Improved genotyping and sequencing success rates for North American river otter (Lontra canadensis)

Identification of three Asian otter species (Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata) using a novel noninvasive PCR‐RFLP analysis

Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth‐coated otter, Asian small‐clawed otter, and hairy‐nosed otter have been reliably reported as residents. We designed a replicable and cost‐efficient PCR‐RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR‐RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D‐loop region and a 300‐bp fragment of the mt ND4 gene using primer sets TanaD, TanaD‐Mod, and OTR‐ND4, respectively. Amplification products were digested with restriction enzymes to generate species‐specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD‐Mod primer amplifying DNA from all 33 spraints. TanaD and OTR‐ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD‐Mod provided the expected species‐specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR‐ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR‐ND4 primer–enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD‐Mod (455 USD). We suggest the use of both OTR‐ND4 and TanaD‐Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR‐RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition and increase genotyping success. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii, California, US, and Morafka's desert tortoise, G. morafkai, Arizona, US) and the common chuckwalla (Sauromalus atar) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, was 15% for the study of Agassiz's desert tortoise and for the study of 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study indicates that genotypes can successfully be obtained from swabs of scat from herbivorous reptiles collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for the genetic identification of individuals from non-invasive samples.

Highly contaminated river otters (Lontra canadensis) are effective biomonitors of environmental pollutant exposure

River otters (Lontra canadensis) are apex predators that bioaccumulate contaminants via their diet, potentially serving as biomonitors of watershed health. They reside throughout the Green-Duwamish River, WA (USA), a watershed encompassing an extreme urbanization gradient, including a US Superfund site slated for a 17-year remediation. The objectives of this study were to document baseline contaminant levels in river otters, assess otters' utility as top trophic-level biomonitors of contaminant exposure, and evaluate the potential for health impacts on this species. We measured a suite of contaminants of concern, lipid content, nitrogen stable isotopes (δ¹⁵N), and microsatellite DNA markers in 69 otter scat samples collected from twelve sites. Landcover characteristics were used to group sampling sites into industrial (Superfund site), suburban, and rural development zones. Concentrations of polychlorinated biphenyls (PCBs), polybrominated diphenyl ether flame-retardants (PBDEs), dichlorodiphenyl-trichloroethane and its metabolites (DDTs), and polycyclic aromatic hydrocarbons (PAHs) increased significantly with increasing urbanization, and were best predicted by models that included development zone, suggesting that river otters are effective biomonitors, as defined in this study. Diet also played an important role, with lipid content, δ¹⁵N or both included in all best models. We recommend river otter scat be included in evaluating restoration efforts in this Superfund site, and as a potentially useful monitoring tool wherever otters are found. We also report ΣPCB and ΣPAH exposures among the highest published for wild river otters, with almost 70% of samples in the Superfund site exceeding established levels of concern.

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.

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.

The Gut Microbial Community Structure of the North American River Otter (Lontra canadensis) in the Alberta Oil Sands Region in Canada: Relationship with Local Environmental Variables and Metal Body Burden

The Alberta Oil Sands Region in Canada is home to one of the largest oil bitumen deposits in the world. The North American river otter (Lontra canadensis) is a top predator with a small home range and is sensitive to disturbances; it has been designated as a sentinel species for the potential impacts of the natural resource exploitation on freshwater ecosystems in the Alberta Oil Sands Region. With an increasing interest in noninvasive biomarkers, recent studies suggest that gut microbiota can be used as a potential biomarker of early biological effects on aquatic wildlife. The goal of the present study was to determine the river otter gut microbial structure related to environmental variables characterizing mining activities and metal body burden. We obtained 18 trapped animals from and surrounding the surface mineable area of the Alberta Oil Sands Region. The gut microbial community structure was characterized using high-throughput sequencing of 16S rRNA gene amplicon analyses. Trace metal concentrations in the liver were measured by inductively coupled plasma-mass spectrometry. Our study revealed that the gut bacteria of river otters in the Alberta Oil Sands Region clustered in 4 groups dominated by Peptostreptococcaceae, Carnobacteriaceae, Enterobacteriaceae, Clostridiaceae, and Nostocaceae. We show that arsenic, barium, rubidium, liver-body weight ratio, and δ¹⁵ N were associated with each cluster. When comparing affected versus less affected sites, we show that river otter gut bacterial community and structure are significantly related to trophic level of the river otter but not to Alberta Oil Sands Region mining activities. Our study reveals that the gut bacterial dynamics can provide insights into the diet and habitat use of river otters but that more work is needed to use it as a pollution biomarker. Environ Toxicol Chem 2020;39:2516-2526. © 2020 SETAC.