Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).
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DOI：
10.1186/1471-2105-11-401
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发表时间：
2010-07-28
影响因子：
3
通讯作者：
Estoup A
中科院分区：
文献类型：
--
作者：
Cornuet JM;Ravigné V;Estoup A
近似贝叶斯计算（ABC）是最近一类灵活的蒙特卡罗算法，越来越多地用于对影响自然种群的复杂进化场景进行基于模型的推理。DIYABC软件提供了一个用户友好的界面，允许非专业用户考虑人口历史，包括人口差异、外加剂和人口规模变化的任何组合。我们在这里描述和说明了该软件的新发展，主要包括(i)从DNA序列数据中推断除了或单独的微卫星数据，（ii）考虑平衡或不平衡性别比例分析五类位点的可能性：常染色体二倍体，常染色体单倍体，x连锁，y连锁和线粒体，以及（iii）执行模型检查计算以评估模型的“拟合优度”的可能性，这是ABC分析迄今为止被忽视的一个特征。我们使用在进化情景下产生的受控模拟数据集，包括各种分化和混合事件，来评估混合常染色体微卫星、mtDNA和/或核常染色体DNA序列数据对推断的影响。该评估包括竞争情景的比较及其相对支持度的量化，以及给定情景下参数后验分布的估计。我们还考虑了在对入侵物种引入路径进行ABC推断时经常比较的一组场景，以说明DIYABC的新模型检查选项对评估模型不拟合的兴趣。我们新开发的集成软件DIYABC对于推断涉及近代和古代历史事件的复杂进化情景以及使用二倍体或单倍体生物的各种类型的分子标记特别有用。它们为非专业用户在ABC框架内实现模型检查计算提供了一种方便的方法，从而填补了ABC分析的空白。DIYABC V1.0软件可在http://www1.montpellier.inra.fr/CBGP/diyabc免费获得。
Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. We used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit. Our new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking computation within an ABC framework, hence filling up a gap of ABC analysis. The software DIYABC V1.0 is freely available at http://www1.montpellier.inra.fr/CBGP/diyabc.
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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：
3.4
作者：
Hickerson, Michael J.;Meyer, Christopher P.
通讯作者：
Meyer, Christopher P.
影响因子：
3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.3
作者：
Excoffier, L;Estoup, A;Cornuet, JM
通讯作者：
Cornuet, JM