Is the standard Eurasian otter Lutra lutra survey strategy suitable for surveying the American mink Neovison vison?

The American mink Neovison vison is an elusive mustelid that is monitored mostly through the detection of its field signs, namely, footprints and scats. In Europe, the American mink has been often monitored using the standard otter survey strategy developed specifically for the Eurasian otter Lutra lutra, requiring to walk transects of 600 m spaced at least 5 km apart. We tested whether the standard otter survey strategy was appropriate for surveying mink. We studied a high-density population of mink along a 9-km stretch of river between December 2004 and April 2005. Monthly surveys were conducted and scats and footprints were recorded within 100-m sections along the river. The results showed a monthly variation in signs recovery, with the months of December, January and February being the best ones for surveying. Transects of 600 m detected mink between 74 and 90 % of the times in all months, excluding March when detection was as low as 56 %. Taken all together, the results suggest that the standard otter survey strategy was adequate to detect mink, at least in this case where species density was high. The study also highlighted monthly differences in signs detection, suggesting that temporal variations should be taken into account when designing the sampling strategy and the length of the sampling units (transects). In the months immediately following the mating season (and possibly in lower-density mink populations), it may be advisable to increase the length of transects to increase detection of mink.     

A Comparison of the diet and distribution of southern river otter (Lutra provocax) and mink (Mustela vison) in Southern Chile

In Chile, between latitudes 39S and 4330'S, southern river otter ( Lutra provocax ) and introduced mink ( Mustela vison ) scats were collected. Mink sign was recorded in 29% of the aquatic habitat where otter sign was found. Sixty-eight per cent of mink scats were collected at otter rest sites. A significant difference between the diets and low percentage of habitat use overlap of the two species (5-22%) suggest that, in Chile, river otter and mink coexist with little competition for space or food. There are no data supporting a relationship between the introduction of mink and the decline of southern river otters.     

Effectiveness of Scat Detection Dogs for Detecting Forest Carnivores

Abstract: We assessed the detection and accuracy rates of detection dogs trained to locate scats from free-ranging black bears (Ursus americanus), fishers (Martes pennanti), and bobcats (Lynx rufus). During the summers of 2003-2004, 5 detection teams located 1,565 scats (747 putative black bear, 665 putative fisher, and 153 putative bobcat) at 168 survey sites throughout Vermont, USA. Of 347 scats genetically analyzed for species identification, 179 (51.6%) yielded a positive identification, 131 (37.8%) failed to yield DNA information, and 37 (10.7%) yielded DNA but provided no species confirmation. For 70 survey sites where confirmation of a putative target species' scat was not possible, we assessed the probability that ≤1 of the scats collected at the site was deposited by the target species (probability of correct identification; P_ID). Based on species confirmations or P_ID values, we detected bears at 57.1% (96) of sites, fishers at 61.3% (103) of sites, and bobcats at 12.5% (21) of sites. We estimated that the mean probability of detecting the target species (when present) during a single visit to a site was 0.86 for black bears, 0.95 for fishers, and 0.40 for bobcats. The probability of detecting black bears was largely unaffected by site- or visit-specific covariates, but the probability of detecting fishers varied by detection team. We found little or no effect of topographic ruggedness, vegetation density, or local weather (e.g., temp, humidity) on detection probability for fishers or black bears (data were insufficient for bobcat analyses). Detection dogs were highly effective at locating scats from forest carnivores and provided an efficient and accurate method for collecting detection-nondetection data on multiple species.     

Feeding habits of invasive American mink (Neovison vison) in northern Germany—potential implications for fishery and waterfowl

In order to collect ecological data of invasive American mink (Neovison vison) at a fishpond area in northeastern Germany, we conducted a telemetry study in which 14 mink were radio-tracked. During this project, 2,502 scats from radio-tracked individuals were collected in the period from October 2003 to October 2005. Investigated mink principally prey on fish, small mammals and birds (eggs inclusive), whereas amphibians, reptiles and invertebrates were caught infrequently. Analysing mink scats of different seasons, we found significant seasonal variations of diet composition. In spring, fish, mammals and birds were hunted in similar amounts. During summer, birds made up the main part of the diet followed by mammals. In autumn, the proportion of birds in the mink diet decreased, whereas fish gained in importance. This trend continued during the winter period, when mink preyed almost exclusively on fish. Amphibians, crustaceans, insects, molluscs and reptiles were found only occasionally in scat samples. Among birds, the mink preyed mainly on the Eurasian Coot (Fulica atra) followed by the Mallard (Anas platyrhynchos). Mammalian prey was clearly dominated by the water vole (Arvicola terrestris) and among fish, mink hunted especially perch (Perca fluviatilis), roach (Rutilus rutilus) and carp (Cyprinus carpio). Results clearly demonstrate that mink is an opportunistic predator, which hunts its prey according to availability and vulnerability, respectively. Despite the high portions of fish in their autumn and winter diet, the economic damage caused by mink seems to be negligible. However, high predation rates on birds during the breeding season indicate a potential negative impact of mink on waterfowl.     

