Biology subjects

Covain, R.

Publications and source records attributed to Covain, R..

3 recordsLinked to original sources

bioRxiv2026

Variable performances of commercial eDNA inventories challenge their use for surveying stream fish communities

1. Environmental DNA (eDNA) metabarcoding of water samples is increasingly used to detect fish species in streams. Several studies have concluded that it can outperform traditional inventory methods and recommend using it at large scales for fish-based ecological assessments. However, there is no standard protocol that can guarantee sufficient detection rates and repeatability, despite companies offering an extensive range of analyses. 2. We compared eDNA metabarcoding performed by four companies. Following their guidelines, samples were collected in a small tropical stream in the Maroni River (French Guiana) that hosts a species-rich fish community. We compared their inventories to each other and to a list of species captured during an extensive fish inventory performed immediately after sampling eDNA, as well as to current data on the species distributions. 3. The number of species detected by eDNA metabarcoding ranged from 5 to 48 among the companies, but these inventories contained many inaccuracies. All companies combined, 63 species were detected, of which 10 (16%) had never been reported in the Maroni River. The extensive inventory identified 50 species in the local fish community, of which 16-46 were not detected by eDNA metabarcoding (i.e. false negative detection rate of 32%-92% among the companies). 4. Reanalysis of raw sequencing data decreased differences among companies greatly, highlighting the importance of using a comprehensive and accurate DNA barcode database to assign species. Dissimilarity indices, calculated to compare the local fish community (based on presence/absence or fish catches) to eDNA detection, revealed large differences regardless of the company. 5. Summary and applications. The large percentage of species not detected by eDNA metabarcoding of water samples could strongly bias fish-diversity inventories in streams that host species-rich communities. This issue is not well documented in the literature, and we recommend that similar studies in the future focus on other stream contexts. The large differences between commercial eDNA inventories and the local fish community challenge the use of eDNA metabarcoding for fish-based ecological assessments of streams. The variable performance of eDNA companies indicates the need for a standard protocol and access to a comprehensive DNA database before beginning large-scale eDNA programmes. Highlights- eDNA metabarcoding of water samples is widely used to detect species in streams - Detection performances of 4 private companies were compared to an exhaustive fish inventory - The number of undetected species varies from 32 to 92% depending on the company - Such discrepancies challenge the use of eDNA for fish-based ecological assessments

ecology↗

bioRxiv2021

Western Amazon was a center of Neotropical fish dispersal, as evidenced by the continental-wide time-stratified biogeographic analysis of the hyper-diverse Hypostomus catfish

The Amazon is probably the most diverse realm on Earth, and is considered to be the primary source of diversity and a center of dispersal for Neotropical terrestrial organisms. Yet, the assumption that the Amazon basin is a primordial place of fish species origination and dispersal into other drainages still need to be tested. We addressed this issue by inferring a time-stratified biogeographic history and reconstructing the ancestral habitat preference of Hypostomus, a continentally widespread and species-rich Neotropical genus. We found that Hypostomus emerged in the Western Amazon ([~]14.7 Ma), when the Western Amazon River was flowing northwards and disconnected from the Eastern Amazon. We show that dispersal events in the first half of Hypostomus evolution occurred from the Western Amazon into adjacent basins, initiating its Neotropical radiation. The ancestral preferred habitat consisted in small rivers with running waters, a predominant habitat in river headwaters. Because of strong niche conservatism in the early evolution of Hypostomus, we suggest that most of the out-of-Western-Amazon dispersal occurred via headwater captures. The radiation of Hypostomus was further promoted by major reconfigurations of river basins, which opened dispersal opportunities into new drainages. Diversification in habitat preference coincided with colonization of basins already occupied by congenerics, indicative of niche shifts triggered by inter-specific competition and species coexistence. By analyzing the evolutionary history of Hypostomus, we show that Western Amazon was the main center of fish dispersal in the Neotropical Region from Middle Miocene to the present, supporting the cradle hypothesis of fish origination and dispersal.

evolutionary biology↗

bioRxiv2021

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

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 to include eDNA 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 Earths 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.

ecology↗