Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.
Mol Ecol. 2022 May;31(10):2814-2829. doi: 10.1111/mec.16433. Epub 2022 Apr 4.
Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet, in real data sets intralocus recombination causes different sites of the same locus to have different genealogical histories so that the model is misspecified. The impact of recombination on various coalescent-based phylogenomic analyses has not been systematically examined. Here, we conduct a computer simulation to examine the impact of recombination on several Bayesian analyses of multilocus sequence data, including species tree estimation, species delimitation (by Bayesian selection of delimitation models) and estimation of evolutionary parameters such as species divergence and introgression times, population sizes for modern and extinct species, and cross-species introgression probabilities. We found that recombination, at rates comparable to estimates from the human being, has little impact on coalescent-based species tree estimation, species delimitation and estimation of population parameters. At rates 10 times higher than the human rate, recombination may affect parameter estimation, causing positive biases in introgression times and ancestral population sizes, although species divergence times and cross-species introgression probabilities are estimated with little bias. Overall, the simulation suggests that phylogenomic inferences under the multispecies coalescent model are robust to realistic amounts of intralocus recombination.
系统发育基因组分析假设在同一基因座内没有重组，并且基因座之间可以自由重组。然而，在实际数据集，基因座内重组导致同一基因座的不同位点具有不同的系统发育历史，从而使模型出现误判。重组对各种基于合并的系统发育基因组分析的影响尚未得到系统研究。在这里，我们进行了计算机模拟，以研究重组对多基因座序列数据的几种贝叶斯分析的影响，包括物种树估计、物种划分（通过贝叶斯选择划分模型）以及物种分化和基因渐渗时间、现代和灭绝物种的种群大小以及跨物种基因渐渗概率等进化参数的估计。我们发现，与人类的估计值相当的重组率对基于合并的物种树估计、物种划分和种群参数估计的影响很小。在比人类速度高 10 倍的重组率下，重组可能会影响参数估计，导致基因渐渗时间和祖先种群大小出现正偏差，尽管物种分化时间和跨物种基因渐渗概率的估计偏差较小。总体而言，模拟表明，多物种合并模型下的基因组推断对真实的基因座内重组具有很强的鲁棒性。
