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The most traditional method used to monitor the distribution of otters is spraint density surveys, but there has been long-standing debate regarding whether this approach is sufficiently accurate. In response to this debate, the effectiveness and reliability of spraint density surveys as a method for assessing the otter distribution within urban areas were evaluated by comparing their results with those achieved using two alternative methods: genetic analysis and camera trap-based density based on the random encounter model. In addition, the spraint density was tested as an indicator of otter habitat preferences by modeling 19 environmental factors (seven associated with prey, nine with land use, and three with the river environment) using a pcount model. Spraint surveys, genetic analysis, and camera trapping were conducted at 36, 22, and 12 sites within Daegu Metropolitan City, respectively. A regression model indicated that the spraint density was strongly associated with the other two methods, while it was also found to accurately represent otter habitat preferences, with otters in urban areas preferring sites with a high density of large fish and river islets. Consequently, spraint density surveys were the most time-effective, cost-effective, and reliable method for investigating the otter distribution in this urban environment. As a result, population status assessment using spraint density surveys can provide important information for the conservation management of urban otters.

Effective, evidence‐based management is required to ensure long‐term coexistence between people and wildlife in an increasingly humanized world. Although behavioural individuality is recognized as a key factor affecting evolutionary and ecological processes, it has rarely been explicitly assessed in relation to human–wildlife conflicts. The 'problem individual' paradigm states that some conspecifics within a given population have a disproportionately large contribution to conflicts. To the best of our knowledge, no studies have so far systematically tested this assumption in large carnivores.Here, we investigated the variation in conflict behaviour among brown bears Ursus arctos within the population inhabiting the Polish Eastern Carpathians. We inspected all sites notified as damaged by bears in 2014–2017 to determine the number and sex of the individuals involved. We conducted systematic noninvasive genetic sampling to estimate the size of the local population by spatially explicit capture–recapture models. We assessed the fraction and sex ratio of damage‐making bears in relation to the population, as well as the behavioural patterns by classifying and differentiating between occasional and repetitive damage‐makers.Approximately one‐third of the estimated 72 (95% CI 45.2–115.5) brown bears inhabiting the Polish Eastern Carpathians were responsible for damage occurrence in the region. The majority of damage‐makers were female (65% vs. 35% of male), which reflected the sex ratio of the local population (0.57). Thirty‐three per cent of the damage‐making bears (i.e. nine individuals) were classified as 'problem individuals', exhibiting repetitive conflict behaviour.Synthesis and applications. This study provides evidence of intraspecific differences in conflict behaviour in a large carnivore species, the brown bear, and indicates that damage‐making behaviour is not exhibited with the same frequency by all individuals within a population. Managers and policy‐makers should be aware that targeting individuals involved in conflicts without reference to the whole population may lead to misleading conclusions or an incomplete picture of the mechanisms underlying the conflicts, and thus, to mismanagement. Unravelling the behavioural patterns of individual engagement in damage through large‐scale and population‐wide studies is needed to accurately assess the magnitude of damage and enhance human–wildlife coexistence in areas experiencing conflicts. [ABSTRACT FROM AUTHOR]

Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item. [ABSTRACT FROM AUTHOR]

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session NGS sampling of hares. We compared spatial capture-recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost-effective sampling protocols.

Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (

Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive and at‐risk species. We developed and optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using noninvasive samples to inform the management of invasive Sitka black‐tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive fecal and hair samples to simultaneously distinguish individuals, identify sex, and reconstruct kinship among deer sampled across the archipelago, then provided a proof‐of‐concept application using field‐collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high‐quality tissue samples genotyped using restriction‐site associated DNA sequencing (92.4%), while genotyping discordance between paired high‐quality tissue and noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT‐seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where noninvasive genetic sampling is employed. [ABSTRACT FROM AUTHOR]

Subsidization of predator populations increases predation pressure on prey species, which is exacerbated when natural resources are scarce. Estimating the frequency of predation by subsidized predators on vulnerable species, especially low‐density, long‐lived species such as the federally threatened Mojave desert tortoise (Gopherus agassizii), allows landscape managers to evaluate the need for actions like reducing subsidies, discouraging predation by taste aversion, or predator removal. Most studies of Mojave desert tortoise predation have relied on morphological analysis to identify hard parts in predator scat. Here, we developed and validated a qPCR assay to test for the presence of Mojave desert tortoise in DNA extracted from scat and pellets. We used the assay to detect tortoise DNA in scat and pellets collected in a conservation easement adjacent to Boulder City, Nevada, from three Mojave desert tortoise predators: coyotes (Canis latrans), desert kit foxes (Vulpes macrotis arsipus), and common ravens (Corvus corax)—all of which consume anthropogenic resources. We compared the results of our qPCR assay to results from morphological analysis of the same samples and found that the qPCR method is much more sensitive at detecting the presence of tortoise remains. Although neither method can determine whether consumption was the result of predation or scavenging, nor how many individual tortoises were consumed, our findings indicate that conservation managers may benefit from focusing efforts on reducing subsidies that attract and support predators and on reducing tortoise mortality from predation. [ABSTRACT FROM AUTHOR]

Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in‐solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat‐derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field‐collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low‐quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples. [ABSTRACT FROM AUTHOR]

Abstract Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive and at‐risk species. We developed and optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using noninvasive samples to inform the management of invasive Sitka black‐tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive fecal and hair samples to simultaneously distinguish individuals, identify sex, and reconstruct kinship among deer sampled across the archipelago, then provided a proof‐of‐concept application using field‐collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high‐quality tissue samples genotyped using restriction‐site associated DNA sequencing (92.4%), while genotyping discordance between paired high‐quality tissue and noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT‐seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where noninvasive genetic sampling is employed.

Abstract Accurately estimating abundance is a critical component of monitoring and recovery of rare and elusive species. Spatial capture–recapture (SCR) models are an increasingly popular method for robust estimation of ecological parameters. We provide an analytical framework to assess results from empirical studies to inform SCR sampling design, using both simulated and empirical data from noninvasive genetic sampling of seven boreal caribou populations (Rangifer tarandus caribou), which varied in range size and estimated population density. We use simulated population data with varying levels of clustered distributions to quantify the impact of nonindependence of detections on density estimates, and empirical datasets to explore the influence of varied sampling intensity on the relative bias and precision of density estimates. Simulations revealed that clustered distributions of detections did not significantly impact relative bias or precision of density estimates. The genotyping success rate of our empirical dataset (n = 7,210 samples) was 95.1%, and 1,755 unique individuals were identified. Analysis of the empirical data indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges. The number of captures and spatial recaptures was strongly correlated with precision, but not absolute relative bias. The best sampling designs did not differ with estimated population density but differed between large and small ranges. We provide an efficient framework implemented in R to estimate the detection parameters required when designing SCR studies. The framework can be used when designing a monitoring program to minimize effort and cost while maximizing effectiveness, which is critical for informing wildlife management and conservation.

Climate-caused changes in prey abundance may alter predator–prey dynamics in the Arctic food web. Lemmings (Dicrostonyx spp.) are important prey for Arctic foxes (Vulpes lagopus) and their annual population fluctuations drive fox reproduction, creating strongly linked predator–prey population cycles. Winter diet directly impacts Arctic fox reproductive success, but winter prey diversity on the tundra is low. Strategies such as using the marine environment to scavenge seals have allowed Arctic foxes to persist during years of low lemming abundance. However, warming winters have decreased snowpack quality, preventing lemmings from reaching their previous high abundances, which may reduce their impact on predator dynamics. We investigated Arctic fox dietary response to lemming abundance by reconstructing Arctic fox winter diet in the low Arctic. Next-generation sequencing of fecal DNA, from samples (n = 627) collected at dens in winters of 2011–2018, identified prey both from terrestrial and marine environments. Despite lemming cycle damping, Arctic foxes still increased lemming consumption during years of higher lemming abundance. Alternative prey such as marine resources were consumed more during years of low lemming abundance, with up to 45% of samples containing marine resources in low lemming years. In addition, Arctic foxes consumed high proportions of meadow voles (Microtus pennsylvanicus), which may represent a new alternative prey, suggesting climate change may be creating new foraging opportunities. Changes in prey abundance illustrate how climate-caused disturbances are altering Arctic food-web dynamics. Dietary flexibility and availability of alternative prey may become increasingly important for Arctic predators as the Arctic continues to change. [ABSTRACT FROM AUTHOR]

Spatial capture–recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark–resight, gSMR), or no individual identification (spatial count or spatial presence–absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real‐world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a hybrid model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species, we genotyped fecal DNA collected with detection dogs during a 20‐d period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 d contemporaneous with scat collection. Camera‐based gSMR models produced density estimates that differed by <10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple data sets are incorporated when possible. [ABSTRACT FROM AUTHOR]

La variabilidad genética intrapoblacional de Vultur gryphus (cóndores andinos) de las regiones de Cusco y Apurímac fue evaluada mediante amplificación y secuenciación del ADN mitocondrial correspondientes a la región control y subunidad ribosomal 12S (D-Loop-ARNr12S), y a los genes Citocromo Oxidasa subunidad I (COI) y NADH deshidrogenasa subunidad II (ND2). El ADN se extrajo a partir de cálamos de plumas de muda de ejemplares en cautiverio y silvestres. Se analizaron los principales índices de diversidad genética como son: la diversidad haplotípica, la diversidad nucleotídica, el número promedio de diferencias nucleotídicas y el número de sitios polimórficos. La tasa de éxito de amplificación mediante PCR fue de 100% para las tres regiones de ADN analizadas. Se secuenció 600 pb de la región D-Loop-ARNr12S caracterizándose cuatro haplotipos, 704 pb del gen COI caracterizándose seis haplotipos y 1090 pb del gen ND2 caracterizándose cinco haplotipos. El gen COI presentó el mayor valor de diversidad haplotípica (Hd = 0.468), la región del gen D-Loop-ARNr12S presentó el mayor índice de diversidad nucleotídica (π = 0.00086), mientras que el gen COI presentó el mayor número promedio de diferencias nucleotídicas (K = 0.52615). Los resultados muestran bajos niveles de variabilidad genética en los genes mitocondriales de los cóndores andinos de la zona de estudio, que indicarían una población con estructura genética homogénea.

