The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach

Diet composition of wild columbiform birds: next-generation sequencing of plant and metazoan DNA in faecal samples

Accurate knowledge of a species' diets is fundamental to understand their ecological requirements. Next-generation sequencing technology has become a powerful and non-invasive tool for diet reconstruction through DNA metabarcoding. Here, we applied those methods on faecal samples of Common Woodpigeons Columba palumbus, European Turtle Doves Streptopelia turtur, and Stock Doves C. oenas to investigate their dietary composition. By applying primer pairs targeting both the ITS2 region of plant nuclear DNA and the mitochondrial COI region of metazoan DNA, we provide a complete picture of the food ingested and estimate the dietary overlap between the columbiform species during the breeding season. Animal DNA was present very rarely, and a diverse range of plants from the class Spermatopsida dominated the diet, with Asteraceae, Brassicaceae, Cucurbitaceae, Fabaceae, and Poaceae as the most frequently represented families. Generally, we detected a variability between species but also amongst individual samples. Plant species already known from previous studies, mainly visual analyses, could be confirmed for our individuals sampled in Germany and the Netherlands. Our molecular approach revealed new plant taxa, e.g. plants of the families Malvaceae for Woodpigeons, Lythraceae for Turtle Doves, and Pinaceae for Stock Doves, not found in previous studies using visual analyses. Although most of the plant species observed were of wild origin, the majority of cultivated plants found were present in higher frequencies of occurrence, suggesting that cultivated food items likely constitute an important part of the diet of the studied species. For Turtle Doves, a comparison with previous studies suggested regional differences, and that food items (historically) considered as important part of their diet, such as Fumitory Fumaria sp. and Chickweed Stellaria media, were missing in our samples. This indicates that regional variations as well as historic and current data on diet should be considered to plan tailored seed mixtures, which are currently proposed as an important management measure for conservation of the rapidly declining Turtle Dove.

Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains

Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.

Can the Eurasian otter (Lutra lutra) be used as an effective sampler of fish diversity? Using molecular assessment of otter diet to survey fish communities

The Eurasian otter Lutra lutra is a generalist carnivore that is widely distributed in many aquatic ecosystems. Based on its inherent attributes of opportunistic foraging behaviour and broad dietary range, it is naturally considered a potential sampler of the diversity of aquatic vertebrates. To test the ability and efficiency of otters as a diversity sampler, we used DNA metabarcoding to investigate the composition in vertebrates of the diet of otters that inhabit a forest stream area in northeast China. Twenty vertebrate prey taxa were detected in 98 otter spraints. Otter diet mainly comprised aquatic fishes (59.4%) and amphibians (39.0%). We also used traditional approaches to investigate fish communities at 60 sampling sites in the same area to determine the relationship between fish population composition in the environment and otter diet. The comparison revealed that 28 species of fish were distributed in this area, of which five are simultaneously detected in otter spraints. This indicates that molecular analysis of the diet of otters is not an ideal approach for investigating fish diversity, at least when using the 12SV5 primer pair. Based on a review of the available molecular research on otter diet, we conclude that the low species resolution may be due to the presence of many closely-related prey species in native habitats and lack of suitable barcodes. Considering the remarkable power of diet metabarcoding analysis in capturing elusive and rare species, it represents an approach that can compensate for the defects associated with fishing methods and we suggest that it can be used as an auxiliary means of measuring traditional fish diversity.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

Assessing the Diet of a Predator Using a DNA Metabarcoding Approach

The diet of top predators is vital information needed to determine their ecological function and for their conservation management. However, the elusive habit and low population density of many predators constrains determination of their diets. While the morphological identification of scat contents is the traditional method, DNA metabarcoding has lately proven a more efficient and accurate method of identifying prey taxa. We applied DNA metabarcoding to analyzing the diet of the Eurasian otter (Lutra lutra), a top predator in freshwater ecosystems, using 12S and 16S rRNA mitochondrial primers target vertebrate prey. Diet did not vary among different data removal thresholds of 0.1, 1, 3, and 5%, comprising fishes (>90%), amphibians and birds (>2%), and occasionally mammals (<2%). Both 12S and 16S primers revealed similar otter diets, indicating that a single set of primers with a higher threshold is cost-effective for detecting the main prey taxa. Using 12S primers and a 5% threshold, we found no seasonal variation of otter diet in the Tangjiahe National Nature Reserve. A different prey community was found outside the reserve, which resulted in different prey composition for otters. However, prey taxon richness was not different between otters in- and outside the reserve. Otters preferred Schizothorax spp., the largest-sized fish species in the reserve, whereas they mainly preyed on Triplophysa bleekeri, a small-sized fish species, outside the reserve. Otters’ flexible feeding strategy reflect their high adaptability. However, greater human disturbance outside the reserve may present significant challenges to otters by altering prey communities and reducing prey profitability. Combining fecal DNA metabarcoding and local fish survey will provide opportunities for more detailed studies on the impact of different levels of human disturbances on prey communities and otters.

Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of F_ST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised F_ST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.

A barcoding-based scat-analysis assessment of Eurasian otter Lutra lutra diet on Kinmen Island

While it is well known that Eurasian otters principally feed on fishes and crustaceans, their detailed diet taxonomies are not fully understood. This is partly due to their nocturnal behavior and the limited resolving power of traditional morphological identification from scat. A suitable, reliable molecular method for diet studies is therefore needed.I performed a series of Sanger-sequencing reactions, utilizing nine primer sets for Eurasian otter diet research. These are mainly based on the barcoding concept to determine the taxonomic composition of spraints. The primer sets target different types of animals, amplifying each separately. This procedure was used to detect the prey contents of 64 spraint samples collected from Kinmen Island. Through high-resolution gel electrophoresis and sequencing, it was evident that PCR products could be successfully amplified by the different primer sets and from spraint samples comprising multiple prey species.Extracted DNA from all spraint samples was PCR-amplified with 9 primer sets. In total, 16 prey types were identified across all 64 samples. Fourteen were identified at the species level.The aim of this study was to develop and apply a novel diet research method to Eurasian otters. Eight of the primers are universal primers designed for COI segments of different animal groups, and one primer set was designed specifically for tilapia groups. This method can be applied to study the diets of not only Kinmen Eurasian otter populations, but also other Eurasian otter populations and other small carnivorous animals.

Social organization of otters in relation to their ecology

Otter species are known to fluctuate intraspecifically from a solitary lifestyle to group-living arrangements. By examining what is known about habitat use and foraging style in otters of 13 different species, based on 93 studied sites, we assessed (1) the relationship between social habits and preferred habitats, (2) the relationship between species and prey preferences, and (3) the effect of predator avoidance on their social organization in order to assess the socio-ecological factors influencing otters. Females remain the core of their social stability. We show the major influence of habitats and feeding strategies (i.e. socio-ecology) of otters. The different species of solitary otters most often inhabit linear environments, such as freshwater ecosystems or wave-exposed marine coasts, and their habitat is often subject to disturbances that fragment their functional continuity. Social otters are more often found in extensive habitats with high plant cover, regular food resources and in areas with large predators compared to solitary species. The maintenance of regular resources and the fact that the main trophic resources are replenished rapidly might be determining factors driving sociality. Group-living and bachelor congregations among otters can also respond to pressure from large predators. This suggests that foraging, habitat use and the presence of large predators may be the drivers of sociality in otters. We conclude that most otters have a greater social potential than previously assumed, which is confirmed by their various vocalizations recently described.

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