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Hierarchical heuristic species delimitation under the multispecies coalescent model with migration

Kornai, Daniel1; Jiao, Xiyun2; Ji, Jiayi1; Flouris, Thomas1; Yang, Ziheng1

Published Sep 13, 2023; Updated Sep 10, 2024 on Dryad. https://doi.org/10.5061/dryad.jm63xsjhc

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Sep 13, 2023 version files 191.44 KB
Sep 10, 2024 version files 2.63 MB

Abstract

The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g., MSC for one species versus MSC for two species) and compared using Bayesian model selection. This approach, implemented in the program bpp, has been found to be prone to over-splitting. Alternatively heuristic criteria based on population parameters (such as population split times, population sizes, and migration rates) estimated from genomic data may be used to delimit species. Here we develop hierarchical merge and split algorithms for heuristic species delimitation based on the genealogical divergence index (𝑔𝑑𝑖) and implement them in a python pipeline called hhsd. We characterize the behavior of the 𝑔𝑑𝑖 under a few simple scenarios of gene flow. We apply the new approaches to a dataset simulated under a model of isolation by distance as well as three empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria.