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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.

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]

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.

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.

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]

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]

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]

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]

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]

ABSTRACT Various monitoring methods have been developed for large carnivores, but not all are practical or sufficiently accurate for long-term monitoring over large spatial scales. From 2009 to 2010, we used a predictive habitat model to locate gray wolf rendezvous sites in 4 study areas in Idaho, USA and conducted noninvasive genetic sampling (NGS) of scat and hair found at the sites. We evaluated species and individual identification PCR success rates across the study areas, and estimated population size with a single-session population estimator using 2 different recapture-coding methods. We then compared NGS population estimates to estimates generated concurrently from telemetry data. We collected 1,937 scat and 166 hair samples and identified 193 unique individuals over 2 years. For fecal DNA samples, species identification success rates were consistently high (>92%) across areas. Individual identification success rates ranged from 78% to 80% in the drier study areas and dropped to 50% in the wettest study area. The degree of agreement between NGS- and telemetry-derived population estimates varied by recapture-coding method with considerable variability in 95% confidence intervals. Population estimates derived from NGS methods were most influenced by the average number of detections per individual. We demonstrate how changes in field effort and recapture-coding method can affect population estimates in a widely used single-session population estimation model. Our study highlights the need to further develop reliable population estimation tools for single-session NGS data, especially those with large differences in capture frequencies among individuals stemming from severe capture heterogeneity (i.e., overdispersion). © 2014 The Wildlife Society. [ABSTRACT FROM AUTHOR]

Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly ( Ursus arctos) and black bear ( Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations in Banff National Park. Conectividad Demográfica para Poblaciones de Úrsidos en Estructuras para Cruce de Vida Silvestre en el Parque Nacional Banff [ABSTRACT FROM AUTHOR]

The Amur tiger, Panthera tigris altaica, is currently distributed across the southern part of the Russian Far East and parts of northeastern China. Most Amur tigers are found in Russia, where their range is fragmented into at least 3 populations (a large population centered in the Sikhote-Alin Mountains and 2 smaller populations in northwest and southwest Primorye Krai). Traditionally, track-based techniques have been used for surveys of tigers in Russia. However, such techniques involve problems such as misinterpretation of track sizes due to snow degradation, and thus, other survey protocols have been needed. This study aimed to identify individuals and estimate population size using noninvasive genetic samples, such as feces, hairs, and saliva, collected from southwest Primorye Krai during 4 winters (2000-2001, 2001-2002, 2002-2003, and 2004-2005). During these winters, we identified 12 tigers (5 males and 7 females) using 10 microsatellite markers. Population size estimated from the 2002-2003 samples was 12 (95% confidence interval = 9-19), which was comparable to the estimate from the track count survey. Of the 3 types of noninvasive genetic samples we collected, feces were the most useful in terms of genotyping success rate and sampling efficiency. The noninvasive genetic methods developed in this study can contribute to population monitoring and management assessment of tiger conservation in the Russian Far East. [ABSTRACT FROM AUTHOR]

Across much of North America, river otter (Lontra canadensis) populations were extirpated or greatly reduced by the early 20th century. More recently, reintroductions have resulted in restored populations and the recommencement of managed trapping. Perhaps the best example of these river otter reintroductions occurred in Missouri, regarded as one of the most successful carnivore recovery programs in history. However, abundance estimates for river otter populations are difficult to obtain and often contentious when used to underpin management activities. We assessed the value of latrine site monitoring as a mechanism for quantifying river otter abundance. Analyses of fecal DNA to identify individual animals may result in an improved population estimate and have been used for a variety of mammal species. We optimized laboratory protocols, redesigned existing microsatellite primers, and calculated genotyping error rates to enhance genotyping success for a large quantity of river otter scat samples. We also developed a method for molecular sexing. We then extracted DNA from 1,421 scat samples and anal sac secretions (anal jelly) collected during latrine site counts along 22-34-km stretches representing 8-77% of 8 rivers in southern Missouri in 2009. Error rates were low for the redesigned microsatellites. We obtained genotypes at 7-10 microsatellite loci for 24% of samples, observing highest success for anal jelly samples (71%) and lowest for fresh samples (collected within 1 day of defecation). We identified 63 otters (41 M, 22 F) in the 8 rivers, ranging from 2 to 14 otters per river. Analyses using program CAPWIRE resulted in population estimates similar to the minimum genotyping estimate. Density estimates averaged 0.24?otters/km. We used linear regression to develop and contrast models predicting population size based on latrine site and scat count indices, which are easily collected in the field. Population size was best predicted by a combination of scats per latrine and latrines per kilometer. Our results provide methodological approaches to guide wildlife managers seeking to initiate similar river otter fecal genotyping studies, as well as to estimate and monitor river otter population sizes. [ABSTRACT FROM AUTHOR]

