title: SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.
abstract: The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 6112: Laboratoire de Planétologie et de Géodynamique - Bioindicateurs Actuels et Fossiles, Université d'Angers, Angers, France.
authors.forename: Aurore
authors.initials: A
authors.lastname: André
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Quillévéré
authors.affiliation: Zentrum für marine Umweltwissenschaften MARUM, Universität Bremen, Bremen, Germany.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Morard
authors.affiliation: Department of Biology, Shinshu University, Matsumoto, Japan.
authors.forename: Yurika
authors.initials: Y
authors.lastname: Ujiié
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5276: Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Université Lyon 1, Villeurbanne, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Escarguel
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144: Evolution des Protistes et des Ecosystèmes Pélagiques, Université Pierre et Marie Curie-Station Biologique de Roscoff, Roscoff, France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.affiliation: Centre National de la Recherche Scientifique, Centre de Recherche et d'Enseignement de Géosciences de l'Environnement, Université Aix-Marseille, Aix-en-Provence, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: de Garidel-Thoron
authors.affiliation: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5023: Ecologie des Hydrosystèmes Fluviaux, Université Lyon 1, Villeurbanne, France; Institut Universitaire de France, Paris, France.
authors.forename: Christophe J
authors.initials: CJ
authors.lastname: Douady
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D056908:Foraminifera / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D008386:Marine Biology / Q000379:methods; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010163:Paleontology / Q000379:methods; D058974:Phylogeography; D010933:Plankton / Q000145:classification / Q000235:genetics*; D054679:Ribosome Subunits, Small / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity