The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

Abstract

Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth’s hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities

“…Overall, FARMS are a simple, standardized, broadly accessible 2022, no other specimens of P. laurae had been observed or collected (Baldwin et al, 2018;Tornabene et al, 2016). This suggests that deploying FARMS in undersampled habitats such as deep reefs may yield a additional taxonomic records that help us gain a better understanding of cryptobenthic fish diversity and distribution patterns, while also yielding critically important specimens and tissue samples that can support emerging molecular survey methods (de Santana et al, 2021;Gold et al, 2021).…”

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

“…eDNA studies carried out so far on the Neotropical ichthyofauna [ 25 – 28 ], although limited by the size of the reference database for the mitochondrial gene 12S used, have faced varying degrees of success. Jackman et al (2021) identified 84 molecular taxonomic units (MOTU), of which only 4 to the species level (1.6%), out of the 258 fish species detected using traditional sampling methods in the Adolpho Ducke Forest Reserve near Manaus in the Brazilian Amazon.…”

“…Very few eDNA studies were carried out so far on the ichthyofauna of the Neotropics (e.g. [ 25 – 28 ]), and even fewer in the most species-rich basin of the Neotropics: the Amazon basin [ 27 , 28 ]. All these studies were limited by the size of the reference database.…”

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

“…Whichever approach is used, they all ultimately rely on the accuracy and completeness of a reference database for subsequent taxonomic assignment (Dugal et al, 2022; Jackman et al, 2021). Reference databases therefore should be a major consideration of any metabarcoding study as they underpin the successful and accurate taxonomic assignments (de Santana et al, 2021; Rodríguez‐Ezpeleta et al, 2021). Ideally, these databases consist of verified barcodes, including taxa known to occur in the study area (Taberlet et al, 2007).…”