title: Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations.
abstract: Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.
authors.affiliation: UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France; UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Rougemont
authors.affiliation: Department of Ecology and Evolution, Université de Lausanne , Lausanne , Switzerland.
authors.forename: Camille
authors.initials: C
authors.lastname: Roux
authors.affiliation: Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland.
authors.forename: Samuel
authors.initials: S
authors.lastname: Neuenschwander
authors.affiliation: Department of Ecology and Evolution, Université de Lausanne , Lausanne , Switzerland.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Goudet
authors.affiliation: UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France; UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Launey
authors.affiliation: UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France; UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Evanno
keywords: Approximate Bayesian computation; Divergence history; Gene flow; Lampetra fluviatilis; Lampetra planeri; Random forest; Speciation