Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
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DOI：
10.1101/2023.09.10.557025
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发表时间：
2023-09
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影响因子：
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通讯作者：
Daniel Kornai;T. Flouri;Ziheng Yang
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作者：
Daniel Kornai;T. Flouri;Ziheng Yang
多物种聚结（MSC）模型适应了整个基因组的谱系波动，为基因组序列数据的比较分析提供了一个自然的框架，以推断物种分化和基因流动的历史。给定一组种群，物种划分（和物种系统发育）的假设可能被制定为MSC模型的实例（例如，一个物种的MSC与两个物种的MSC），并使用贝叶斯模型选择进行比较。在程序bpp中实现的这种方法已被发现容易过度拆分。或者，根据基因组序列数据估计的MSC模型下的种群参数（如种群/物种分化时间、种群大小和迁移率）的启发式标准可用于划分物种。本文扩展了使用谱系分化指数（gdi）的物种划分方法，开发了启发式物种划分的分层合并和分裂算法，并在一个名为hhsd的python管道中实现。应用于距离隔离模型下模拟的数据，该方法能够恢复正确的物种划分，而bpp模型比较失败。对经验数据集的分析表明，该过程可能不太容易过度分裂。我们讨论了可能的策略，以适应在程序中的超种，以及基于启发式标准的物种划分的挑战。
The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g., MSC for one species versus MSC for two species) and compared using Bayesian model selection. This approach, implemented in the program bpp, has been found to be prone to over-splitting. Alternatively heuristic criteria based on population parameters under the MSC model (such as population/species divergence times, population sizes, and migration rates) estimated from genomic sequence data may be used to delimit species. Here we extend the approach of species delimitation using the genealogical divergence index (gdi) to develop hierarchical merge and split algorithms for heuristic species delimitation, and implement them in a python pipeline called hhsd. Applied to data simulated under a model of isolation by distance, the approach was able to recover the correct species delimitation, whereas model comparison by bpp failed. Analyses of empirical datasets suggest that the procedure may be less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the procedure, as well as the challenges of species delimitation based on heuristic criteria.