Studying the ecology and behavior of pack animals often requires that most, or all, of the pack members are sampled. A unique opportunity to sample all gray wolf (Canis lupus) pack members arises during the summer months when reproductive packs localize in rendezvous sites. We collected 155-296 scat and hair samples from each of 5 wolf rendezvous sites in central Idaho to evaluate intrapack relationships and determine the efficacy of noninvasive genetic sampling (NGS) for estimating pack size and family relationships. We detected 65 wolves (5-20 wolves per pack) with NGS, and the pack counts from NGS were the same or higher for adults and the same or slightly lower for pups compared with the counts from observation and telemetry. The wolves in each pack were closely related to one another, and all packs included at least 2 years of offspring from the current breeding pair. Three of the packs had additional breeding adults present. In 1 pack pups were produced by a parent--offspring pair and a pair of their inbred full siblings, indicating multiple cases of inbreeding. This targeted NGS approach shows great promise for studying pack size and wolf social structure without the use of radiotelemetry or direct observations. [ABSTRACT FROM AUTHOR]

Conventional methods for monitoring cougar, Puma concolor, populations involve capture, tagging, and radio-collaring, but these methods are time-consuming, expensive, and logistically challenging. For difficult-to-study species such as cougars, noninvasive genetic sampling (NGS) may be a useful alternative. The ability to identify individuals from samples collected through NGS methods provides many opportunities for developing population-monitoring tools, but the utility of these survey methods is dependent upon collection of samples and accurate genotyping of those samples. In January 2003, we initiated a 3-yr evaluation of NGS methods for cougars using a radio-collared population in Yellowstone National Park (YNP), USA. Our goals were to: 1) determine which DNA collection method, hair snares or snow tracking, provided a better method for obtaining samples for genetic analysis, 2) evaluate reliability of the genetic data derived from hair samples collected in the field, and 3) evaluate the potential of NGS for demographic monitoring of cougar populations. Snow tracking yielded more hair samples and was more cost effective than snagging hair with rub pads. Samples collected from bed sites and natural hair snags (e.g., branch tips, thorn bushes) while snow tracking accurately identified and sexed 22 individuals (9 F, 13 M). The ratio of the count from snow tracking to the count from radio-telemetry was 15:24 in winter 2004, 13:12 in 2005, and 22:29 for both years combined. Annual capture probabilities for obtaining DNA from snow tracking varied considerably between years for females (0.42 in 2004 and 0.88 in 2005) but were more consistent for males (0.77 in 2004 and 0.88 in 2005). Our results indicate that snow tracking can be an efficient, reliable NGS method for cougars in YNP and has potential for estimating demographic and genetic parameters of other carnivore populations in similar climates. [ABSTRACT FROM AUTHOR]

The article presents the study on appropriate microsatellite markers for the production of multiplex sets to be used in the noninvasive population genetic study of the Tatra chamois Rupicapra rupicapra tatrica. For the optimisation of three multiplex sets, the polymorphic loci were used, that revealed a mean number of alleles of 2.1 and mean expected heterozygosity of 0.331 for the Tatra population. The Low Tatra population showed low genetic diversity compared to slightly higher values taken for Alpine chamois population in Slovenský raj. It determined the effectivity of the developed polymorphic microsatellite sets as a tool for population genetic study of the endangered Tatra chamois.

