Evaluating river otter demography using noninvasive genetic methods

Nutritional ecology of a prototypical generalist predator, the red fox (Vulpes vulpes)

Generalist species, which exploit a wide range of food resources, are expected to be able to combine available resources as to attain their specific macronutrient ratio (percentage of caloric intake of protein, lipids and carbohydrates). Among mammalian predators, the red fox Vulpes vulpes is a widespread, opportunistic forager: its diet has been largely studied, outlining wide variation according to geographic and climatic factors. We aimed to check if, throughout the species' European range, diets vary widely in macronutrient composition or foxes can combine complementary foods to gain the same nutrient intake. First, we assessed fox's intake target in the framework of nutritional geometry. Secondly, we aimed to highlight the effects of unbalanced diets on fox density, which was assumed as a proxy for Darwinian fitness, as assessed in five areas of the western Italian Alps. Unexpectedly, the target macronutrient ratio of the fox (52.4% protein-, 38.7% lipid- and 8.9% carbohydrate energy) was consistent with that of hypercarnivores, such as wolves and felids, except for carbohydrate intakes in urban and rural habitats. The inverse relation between density and the deviation of observed macronutrient ratios from the intake target suggests that fox capability of surviving in a wide range of habitats may not be exempt from fitness costs and that nutrient availability should be regarded among the biotic factors affecting animal abundance and distribution.

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.

Microsatellite mutation frequencies in river otters (Lontra Canadensis) from the Athabasca Oil Sands region are correlated to polycyclic aromatic compound tissue burden

Mining activities in the Athabasca oil sands region (AOSR) have contributed to an increase of polycyclic aromatic compounds (PACs) locally. However, many PACs found in the AOSR, and the combined effects of PAC mixtures have not been evaluated for genotoxicity in wildlife. Here, we examine whether mutation frequencies in AOSR river otters are correlated to PAC tissue burdens. We used single-molecule polymerase chain reaction (SM-PCR) to measure the mutant frequency of unstable DNA microsatellite loci in the bone marrow of wild river otters (n = 11) from the AOSR. Microsatellite mutation frequencies were regressed against liver PAC burden (total, low/high molecular weight [LMW/HMW], and parent/alkylated PACs), and to the distances from where the samples were collected to nearby bitumen upgraders. We found that microsatellite mutation frequency was positively correlated with total liver PAC burden. LMW and alkylated PACs were detected at higher levels and had a stronger positive relationship with mutation frequency than HMW (alkylated and parent) PACs. There were no significant relationships detected between mutation frequency and LMW parent PACs or the distance from bitumen upgraders. Furthermore, pyrogenic and petrogenic signatures suggest PACs in animals with high mutation frequencies were associated with combustion processes; although further investigation is warranted, due to limitations of diagnostic ratio determination with biotic models. Our findings support the hypothesis that PACs found in the AOSR increase mutation frequency in wildlife. Further investigation is required to determine if the elevated PAC levels associated with higher mutation frequency are due to natural exposure or elevated human activity.

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.

Variation in diet and activity of river otters (Lontra canadensis) by season and aquatic community

Keystone predators can impact many prey species, including those that are endangered. A requisite to assess the impact predators have on different prey populations is to identify the species being consumed in different types of communities, while accounting for possible seasonal variation in consumption. Here we used analysis of North American river otter (Lontra canadensis) scat to assess the impact river otters have on their prey populations, particularly endangered salmonids and migrating birds. We analyzed the prey composition of 1,411 river otter scats collected from 10 sites in Humboldt County, California, between 2011 and 2012. Analysis of prey items in scat placed study sites into four distinct clusters based on diet. Fish, mostly from the families Gasterosteidae, Cottidae, and Pholidae, formed the primary prey component, and crustaceans, birds, amphibians, and insects, also were important components of river otter diet. Salmonids constituted < 5% of overall diet, but river otters consumed the largest percentage of salmon during salmon spawning season at the inland cluster where salmonids spawn. Scat marking intensity varied between clusters and seasons, with the most scats collected in the autumn and the fewest in the winter/spring, except at the inland cluster where the pattern of marking activity was reversed. River otters may be responding to seasonal migrations of endangered and threatened salmonids. Diet surveys of this type are useful for monitoring resource use by top predators in aquatic ecosystems.

Spatial ecology of the stone marten in an Alpine area: combining camera-trapping and genetic surveys

A species’ potential distribution can be modelled adequately only if no factor other than habitat availability affects its occurrences. Space use by stone marten Martes foina is likely to be affected by interspecific competition with the strictly related pine marten Martes martes, the latter being able to outcompete the first species in forested habitats. Hence, to point out the environmental factors which determine the distribution and density of the stone marten, a relatively understudied mesocarnivore, we applied two non-invasive survey methods, camera-trapping and faecal-DNA based genetic analysis, in an Alpine area where the pine marten was deemed to be absent (Val Grande National Park N Italy). Camera trapping was conducted from October 2014 to November 2015, using up to 27 cameras. Marten scats were searched for between July and November 2015 and, to assess density, in spring 2017. Species identification was accomplished by a PCR-RFLP method, while 17 autosomal microsatellites were used for individual identification. The stone marten occurred in all available habitats (83% of trapping sites and 73.2% of scats); nonetheless, habitat suitability, as assessed using MaxEnt, depended on four major land cover variables—rocky grasslands, rocks and debris, beech forests and chestnut forests—, martens selecting forests and avoiding open rocky areas. Sixteen individuals were identified, of which 14 related to each other, possibly forming six different groups. Using capwire estimators, density was assessed as 0.95 (0.7–1.3) ind/km2. In the study area, the widespread stone marten selected forested areas, attaining density values like those reported for the pine marten in northern Europe and suggesting that patterns of habitat selection may depend on the relative abundance of the two competing martens.

Quantification of immunoreactive testosterone and estradiol-17ß metabolites to identify the sex of Neotropical otters (Lontra longicaudis annectens) in the field

Before there was use of ultrasonographic imaging, determination of the ratio of estrogens to androgens in the same individual was a technique used for differentiating the sex of monomorphic animals in captivity, with larger estrogen concentrations in the females. Due to species-specific differences in both concentration and changes throughout the year of these hormones, corroboration of the method is needed in each case. In this study, there was use of a chemo-immuno assay to quantify sex steroids in fecal samples collected from seven (five females and two males) Neotropical otters, Lontra longicaudis. The reproductive season for this species was determined to be between October and March, with increased estradiol in the females and relatively greater concentrations of testosterone in the males as compared with other seasons of the year. Results from utilization of a k-means analysis procedure indicated that the use of steroid ratios in fecal samples to differentiate otter sex is an effective technique when there are evaluations during the breeding season. The estrogen to androgen ratios during this period, however, are the inverse of what was expected, with there being larger testosterone concentrations in the female otters. The ratio of estrogens to androgens in feces of captive otters can be effectively used to determine the sex of otters in the field. We propose this method is reliable for sex determination in wild otter populations during the reproductive season.

Assessment of river otter abundance following reintroduction

Context By the early 1900s, river otters (Lontra canadensis) were extirpated across large parts of their range in North America. Over the last several decades they have made a remarkable recovery through widespread reintroduction programs. River otters were reintroduced in Ohio, USA, between 1988 and 1993, and restricted and limited harvesting of this population began in 2005. While circumstantial evidence points to rapid population growth following the reintroduction, changes in population size over time is unknown. Aims We sought to model river otter population growth following reintroduction, and to assess the impact of harvesting. Methods We used empirical and literature-based data on river otter demographics in Ohio to estimate abundance from 1988–2008 using an age- and sex-specific stochastic Leslie matrix model. Additionally, we used statistical population reconstruction (SPR) methods to estimate population abundance of river otters in Ohio from 2006 to 2008. Results Our Leslie matrix model predicted a population size of 4115 (s.d. = 1169) in 2005, with a population growth rate (λ) of 1.28 in 2005. Using SPR methods we found that both trapper effort and initial population abundance influenced our population estimates from 2006 to 2008. If we assumed that river otter pelt price was an accurate index of trapper effort, and if the initial population was between 2000 and 4000, then we estimated the λ to be 1.27–1.31 in 2008 and the exponential rate to be 0.17–0.21 from 2006 to 2008. Conversely, if the river otter population in 2005 was 1000, then we estimated λ to be 1.20 in 2008 and the exponential rate to be 0.08 from 2006 to 2008. Conclusions The river otter population in Ohio appears to have had the potential to grow rapidly following reintroduction. The ultimate effect of the harvesting regime on population abundance, however, remains clouded by limited data availability and high variability. Implications The considerable uncertainty surrounding population estimates of river otters in Ohio under the harvesting regime was largely driven by lack of additional data. This uncertainty clouds our understanding of the status of river otters in Ohio, but a more robust, long-term monitoring effort would provide the data necessary to more precisely monitor the population.

An Analysis of Citizen Science Based Research: Usage and Publication Patterns

The use of citizen science for scientific discovery relies on the acceptance of this method by the scientific community. Using the Web of Science and Scopus as the source of peer reviewed articles, an analysis of all published articles on “citizen science” confirmed its growth, and found that significant research on methodology and validation techniques preceded the rapid rise of the publications on research outcomes based on citizen science methods. Of considerable interest is the growing number of studies relying on the re-use of collected datasets from past citizen science research projects, which used data from either individual or multiple citizen science projects for new discoveries, such as for climate change research. The extent to which citizen science has been used in scientific discovery demonstrates its importance as a research approach. This broad analysis of peer reviewed papers on citizen science, that included not only citizen science projects, but the theory and methods developed to underpin the research, highlights the breadth and depth of the citizen science approach and encourages cross-fertilization between the different disciplines.

Density of river otters (Lontra canadensis) in relation to energy development in the Green River Basin, Wyoming

Exploration and extraction of oil and natural gas have increased in recent years and are expected to expand in the future. Reduction in water quality from energy extraction may negatively affect water supply for agriculture and urban use within catchments as well as down river. We used non-invasive genetic techniques and capture-recapture modeling to estimate the abundance and density of North American river otters (Lontra canadensis), a sentinel species of aquatic ecosystems, in Southwestern Wyoming. While densities in two of three river reaches were similar to those reported in other freshwater systems in the western US (1.45-2.39 km per otter), otters appeared to avoid areas near energy development. We found no strong difference in habitat variables, such as overstory cover, at the site or reach level. Also, fish abundance was similar among the three river reaches. Otter activity in our study area could have been affected by elevated levels of disturbance surrounding the industrial gas fields, and by potential surface water contamination as indicated by patterns in water conductivity. Continued monitoring of surface water quality in Southwestern Wyoming with the aid of continuously recording devices and sentinel species is warranted.

Landscape genetics for the empirical assessment of resistance surfaces: the European pine marten (Martes martes) as a target-species of a regional ecological network

Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale.