Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

/pdf/whole-genome-sequences-from-non-invasively-collected-caribou-1zrrdv3h9t.pdf

Whole genome sequences from non-invasively collected caribou faecal samples

Genetic influences on male and female variance in reproductive success and implications for the recovery of severely endangered mountain caribou

In social species, reproductive success and rates of dispersal vary among individuals resulting in spatially structured populations. Network analyses of familial relationships may provide insights on how these parameters influence population-level demographic patterns. These methods, however, have rarely been applied to genetically derived pedigree data from wild populations.Here, we use parent-offspring relationships to construct familial networks from polygamous boreal woodland caribou (Rangifer tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We collected samples from 933 individuals at 15 variable microsatellite loci along with caribou-specific primers for sex identification. Using network measures, we assess the contribution of individual caribou to the population with several centrality measures and then determine which measures are best suited to inform on the population demographic structure. We investigate the centrality of individuals from eighteen different local areas, along with the entire population.We found substantial differences in centrality of individuals in different local areas, that in turn contributed differently to the full network, highlighting the importance of analyzing networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative measures to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and family cohesion across the range. We found varied levels of dispersal, fitness, and cohesion in family groups. Synthesis and applications: Our results demonstrate the value of different network measures in assessing genetically derived familial networks. The spatial application of the familial networks identified individuals presenting different fitness levels, short- and long-distance dispersing ability across the range in support of population monitoring and recovery efforts.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7345

Spatial familial networks to infer demographic structure of wild populations.

https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3443

Integrating counts, telemetry, and non-invasive DNA data to improve demographic monitoring of an endangered species

Genetic networks in ecology: A guide to population, relatedness, and pedigree networks and their applications in conservation biology

Determining age structure of populations is a valuable parameter in wildlife management, but is often difficult to obtain. Here, we tested a noninvasive method via fecal DNA, hormones, and pellet morphometrics to distinguish calf from adult in Central Mountain and Boreal woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)) populations. Annual surveys of fall-sampled Central Mountain caribou were done in Jasper National Park, Alberta, between 2006 and 2011 and winter-sampled Boreal caribou were surveyed in the North Interlake area, Manitoba, between 2004 and 2010. Samples were amplified at 10 microsatellite loci to identify unique individuals and capture histories were used to identify putative calves and adults. Fecal pellets were measured for length, width, depth, dry mass, and analyzed for progesterone, estrogen, and testosterone concentrations. Results showed significant differences in fecal pellet size between putative calves and adults for both sexes and populations–seasons. Progesterone conce...

/pdf/fecal-dna-hormones-and-pellet-morphometrics-as-a-noninvasive-3syj61scif.pdf

Fecal DNA, hormones, and pellet morphometrics as a noninvasive method to estimate age class: an application to wild populations of Central Mountain and Boreal woodland caribou (Rangifer tarandus caribou)

Abstract: An emaciated, 14-yr-old female boreal woodland caribou (Rangifer tarandus caribou) was found dead with an ulcerated wound on the left side of the head. Radiographs documented osteolysis of portions of the mandible and cranium. Histopathology revealed an invasive adenocarcinoma infiltrating the soft tissues and bones of the head.

Invasive Adenocarcinoma of the Head of a Boreal Woodland Caribou (Rangifer tarandus caribou), Alberta, Canada

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Fecal DNA, hormones, and pellet morphometrics as a noninvasive method to estimate age class: an application to wild populations of Central Mountain and Boreal woodland caribou (Rangifer tarandus caribou)

Genetic influences on male and female variance in reproductive success and implications for the recovery of severely endangered mountain caribou

Invasive Adenocarcinoma of the Head of a Boreal Woodland Caribou (Rangifer tarandus caribou), Alberta, Canada