Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago

Abstract

This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Elasmobranchs’ metabarcoding requires a pragmatic approach to reach its promises

“…Concerning the samples, the authors would like to express their gratitude to the ICMBio Fernando de Noronha for their help and their support. Liu et al, 2022), protect on ice until filtering (Simpfendorfer et al, 2016) and filter the samples as soon as possible (Barnes et al, 2014) Incidental amplification of non-target DNA Further research into the primers used (Dunn et al, 2022) Capturing elusive species To collect water as much as logistically possible (Bessey et al, 2020); but good results with 4 L (Bakker et al, 2017;Boussarie et al, 2018;and Mariani et al, 2021) Capturing migratory species To sample seasonally (Postaire et al, 2020) Capturing benthic batoids species To collect sediment environments (Ip et al 2021) and/or to sample replications from varying standardized depths (Marwayana et al 2021) Studying heterogeneous ecosystems To sample horizontally, varying across habitats (Jeunen et al, 2019;West et al, 2020;Marwayana et al, 2021) General recommendation To use a regional-specific reference library Box 2: Compilation of Elasmobranchs' Metabarcoding studies.…”

“…The metabarcoding approach has been proven to be an efficient tool for marine monitoring and ecosystem health assessment (Thomsen et al, 2012; Leray and Knowlton, 2015). And, recent studies provided a proof-of-concept that sharks, rays, and their relatives can be monitored using eDNA metabarcoding (Fraija-Fernández et al, 2020; Ip et al, 2021; Mariani et al, 2021; Marwayana et al, 2021; Monuki et al, 2021; Liu et al, 2022; Dunn et al, 2022).…”

“…Metabarcoding is often recommended as a cost-effective and easily replicated technique that could potentially be the answer to this and other monitoring gaps (Miya et al, 2015; Marwayana et al, 2021; Monuki et al, 2021). However, the elasmobranchs’ metabarcoding needs validation in realistic situations before being guaranteed as a routine monitoring tool.…”

Metabarcoding the marine environment: from single species to biogeographic patterns

“…With much of the biodiversity in the Coral Triangle under threat, management and conservation decision making requires a better understanding of the spatiotemporal patterns of biodiversity. In this issue, Marwayana et al (2021) sampled across the Indonesian Archipelago and demonstrated that 12S rRNA metabarcoding of eDNA could detect regional patterns of fish biodiversity, such as distinguishing between Indian and Pacific Ocean communities. However, they cite the lack of a complete reference database as a significant obstacle to assigning OTUs to species, which likely led to low rates of assignment for some sites.…”

A CONTRAST PATTERN OF REEF FISH SPECIES DIVERSITY AND DISTRIBUTION USING ENVIRONMENTAL DNA (eDNA) METABARCODING IN LONGITUDINAL DISTANCE FROM JAKARTA BAY

“…In the other hand, species in economically family are observed on higher number (i.e Carangidae, Scrombidae, Serranidae, and Lutjanidae). A study by Marwayana et al, (2021) found that eDNA metabarcoding analysis was able to capture a spectrum of fish species that were rarely recorded when using the visual census method.…”