Genotypic diversity,molecular markers and spatial distribution of genets in clonal plants,a literature survey

We present a literature survey of studies using molecular markers to investigate genet diversity and structure in clonal plants. The data from 40 studies comprised 45 species of which only two were studied by DNA methods, the rest by isozyme markers. Less than one third of the studies provided information about the spatial distribution of individual genets within populations, and only 12.5% of the studies used mapping of all ramets within plots or part of the population in combination with identification of multilocus genotypes. We also present two case studies. InGlechoma hederacea morphological criteria were used to select clones. Multi-samples of ramets within these “clones” turned out to be variable using isozymes indicating that these “clones” in most cases consisted of several genets. One individual multilocus genotype covered tens of square metres. InHylocomium splendens samples from 10×10 cm plots usually consisted of a mixture of multilocus genotypes, but occasionally the whole plot consisted of one genet.     

The impact of American mink Mustela vison and European mink Mustela lutreola on water voles Arvicola terrestris in Belarus

In the U.K. the impact of introduced American mink Mustela vison , on water voles Arvicola terrestris , may be exacerbated by habitat loss and fragmentation. Pristine wetlands in Belarus, which American mink invaded in the early 1990s, provide a three-pronged opportunity to test this hypothesis. First, we examine the evidence that, even in the unmanaged wetlands of our Belarussian study site, American mink have reduced water vole populations. Second, we ask whether habitat size, type and isolation mitigate the impact of American mink predation. Thirdly, we explore whether water voles are at greater risk of predation from American than European mink because of their patterns of habitat use. Following the invasion of American mink, water voles were most abundant in small, still-water sites, far from river banks, while American mink were most active in large, running-water sites. Small mammal remains were found in a higher percentage of American than European mink scats, and of these, more were water vole in American mink scats. The occurrence of water voles in scats of both mink species declined after the American mink invaded and established. Our results provide at least circumstantial evidence that American mink limit water vole populations even in unmanaged wetland eco-systems, and that they have a greater impact than their European congener at least partly because they make greater use of isolated marshes. Although by no means providing complete protection, the configuration and dispersion of available habitat mitigated the impact of American mink on water voles. This raises the possibility that habitat restoration, especially through the establishment of isolated enclaves, could help reduce the effect of American mink in the U.K. These observations are of broader interest in the context of assessing the effect of multiple pressures on vulnerable species.     

A systematic re-sampling approach to assess the probability of detecting otters Lutra lutra using spraint surveys on small lowland rivers

Assessing and monitoring populations of elusive species frequently rely on the identification of indirect signs such as faeces. The absence of signs does not necessarily denote the absence of a species, thus, the ability to determine the presence/absence is susceptible to false negative results. The probability of detection is central to the interpretation and utility of data from field sign surveys. A low probability of detection may introduce considerable error into distribution patterns, resulting in inaccurate ecological conclusions.We used a systematic resampling approach, based on sequential spatial replication of spraint surveys, to investigate the probability of detecting Eurasian otters (Lutra lutra L.) with different survey designs. This included the standard otter transect survey methodology, which is widely used in conservation and scientific studies. In particular, we focus on the impact of applying broad scale population assessment techniques at smaller spatial scales. Fortnightly catchment-level otter surveys were undertaken on four lowland rivers in South Wales, over a period of two years. GIS was used to construct binary vectors for each survey, denoting the presence (1) or absence (0) of otters at each 50 m section of river. Vectors from all study rivers were pooled and resampled to test the different survey designs. The mean probability of detecting otters based on the standard protocol of a single 600 m transect survey was very low (0.26 ± 0.01 SE). The best way of obtaining a detection probability of 0.8 was to undertake three repeat surveys at two separate sites, using a transect of 800–1000 m.We demonstrate how sequentially collected spatial data can be analysed to determine the reliability of field sign surveys. Increasing the number of visits and study sites was a more efficient means of improving detection power than increasing transect length alone. The study emphasises the importance of determining detection probabilities and designing field sign surveys according to study scale and objectives. Our findings question the value of survey designs that aim to provide an instantaneous assessment of species presence/absence.     

