SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications
International audience 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 compos...
Published in: | PLoS ONE |
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Main Authors: | , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2014
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Subjects: | |
Online Access: | https://hal.sorbonne-universite.fr/hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608/document https://hal.sorbonne-universite.fr/hal-01100608/file/Andr%C3%A9_2014_SSU_rDNA_Divergence.pdf https://doi.org/10.1371/journal.pone.0104641 |
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Open Polar |
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Institut national des sciences de l'Univers: HAL-INSU |
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ftinsu |
language |
English |
topic |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDE]Environmental Sciences |
spellingShingle |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDE]Environmental Sciences André, Aurore Frédéric, Quillévéré Morard, Raphaël Ujiié, Yurika Escarguel, Gilles de Vargas, Colomban Garidel-Thoron, Thibault Douady, Christophe Jean SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
topic_facet |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDE]Environmental Sciences |
description |
International audience 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 39end 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. |
author2 |
Laboratoire de Planétologie et Géodynamique UMR 6112 (LPG) Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE) École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS) Center for Marine Environmental Sciences Bremen (MARUM) Universität Bremen Department of Biology Shinshu University Nagano Evolution des Protistes et Ecosystèmes Pélagiques (EPEP) Adaptation et diversité en milieu marin (AD2M) Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE) Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Universitaire de France (IUF) Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.) Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF) Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA) Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS) ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011) |
format |
Article in Journal/Newspaper |
author |
André, Aurore Frédéric, Quillévéré Morard, Raphaël Ujiié, Yurika Escarguel, Gilles de Vargas, Colomban Garidel-Thoron, Thibault Douady, Christophe Jean |
author_facet |
André, Aurore Frédéric, Quillévéré Morard, Raphaël Ujiié, Yurika Escarguel, Gilles de Vargas, Colomban Garidel-Thoron, Thibault Douady, Christophe Jean |
author_sort |
André, Aurore |
title |
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
title_short |
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
title_full |
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
title_fullStr |
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
title_full_unstemmed |
SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
title_sort |
ssu rdna divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications |
publisher |
HAL CCSD |
publishDate |
2014 |
url |
https://hal.sorbonne-universite.fr/hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608/document https://hal.sorbonne-universite.fr/hal-01100608/file/Andr%C3%A9_2014_SSU_rDNA_Divergence.pdf https://doi.org/10.1371/journal.pone.0104641 |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01100608 PLoS ONE, 2014, 9 (8), pp.e104641. ⟨10.1371/journal.pone.0104641⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0104641 hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608/document https://hal.sorbonne-universite.fr/hal-01100608/file/Andr%C3%A9_2014_SSU_rDNA_Divergence.pdf doi:10.1371/journal.pone.0104641 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0104641 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
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container_start_page |
e104641 |
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1790606933658435584 |
spelling |
ftinsu:oai:HAL:hal-01100608v1 2024-02-11T10:08:01+01:00 SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications André, Aurore Frédéric, Quillévéré Morard, Raphaël Ujiié, Yurika Escarguel, Gilles de Vargas, Colomban Garidel-Thoron, Thibault Douady, Christophe Jean Laboratoire de Planétologie et Géodynamique UMR 6112 (LPG) Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST) Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE) École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS) Center for Marine Environmental Sciences Bremen (MARUM) Universität Bremen Department of Biology Shinshu University Nagano Evolution des Protistes et Ecosystèmes Pélagiques (EPEP) Adaptation et diversité en milieu marin (AD2M) Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE) Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut Universitaire de France (IUF) Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.) Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF) Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA) Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS) ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011) 2014-08-13 https://hal.sorbonne-universite.fr/hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608/document https://hal.sorbonne-universite.fr/hal-01100608/file/Andr%C3%A9_2014_SSU_rDNA_Divergence.pdf https://doi.org/10.1371/journal.pone.0104641 en eng HAL CCSD Public Library of Science info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0104641 hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608 https://hal.sorbonne-universite.fr/hal-01100608/document https://hal.sorbonne-universite.fr/hal-01100608/file/Andr%C3%A9_2014_SSU_rDNA_Divergence.pdf doi:10.1371/journal.pone.0104641 info:eu-repo/semantics/OpenAccess ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01100608 PLoS ONE, 2014, 9 (8), pp.e104641. ⟨10.1371/journal.pone.0104641⟩ [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDE]Environmental Sciences info:eu-repo/semantics/article Journal articles 2014 ftinsu https://doi.org/10.1371/journal.pone.0104641 2024-01-24T17:40:17Z International audience 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 39end 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. Article in Journal/Newspaper Planktonic foraminifera Institut national des sciences de l'Univers: HAL-INSU PLoS ONE 9 8 e104641 |