MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.
MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.
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DOI：
10.1186/1471-2105-12-1
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发表时间：
2011-01-03
影响因子：
3
通讯作者：
Hickerson MJ
中科院分区：
文献类型：
--
作者：
Huang W;Takebayashi N;Qi Y;Hickerson MJ
MTML-msBayes使用层次近似贝叶斯计算（HABC）的合并模型下推断的时间模式的分歧和基因流跨共分布的分类对。在多个共分布类群的模式下，分化成类群对，随后的基因流或隔离，可以估计超参数，量化的平均值和变异的分歧时间或测试模型的迁移和隔离。该软件使用从多个分类群对收集的多位点DNA序列数据，并允许在人口统计学参数中的分类群之间的变化以及在基因座之间的DNA突变率的异质性。该方法还允许一个灵活的采样方案：不同数量的基因座的长度不同，可以从不同的分类对采样。模拟测试显示，随着越来越多的位点的权力时，试图区分时间的一致性，从不一致的分歧时间跨分类对。这些结果对DNA突变率异质性具有稳健性。估计平均发散时间和测试同时发散是不太准确的迁移，但改善，如果一个指定正确的迁移模型。模拟验证测试表明，人们可以检测到正确的迁移或隔离模型的概率很高，这HABC模型测试程序大大提高了合并的汇总统计最初开发的这项任务（韦克利的ESPW）。该方法被应用到三个澳大利亚鸟类分类群对的经验数据集，并推断与一些随后的基因流的同时发散的结果。为了保持与现有生物信息学工具的灵活性和兼容性，MTML-msBayes是一个管道软件包，由通过命令行执行的Perl，C和R程序组成。源代码和二进制文件可以在开放源代码许可证（GNU公共许可证）下在http://msbayes.sourceforge.net/上下载。
MTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs. Simulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred. To retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).
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影响因子：
5.8
作者：
Cornuet, Jean-Marie;Santos, Filipe;Beaumont, Mark A.;Robert, Christian P.;Marin, Jean-Michel;Balding, David J.;Guillemaud, Thomas;Estoup, Arnaud
通讯作者：
Estoup, Arnaud
影响因子：
3.3
作者：
Excoffier, L;Estoup, A;Cornuet, JM
通讯作者：
Cornuet, JM
DOI：
10.1198/106186006x136976
发表时间：
2006-09-01
影响因子：
2.4
作者：
Cook, Samantha R.;Gelman, Andrew;Rubin, Donald B.
通讯作者：
Rubin, Donald B.
DOI：
10.1073/pnas.0901649106
发表时间：
2009-11-17
影响因子：
11.1
作者：
Graham, Catherine H.;Parra, Juan L.;McGuire, Jimmy A.
通讯作者：
McGuire, Jimmy A.
影响因子：
4.9
作者：
Carstens, Bryan C.;Stoute, Holly N.;Reid, Noah M.
通讯作者：
Reid, Noah M.