Global gap-analysis of amphipod barcode library.

Anna Maria Jażdżewska,Saskia Brix,Tammy Horton,Anne Helene S Tandberg

doi:10.7717/peerj.12352

Anna Maria Jażdżewska, Saskia Brix + Show 2 more

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https://doi.org/10.7717/peerj.12352

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Abstract

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.

Highlights

Nature in the age of Anthropocene is facing numerous global changes and challenges
The combined factors of high diversity and the important role played by amphipods in the aquatic ecosystem highlight the need for accurate species identifications which are required for biological monitoring programs
At the time of download they were represented by almost 26,000 records (3,835 Barcode Index Number (BIN)), and by the end of August there were more than 34,000 public sequences (3,914 BINs) (BOLD accessed on 20-08-2020), indicating the great intensity of molecular studies involving this crustacean group, and that the data in Barcode of Life Data System (BOLD) are actively growing

Summary

Introduction

Nature in the age of Anthropocene is facing numerous global changes and challenges. One of the drastic results of human associated activities is the acceleration of species extinctions, with one million species estimated to be presently critically endangered (IPBES, 2019). The rate of species discovery grows, large numbers of species remain undescribed and it is believed many will not be recognized before they go extinct (Mora et al, 2011; Brix et al, 2020) This raises the challenge of efficient environmental monitoring, which is crucial for biodiversity recognition and preservation. The use of metabarcoding in assessing the status of ecosystems has already received the new term ‘‘Biomonitoring 2.0’’ (Bush et al, 2019) Such approaches require the existence of well-established barcode fragment libraries, which allow accurate recognition of organisms in the environment (Cristescu, 2014; Cowart et al, 2015; Oliveira et al, 2016; Múrria et al, 2020). Recent studies indicate that the use of barcoding in biomonitoring has great advantages over morphological identification, the current gaps in barcode libraries may hinder their use (Weigand et al, 2019; Duarte, Vieira & Costa, 2020; Feio et al, 2020; Hestetun et al, 2020; Leite et al, 2020; Múrria et al, 2020; Vieira et al, 2021)

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