ArticleSystematic biology2024
Hierarchical Heuristic Species Delimitation Under the Multispecies Coalescent Model with Migration.
Article in Systematic biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (Phrynosoma modestum).Genome biology and evolution · 2026Article
- A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum.Systematic biology · 2026Article
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection.Journal of molecular evolution · 2026Article
- Extending GroupStruct2: a Bayesian and machine-learning framework for testing taxonomic hypotheses using morphometric data.ZooKeys · 2026Article
- Global species delimitation of smooth-shelled blue mussels in the Mytilus edulis complex.Scientific reports · 2025Article
- More than one species of the naked mole-rat, a new biomedical model.Communications biology · 2025Article
- When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi's paleo-archipelago.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A New Species ofAnimals : an open access journal from MDPI · 2025Article
- The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- Distinguishing species boundaries from geographic variation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Establishing species boundaries in Bornean geckos.Biology letters · 2024Article
- Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea).The Journal of heredity · 2024Article
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5 authors.
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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 1 species versus MSC for 2 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 3 empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to oversplitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria.
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