Shedding light on the grey zone of speciation along a continuum of genomic divergence Journal Article


Author(s): Roux, Camille; Fraisse, Christelle; Romiguier, Jonathan; Anciaux, Youann; Galtier, Nicolas; Bierne, Nicolas
Article Title: Shedding light on the grey zone of speciation along a continuum of genomic divergence
Affiliation IST Austria
Abstract: Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.
Keywords: Gene Flow; Genetic Drift; Mutation; Prevalence; Probability; introgression; gene pool; model; Ecology; life history trait; mating; species differentiation
Journal Title: PLoS Biology
Volume: 14
Issue 12
ISSN: 1545-7885
Publisher: Public Library of Science  
Date Published: 2016-12-27
Start Page: Article number: e2000234
Copyright Statement: CC BY 4.0
URL:
DOI: 10.1371/journal.pbio.2000234
Notes: European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project. We thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.
Open access: yes (OA journal)
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