Biology subjects

Quemere, E.

Publications and source records attributed to Quemere, E..

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↗

bioRxiv2024

When does a parasite become a disease? eDNA unravels complex host-pathogen dynamics across environmental stress gradients in wild salmonid populations

Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasites infective stages, as well as the hosts ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modeling at a regional scale, we uncovered the biotic and abiotic drivers of a lethal infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water--i.e., the propagule pressure-- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts--i.e., proxies for disease emergence--were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by compromising the hosts ability to fight the parasite. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on disease emergence.

ecology↗

bioRxiv2018

RAD-sequencing for estimating GRM-based heritability in the wild: a case study in roe deer

Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the SNP calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7000). GRM-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP dataset. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.

genomics↗