Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow

作     者：Xiyun Jiao Tomá■ Flouri Ziheng Yang Xiyun Jiao;Tomá(s) Flouri;Ziheng Yang

作者机构：Department of GeneticsEvolution and EnvironmentUniversity College London Department of Statistics and Data ScienceSouthern University of Science and Technology 

出 版 物：《National Science Review》 (国家科学评论(英文版))

年 卷 期：2021年第8卷第12期

页      面：86-103页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 07[理学] 08[工学] 

基　　金：supported by Biotechnology and Biological Sciences Research Council grants (BB/P006493/1 and BB/T003502/1) to Z.Y 

主　　题：anomaly zone BPP deep coalescence gene flow Markov chain Monte Carlo multispecies coalescent species tree 

摘      要：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.