Procedures to genotype problematic non-invasive otter (Lutra lutra) samples

Faecal DNA-based genetic survey of a relict Eurasian otter (Lutra lutra) population (Sila Massif, S Italy)

Faecal DNA-based genetic analysis is a suitable tool for assessing both population size and genetic diversity of threatened and elusive species. We applied microsatellite analysis and mtDNA sequencing for investigating the southernmost Italian (Sila Massif, Calabria Region) population of the Eurasian otter (Lutra lutra). This relict population, filed as extinct in the mid-1980s, is currently expanding but still quite isolated. On the two main rivers hosting otters permanently since 2014, we collected 47 spraints, out of which 24 (51.1%) were successfully genotyped (on average 2.0 alleles per locus). Thirteen individuals were identified: seven females and three males (sex identification success of 76.9%). Population size was assessed as 16 individuals (13–22), corresponding to a density of 0.15 (0.13–0.21) ind/km. Successfully amplified mtDNA samples (N = 16) confirmed the occurrence of a haplotype—H10—which had been previously reported only for Southern Italy, bringing new evidence of the unicity of the Italian otter population. Although density values complied with those reported for the core area of otter Italian range, the small size and genetic isolation of this population require special attention. To assist the ongoing re-colonisation of the Sila Massif, habitat management should aim to enhance fish availability and connectivity with the core area.

A Noninvasive Genetic Insight into the Spatial and Social Organization of an Endangered Population of the Eurasian Otter (Lutra lutra, Mustelidae, Carnivora)

The Eurasian otter is endangered in Italy, only surviving in southern river basins. The spatial and social structure of a population living at the border of the current range was explored through a noninvasive genetic study along 174 km of the Sangro river. Sampling was conducted in 2011 and 2012, collecting spraints and anal jellies at 62 marking sites. Samples were successfully genotyped at 13 nuclear microsatellites and the ZFX/ZFY locus for molecular sexing, resulting in 14 distinct genotypes (4 females, 2 possible females, 8 males), from 35 marking sites. Mean captures/recaptures rate was 3.8 captures/individual, with males being recaptured more frequently than females. Spatial overlap among individuals was analyzed through a linear regression model fitted against sibship categories and sex pairing. Nine out of the fourteen genotyped individuals belonged to three full-sib clusters, while five individuals had no full-sibs in the population. Full-sibs overlapped more than half-sibs, while male–male pairs showed significantly higher spatial overlap than both male–female and female–female pairs. Estimated mean density was 0.152 otters/km and 2.4 individuals/10 × 10 km grid cell. Accordingly, the 3440 grid cells of otter occurrence in Italy could likely host about 8000 otters, suggesting the current population has become larger than the minimum viable population size.

Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture-recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23-0.28 otter/km, or 1 otter/3.57-4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83-104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12-1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8-10 years post-reintroduction, including 13-21% genetic diversity loss, 84%-87% genetic effective population size decline, and rapid divergence from the source population (F ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non-invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.

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.

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.

Marking behaviour and census of Eurasian otters (Lutra lutra) in riverine habitats: what can scat abundances and non-invasive genetic sampling tell us about otter numbers?

Growing human-wildlife conflicts and legal conservation obligations increased the need for precise information on Eurasian otter (Lutra lutra) population parameters for species status assessment and wildlife management measures. Scat surveys have become the method of choice to monitor species distribution range, abundance and habitat use. Although methodological concerns exist, scat abundance is often used as main indicator for otter population estimates and trends. To evaluate whether scat counts serve as good proxy for otter densities in linear stream habitats, we modelled the relationship between old/fresh scat abundance and otter numbers on two spatial scales, including also seasonal effects. Actual otter densities and marking behaviour were ascertained by genotyping of otter faeces collected at 218 marking sites along 132.6 km of four salmonid streams. Otter densities in our study areas ranged from 0.16 to 0.28 otters per stream kilometre. The age of scats and the level of spatial scale were determining factors when evaluating the suitability of scat abundance as index for otter densities. Covering large parts of an otter’s territory, fresh scat abundance increased with otter density, irrespectively of season. On the spatial scale of single marking sites, the relationship was not well supported, and no relationship could be found when using old scats in the models. Otter marking behaviour and differences in marking site use intensity, as well as seasonal differences in traceability and accumulation of old scats were discussed to bias the relationship between scat abundance and otter numbers.

The effect of a major drainage divide on the gene flow of a semiaquatic carnivore, the Eurasian otter

Major drainage divides (separating the water flow draining to different seas) may significantly affect the dispersal, distribution, and genetic structure of semiaquatic animals. Assessing this effect is important for the proper management of both endangered and invasive riparian species. Here, I determined the fine-scale impact of the drainage divide between the Baltic Sea and the Black Sea drainage basins on the genetic structure and dispersal of the Eurasian otter (Lutra lutra) in the Bieszczady Mountains (Poland and Slovakia). I investigated the genetic structure of the otter population and assessed 3 alternative dispersal models using 6 landscape genetics methods. The analyses were based on 48 individual genotypes obtained from 622 fecal and gland secretion samples collected in 2008–2011. Results indicate that the major drainage divide is not a barrier to gene flow for this population. This was established by analyses of population genetic structure and confirmed by analysis of the spatial distribution of samples originating from closely related individuals. In line with these findings, the best-supported dispersal model assumed that otters migrate through mountain passes, away from streams, thus revealing that they are able to cross a drainage divide. The genetic structure of the population studied exhibits an isolation-by-distance pattern; however, the locations of several repeatedly recorded or closely related individuals revealed the occurrence of long-distance movements. Confirmation of the high mobility of otters and their ability to cross a major drainage divide ridge suggest that landscape obstacles and discontinuity of river network are unlikely to stop otter dispersal, gene flow, and recolonization of new areas.