Invasion and eradication of the American mink in the Atlantic Islands National Park (NW Spain): a retrospective analysis

Alien predators exert severe effects on island ecosystems, and their eradication from island habitats may therefore be necessary to conserve the native biota. Efforts are being made to eradicate the American mink (Neovison vison) from the Atlantic Islands of Galicia National Park (NW Spain), a protected site inhabited by vulnerable island fauna. We applied a molecular genetic approach to elucidate the source of the invaders and to evaluate the effectiveness of the trapping programme. We collected mink scats in the field and obtained tissue samples from culled mink. Populations of feral mink were known to be present in coastal areas close to the National Park archipelagos in the 1980–1990s. However, the molecular findings suggest that these populations were not the main source of the mink populations that colonized the islands during the 2000s. Recent releases from farms directly on to the islands are a more likely source of these invaders. Genetic analysis suggested that mink reproduced successfully on the islands and were relatively isolated from other mainland populations. The findings also suggest that most of the culled mink were juveniles, probably because it was more difficult to catch adults. Since mink are short-lived animals, it seems that eradication may also be achieved when a large proportion of juveniles are culled in isolated and small populations.     

Developing noninvasive methodologies to assess koala population health through detecting Chlamydia from scats

Wildlife diseases are a recognized driver of global biodiversity loss, have substantial economic impacts, and are increasingly becoming a threat to human health. Disease surveillance is critical but remains difficult in the wild due to the substantial costs and potential biases associated with most disease detection methods. Noninvasive scat surveys have been proposed as a health monitoring methodology to overcome some of these limitations. Here, we use the known threat of Chlamydia disease to the iconic, yet vulnerable, koala Phascolarctos cinereus to compare three methods for Chlamydia detection in scats: multiplex quantitative PCR, next generation sequencing, and a detection dog specifically trained on scats from Chlamydia‐infected koalas. All three methods demonstrated 100% specificity, while sensitivity was variable. Of particular interest is the variable sensitivity of these diagnostic tests to detect sick individuals (i.e., not only infection as confirmed by Chlamydia‐positive swabs, but with observable clinical signs of the disease); for koalas with urogenital tract disease signs, sensitivity was 78% with quantitative PCR, 50% with next generation genotyping and 100% with the detection dog method. This may be due to molecular methods having to rely on high‐quality DNA whereas the dog most likely detects volatile organic compounds. The most appropriate diagnostic test will vary with disease prevalence and the specific aims of disease surveillance. Acknowledging that detection dogs might not be easily accessible to all, the future development of affordable and portable “artificial noses” to detect diseases from scats in the field might enable cost‐effective, rapid and large‐scale disease surveillance.     

Shifts in fisher (Pekania pennanti) diet in response to climate-induced tree mortality in California assessed with DNA metabarcoding

A recent climate-induced tree mortality event in California, USA has led to dramatic landscape-level changes in the southern Sierra Nevada. Wide-spread conifer mortality was documented in habitat occupied by fisher (Pekania pennanti), a mature-forest associated species of conservation concern in this region. We analyzed fisher scats collected on the Sierra National Forest from the pre-tree-mortality period (PreTM, 2011 – 2013) and post-tree-mortality period (PostTM, 2017 – 2018). We used DNA metabarcoding to successfully identify taxa and summarized diet composition for 109 PreTM and 102 PostTM fisher scats. We observed 48 different diet items (33 assigned to species and 15 to genus). Mammals, birds, and plants of the Ribes genus (gooseberries and currents) comprised the highest proportions of diet items, although scats also contained DNA from reptiles, insects, arachnids, snails, and fungi. The frequency of occurrence of mammalian prey items was lower in PostTM (49.0%) versus PreTM scats (81.7%) with a reduction in the occurrence of two tree squirrels (Douglas squirrel and Humboldt’s flying squirrel). A higher proportion of scats collected PostTM (46.1%) contained DNA from Ribes spp. versus scats collected PreTM (19.3%). Our data reveal potential cascading effects of climate-induced tree mortality on fisher diet in the southern Sierra Nevada. Flexibility in fisher diet, however, may allow resilience to ecological change though future studies should consider the behavioral, energetic, demographic or fitness consequences from a shift away from medium-sized mammalian prey to plants.     

