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

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.

Automated summary

The Multispecies Coalescent (MSC) model extends the single-population coalescent model to multiple species, allowing for estimation of species divergence times, population sizes, species trees, and inference of cross-species gene flow and species delimitation. This framework faces statistical and computational challenges, but research advancements are leading the way towards breakthroughs in the field in the next few years.