Multispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes, estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years.

中文翻译：

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多物种聚结及其在推断物种系统发育和跨物种基因流中的应用

多物种聚结（MSC）是单种群聚结模型对多个物种的扩展。它整合了物种分化的系统发育过程和聚结的种群遗传过程，并为使用来自多个物种的基因组序列数据的许多推理问题提供了强大的框架，包括估计物种分化时间和种群大小，估计物种树适应不一致的基因树，跨物种基因流动和物种划界的推断。在这篇综述中，我们介绍了 MSC 模型的主要特征，讨论了物种树估计的全似然和启发式方法，并总结了跨物种基因流推断的最新方法学进展。