The hitchhiker's guide to single-locus species delimitation

Molecular Ecology Resources
Simon Dellicour, Jean-François Flot

Abstract

Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) and tree-based approaches (GMYC, "generalized mixed Yule-coalescent" and PTP, "Poisson tree processes") to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting,...Continue Reading

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Citations

Jun 19, 2019·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Marcos O R da CruzJoão Alves de Oliveira
Dec 25, 2019·Scientific Reports·María Angélica LarraínCristián Araneda
Nov 8, 2020·BMC Evolutionary Biology·Leona LovrenčićIvana Maguire
Oct 16, 2020·Molecular Ecology Resources·Nicolas PuillandreGuillaume Achaz
Jan 24, 2021·Journal of Fish Biology·Bruno GuinandChristelle Tougard
Jan 20, 2020·Trends in Ecology & Evolution·Jonas EberleBernhard Misof
Feb 11, 2021·Molecular Ecology Resources·Giulia MagogaMatteo Montagna
Apr 3, 2021·Journal of Phycology·Frederik Leliaert
Feb 18, 2021·Genome Génome / Conseil National De Recherches Canada·Mario Alejandro MarínCarlos Federico Álvarez
Jul 2, 2021·Molecular Phylogenetics and Evolution·Tobias PfingstlStephan Koblmüller
Sep 21, 2021·Systematic Biology·Catalina Ramírez-PortillaJean-François Flot

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