Faecal material has increasingly become an important non-invasive source of DNA for wildlife population genetics. However, DNA from faecal sources can have issues associated with quantity (lowtemplate and/or low target-to-total DNA ratio) and quality (degradation and/or low DNA-to-inhibitor ratio). A number of studies utilizing faecal material assume and compensate for the above properties with minimal characterization of quantity or quality of target DNA, which can unnecessarily increase the risk of downstream technical problems. Here, we present a protocol which quantifies faecal DNA using a two step approach: (1) estimating total DNA concentration using a Picogreen TM fluorescence assay and (2) estimating target nuclear DNA concentration by comparing amplification products of field samples at suspected concentrations to those of control DNA at known concentrations. We applied this protocol to faecal material collected in the field from two species: woodland caribou (Rangifer tarandus) and swift fox (Vulpes velox). Total DNA estimates ranged from 6.5 ng/ll to 28.6 ng/ll (X = 16.2 ng/ll) for the caribou extracts and 1.0-26.1 ng/ll (X = 7.5 ng/ll) for the swift fox extracts. Our results showed high concordance between total and target DNA estimates from woodland caribou faecal extracts, with only 10% of the samples showing relatively lower target-to-total DNA ratios. In contrast, DNA extracts from swift fox scat exhibited low target DNA yields, with only 38% (19 of 50) of the samples showing comparative target DNA amplification of at least 0.1 ng. With this information, we were able to estimate the amount of target DNA entered into PCR amplifications, and identify samples having target DNA below a lower threshold of 0.2 ng and requiring modification to genotyping protocols such as multiple tube amplification. Our results here also show that this approach can easily be adapted to other species where faeces are the primary source of DNA template.

Individual-based clustering (IBC) methods have become increasingly popular for the characterization and delineation of genetic population units for numerous species. These methods delineate populations based on the genetic assumptions of a breeding unit which may provide a better representation of the behaviour of the species. The increasing use of IBC has resulted in the development of several analytical models all of which vary in their theoretical assumptions to infer genetic population structure. In this paper, we report a comparative strategy utilizing three IBC methods to characterize the spatial genetic structure of the boreal population of woodland caribou (Rangifer tarandus caribou) in central Canada. In addition, we implement both tests for isolation-by-distance (IBD) and frequency-based assignment tests to validate the consensus genetic clusters as defined by IBC. We also compare indirect metrics of genetic diversity and gene flow using both a priori defined herds and the IBC defined populations. Although our results show some concordance between both pre-defined herds and IBC derived genetic clusters, the IBC analyses identified a cluster that was cryptic to observation-based caribou herds and found no difference between several adjacent herds. By comparing multiple IBC methods and integrating both IBD and indirect genetic diversity metrics a posteriori, our strategy provides an effective means to delineate wildlife population structure and accurately assess genetic diversity and connectivity.

Outbreaks of many vector‐borne human diseases are broadly correlated with climatic variation, but evidence of similar fluctuations in disease in natural host populations is rare. Here, we use 21 years of monitoring of black‐tailed prairie dog (Cynomys ludovicianus) colonies to demonstrate a link between extinctions of colonies attributed to plague (Yersinia pestis) and climatic fluctuations associated with El Ninì Southern Oscillation events that promote the growth of flea vector and rodent host populations. During epizootics, rates of extinction of the largest colonies (>16 ha) were nearly as high (>60%) as for the smallest ones (<3 ha), but only a third of intermediate‐sized colonies were extirpated. The probability of extinction was influenced by the size and fate of adjacent colonies, but there was no predictable relationship between extinction probabilities and intercolony distance, indicating that spatial isolation does not reduce the vulnerability of colonies to plague. By causing sporadic extinctions of colonies, plague creates a metapopulation structure that has altered the dynamics of prairie dog colonies as they respond to a century of human persecution and habitat loss.

Elaphostrongylus rangiferi was introduced to caribou (Rangifer tarandus caribou) of Newfoundland by infected reindeer (R. t. tarandus) from Norway and has caused at least two epizootics of cerebrospinal elaphostrongylosis (CSE), a debilitating neurologic disease. In an attempt to understand the conditions necessary for such outbreaks, we examined the effects of herd density and climatic factors on parasite abundance. The abundance of E. rangiferi was represented by counts of first-stage larvae in feces collected from young caribou (calves and yearlings) in 7 distinct caribou herds in Newfoundland. Abundance of E. rangiferi was highest in February and in the Avalon (632 ± 14 (mean ± SE)) and St. Anthony (526 ± 145) herds, the 2 herds in which CSE was most frequently reported. Mean abundance in February samples from young animals correlated positively with mean annual minimum temperature (rS = 0.829, df = 6, P = 0.04) and the number of days per year above 0°C (rS = 0.812, df = 6, P = 0.05) and negatively with mean summer temperatures (rS = –0.830, df = 6, P = 0.04). Results suggest that abundance of E. rangiferi and the likelihood of cases of CSE are increased by moderate summer temperatures suitable for the activity and infection of gastropod intermediate hosts and by mild winters with little snow that extend the transmission period. Abundance of larvae was not correlated with herd density. Animals in all 7 herds also had the muscle worm Parelaphostrongylus andersoni, a related nematode with similar dorsal-spined larvae. In 2 additional herds (Cape Shore and Bay de Verde), P. andersoni occurred alone and larvae were passed only by young caribou. In herds with dual infections, numbers of P. andersoni larvae were depressed, declined more quickly in young animals, and were considered to be present in only low numbers in February samples used for E. rangiferi analysis. Upon initial infection, young caribou develop a resistance to E. rangiferi that prevents or reduces reinfection later in life. This was demonstrated by examining the brains of caribou for recently acquired worms, which must develop there for up to 90 days before continuing their tissue migration into the skeletal muscles. Recent infections were detected in only calves and yearlings in all herds with E. rangiferi except the Avalon herd, where developing worms were also found on the brains of older caribou. The infection of older animals in the Avalon herd may reflect a lower immunocompetence of a naive herd that has only recently been exposed to E. rangiferi.