Monitoring site occupancy for American mink in its native range

American mink (Neovison vison) are secretive, semi-aquatic carnivores that often require noninvasive methods based on field signs such as tracks and scat for determining their spatial distribution. Most previous assessments of survey methods for American mink have been conducted in the United Kingdom where mink are an invasive species. We evaluated survey techniques for American mink in riparian habitat in its native range in the midwestern United States. We used occupancy modeling to compare detection rates between walking surveys and mink raft surveys, and we evaluated the potential for environmental covariates and observer bias to influence detectability from walking surveys. Per-survey detection probabilities were greater for walking surveys (0.72) than for mink rafts (0.39). Walking surveys also were cheaper and easier to conduct in small streams prone to flooding when compared to mink raft surveys. However, detection probabilities from walking surveys were affected by observer bias, recent rainfall, substrate, and date. We recommend walking surveys for determining the distribution of American mink in riparian habitat in the Midwest if occupancy modeling is applied to adjust for environmental and observer effects on detectability. We used such an approach to demonstrate occupancy dynamics of mink were related to variable water depths, which has implications for how this carnivore might be influenced by climate change. Mink rafts standardize the substrate for recording mink tracks and reduce the likelihood of observer effects. For studies using many volunteers, we recommend mink rafts for determining site occupancy by American mink. © 2011 The Wildlife Society.     

Determining Observer Reliability in Counts of River Otter Tracks

ABSTRACT In many research projects, reliability of collected data is dependent on reliability of field observers. However, it is uncommon for observer reliability to be either measured or reported in wildlife research. We tested whether observer skill affected outcomes of a northern river otter (Lontra canadensis) track survey conducted by the Texas Parks and Wildlife Department. Observers recorded presence of tracks at bridge sites (n = 250) throughout a 27-county region in east Texas, USA. Logistic regression indicated that observers were significantly associated with frequency of reported otter tracks. Because observers were not assigned to bridges at random, we tested and found associations between the bridges surveyed by each observer (SURVEY ROUTE) and habitat variables (WATERSHED, VEGETATION-TYPE, WATER-TYPE, BRIDGE-AREA) that may have influenced otter presence and probability of detection. A standardized tracker evaluation procedure indicated that experienced observers (n = 7) misidentified 37% of otter tracks. Additionally, 26% of tracks from species determined to be “otter-like” were misidentified as otter tracks. We recommend that observer skill in identification of animal tracks and other indirect signs be measured to detect and reduce observer errors in wildlife monitoring.     

Estimating the relative abundance of American mink <Emphasis Type="Italic">Mustela vison</Emphasis> on lowland rivers: evaluation and comparison of two techniques

Monitoring elusive species, which are ‘difficult to study’, often relies on the use of indirect indices to estimate relative abundance. It is important to know the accuracy of such indices and factors affecting it. For the American mink Mustela vison (an invasive species of conservation concern in the UK), we compare two indices of relative abundance: sign surveys (based on the detection of scats) and a new method based on the use of tracking plates on rafts. We found that raft surveys consistently performed better than did sign surveys and that estimates of relative abundance derived from both raft and sign surveys were linearly related to the number of individuals captured (but statistically significantly so only for raft surveys). Although both indices were highly correlated, there was considerable unexplained variation in the relationship between them. No statistically significant seasonal effects were detected for either method. Costs of the two methods were comparable after the first 2 years (based on four surveys per year), although raft surveys were more economical than were sign surveys in the longer term. In areas where polecats M. putorius are sympatric with mink, it will be important to develop methods to minimise confusion between the tracks of polecats and mink.     

Do alien North American mink compete for resources with native South American river otter in Argentinean Patagonia?

