ratio test (LRT) of speciation with gene flow. We conduct computer simulations to evaluate the LRT and found that the test is in general conservative, with the false positive rate well below the significance level. For the test to have substantial power, hundreds of loci are needed. Application of the test to a human-chimpanzee-gorilla genomic data set suggests gene flow around the time of speciation of the human and the chimpanzee.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Zhu T,Yang Zdoi
10.1093/molbev/mss118subject
Has Abstractpub_date
2012-10-01 00:00:00pages
3131-42issue
10eissn
0737-4038issn
1537-1719pii
mss118journal_volume
29pub_type
杂志文章abstract::Identification of recently gained spliceosomal introns would provide crucial evidence in the continuing debate concerning the age and evolutionary significance of introns. A previously published genomic analysis reported to have identified 122 introns that had been gained since the divergence of the nematodes Caenorha...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl098
更新日期:2006-12-01 00:00:00
abstract::Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as the highest plateau in the world, may offer a unique opportunity to understand the biological adaptations of human beings to high-altitude environments. We conducted a genome-wide study of 1,000,000 genet...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq277
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journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msl021
更新日期:2006-08-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi107
更新日期:2005-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss170
更新日期:2012-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn136
更新日期:2008-09-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv348
更新日期:2016-04-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh084
更新日期:2004-05-01 00:00:00
abstract::In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss136
更新日期:2012-10-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh117
更新日期:2004-07-01 00:00:00
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040213
更新日期:1995-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040173
更新日期:1994-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm278
更新日期:2008-03-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx158
更新日期:2017-09-01 00:00:00
abstract::Eutrema salsugineum and Schrenkiella parvula are salt-tolerant relatives of the salt-sensitive species Arabidopsis thaliana. An important component of salt tolerance is the regulation of Na(+) ion homeostasis, which occurs in part through proteins encoded by the Cation/Proton Antiporter-1 (CPA1) gene family. We used a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu152
更新日期:2014-08-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy047
更新日期:2018-06-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz218
更新日期:2020-02-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz039
更新日期:2019-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026271
更新日期:2000-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh230
更新日期:2004-12-01 00:00:00
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journal_title:Molecular biology and evolution
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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
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更新日期:2003-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a039999
更新日期:1993-01-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy043
更新日期:2018-07-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg156
更新日期:2003-09-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 信件
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更新日期:2015-08-01 00:00:00
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025798
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pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040360
更新日期:1985-09-01 00:00:00