Biology subjects

Watson, H. V.

Publications and source records attributed to Watson, H. V..

4 recordsLinked to original sources

bioRxiv2020

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals. eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.

molecular biology↗

bioRxiv2020

Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments

The European eel Anguilla anguilla (eel hereafter) is critically endangered and has a catadromous lifecycle, which means adult eels that live in pumped catchments must pass through pumps during their downstream spawning migration. We are currently lacking detailed site-by-site eel distribution information in order to estimate the overall impact of individual pumping stations on eel escapement, and as such lack the data to enable informed prioritisation of pumping station management and targeted mitigation. In this study, we investigated whether environmental DNA (eDNA) metabarcoding can provide increased detection sensitivity for eel and fish community structure in highly regulated pumped catchments, when compared directly to current standard practice fish survey protocols (seine netting/electric fishing). Eels were detected in 14/17 sites (82.4%) using eDNA metabarcoding in contrast to 3/17 (17.6%) using traditional catch methods. Additionally, when using eDNA monitoring species richness was higher in 16/17 sites (94.1%) and site occupancy [≥] traditional methods for 23/26 of the fish species detected (88.5%). While eDNA methods presented significantly higher average species richness and species site occupancy overall, eDNA and Catch methods were positively correlated in terms of species richness and site occupancy. We therefore found that eDNA metabarcoding was a high sensitivity method for detecting eels in pumped catchments, while also increasing the detection of overall fish community structure compared to traditional catch methods. In addition, we highlight how eDNA monitoring is especially suited to increased detection of particular species, with traditional methods sufficient for others. This high sensitivity, coupled with the ability to sample multiple sites in a short time frame suggests eDNA metabarcoding could be an invaluable tool when prioritising pumping station management.

ecology↗

bioRxiv2020

DNA metabarcoding shows strong potential for investigating diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)

In the UK, the native European otter (Lutra lutra) and invasive American mink (Neovison vison) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in decline due to population control and probable interspecific interaction with the otter. We explored the potential of DNA metabarcoding for investigating diet and niche partitioning between these mustelids. Otter spraints (n = 171) and mink scats (n = 19) collected from three sites (Malham Tarn, River Hull, and River Glaven) in northern and eastern England were screened for vertebrates using high-throughput sequencing. Otter diet mainly comprised aquatic fishes (81.0%) and amphibians (12.7%), whereas mink diet predominantly consisted of terrestrial birds (55.9%) and mammals (39.6%). The mink used a lower proportion (20%) of available prey (n = 40 taxa) than the otter, and low niche overlap (0.267) was observed between these mustelids. Prey taxon richness of mink scats was lower than otter spraints, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter and mink consumed different prey taxa). Considering otter diet only, prey taxon richness was higher in spraints from the River Hull catchment, and beta diversity of prey communities was driven by taxon turnover (i.e. the otter consumed different prey taxa at each site). Studies using morphological faecal analysis may misidentify the predator as well as prey items. Faecal DNA metabarcoding can resolve these issues and provide more accurate and detailed dietary information. When upscaled across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink.

ecology↗

bioRxiv2018

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non-invasive biodiversity monitoring. In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of eDNA in two ponds following the introduction and removal of two rare fish species. When two rare species were introduced and kept at a fixed location in the ponds, eDNA concentration (i.e., proportional read counts abundance) of the introduced species typically peaked after two days. Thereafter, it gradually declined and stabilised after six days. These findings are supported by the highest community dissimilarity of different sampling positions being observed on the second day after introduction, which then gradually decreased over time. On the sixth day, there was no longer a significant difference in community dissimilarity between sampling days. The introduced species were no longer detected at any sampling positions 48 hrs after removal from the ponds. The eDNA signal and detection probability of the introduced species were strongest near the keepnets, resulting in the highest community variance of different sampling events at this position. Thereafter, the eDNA signal significantly decreased with increasing distance, although the signal increased slightly again at 85 m position away from the keepnets. Collectively, these findings reveal that eDNA distribution in lentic ecosystems is highly localised in space and time, which adds to the growing weight of evidence that eDNA signal provides a good approximation of the presence and distribution of species in ponds. Moreover, eDNA metabarcoding is a powerful tool for detection of rare species alongside more abundant species due to the use of generic PCR primers, and can enable monitoring of spatial and temporal community variance.

molecular biology↗