SODA: multi-locus species delimitation using quartet frequencies.

Abstract

Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in computational evolutionary biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years. In this article, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy. The code and data presented here are available on https://github.com/maryamrabiee/SODA. Supplementary data are available at Bioinformatics online.