Although diversionary feeding has been used as a management strategy to limit problem bear behaviors or reduce human-wildlife conflict, the underlying mechanisms determining the success or failure of diversionary feeding programs are infrequently assessed. Further, molecular methods, commonly applied in wildlife research, have not been used to examine diet composition of target species in response to diversionary feeding. Here, we used molecular methods to evaluate the consumption of ungulates by American black bears (Ursus americanus) as influenced by the composition of supplemental foods during a diversionary feeding program originally implemented to reduce predation on woodland caribou (Rangifer tarandus caribou) calves in Newfoundland, Canada. We used a previously developed mitochondrial DNA prey identification test to determine the proportion of American black bear scats containing caribou and moose (Alces alces) DNA in 2010 and 2011 at a study site where supplemental foods were provided. The composition of supplemental foods varied between years: bakery waste was provided in 2010, whereas both bakery waste and beaver (Castor canadensis) carcasses were provided in 2011. We also evaluated differences in the consumption of caribou and moose between male and female American black bears at the experimental site and an additional site where diversionary feeding was not implemented. We anticipated that male bears' larger body size and greater nutritional requirements would lead them to more frequently consume caribou and moose. In contrast to our predictions, the proportion of scats found to contain caribou and moose did not differ between years at the site where diversionary feeding was implemented, and there were no differences in the consumption of caribou and moose by male and female bears. This research demonstrates the utility of noninvasive molecular methods to reveal a mechanistic understanding of the effectiveness, or in this case ineffectiveness, of diversionary feeding. [ABSTRACT FROM AUTHOR]

Genetic monitoring has proven helpful in estimating species presence and abundance, and detecting trends in genetic diversity, to be incorporated in providing data and recommendations to management authorities for action and policy development. We reviewed 148 genetics research papers conducted on the bear species worldwide retrieved from Web of Science, SCOPUS, and Google Scholar. This review aims to reveal sampling methodology and data collection instructions, and to unveil innovative noninvasively genetic monitoring techniques that may be integrated into the genetic monitoring of a large bear population. In North American studies, hair samples were collected more often than faeces, whereas in Europe, both faeces and hair samples surveys are recommended, usually focusing on faeces. The use of the Isohelix sample collection method, previously tested locally and, if suitable, applied at the national level, could generate numerous advantages by reducing shortcomings. Additionally, dogs trained for faeces sampling could be used in parallel with hunting managers, foresters, and volunteers for sample collection organised during autumn and winter. It was stated that this is the best period in terms of cost-efficiency and high quality of the gathered samples. We conclude that large-scale noninvasive genetic monitoring of a large bear population represents a challenge; nevertheless, it provides valuable insights for biodiversity monitoring and actions to respond to climate change.

Abundance estimators are often evaluated with simulations, or by comparing estimates to populations of known size. Advances in noninvasive genetic sampling have fueled an increase in the use of noninvasive genetic sampling-based capture–recapture. However, when working with free-ranging populations of unknown size, managers often lack data necessary to select the appropriate estimator. This leads to uncertainty regarding how choice of estimator or sampling design influence estimates, and managers may select estimators based on funding or logistical constraints. Alternatively, comparing estimates from multiple estimators can provide managers with greater confidence in estimates, or highlight potential differences. We used noninvasive genetic sampling to estimate the abundance of free-ranging kit foxes Vulpes macrotis and coyotes Canis latrans. We generated estimates of abundance with two non-spatial likelihood-based estimators: 1) robust design Huggins capture–recapture models and 2) single-occasion capture with replacement (CAPWIRE) models. We compared these with recently published estimates derived from spatially explicit capture–recapture (SECR) models. For both species, estimates from Huggins models were generally lower than those from SECR. Abundance estimates from CAPWIRE, which was developed specifically for noninvasive genetic sampling and generates estimates from a single sampling occasion, tended to be biased low with high precision. Our results suggest that choice of estimator and sampling design can significantly influence estimates, and that the relationship between estimators varied between species. Our results further suggest that single-occasion sampling often employed with CAPWIRE abundance estimation may produce biased results and be inappropriate for species requiring dispersed sampling strategies. [ABSTRACT FROM AUTHOR]

Accurately estimating abundance is a critical component of monitoring and recovery of rare and elusive species. Spatial capture–recapture (SCR) models are an increasingly popular method for robust estimation of ecological parameters. We provide an analytical framework to assess results from empirical studies to inform SCR sampling design, using both simulated and empirical data from noninvasive genetic sampling of seven boreal caribou populations (Rangifer tarandus caribou), which varied in range size and estimated population density. We use simulated population data with varying levels of clustered distributions to quantify the impact of nonindependence of detections on density estimates, and empirical datasets to explore the influence of varied sampling intensity on the relative bias and precision of density estimates. Simulations revealed that clustered distributions of detections did not significantly impact relative bias or precision of density estimates. The genotyping success rate of our empirical dataset (n = 7,210 samples) was 95.1%, and 1,755 unique individuals were identified. Analysis of the empirical data indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges. The number of captures and spatial recaptures was strongly correlated with precision, but not absolute relative bias. The best sampling designs did not differ with estimated population density but differed between large and small ranges. We provide an efficient framework implemented in R to estimate the detection parameters required when designing SCR studies. The framework can be used when designing a monitoring program to minimize effort and cost while maximizing effectiveness, which is critical for informing wildlife management and conservation. [ABSTRACT FROM AUTHOR]