American mink Mustela vison , originally bred in fur farms, have become established in areas occupied by native endangered Southern river otter Lontra provocax , in Patagonia. In accordance with European experience, this biological invasion in South America raises questions about the interaction between invasive mink and native otter, from the viewpoints of both community assembly and conservation. We set out (1) to find which aspects of habitat structure were related to the distribution of signs of both this invasive species and Southern river otter Lontra provocax , in Argentinean Patagonia and their most common prey and (2) to test general predictions of niche partitioning between these two species. Based on surveys of 447 of 600 m transects for otter and mink scats/footprints along the waterside of lakes and rivers in the Andean Patagonian region, we compared diet composition (from scat analysis) and micro-habitat preferences (from field signs) of the two species. Otters were more specialist than mink in habitat use and diet. Mink used different habitats in other river basins where otters were absent. Where they occurred together in the basin of the Limay River, the distributions of their signs were similar, and mink diet was more similar to that of otters. There was no detectable difference in otter diet before and after mink arrival in the Limay basin. Contrary to the prediction of niche partitioning, and to the findings of European studies, resource use by mink was more similar to that of otters where the species occurred sympatrically than where they were allopatric.     

Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification

Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR‐based generation of DNA references into shotgun sequencing‐based “genome skimming” alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its “DNA‐mark”) for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such “DNA‐marks,” it will enable future DNA‐based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.     

Using remote sensing data to model European wild rabbit (Oryctolagus cuniculus) occurrence in a highly fragmented landscape in northwestern Spain

We model the occurrence of European wild rabbit in fragmented environments in a mountainous area of northwestern Spain (Gerês–Xurés Biosphere Reserve). We carried out a field survey by sampling the presence/absence of pellets in 237 plots (100?×?100 m) selected at random below an altitude of 800 m. For modelling purposes, we considered eight predictors related to vegetation, topography, human influence and heterogeneity. We obtained vegetation and ecological predictors from land use/land cover maps derived from Landsat Enhanced Thematic Mapper Plus images (acquired at the same time as the field data) and calculated vegetation indices by using a supervised classification method. We obtained topographical predictors from a Global Digital Elevation Model (GDEM) and used a generalized linear model to describe the occurrence of the European wild rabbit. The overall accuracy of the Landsat-derived map in Baixa Limia was 87.51 %, and the kappa coefficient was 0.85. The most parsimonious model included “grassland and crops”, “mean slope”, “distance to roads”, “urban settlements” and “ecotone scrubland-forest”. Five predictors were consequential, three of them with a positive sign for the presence of the species (scrub, urban settlements and ecotone scrubland-forest) and two with a negative sign (mean slope and distance to roads). The information on habitat requirements of European wild rabbit in the area provides a good framework for determining the habitat requirements of this keystone species in mountainous ecosystems in northwestern Iberian Peninsula.     

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA‐based methods applied to detect prey in predators’ scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species‐specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high‐throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost‐efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.     

Exonuclease VII is involved in “reckless” DNA degradation in UV-irradiated Escherichia coli

The recA mutants of Escherichia coli exhibit an abnormal DNA degradation that starts at sites of double-strand DNA breaks (DSBs), and is mediated by RecBCD exonuclease (ExoV). This “reckless” DNA degradation occurs spontaneously in exponentially growing recA cells, and is stimulated by DNA-damaging agents. We have previously found that the xonA and sbcD mutations, which inactivate exonuclease I (ExoI) and SbcCD nuclease, respectively, markedly suppress “reckless” DNA degradation in UV-irradiated recA cells. In the present work, we show that inactivation of exonuclease VII (ExoVII) by an xseA mutation contributes to attenuation of DNA degradation in UV-irradiated recA mutants. The xseA mutation itself has only a weak effect, however, it acts synergistically with the xonA or sbcD mutations in suppressing “reckless” DNA degradation. The quadruple xseA xonA sbcD recA mutants show no sign of DNA degradation during post-irradiation incubation, suggesting that ExoVII, together with ExoI and SbcCD, plays a crucial role in regulating RecBCD-catalyzed chromosome degradation. We propose that these nucleases act on DSBs to create blunt DNA ends, the preferred substrates for the RecBCD enzyme. In addition, our results show that in UV-irradiated recF recA⁺ cells, the xseA, xonA, and sbcD mutations do not affect RecBCD-mediated DNA repair, suggesting that ExoVII, ExoI and SbcCD nucleases are not essential for the initial targeting of RecBCD to DSBs. It is possible that the DNA-blunting activity provided by ExoVII, ExoI and SbcCD is required for an exchange of RecBCD molecules on dsDNA ends during ongoing “reckless” DNA degradation.     

Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide‐ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture–recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1–112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture–recapture analyses, overall cost‐efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.