nthropogenic habitat loss and fragmentation have been implicated in the endangerment and extinction of many species. Here we assess genetic variation and demographic history in the southernmost population of giant pandas ( Ailuropoda melanoleuca) that continues to be threatened by habitat degradation and fragmentation, using noninvasive genetic sampling, mitochondrial control region sequence and 12 microsatellite loci. Compared to other giant panda populations, this population has medium-level genetic diversity based on the measure of both mitochondrial and nuclear markers. Mitochondrial DNA-based demographic analyses revealed that no historical population expansion or contraction has occurred, indicating a relatively stable population size. However, a Bayesian-coalescent method based on the observed allele distribution and allele frequencies of microsatellite clearly did detect, quantify and date a recent decrease in population size. Overall, the results indicate that a population contraction in the order of 95-96% has taken place over the last 910-999 years and is most likely due to anthropogenic habitat loss. These findings highlight the need for a greater focus on habitat protection and restoration for the long-term survival of this giant panda population. [ABSTRACT FROM AUTHOR]

Wildlife managers need reliable estimates of population size, trend, and distribution to make informed decisions about how to recover at-risk populations, yet obtaining these estimates is costly and often imprecise. The grizzly bear (Ursus arctos) population in northwestern Montana, USA, has been managed for recovery since being listed under the United States Endangered Species Act in 1975, yet no rigorous data were available to evaluate the program's success. We used encounter data from 379 grizzly bears identified through bear rub surveys to parameterize a series of Pradel model simulations in Program MARK to assess the ability of noninvasive genetic sampling to estimate population growth rates. We evaluated model performance in terms of 1) power to detect gender-specific and population-wide declines in population abundance, 2) precision and relative bias of growth rate estimates, and 3) sampling effort required to achieve 80% power to detect a decline within 10 years. Simulations indicated that ecosystem-wide, annual bear rub surveys would exceed 80% power to detect a 3% annual decline within 6 years. Robust-design models with 2 simulated surveys per year provided precise and unbiased annual estimates of trend, abundance, and apparent survival. Designs incorporating one survey per year require less sampling effort but only yield trend and apparent survival estimates. Our results suggest that systematic, annual bear rub surveys may provide a viable complement or alternative to telemetrybased methods for monitoring trends in grizzly bear populations. [ABSTRACT FROM AUTHOR]

Noninvasive genetic sampling has become a popular method for obtaining population parameter estimates for black (Ursus americanus) and brown (U. arctos) bears. These estimates allow wildlife managers to develop appropriate management strategies for populations of concern. Black bear populations at Great Dismal Swamp (GDSNWR), Pocosin Lakes (PLNWR), and Alligator River (ARNWR) National Wildlife Refuges in coastal Virginia and North Carolina, USA, were perceived by refuge biologists to be at or above cultural and perhaps biological carrying capacity, but managers had no reliable abundance estimates upon which to base population management. We derived density estimates from 3,150 hair samples collected noninvasively at each of the 3 refuges, using 6-7 microsatellite markers to obtain multilocus genotypes for individual bears. We used Program MARK to calculate population estimates from capture histories at each refuge. We estimated densities using both traditional buffer strip methods and Program DENSITY. Estimated densities were some of the highest reported in the literature and ranged from 0.46 bears/km² at GDSNWR to 1.30 bears/km² at PLNWR. Sex ratios were male-biased at all refuges. Our estimates can be directly utilized by biologists to develop effective strategies for managing and maintaining bears at these refuges, and noninvasive methods may also be effective for monitoring bear populations over the long term. [ABSTRACT FROM AUTHOR]