Little is known about the relatedness structure of carnivores living in urban areas, where green spaces may vary in size and resource availability. We examined the minimum population size, relatedness structure, and genetic diversity of a recently established population of eastern coyotes (Canis latrans) inhabiting New York City (NYC). The population has been established for approximately 25 years, and sample collection for genetic analysis has been ongoing since 2010. We genotyped 234 scat, eight tissue, and three blood samples at nine microsatellite loci. We identified 45 individual coyotes with a male-biased sex ratio of 2.2:1. We also found moderate to high levels of genetic diversity, with average observed heterozygosity of 0.779 and mean number of alleles per locus of 7.8. Most of the green spaces surveyed supported a single group of closely related coyotes in each. Relatedness comparisons between parks also indicated that coyotes compared across different parks were also closely related. We identified two unrelated mated pairs and found no support for polygamy. The high incidence of relatedness suggests that the coyote population is descended from a small number of founding individuals. Additionally, we genetically recaptured several coyotes, including one individual sampled in the Bronx and in Queens, with a median of 103 days between resampling. This result indicates that the coyotes are persisting in some of the isolated greenspaces of New York City and able to move successfully between them. [ABSTRACT FROM AUTHOR]

Monitoring population performance in the years following species reintroductions is key to assessing population restoration success and evaluating assumptions made in planning species restoration programs. From 2008–2010 we translocated 90 fishers (Pekania pennanti) from British Columbia, Canada, to Washington's Olympic Peninsula, USA, providing the opportunity to evaluate modeling assumptions used to identify the most suitable reintroduction areas in Washington and enhance understanding of fisher habitat associations in the late‐successional forest ecosystems in the coastal Pacific Northwest. From 2013–2016, we deployed 788 motion‐sensing cameras and hair (DNA)‐snaring devices distributed among 263 24‐km2 primary sampling units across the Olympic Peninsula. Our objectives were to determine whether occupancy patterns of the reestablishing population supported assumptions of the initial habitat assessment models, whether the population had expanded or shifted in distribution since the initial reintroductions, compare physical habitat attributes among land‐management designations, and determine whether the founding fishers had successfully reproduced. We predicted that site occupancy by fishers would be associated with landscapes characterized by high proportional coverage of dense forest canopies and medium‐sized and large trees, a diversity of stand structural classes, and area near the administrative boundary separating wilderness from more intensively managed forest lands. We detected fishers across designated wilderness, federal lands outside of wilderness, and other land designations in proportion to land availability on the Peninsula. We found negligible support for predictions that occupancy by fishers was associated with percent forest cover, tree‐size class, or structural class diversity. Rather, occupancy was strongly associated with lands near the wilderness boundary on both sides. We speculate that the boundary between wilderness and more intensively managed forest lands provided fishers with the most suitable prey in proximity to contiguous expanses of low‐ to mid‐elevation late‐successional forests that provided optimal resting, denning, and security values. Occupancy patterns shifted toward the west and south along a precipitation gradient during the study, indicating that population distribution had not yet stabilized 5–8 years following translocation. Genetic results indicated that ≥2 generations of fishers have been produced on the Peninsula. Annual occupancy rates across the Peninsula (0.08–0.24) were lower than in other previously studied and established fisher populations, indicating that not all habitat was fully occupied or that initial estimates of the extent of habitat was overestimated. The strong selection fishers exhibited for wilderness edge and weak selection against extensive forested wilderness areas suggested that habitat managers should strive for maintaining a suitable interspersion of required forest structures and biotic habitat components, such as prey resource availability. © 2019 The Wildlife Society. Site occupancy in a recently reintroduced population of fishers was associated primarily with the boundary separating late‐successional forest wilderness from more intensively managed forests on Washington's Olympic Peninsula. Occupancy patterns varied among years along a precipitation gradient as new generations of fishers were produced and increasingly occupied the wetter western and southern portions of the Peninsula. Evidence of stable occupancy rate, reproduction, and potential population expansion are positive indicators of successful population restoration. [ABSTRACT FROM AUTHOR]

The measurement of glucocorticoid metabolites (GCMs) in faeces has become a widely used and effective tool for evaluating the amount of stress experienced by animals. However, the potential sampling bias resulting from an oversampling of individuals in different states of pregnancy has rarely been investigated. In this study, we validate a noninvasive method for measuring gestagen metabolites in female mountain hares (Lepus timidus) under controlled conditions. We also measured the concentration of gestagen metabolites of females in a free-ranging population during the early breeding and post-breeding periods from 2014 to 2019. We found significant yearly variations in gestagen metabolites, which were related to the condition of the females due to the snow cover duration before and at the start of the reproduction period. GCMs were significantly influenced by the gestagen metabolite levels. These results are important for improving the interpretation of GCM concentrations in free-ranging populations during the breeding and reproductive periods.

