Abstract:
:Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MAdoi
10.1093/molbev/mss265subject
Has Abstractpub_date
2013-03-01 00:00:00pages
713-24issue
3eissn
0737-4038issn
1537-1719pii
mss265journal_volume
30pub_type
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journal_title:Molecular biology and evolution
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abstract::This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibli...
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doi:10.1093/oxfordjournals.molbev.a040625
更新日期:1990-11-01 00:00:00
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更新日期:2004-01-01 00:00:00
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pub_type: 杂志文章
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更新日期:1997-10-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 评论,杂志文章
doi:10.1093/oxfordjournals.molbev.a026374
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abstract::Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of noncanc...
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更新日期:2017-04-01 00:00:00
abstract::Insertion and deletion (indel)-based analyses have great potential for rooting the tree of life, but their use has been limited because they require ubiquitous sequences that have not been horizontally/laterally transferred. Very few such sequences exist. Here we describe and demonstrate a new algorithm that can use n...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl140
更新日期:2007-01-01 00:00:00
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journal_title:Molecular biology and evolution
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doi:10.1093/molbev/msw219
更新日期:2017-01-01 00:00:00
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journal_title:Molecular biology and evolution
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更新日期:2016-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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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
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更新日期:2020-02-01 00:00:00
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pub_type: 杂志文章
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journal_title:Molecular biology and evolution
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更新日期:2015-07-01 00:00:00
abstract::The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extre...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
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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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更新日期:2019-07-01 00:00:00