Global gap-analysis of amphipod barcode library

In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cyt...

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Autores principales:	Anna Maria Jażdżewska, Anne Helene S. Tandberg, Tammy Horton, Saskia Brix
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	DNA barcoding Crustacea Marine realm Freshwaters Semi-terrestrial Taxonomic identification Medicine R
Acceso en línea:	https://doaj.org/article/09b259d286654e0e8ec2d92e7f2e3546
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id	oai:doaj.org-article:09b259d286654e0e8ec2d92e7f2e3546
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spelling	oai:doaj.org-article:09b259d286654e0e8ec2d92e7f2e35462021-11-06T15:05:26ZGlobal gap-analysis of amphipod barcode library10.7717/peerj.123522167-8359https://doaj.org/article/09b259d286654e0e8ec2d92e7f2e35462021-11-01T00:00:00Zhttps://peerj.com/articles/12352.pdfhttps://peerj.com/articles/12352/https://doaj.org/toc/2167-8359In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.Anna Maria JażdżewskaAnne Helene S. TandbergTammy HortonSaskia BrixPeerJ Inc.articleDNA barcodingCrustaceaMarine realmFreshwatersSemi-terrestrialTaxonomic identificationMedicineRENPeerJ, Vol 9, p e12352 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA barcoding Crustacea Marine realm Freshwaters Semi-terrestrial Taxonomic identification Medicine R
spellingShingle	DNA barcoding Crustacea Marine realm Freshwaters Semi-terrestrial Taxonomic identification Medicine R Anna Maria Jażdżewska Anne Helene S. Tandberg Tammy Horton Saskia Brix Global gap-analysis of amphipod barcode library
description	In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
format	article
author	Anna Maria Jażdżewska Anne Helene S. Tandberg Tammy Horton Saskia Brix
author_facet	Anna Maria Jażdżewska Anne Helene S. Tandberg Tammy Horton Saskia Brix
author_sort	Anna Maria Jażdżewska
title	Global gap-analysis of amphipod barcode library
title_short	Global gap-analysis of amphipod barcode library
title_full	Global gap-analysis of amphipod barcode library
title_fullStr	Global gap-analysis of amphipod barcode library
title_full_unstemmed	Global gap-analysis of amphipod barcode library
title_sort	global gap-analysis of amphipod barcode library
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/09b259d286654e0e8ec2d92e7f2e3546
work_keys_str_mv	AT annamariajazdzewska globalgapanalysisofamphipodbarcodelibrary AT annehelenestandberg globalgapanalysisofamphipodbarcodelibrary AT tammyhorton globalgapanalysisofamphipodbarcodelibrary AT saskiabrix globalgapanalysisofamphipodbarcodelibrary
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Global gap-analysis of amphipod barcode library

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