SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications
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 morphospecies of planktonic foraminifera are composed of a complex of sever...
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Public Library Science
2014
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Online Access: | https://archimer.ifremer.fr/doc/00290/40107/38859.pdf https://archimer.ifremer.fr/doc/00290/40107/38860.pdf https://archimer.ifremer.fr/doc/00290/40107/38861.xls https://archimer.ifremer.fr/doc/00290/40107/38862.xlsx https://archimer.ifremer.fr/doc/00290/40107/38863.zip https://archimer.ifremer.fr/doc/00290/40107/38864.pdf https://doi.org/10.1371/journal.pone.0104641 https://archimer.ifremer.fr/doc/00290/40107/ |
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ftarchimer:oai:archimer.ifremer.fr:40107 2023-05-15T18:00:24+02:00 SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications Andre, Aurore Quillevere, Frederic Morard, Raphael Ujiie, Yurika Escarguel, Gilles De Vargas, Colomban De Garidel-thoron, Thibault Douady, Christophe J. 2014-08-13 application/pdf https://archimer.ifremer.fr/doc/00290/40107/38859.pdf https://archimer.ifremer.fr/doc/00290/40107/38860.pdf https://archimer.ifremer.fr/doc/00290/40107/38861.xls https://archimer.ifremer.fr/doc/00290/40107/38862.xlsx https://archimer.ifremer.fr/doc/00290/40107/38863.zip https://archimer.ifremer.fr/doc/00290/40107/38864.pdf https://doi.org/10.1371/journal.pone.0104641 https://archimer.ifremer.fr/doc/00290/40107/ eng eng Public Library Science https://archimer.ifremer.fr/doc/00290/40107/38859.pdf https://archimer.ifremer.fr/doc/00290/40107/38860.pdf https://archimer.ifremer.fr/doc/00290/40107/38861.xls https://archimer.ifremer.fr/doc/00290/40107/38862.xlsx https://archimer.ifremer.fr/doc/00290/40107/38863.zip https://archimer.ifremer.fr/doc/00290/40107/38864.pdf doi:10.1371/journal.pone.0104641 https://archimer.ifremer.fr/doc/00290/40107/ 2014 André et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited info:eu-repo/semantics/openAccess restricted use CC-BY Plos One (1932-6203) (Public Library Science), 2014-08-13 , Vol. 9 , N. 8 , P. 1-19 text Publication info:eu-repo/semantics/article 2014 ftarchimer https://doi.org/10.1371/journal.pone.0104641 2021-09-23T20:26:50Z 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 morphospecies 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. Article in Journal/Newspaper Planktonic foraminifera Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) PLoS ONE 9 8 e104641 |
institution |
Open Polar |
collection |
Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
description |
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 morphospecies 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. |
format |
Article in Journal/Newspaper |
author |
Andre, Aurore Quillevere, Frederic Morard, Raphael Ujiie, Yurika Escarguel, Gilles De Vargas, Colomban De Garidel-thoron, Thibault Douady, Christophe J. |
spellingShingle |
Andre, Aurore Quillevere, Frederic Morard, Raphael Ujiie, Yurika Escarguel, Gilles De Vargas, Colomban De Garidel-thoron, Thibault Douady, Christophe J. SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications |
author_facet |
Andre, Aurore Quillevere, Frederic Morard, Raphael Ujiie, Yurika Escarguel, Gilles De Vargas, Colomban De Garidel-thoron, Thibault Douady, Christophe J. |
author_sort |
Andre, 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 |
Public Library Science |
publishDate |
2014 |
url |
https://archimer.ifremer.fr/doc/00290/40107/38859.pdf https://archimer.ifremer.fr/doc/00290/40107/38860.pdf https://archimer.ifremer.fr/doc/00290/40107/38861.xls https://archimer.ifremer.fr/doc/00290/40107/38862.xlsx https://archimer.ifremer.fr/doc/00290/40107/38863.zip https://archimer.ifremer.fr/doc/00290/40107/38864.pdf https://doi.org/10.1371/journal.pone.0104641 https://archimer.ifremer.fr/doc/00290/40107/ |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Plos One (1932-6203) (Public Library Science), 2014-08-13 , Vol. 9 , N. 8 , P. 1-19 |
op_relation |
https://archimer.ifremer.fr/doc/00290/40107/38859.pdf https://archimer.ifremer.fr/doc/00290/40107/38860.pdf https://archimer.ifremer.fr/doc/00290/40107/38861.xls https://archimer.ifremer.fr/doc/00290/40107/38862.xlsx https://archimer.ifremer.fr/doc/00290/40107/38863.zip https://archimer.ifremer.fr/doc/00290/40107/38864.pdf doi:10.1371/journal.pone.0104641 https://archimer.ifremer.fr/doc/00290/40107/ |
op_rights |
2014 André et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited info:eu-repo/semantics/openAccess restricted use |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0104641 |
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PLoS ONE |
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9 |
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8 |
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e104641 |
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