Evaluation of a Bayesian Coalescent Method of Species Delimitation
Evaluation of a Bayesian Coalescent Method of Species Delimitation
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DOI：
10.1093/sysbio/syr071
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发表时间：
2011-12-01
影响因子：
6.5
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
--
作者：
Zhang, Chi;Zhang, De-Xing;Yang, Ziheng
最近提出了一种基于贝叶斯聚结的方法，使用多位点遗传序列数据来划分物种。采用可逆跳马尔可夫链蒙特卡罗算法计算了不同物种划界模型的后验概率。该方法占现存和灭绝的物种的物种遗传和合并事件，并容纳谱系排序和基因树的不确定性。虽然该方法在理论上很有吸引力，但其在实际数据分析中的实用性还有待严格审查。特别是，分析可能是敏感的祖先的人口规模和物种的分歧时间和物种之间的基因流的先验。在这里，我们进行了计算机模拟，以评估该方法的统计性能，如假阴性（将多个物种归为一个的错误）和假阳性（将一个物种分成几个的错误）。我们发现，正确的物种模型推断与高后验概率只有一个或两个位点时，5或10个序列从每个群体，或50个位点时，只有一个序列被采样。我们还模拟了两个物种模型，大陆岛屿模型和踏脚石模型下的迁移数据，以评估基因流（杂交或渐渗）的影响。根据迁移率的不同，该方法的行为完全不同。每代< 0.1个迁移者的低比率实际上没有影响，因此该方法虽然假设物种之间没有杂交，但尽管有少量的基因流动，仍然可以识别出不同的物种。这种行为似乎与生物学家的做法一致。与此相反，较高的迁移率>= 10移民每一代的方法，以推断一个物种。在中等水平的迁移中，该方法是不确定的。我们的研究结果表明，贝叶斯分析下的多物种结合模型可能提供重要的见解，人口分歧，并可能是有用的物种划界产生的假设，从解剖，行为和生态数据的独立信息进行评估。
A Bayesian coalescent-based method has recently been proposed to delimit species using multilocus genetic sequence data. Posterior probabilities of different species delimitation models are calculated using reversible-jump Markov chain Monte Carlo algorithms. The method accounts for species phylogenies and coalescent events in both extant and extinct species and accommodates lineage sorting and uncertainties in the gene trees. Although the method is theoretically appealing, its utility in practical data analysis is yet to be rigorously examined. In particular, the analysis may be sensitive to priors on ancestral population sizes and on species divergence times and to gene flow between species. Here we conduct a computer simulation to evaluate the statistical performance of the method, such as the false negatives (the error of lumping multiple species into one) and false positives (the error of splitting one species into several). We found that the correct species model was inferred with high posterior probability with only one or two loci when 5 or 10 sequences were sampled from each population, or with 50 loci when only one sequence was sampled. We also simulated data allowing migration under a two-species model, a mainland-island model and a stepping-stone model to assess the impact of gene flow (hybridization or introgression). The behavior of the method was diametrically different depending on the migration rate. Low rates at < 0.1 migrants per generation had virtually no effect, so that the method, while assuming no hybridization between species, identified distinct species despite small amounts of gene flow. This behavior appears to be consistent with biologists' practice. In contrast, higher migration rates at >= 10 migrants per generation caused the method to infer one species. At intermediate levels of migration, the method is indecisive. Our results suggest that Bayesian analysis under the multispecies coalescent model may provide important insights into population divergences, and may be useful for generating hypotheses of species delimitation, to be assessed with independent information from anatomical, behavioral, and ecological data.