Sampling DNA noninvasively has advantages for identifying animals for uses such as mark–recapture modeling that require unique identification of animals in samples. Although it is possible to generate large amounts of data from noninvasive sources of DNA, a challenge is overcoming genotyping errors that can lead to incorrect identification of individuals. A major source of error is allelic dropout, which is failure of DNA amplification at one or more loci. This has the effect of heterozygous individuals being scored as homozygotes at those loci as only one allele is detected. If errors go undetected and the genotypes are naively used in mark–recapture models, significant overestimates of population size can occur. To avoid this it is common to reject low-quality samples but this may lead to the elimination of large amounts of data. It is preferable to retain these low-quality samples as they still contain usable information in the form of partial genotypes. Rather than trying to minimize error or discarding error-prone samples we model dropout in our analysis. We describe a method based on data augmentation that allows us to model data from samples that include uncertain genotypes. Application is illustrated using data from the European badger ( Meles meles). [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. [ABSTRACT FROM AUTHOR]

Estimation of abundance is important for assessing population responses to management actions. Accurate abundance estimates are particularly critical for monitoring temporal variation following reintroductions when the management goal is to attain population sizes capable of sustaining harvest. Numerous reintroductions have taken place in the Great Lakes region of North America, including efforts to restore extirpated fishers (Martes pennanti) and American martens (M. americana). We used a DNA-based noninvasive hair-snaring method based on one trap design and trapping -grid configuration, and evaluated capture-mark-recapture (CMR) analytical approaches to simultaneously estimate population size for co-distributed fishers and American martens in a 671-km7sup2; area of the Ottawa National Forest in the western Upper Peninsula of Michigan, USA. We included harvest as a final recapture period to increase probability of recapture and to evaluate potential violations of geographic closure assumptions. We used microsatellite markers to identify target species, eliminate congener species, and provide individual identity for estimation of abundance. Population estimates for fishers and martens on the study area ranged from 35 to 60 and 8 to 28, respectively. Estimators incorporating harvest data resulted in up to a 40% increase in abundance estimates relative to estimators without harvest. We considered population estimates not including harvest data the most appropriate for the study due to timing of sampling and environmental factors, but inclusion of harvested individuals was shown to be useful as a means to detect violations of the assumption of geographic closure. We suggest improvements on future CMR sampling designs for larger landscape scales of relevance to management through incorporation of habitat or historical harvest data. Noninvasive genetic methods that simultaneously estimate the numerical abundance of co-distributed species can greatly decrease assessment costs relative to traditional methods, and increase resulting demographic and ecological information. [ABSTRACT FROM AUTHOR]

We present the first rigorous estimate of grizzly bear (Ursus arctos) population density and distribution in and around Glacier National Park (GNP), Montana, USA. We used genetic analysis to identify individual bears from hair samples collected via 2 concurrent sampling methods: 1) systematically distributed, baited, barbed-wire hair traps and 2) unbaited bear rub trees found along trails. We used Huggins closed mixture models in Program MARK to estimate total population size and developed a method to account for heterogeneity caused by unequal access to rub trees. We corrected our estimate for lack of geographic closure using a new method that utilizes information from radiocollared bears and the distribution of bears captured with DNA sampling. Adjusted for closure, the average number of grizzly bears in our study area was 240.7 (95% CI = 202-303) in 1998 and 240.6 (95% CI = 205-304) in 2000. Average grizzly bear density was 30 bears/ 1,000 km², with 2.4 times more bears detected per hair trap inside than outside GNP. We provide baseline information important for managing one of the few remaining populations of grizzlies in the contiguous United States. [ABSTRACT FROM AUTHOR]

The article reports on the research conducted by John Boulanger and colleagues on the significance of multiple data sources to improve DNA-based mark-recapture population of Grizzly bears in the U.S. It reveals that the primary challenge in estimating the population size of mark-recapture method is heterogenous capture probabilities and subsequent bias of population estimates. To address the situation, one must have a substantial sampling effort of some species. Researchers formulated a methodology that uses two data sources to deal with heterogeneity and applied it to DNA mark-recapture data. With such process, they were able to improve population estimates of the bears.

Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field. [ABSTRACT FROM AUTHOR]

Resolving conflicts between predators and livestock producers depends on obtaining reliable information about the predators that kill livestock. We used salivary DNA obtained from attack wounds on domestic sheep carcasses to identify the species of predator responsible for the kill, as well as the sex and individual identity of coyotes (Canis latrans) that killed sheep. Coyotes killed 36 of 37 depredated sheep. Breeding pairs whose territories overlapped sheep grazing areas were the primary predators on domestic sheep, and only breeding pairs killed multiple sheep. Breeding males, acting alone or with their mate, were involved in 21 of 25 kills. Breeding females participated in 13 kills, but only 1 breeding female killed sheep on her own. Transient females did not kill sheep, and both kills by transient males occurred in territories with a breeding vacancy. Our results suggest that predator control should be targeted at breeding male coyotes. Salivary DNA is a potentially powerful means of both investigating predation patterns and evaluating the effectiveness of control at targeting individuals that kill livestock. [ABSTRACT FROM AUTHOR]

The southern hairy-nosed wombat (Lasiorhinus latifrons) is a cryptic, primarily nocturnal marsupial, for which behavioral information is notably lacking. Animals that are difficult to observe can be identified and tracked by individual-specific genotypes obtained from remotely collected DNA sources; wombats are excellent candidates for such an approach because freshly plucked hair is easily captured at burrow entrances. Twice a year during 1999-2001, we employed an intensive remote hair-collection regime coupled with individual-resolution genetic analysis to sample a South Australian population in a 63.3-km² protected conservation reserve. Individuals were identified using 5 highly polymorphic microsatellite markers and further examined using another 10 markers to resolve ambiguities, enabling assessment of burrow- and space-use patterns. Analyses of rate of discovery of new individuals indicated that nearly all wombats inhabiting the study area were detected (102); there were > 1,000) "capture" events, and 90% of individuals were detected multiple times. Surprisingly, a female sex bias existed despite females being the dispersing sex. Space use was conservative and likely a reflection of adaptations enabling energy conservation. Transits between the northern and southern sections of the study area were nearly nonexistent. No sex or consistent seasonal differences were found in burrow, warren, or space use, other than in interaction with other factors. However, a strong increase in activity and space use in September 2001 relative to other sampling periods may be attributed to activities associated with mating. The thoroughness and evenness of this study's sampling strategy was markedly effective for this species, as, with appropriate modification and optimization, it will likely be for other shy and cryptic organisms. [ABSTRACT FROM AUTHOR]

Noninvasive genetic sampling provides great potential for research and management applications in wildlife biology. Researchers can obtain DNA from a variety of sources including hair, feces, urine, feathers, shed skin, saliva, and egg shells without handling or observing animals. These samples can then be used to identify tile presence of rare or elusive species, count and identify individuals, determine gender, and identify diet items, or samples can be used to evaluate genetic diversity, population structure, and mating system. We review tile recent advancements and techniques used for identifying species, individuals, and gender. We also address tile potential pitfalls of noninvasive genetic sampling and provide recommendations for laboratory- and field-based methods to improve the reliability and accuracy of data collected from noninvasive genetic samples. [ABSTRACT FROM AUTHOR]

Simple Summary: The measurement of stress hormones has become a widely used and effective tool for evaluating adrenocortical activity in animals. However, to correctly interpret stress measurements, the potential sampling bias resulting from an oversampling of individuals in different states of pregnancy has rarely been investigated. We found significant yearly variations in states of pregnancy, which is related to the conditions of the females due to the snow cover duration before and at the start of the reproductive period. These results are important for improving the interpretation of stress hormone concentrations in free-ranging populations during the breeding and reproductive periods. 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. [ABSTRACT FROM AUTHOR]