In defence of model-based inference in phylogeography.
In defence of model-based inference in phylogeography.
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DOI：
10.1111/j.1365-294x.2009.04515.x
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发表时间：
2010-03
影响因子：
4.9
通讯作者：
Excoffier L
中科院分区：
文献类型：
--
作者：
Beaumont MA;Nielsen R;Robert C;Hey J;Gaggiotti O;Knowles L;Estoup A;Panchal M;Corander J;Hickerson M;Sisson SA;Fagundes N;Chikhi L;Beerli P;Vitalis R;Cornuet JM;Huelsenbeck J;Foll M;Yang Z;Rousset F;Balding D;Excoffier L
最近的论文认为，基于模型的方法，特别是基于近似贝叶斯计算(ABC)的方法，在许多方面都存在缺陷，因此不适合于系统地理数据的分析。这些论文进一步认为，嵌套的分支系统地理分析(NCPA)在统计系统地理学中提供了最好的方法。为了消除这些论文带来的混淆和误解，我们证明并解释了基于模型推理背后的推理。我们认为，ABC是一种统计上有效的方法，与其他计算统计技术一起，已经成功地用于推断参数和比较种群遗传学中的模型。我们还检查了NCPA方法，并强调了许多不足之处，无论是在使用单基因座还是多基因座时。我们进一步表明，分支的年龄被粗心地用于推断人口事件的年龄，这些年龄是在一个简单的泛混合和人口平稳性模型下估计的，但然后在不同的和未指定的模型下用于检验假设，这种使用使这些测试过程无效。最后，我们鼓励研究人员在群体遗传学中研究和使用基于模型的推理。
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.