Comparing inference under the multispecies coalescent with and without recombination
Comparing inference under the multispecies coalescent with and without recombination
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DOI：
10.1016/j.ympev.2023.107724
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发表时间：
2023-02-03
影响因子：
4.1
通讯作者：
Nakhleh, Luay
中科院分区：
文献类型：
--
作者：
Yan, Zhi;Ogilvie, Huw A.;Nakhleh, Luay
种群参数的准确推断在揭示进化历史方面发挥着关键作用。虽然重组已被普遍认为是有性生殖生物进化的基本过程，但对其进行精确建模仍然具有挑战性。因此，现有的基于合并的方法做出不同的假设或近似以促进系统发育推断，这可能会在存在重组时导致进化参数估计的偏差。在本文中，我们使用三种方法（StarBEAST2、SNAPP 和 diCal2）评估总体参数估计的性能，这三种方法代表三种不同类型的推理。我们进行了全基因组模拟，其中重组率、突变率和不完整谱系排序的水平各不相同。我们表明，使用短或中型基因座的 StarBEAST2 对于实际重组率具有鲁棒性，这与之前的研究一致。正如预期的那样，SNAPP 通常不受重组事件的影响。最令人惊讶的是，diCal2（一种旨在明确解释重组的方法）的表现比其他比较方法要差得多。
Accurate inference of population parameters plays a pivotal role in unravelling evolutionary histories. While recombination has been universally accepted as a fundamental process in the evolution of sexually reproducing organisms, it remains challenging to model it exactly. Thus, existing coalescent-based approaches make different assumptions or approximations to facilitate phylogenetic inference, which can potentially bring about biases in estimates of evolutionary parameters when recombination is present. In this article, we evaluate the performance of population parameter estimation using three methods-StarBEAST2, SNAPP, and diCal2-that represent three different types of inference. We performed whole-genome simulations in which recombination rates, mutation rates, and levels of incomplete lineage sorting were varied. We show that StarBEAST2 using short or mediumsized loci is robust to realistic rates of recombination, which is in agreement with previous studies. SNAPP, as expected, is generally unaffected by recombination events. Most surprisingly, diCal2, a method that is designed to explicitly account for recombination, performs considerably worse than other methods under comparison.