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

Abstract

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 scaled up across multiple habitat types, DNA metabarcoding should greatly improve future understanding of resource use and niche overlap between the otter and mink.

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, 2004Wasser et al, , 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.…”

Assessing the Diet of a Predator Using a DNA Metabarcoding Approach

“…If only one predator was detected, the sample was assigned to this species. If multiple predators were present, the sample was assigned to the species with >90% of the total predator reads (Harper et al, 2020). Scats not identified to otters were excluded from subsequent analysis.…”

“…DNA metabarcoding has its own shortfalls. For example, it cannot provide information on the size or life stage of prey taxa (Harper et al, 2020), and data quality largely depends on the accuracy and wide coverage of DNA reference databases (Nielsen et al, 2018;Traugott et al, 2020). Different primers may focus on different taxa and using a single universal primer influences what prey species can be identified by this method (Da Silva et al, 2019).…”

“…Analyses of otter diet have traditionally been based on morphological identification of undigested prey remains in spraints, usually at a higher taxonomic level than the prey species (Kruuk et al, 1994;Remonti et al, 2010;Reid et al, 2013). Recently, otter researchers have turned to DNA metabarcoding to obtain more accurate prey information, e.g., Eurasian otters (Thalinger et al, 2016;Hong et al, 2019;Kumari et al, 2019;Buglione et al, 2020;Harper et al, 2020;Marcolin et al, 2020;Jang-Liaw, 2021), and giant otters (Pteronura brasiliensis) (Quéméré et al, 2021). In China, the once widespread Eurasian otter populations declined nationwide between the 1950s and 1980s because they were widely harvested (Li and Chan, 2018).…”

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

“…(Janečka et al 2008;Wasser et al 2004;Phoebus et al 2020). Fecal sampling has also been used to identify the contents of animal diets, such as in rodents, hares, and even river otters (Cloutier et al 2019;Buglione et al 2018;Elliott et al 2020;Harper et al 2020), but focused primarily on community identification, and in the context of the host diet rather than the identity of community members. These studies show how powerful and informationally rich fecal sampling can be for population distribution studies While these previous studies focused on macrofauna, this same approach could be used for consumed fungi, which are often used as food sources for many metazoan taxa ranging from fungivorous arthropods to opportunistic small mammals and even many great apes (Yamashita et al 2015;Pyare and Longland 2001;Hanson, Hodge, andPorter 2003, Elliott et al 2020).…”