Abundance estimators are often evaluated with simulations, or by comparing estimates to populations of known size. Advances in noninvasive genetic sampling have fueled an increase in the use of noninvasive genetic samplingbased capture-recapture. However, when working with free-ranging populations of unknown size, managers often lack data necessary to select the appropriate estimator. This leads to uncertainty regarding how choice of estimator or sampling design influence estimates, and managers may select estimators based on funding or logistical constraints. Alternatively, comparing estimates from multiple estimators can provide managers with greater confidence in estimates, or highlight potential differences. We used noninvasive genetic sampling to estimate the abundance of free-ranging kit foxes Vulpes macrotis and coyotes Canis latrans. We generated estimates of abundance with two non-spatial likelihoodbased estimators: 1) robust design Huggins capture-recapture models and 2) single-occasion capture with replacement (CAPWIRE) models. We compared these with recently published estimates derived from spatially explicit capture- recapture (SECR) models. For both species, estimates from Huggins models were generally lower than those from SECR. Abundance estimates from CAPWIRE, which was developed specifically for noninvasive genetic sampling and generates estimates from a single sampling occasion, tended to be biased low with high precision. Our results suggest that choice of estimator and sampling design can significantly influence estimates, and that the relationship between estimators varied between species. Our results further suggest that single-occasion sampling often employed with CAPWIRE abundance estimation may produce biased results and be inappropriate for species requiring dispersed sampling strategies. [ABSTRACT FROM AUTHOR]

Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010–2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1–3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion. [ABSTRACT FROM AUTHOR]

Understanding how environmental factors interact to determine the abundance and distribution of animals is a primary goal of ecology, and fundamental to the conservation of wildlife populations. Studies of these relationships, however, often assume static environmental conditions, and rarely consider effects of competition with ecologically similar species. In many parts of their shared ranges, grizzly bears Ursus arctos and American black bears U. americanus have nearly complete dietary overlap and share similar life history traits. We therefore tested the hypothesis that density patterns of both bear species would reflect seasonal variation in available resources, with areas of higher primary productivity supporting higher densities of both species. We also hypothesized that interspecific competition would influence seasonal density patterns. Specifically, we predicted that grizzly bear density would be locally reduced due to the ability of black bears to more efficiently exploit patchy food resources such as seasonally abundant fruits. To test our hypotheses, we used detections of 309 grizzly and 597 black bears from two independent genetic sampling methods in spatially‐explicit capture–recapture (SECR) models. Our results suggest grizzly bear density was lower in areas of high black bear density during spring and summer, although intraspecific densities were also important, particularly during the breeding season. Black bears had lower densities in areas of high grizzly bear density in spring; however, density of black bears in early and late summer was best explained by primary productivity. Our results are consistent with the hypothesis that smaller‐bodied, more abundant black bears may influence the density patterns of behaviorally‐dominant grizzly bears through exploitative competition. We also suggest that seasonal variation in resource availability be considered in efforts to relate environmental conditions to animal density. [ABSTRACT FROM AUTHOR]

Abstract: The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD‐seq) require large amounts of high‐quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low‐quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next‐generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment. [ABSTRACT FROM AUTHOR]

Population density estimates are necessary to inform management and conservation, yet are difficult to obtain for cryptic species such as carnivores, and often require intensive sampling. We implemented a single-survey, closed session, scat sampling protocol to estimate bobcat density using fecal DNA and spatial capture-recapture at two sites over five sessions in Virginia, USA. We employed a Poisson encounter model to allow for multiple detections on scat transect segments over a single collection interval, and compared single session and multistrata (closed, multi-site, multisession) spatial capture-recapture (SCR) approaches to estimate density for each site and session. We found improved precision for most estimates using the multistrata SCR approach, sharing data on baseline detection and individual movement across sites and sessions. We suggest the summer session estimates are representative of the resident population, that differences in density between summer and winter are representative of potential net recruitment, and that differences between consecutive summer sessions are representative of the net recruitment realized for the population (dependent on survival and emigration). Finally, we assessed factors affecting precision in single session model estimates and provide recommendations to improve detection and reduce credible intervals that may be applicable across the bobcat range and to other carnivore species. The single survey transect methodology provides flexibility in monitoring carnivore populations specifically, or as part of concurrent monitoring for multiple carnivore species. This methodology has potential to dramatically increase the effectiveness of conservation and management dollars, improving our ability to monitor carnivore populations and assess conservation needs and actions. [ABSTRACT FROM AUTHOR]

