Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring

Abstract

Aim DNA metabarcoding has great potential to improve biomonitoring in island's marine ecosystems, which are highly vulnerable to global change and non‐indigenous species (NIS) introductions. However, the depth and accuracy of the taxonomic identifications are mainly dependent on reference libraries containing representative and reliable sequences for the targeted species. In this study, we evaluated the gaps in the availability of DNA sequences and their accuracy for macroinvertebrates inhabiting Macaronesia's shallow marine habitats. Location Macaronesia (Azores, Madeira, Selvagens, Canaries). Methods Checklists of marine invertebrates occurring above 50 m depth were compiled using public databases and published checklists. The availability of cytochrome c oxidase subunit I (COI) and 18S rRNA (18S) gene sequences was verified in BOLD and GenBank. Finally, COI data were audited to check the congruence between morphospecies and Barcode Index Numbers (BINs). Results The taxonomic coverage of different phyla was greater for COI but unbalanced and variable among archipelagos. NIS were better represented in genetic databases (up to 73% and 59%, for COI and 18S, respectively) than native species (up to 47% and 31%, for COI and 18S, respectively). NIS displayed a higher number of discordant records, and native species, a higher quantity of cases of multiple BINs. Notably, DNA sequences generated from specimens collected from Macaronesia were found in less than 10% of the species. Projection of the rates of accretion of DNA sequences suggests that decades will be needed to complete these reference libraries. Main conclusions The level of completion of reference libraries for Macaronesia's marine macroinvertebrates is generally poor. Without a solid effort to speed up the production of sequence data (i.e. generate more DNA barcodes), the ability to employ DNA‐based biomonitoring of such vulnerable fauna is compromised. The high levels of suspected hidden diversity further deepen the expected gaps and reinforce the vulnerability of this endemism‐rich fauna.

Global gap-analysis of amphipod barcode library

“…40% of amphipod species possess barcodes ( Leite et al, 2020 ; Múrria et al, 2020 ). Hestetun et al (2020) conducted a barcode library gap-analysis of the benthic macrofauna of one region of the North Sea, which indicated the barcode coverage varying from 42.4% to 61% (depending on the calculation method) while Vieira et al (2021) found that in Macaronesia 34.2% to 72.6% of macroinvertebrate species have barcode representation with much better coverage of non-indigenous taxa in comparison to the native ones. This indicates that for smaller subset of taxa and specified geographic region it is much easier to produce good barcode coverage.…”

“…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 although 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 ).…”

“…The use of DNA-barcoding may speed up the identification process, but it will only succeed if the barcode library is well-established and robust. Recent gap-analyses of the barcode libraries in aquatic European environments showed very large differences in the coverage between different taxonomic groups and geographic regions ( Weigand et al, 2019 ; Feio et al, 2020 ; Hestetun et al, 2020 ; Leite et al, 2020 ; Vieira et al, 2021 ). These studies used species lists restricted to particular geographic regions or chosen taxonomic groups.…”

Peer Review #1 of "Global gap-analysis of amphipod barcode library (v0.1)"

“…The use of DNA-barcoding may speed up the identification process, but it will only succeed if the barcode library is well-established and robust. Recent gapanalyses of the barcode libraries in aquatic European environments showed very large differences in the coverage between different taxonomic groups and geographic regions (Weigand et al, 2019;Feio et al, 2020;Hestetun et al, 2020;Leite et al, 2020;Vieira et al 2021). These studies used species lists restricted to particular geographic regions or chosen taxonomic groups.…”

Peer Review #2 of "Global gap-analysis of amphipod barcode library (v0.1)"

“…Recent studies indicate that although 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;Feio et al, 2020;Hestetun et al, 2020;Leite et al, 2020;Múrria et al, 2020;Vieira et al 2021).…”