Individual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling ...identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy‐nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01–0.0001).
Evaluating fine-scale population structure of multiple species in the same landscape increases our ability to identify common patterns as well as discern ecological differences among species' ...landscape genetic relationships. In the Palouse bioregion of northern Idaho, USA, 99% of the native prairie has been converted to nonirrigated agriculture and exotic grasslands. Columbia spotted frogs (Rana luteiventris) and long-toed salamanders (Ambystoma macrodactylum) in this area breed almost entirely in artificial ponds on private land. We used genetic distances (FST and Dc) derived from eight microsatellite loci in 783 samples to evaluate the relationships among sympatric breeding populations (N = 20 and 26) of these species in a 213-km² landscape. Both species showed a pattern of isolation by distance that was not improved when distance was measured along drainages instead of topographically corrected straight lines (P < 0.01). After testing for autocorrelation among genetic distances, we used an information theoretic approach to model landscape resistance based on slope, soil type, solar insolation, and land cover, and multi-model inference to rank the resistance of landscape surfaces to dispersal (represented by genetic distance). For both species, urban and rural developed land cover provided the highest landscape resistances. Resistance values for long-toed salamanders followed a moisture gradient where forest provided the least resistance, while agriculture and shrub/clearcut provided the least resistance for Columbia spotted frogs. Comparative landscape genetics can be a powerful tool for detecting similarities and differences between codistributed species, and resulting models can be used to predict species-specific responses to landscape change.
Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using ...conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology, conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.
A large microsatellite data set from three species of bear (Ursidae) was used to empirically test the performance of six genetic distance measures in resolving relationships at a variety of scales ...ranging from adjacent areas in a continuous distribution to species that diverged several million years ago. At the finest scale, while some distance measures performed extremely well, statistics developed specifically to accommodate the mutational processes of microsatellites performed relatively poorly, presumably because of the relatively higher variance of these statistics. At the other extreme, no statistic was able to resolve the close sister relationship of polar bears and brown bears from more distantly related pairs of species. This failure is most likely due to constraints on allele distributions at microsatellite loci. At intermediate scales, both within continuous distributions and in comparisons to insular populations of late Pleistocene origin, it was not possible to define the point where linearity was lost for each of the statistics, except that it is clearly lost after relatively short periods of independent evolution. All of the statistics were affected by the amount of genetic diversity within the populations being compared, significantly complicating the interpretation of genetic distance data.
Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of ...genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term 'landscape genetics', provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.
Genetic monitoring has rarely been used for wildlife translocations despite the potential benefits this approach offers, compared to traditional field-based methods. We applied genetic monitoring to ...the reintroduced brown bear population in northern Italy. From 2002 to 2008, 2781 hair and faecal samples collected noninvasively plus 12 samples obtained from captured or dead bears were used to follow the demographic and geographical expansion and changes in genetic composition. Individual genotypes were used to reconstruct the wild pedigree and revealed that the population increased rapidly, from nine founders to >27 individuals in 2008 (λ = 1.17-1.19). Spatial mapping of bear samples indicated that most bears were distributed in the region surrounding the translocation site; however, individual bears were found up to 163 km away. Genetic diversity in the population was high, with expected heterozygosity of 0.74-0.79 and allelic richness of 4.55-5.41. However, multi-year genetic monitoring data showed that mortality rates were elevated, immigration did not occur, one dominant male sired all cubs born from 2002 to 2005, genetic diversity declined, relatedness increased, inbreeding occurred, and the effective population size was extremely small (Ne = 3.03, ecological method). The comprehensive information collected through genetic monitoring is critical for implementing future conservation plans for the brown bear population in the Italian Alps. This study provides a model for other reintroduction programmes by demonstrating how genetic monitoring can be implemented to uncover aspects of the demography, ecology and genetics of small and reintroduced populations that will advance our understanding of the processes influencing their viability, evolution, and successful restoration.
Knowledge about recruitment in a population can be critical when making conservation decisions, particularly for harvested species. Harvest can affect population demography in complex ways and this ...may be particularly true for cooperatively breeding species whose successful reproduction is often linked with complex social dynamics. We currently have a poor understanding of how harvest affects recruitment in cooperatively breeding species. We used non‐invasive genetic sampling and a natural experiment to estimate recruitment in a population of gray wolves Canis lupus before and after harvest in the northern Rocky Mountains, US (2008–2013). We hypothesized that recruitment would decline after hunting and trapping began and that the decline in recruitment would be attributable to the harvest of pups and not to the subtler mechanisms associated with group dynamics and reduced reproductive success. We collected fecal samples from wolves in 10 packs for 6 consecutive years, extracted DNA and genotyped 154 individual pups across 18 microsatellite loci. Population harvest rates averaged 23.8% (sd = 9.2). Our hypothesis that recruitment would decline was supported; survival from 3 to 15 months of age decreased from 0.60 95% confidence interval (CI): 0.48–0.72 without harvest to 0.38 (95% CI: 0.28–0.48) with harvest and recruitment declined from 3.2 (95% CI: 2.1–4.3) to 1.6 (95% CI: 1.1–2.1) pups per pack after harvest was initiated. We cannot unequivocally dismiss other factors that could have reduced recruitment, however, an increase in recruitment when harvest temporarily ceased lends support to our conclusion that harvest reduced recruitment. We attributed just 18–38% of pup mortality directly to harvest and suggest that there are indirect effects of harvest on recruitment that may be associated with changes in group size and structure. Models that do not include both direct and indirect effects of harvest on recruitment may underestimate the potential impact of harvest on population growth in social species.
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.
A growing number of population genetic studies utilize nuclear DNA microsatellite data from museum specimens and noninvasive sources. Genotyping errors are elevated in these low quantity DNA sources, ...potentially compromising the power and accuracy of the data. The most conservative method for addressing this problem is effective, but requires extensive replication of individual genotypes. In search of a more efficient method, we developed a maximum-likelihood approach that minimizes errors by estimating genotype reliability and strategically directing replication at loci most likely to harbor errors. The model assumes that false and contaminant alleles can be removed from the dataset and that the allelic dropout rate is even across loci. Simulations demonstrate that the proposed method marks a vast improvement in efficiency while maintaining accuracy. When allelic dropout rates are low (0-30%), the reduction in the number of PCR replicates is typically 40-50%. The model is robust to moderate violations of the even dropout rate assumption. For datasets that contain false and contaminant alleles, a replication strategy is proposed. Our current model addresses only allelic dropout, the most prevalent source of genotyping error. However, the developed likelihood framework can incorporate additional error-generating processes as they become more clearly understood.
Range expansions by generalists can alter communities and introduce competitive pressures on native species. In the Great Basin Desert, USA, coyotes (Canis latrans Say, 1823) have colonized and are ...now sympatric with native kit foxes (Vulpes macrotis Merriam, 1888). Since both species have similar diets, dietary partitioning may facilitate coexistence. We analyzed coyote and kit fox diets, then compared our results to an earlier study. Because populations are dynamic, we expected that decreases in prey or increases in predator abundance could alter dietary patterns. We found no significant changes in population-level prey diversity for kit foxes or coyotes, but found high levels of dietary overlap between species. We did detect a significant decrease in the relative importance of leporids (family Leporidae) in the diets of both canids, but they remained important for coyotes. The relative importance of small mammals was greater for kit foxes than coyotes, but their importance had not changed significantly over time. We detected significant declines in prey diversity per sample (scat-level dietary diversity) for both canids, suggesting that during a foraging event, individuals may encounter less diverse prey now than historically. These findings suggested that kit foxes and coyotes were not limited by prey, despite high dietary overlap.
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