Lack of reliable information on the status of species often leads managers to exclusively rely on experiential knowledge, opinions or perceptions, usually derived from personnel associated with natural resource management agencies. Yet, the accuracy of these sources of information remains largely untested. We approached this challenge, which is particularly common for wildlife monitoring programs in developing countries, using a population of Asian brown bears ( Ursus arctos ) in the Iranian Caucasus as case study. We conducted a noninvasive, genetic, spatial capture-recapture (SCR) study to estimate bear density across a core protected area, Arasbaran Biosphere Reserve, and compared our estimate of bear abundance with rangers' perceptions as collated through interviews. The perceived abundance of bears by local rangers was between 3 and 5 times higher than our SCR estimate of 40 bears (2.5–97.5% Bayesian Credible Intervals = 27–70; density: 4.88 bears/100 km 2 ). Our results suggest that basing management of the local bear population on perceptions of population status may result in overestimating the likelihood of population persistence. Our findings offer a scientific baseline for an evidence-based conservation policy for brown bears in Iran, and the broader Caucasus Ecoregion. The majority of threatened terrestrial megafauna occur in developing countries, where collecting and analyzing demographic data remain challenging. Delayed conservation responses due to the lack of, or erroneous knowledge of population status of such imperiled species may have serious consequences. [ABSTRACT FROM AUTHOR]

Noninvasive genetic sampling allows studying wildlife without having to catch, handle or even observe individuals. In this study, factors which may affect the quality of noninvasive samples of Asiatic black bear (Ursus thibetanus) in the subtropical areas were identified. We collected hair and faecal samples from captive Asiatic black bears and quantitatively evaluated the effects of hair age (from fresh to 60 days), faeces age (from fresh to 14 days), faeces sampling locations (i.e. sample collected from either the surface, inside or a mixture of both the surface and inside of faeces), and faeces preservation methods (frozen or kept at room temperature in 95% ethanol) on amplification success rates of mitochondrial DNA fragments of different sizes (450bp, 900bp, and 1600bp). The results showed that the amplification success rates decreased with sample age and amplicon size in both hair and faecal DNA. In subtropical environment, there was no significant difference between amplification success of DNA extracted from fresh and 7-day-old samples of either the hair or faeces. The amplification success rates were not influenced by sampling location of faeces. For faeces preserved in 95% ethanol, the amplification success appeared unaffected by frozen at -20 °C or kept at room temperature in shorter mtDNA fragments, but was significantly influenced when amplicon size was 1600bp. The results of this study will reinforce the optimization of noninvasive sampling approaches in Asiatic black bear research, especially in the subtropics. [ABSTRACT FROM AUTHOR]

The marine otter ( Lontra felina ) can be found on rocky shores from the northern coast of Peru (9°S) to the extreme south of Argentina (56°S). This species is currently classified as endangered but there is little information on population size because marine otters are very difficult to observe and count. Between June and August 2012 we collected 240 samples of marine otter feces from seven localities in Peru. All locations were visited four times. One-hundred and thirty-three samples (55%) were successfully amplified at five to seven microsatellite loci and a sex-linked marker. We identified a minimum of 80 individuals (41 males and 39 females) across all locations for a density estimate of 4.4 otters per km, a value about 2X higher than estimates based on previous visual counts. Estimates using the program CAPWIRE averaged 12.6 otters/km, a value six times higher than estimates based on previous visual counts, although confidence limits were large due to the low number of recaptures. There was a strong positive relationship between the number of fresh scats and the number of unique genotypes, suggesting scat counts might be used to estimate the minimum number of otters at a site. Non-invasive genotyping of marine otter feces and scat counts will be valuable tools for estimating population sizes and monitoring movements of this secretive species. [ABSTRACT FROM AUTHOR]

Monitoring demographic and genetic parameters of reintroduced populations of endangered species is essential for evaluating and informing conservation strategies to maximize the chances of a successful recovery. We applied noninvasive genetic monitoring using fecal DNA to evaluate demographic and genetic parameters as they relate to the recovery of the endangered Columbia Basin pygmy rabbit (Brachylagus idahoensis) in central Washington, United States, during the initial 3 years of a renewed reintroduction effort. We quantified post-release dispersal, apparent survival, and reproduction in the wild, and monitored the genetic diversity and composition of the released cohorts, wild surviving population, and breeding population held in large enclosures. During this study, we reintroduced 1,206 pygmy rabbits into the wild, and detected a total of 176 individuals living on or near the release area during surveys the following winters. Median dispersal distance of juveniles was 776 m, compared to 471 m for adults, and dispersal distances for juveniles decreased for rabbits released later in the release season. Survival of juveniles differed across years and was positively associated with release date, release weight (a surrogate for age), and heterozygosity. Survival of adults was similarly influenced by release day, with some evidence for a positive effect of heterozygosity. Only 14 wild-born individuals were detected during the study. Genetic monitoring was an effective way to evaluate the demographic and genetic status of the reintroduced population within a limited study area, to inform changes to the conservation strategy, and to generate a data set to address long-term research and recovery goals. [ABSTRACT FROM AUTHOR]

