The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

Duhamet, Agnès; Albouy, Camille; Marques, Virginie; Manel, Stéphanie; Mouillot, David

doi:10.1002/ece3.9672

Cited by 6 publications

(3 citation statements)

References 129 publications

(146 reference statements)

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“…Arguably, any detected effect of lacking reference data may have been less pronounced by using another, or multiple primer pairs. For example, some studies suggest that the MiFish primer set provides poor taxonomic resolution and a low success rate in species recovery (Jackman et al, 2021), especially for endemic species (Duhamet et al, 2023) while other studies highlight its usefulness in ecosystem conservation strategies, enhanced taxonomic resolution, and efficient fish biodiversity monitoring (Miya et al, 2015;Schroeter et al, 2020;Zhu & Iwasaki, 2023). Furthermore, our primer evaluations with the more recently released software GAPeDNA (Marques et al, 2021) (released after our experiments were completed) show that, for example, the "Fish 16S" primer set (McInnes et al, 2017) would have covered 249 instead of the 119 New Zealand marine fish species covered by our MiFish 12S data (Table S1).…”

Section: Osmeriformesmentioning

confidence: 99%

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Czechowski,

de Lange,

Heldsinger

et al. 2024

Environmental DNA

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Effective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA (eDNA) by metabarcoding holds promise to achieve this relatively easily. However, taxonomy‐focused eDNA surveys need suitable molecular reference data, which are often lacking, particularly at the species level and for remote locations. To evaluate the comparability of environmental DNA surveys and traditional surveys in a real‐life case study in a marine area of high conservation value, we conducted a biodiversity survey of the fish in remote and pristine Te Wāhipounamu/Fiordland (Aotearoa/New Zealand), incorporating multiple data sources. We compared eDNA‐derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as eDNA. We also cross‐referenced both eDNA and BRUV data against literature and the Ocean Biodiversity Information System (OBIS), with literature and OBIS data representing a summary of multiple traditional surveying approaches. In total, we found 116 fish species in our study area. Environmental DNA detected 43 species; however, only three of those species overlap with species known from the literature, OBIS, or our BRUV analyses. A total of 61 fish species were known from the region from the literature, while OBIS listed 28 species, and our BRUV analyses picked up 26 species. BRUV data coincided more strongly than eDNA data with literature and OBIS data. Twenty of the 26 species detected by BRUV were known from literature and OBIS. We argue that limitated DNA reference databases are the main cause of this discrepancy, and our results indicate that eDNA of rare and endangered species can be detected if matching reference data were available. Environmental DNA analyses can only identify species present among reference data and with relaxed taxonomic assignment parameters may converge on relatives of detected species if the actually existing species themselves are missing among reference data. However, the high number of species detected by our eDNA analyses confirms that eDNA could be a powerful tool for biodiversity surveys if suitable investments in local reference databases were made.

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Section: Osmeriformesmentioning

confidence: 99%

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Czechowski,

de Lange,

Heldsinger

et al. 2024

Environmental DNA

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show abstract

“…Meanwhile, it worked out and successfully discriminated some fish species in other sites (Figure 5). A study has also showed that Teleo primer covered fewer species than MiFish-U could (Duhamet et al 2023). Despite more orders and families detected using MiFish-U primer, a note remains in which Teleo primer could complement the MiFish-U.…”

Section: Comparison Between Mifish-u and Teleo Primermentioning

confidence: 99%

“…The evaluation of five primer pairs for eDNA metabarcoding of Central European fish species based on mock communities discovered differences in primer efficiency depending on the species and primer preferential species in different fish (Macher et al 2023). Furthermore, the genetic coverage of both primers by depth and ocean was assessed, highlighting potential differences in their performance (Duhamet et al 2023). Using different primer pairs can lead to variations in amplification efficiency, taxonomic coverage, and preferential species, potentially contributing to inconsistencies in eDNA analysis results.…”

Section: Comparison Between Mifish-u and Teleo Primermentioning

confidence: 99%

Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia

AMBENG,

IQRAM,

LITAAY

et al. 2024

Biodiversitas

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Abstract. Ambeng, Iqram M, Litaay M, Hasyim Z, Moka WJC, Tinungki GM. 2024. Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia. Biodiversitas 25: 819-828. A newly designated geopark by UNESCO, Maros-Pangkep Global Geopark, South Sulawesi, Indonesia owns great geodiversity, exceptional cultural heritage, and high biodiversity. However, the global biodiversity crisis that has hit the earth might also occur in Maros-Pangkep river systems, potentially threatening endemic freshwater fish and all other biota. It has been reported that there is high pressure on the environment along the watershed in the Maros-Pangkep rivers, including a high sedimentation rate downstream, which is linked to extreme erosion upstream and could eventually affect fish populations such as endemic ones. This should prompt a call for the authorities to build a strategy for monitoring and documenting aquatic biota such as fish to preserve biodiversity. Environmental DNA (eDNA) could be considered a method for monitoring fish species based on the DNA traces they shed in the water. Hence, this study aims to use eDNA to survey fish biodiversity in several rivers in the Maros-Pangkep Global Geopark and compare the result against the traditional gillnet method. The results showed that using two methods, 29 fish species in 19 families and 15 orders were obtained from the three rivers. Despite the majority of detected species, 25 species, as the result of using eDNA, 4 species were only detected using a traditional method which eDNA failed to identify. Among those species, several endemic and non-native species were successfully identified by either one or both methods. This could eventually be a suggestion for responsible authorities in biodiversity conservation to combine both approaches to monitor and conserve local biodiversity.

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New Technologies for Monitoring and Upscaling Marine Ecosystem Restoration in Deep-Sea Environments

Aguzzi,

Thomsen,

Flögel

et al. 2024

Engineering

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The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 6 publications

References 129 publications

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia

New Technologies for Monitoring and Upscaling Marine Ecosystem Restoration in Deep-Sea Environments

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