Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison)

Abstract

<jats:title>Abstract</jats:title><jats:p>In the UK, the native European otter (<jats:italic>Lutra lutra</jats:italic>) and invasive American mink (<jats:italic>Neovison vison</jats:italic>) have experienced parallel 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 (<jats:italic>n</jats:italic> = 171) and mink scats (<jats:italic>n</jats:italic> = 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 (<jats:italic>n</jats:italic> = 40 taxa) than the otter, and low niche overlap (0.267) was observed between these mustelids. Mink scats possessed lower prey taxon richness 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 greatest 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.</jats:p>

On the origin of feces: Fungal diversity, distribution, and conservation implications from feces of small mammals

“…Previous studies have used DNA sequencing of feces to monitor the population of threatened and elusive animals such as snow leopards and grizzly bears, and more recently to identify populations of African elephants to aid in identifying illegal ivory trading routes (Janečka et al, 2008; Phoebus et al, 2020; Wasser et al, 2004, 2015). Fecal sampling has also been used to identify the contents of animal diets, such as in rodents, hares, and even river otters (Buglione et al, 2018; Cloutier et al, 2019; Elliott et al, 2020; Harper et al, 2020), but has focused primarily on community identification, and in the context of the host diet rather than the ecology of community members.…”

Evaluating the Efficiency of DNA Metabarcoding to Analyze the Diet of Hippocampus guttulatus (Teleostea: Syngnathidae)

“…This approach, therefore, virtually enables the identification of all organisms contained in a sample [2,11]. Although it cannot provide information on prey size or life cycle stage nor it is immune to prey taxa retention due to differential digestion and gut transition times, DNA metabarcoding perpetuates non-invasiveness, offers high taxonomic resolution, and has high sensitivity towards soft, highly degraded, and rare prey species [12][13][14]. Since its inception, DNA metabarcoding has been successfully applied in dietary studies of many species, including fish, and provided encouraging results [12,15,16].…”