ABSTRACT Many animals, including gray wolves ( Canis lupus), live in social groups. Genetic techniques can help reveal the structure and composition of social groups, providing valuable information about group and population dynamics. We evaluated the effectiveness of using noninvasive genetic sampling (NGS) of fecal and hair samples at wolf rendezvous sites combined with spatial and genetic assignment criteria for assigning individuals to packs, detecting dispersers and lone wolves, determining the number of packs in an area, and obtaining group metrics. We applied this approach in 4 study areas covering 13,182 km2 in Idaho, USA while concurrently monitoring wolves using telemetry techniques. We assigned pack affiliation to 78-97% of individuals across study areas and identified 12 potential dispersers. We detected a successful gene flow event by reconstructing a breeding male's genotype and tracing it back to a pack of origin using genetic assignment techniques. Average pack size was consistent between our NGS- and telemetry-based counts ( [ABSTRACT FROM AUTHOR]

Population abundance estimates are important for management but can be challenging to determine in low-density, wide-ranging, and endangered species, such as Sonoran pronghorn (Antilocapra americana sonoriensis). The Sonoran pronghorn population has been increasing; however, population estimates are currently derived from a biennial aerial count that does not provide survival or recruitment estimates. We identified individuals through noninvasively collected fecal DNA and used robust-design capture-recapture to estimate abundance and survival for Sonoran pronghorn in the United States from 2013 to 2014. In 2014 we generated separate population estimates for pronghorn gathered near 13 different artificial water holes and for pronghorn not near water holes. The population using artificial water holes had 116 (95% CI 102-131) and 121 individuals (95% CI 112-132) in 2013 and 2014, respectively. For all locations, we estimated there were 144 individuals (95% CI 132-157). Adults had higher annual survival probabilities (0.83, 95% CI 0.69-0.92) than fawns (0.41, 95% CI 0.21-0.65). Our use of targeted noninvasive genetic sampling and capture-recapture with Sonoran pronghorn fecal DNA was an effective method for monitoring a large proportion of the population. Our results provided the first survival estimates for this population in over 2 decades and precise estimates of the population using artificial water holes. Our method could be used for targeted sampling of broadly distributed species in other systems, such as in African savanna ecosystems, where many species congregate at watering sites. [ABSTRACT FROM AUTHOR]

The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently. [ABSTRACT FROM AUTHOR]

When hybridizing species come into contact, understanding the processes that regulate their interactions can help predict the future outcome of the system. This is especially relevant in conservation situations where human activities can influence hybridization dynamics. We investigated a developing hybrid zone between red wolves and coyotes in North Carolina, USA to elucidate patterns of hybridization in a system heavily managed for preservation of the red wolf genome. Using noninvasive genetic sampling of scat, we surveyed a 2880 km2 region adjacent to the Red Wolf Experimental Population Area ( RWEPA). We combined microsatellite genotypes collected from this survey with those from companion studies conducted both within and outside the RWEPA to describe the gradient of red wolf ancestry. A total of 311 individuals were genotyped at 17 loci and red wolf ancestry decreased along an east-west gradient across the RWEPA. No red wolves were found outside the RWEPA, yet half of individuals found within this area were coyotes. Hybrids composed only 4% of individuals within this landscape despite co-occurrence of the two species throughout the RWEPA. The low proportion of hybrids suggests that a combination of active management and natural isolating mechanisms may be limiting intermixing within this hybrid system. [ABSTRACT FROM AUTHOR]

We used molecular genetic analyses to noninvasively identify individual Amur tigers and define subpopulations of tigers in the Russian Far East. We identified 63 individuals after genotyping 256 feces, 7 hair and 11 blood samples collected within southern, central and northern Sikhote-Alin, as well as Southwest Primorye. Analysis of nuclear DNA at 9 microsatellite loci demonstrated greater genetic similarity between animals from southern and northern Sikhote-Alin (some 500 km apart) than between animals from Ussuriskii State Nature Reserve and Southwest Primorye (less than 10 km apart at their nearest point), suggesting that a true barrier exists preventing movements of tigers between Southwest Primorye and the southern Sikhote-Alin Mountains. [ABSTRACT FROM AUTHOR]

An understanding of a species' diet is required to make sound conservation and management decisions. Traditionally, morphological analyses of undigested hard parts from food items remaining in scats have been used to assess diets. More recently, molecular analyses of scats have been used to identify plant and prey species' DNA, but no studies have compared morphological and molecular diet analyses for large, terrestrial carnivores. We used molecular tools to determine the percentage of black bear and coyote scats that contained 3 common prey species (caribou, moose, and snowshoe hares) in Newfoundland and compared the results to a traditional morphological analysis. We found that a ranking of relative prey frequencies was consistent between the 2 methods, but molecular methods tended to detect prey species in a greater percentage of scats for all prey species. However, there were individual scats in which a prey species was detected by morphological methods only, and we provide evidence that molecular methods could result in false negatives if prey DNA is not uniformly distributed throughout a scat or as a result of PCR inconsistency. We also found that the per sample cost comparison between morphological and molecular analyses was dependent upon whether or not a molecular test was needed to identify scats to the predator species, the cost of developing molecular methods, and the number of samples being processed. We recommend that controlled feeding studies be performed to validate molecular methods and investigate the utility of molecular techniques to estimate the proportions of food items consumed. [ABSTRACT FROM AUTHOR]

Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn ( Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling ( NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA ( nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples >7 days old and estimate that a sampling interval of 4-7 days in summer conditions (i.e. extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency. [ABSTRACT FROM AUTHOR]

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 (mt DNA) and nuclear (n DNA) 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, mt DNA amplification success was ≥95% through day 21. Fox n DNA amplification success was ≥70% through day 21 across seasons. Coyote n DNA 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. [ABSTRACT FROM AUTHOR]

Reintroduction is an effective tool for restoring endangered populations. There is increasing concern, however, that demographic restoration may not equate with genetic restoration. We examine the demographic-genetic contrast in the context of one of the world's most successful carnivore population restorations. Beginning in 1982, a total of 835 river otters L ontra canadensis were reintroduced to Missouri, USA, more than 50 years after extirpation. Most otters were translocated from Louisiana, USA, and released at 43 sites across the state. An estimated population of 11 000-18 000 otters existed by 2000, and density estimates for Missouri otters are now similar to those reported for populations across the continent, indicating demographic recovery. We used microsatellite genotyping and mitochondrial sequence analysis of DNA extracted from fecal samples from eight southern Missouri rivers, in conjunction with mitochondrial DNA ( mtDNA) analyses from several native Louisiana otter populations, to evaluate the genetic diversity and population structure of otters within Missouri as compared with Louisiana. The Missouri population showed moderate to high heterozygosity and allelic diversity, similar to that of the source populations, but low mtDNA haplotype diversity. We detected five distinct genetic clusters distributed throughout the eight rivers, with no evidence of isolation by distance. These data collectively suggest that 30 years after restoration efforts commenced, Missouri river otters have retained genetic diversity levels similar to those of the source populations, but that genetic structure has not reached an equilibrium between migration and genetic drift. Thus, the Missouri otter population has made a robust recovery despite retaining the genetic signature of the reintroduction. [ABSTRACT FROM AUTHOR]

Genetic identification of aqueous environmental DNA (eDNA) provides site occupancy inferences for rare aquatic macrofauna that are often easier to obtain than direct observations of organisms. This relative ease makes eDNA sampling a valuable tool for conservation biology. Research on the origin, state, transport, and fate of eDNA shed by aquatic macrofauna is needed to describe the spatiotemporal context for eDNA-based occupancy inferences and to guide eDNA sampling design. We tested the hypothesis that eDNA is more concentrated in surficial sediments than in surface water by measuring the concentration of aqueous and sedimentary eDNA from an invasive fish, bigheaded Asian carp ( Hypophthalmichthys spp.), in experimental ponds and natural rivers. We modified a simple, low-cost DNA extraction method to yield inhibitor-free eDNA from both sediment and water samples. Carp eDNA was 8–1800 times more concentrated per gram of sediment than per milliliter of water and was detected in sediments up to 132 days after carp removal – five times longer than any previous reports of macrobial eDNA persistence in water. These results may be explained by particle settling and/or retarded degradation of sediment-adsorbed DNA molecules. Compared to aqueous eDNA, sedimentary eDNA could provide a more abundant and longer-lasting source of genetic material for inferring current-or-past site occupancy by aquatic macrofauna, particularly benthic species. However, resuspension and transport of sedimentary eDNA could complicate the spatiotemporal inferences from surface water sampling, which is currently the predominant eDNA-based approach. We discuss these implications in the context of conservation-oriented monitoring in aquatic ecosystems. [ABSTRACT FROM AUTHOR]

Accurate and precise estimates of population size are critical for effective management but can be particularly difficult to achieve for small populations of large carnivores. We approached this challenge by integrating multiple noninvasive data sources into a DNA-based mark-recapture framework to estimate the abundance of the small and endangered Apennine brown bear population. To improve sample size and coverage, we collected hair samples from June to September 2011 by concurrently using 4 noninvasive sampling methods: intensive hair-snagging (forty-three 5×5-km cells and five 12-day sampling sessions) plus secondary sampling methods (bear rub trees, alpine buckthorn aggregations, and incidental sampling). Following marker selection based on tissue samples from 55 Apennine bears, we used 13 microsatellites (plus gender) and quality assurance protocols to identify multilocus genotypes from hair samples. We used Huggins closed models in program MARK to estimate population size, which allowed us to account for spatial, temporal, and demographic components of heterogeneity in secondary sampling methods. Based on 529 analyzed hair samples, 80.5% of which yielded high-confidence scores for all markers, we achieved a rather precise ( CV = 7.9%) population estimate of 51 bears (95% CI = 47-66) including cubs. Compared to a previous survey in 2008, our results provide evidence that the Apennine brown bear population has not been declining in recent years. Additionally, the relatively high (closure corrected) density (39.7 bears/1,000 km2; 95% CI = 36.6-51.4) indicates that habitat productivity within the core range is currently adequate for bears and that effective conservation of this small bear population should aim to expand the bears' range across a larger portion of the central Apennines. We examined if a reduction in sampling effort would affect the precision of our population estimates. Reduced sample coverage, small sample size, and low hair-trap-capture probability preclude the adoption of a single sampling method or a subset of such to survey small bear populations if a comparable level of precision is required. [ABSTRACT FROM AUTHOR]