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Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database
INTRODUCTION: Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5723135/ https://www.ncbi.nlm.nih.gov/pubmed/29230362 http://dx.doi.org/10.7717/peerj.4122 |
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author | Vivien, Régis Holzmann, Maria Werner, Inge Pawlowski, Jan Lafont, Michel Ferrari, Benoit J.D. |
author_facet | Vivien, Régis Holzmann, Maria Werner, Inge Pawlowski, Jan Lafont, Michel Ferrari, Benoit J.D. |
author_sort | Vivien, Régis |
collection | PubMed |
description | INTRODUCTION: Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. METHODS: We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. RESULTS: We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. DISCUSSION: Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices. |
format | Online Article Text |
id | pubmed-5723135 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-57231352017-12-11 Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database Vivien, Régis Holzmann, Maria Werner, Inge Pawlowski, Jan Lafont, Michel Ferrari, Benoit J.D. PeerJ Biodiversity INTRODUCTION: Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. METHODS: We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. RESULTS: We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. DISCUSSION: Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices. PeerJ Inc. 2017-12-06 /pmc/articles/PMC5723135/ /pubmed/29230362 http://dx.doi.org/10.7717/peerj.4122 Text en ©2017 Vivien et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biodiversity Vivien, Régis Holzmann, Maria Werner, Inge Pawlowski, Jan Lafont, Michel Ferrari, Benoit J.D. Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title | Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title_full | Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title_fullStr | Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title_full_unstemmed | Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title_short | Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database |
title_sort | cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a swiss reference database |
topic | Biodiversity |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5723135/ https://www.ncbi.nlm.nih.gov/pubmed/29230362 http://dx.doi.org/10.7717/peerj.4122 |
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