Genomics of founders for conservation breeding: the Jasper caribou case.

Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species. Supplementary Information: The online version contains supplementary material available at 10.1007/s10592-023-01540-3.

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus).

BACKGROUND: Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS: From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION: This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Seasonal movements in caribou ecotypes of Western Canada.

BACKGROUND: Several migratory ungulates, including caribou, are dramatically declining. Caribou of the Barren-ground ecotype, which forms its own subspecies, are known to be mainly migratory. By contrast, within the Woodland subspecies, animals of the Boreal ecotype are known to be mainly sedentary, while those within the Northern and Central Mountain ecotypes to be partially migratory, with only some individuals migrating. Promotion of conservation actions (e.g., habitat protection) that are specific to both residents and migrants, as well as to the areas they frequent seasonally (which may be separate for migrants), requires distinguishing migration from other movement behaviours, which might be a challenge. METHODS: We aimed at assessing seasonal movement behaviours, including migratory, resident, dispersing, and nomadic, for caribou belonging to the Barren-ground and Woodland subspecies and ecotypes. We examined seasonal displacement, both planar and altitudinal, and seasonal ranges overlap for 366 individuals that were GPS-collared in Northern and Western Canada. Lastly, we assessed the ability of caribou individuals to switch between migratory and non-migratory movement behaviours between years. RESULTS: We detected migratory behaviour within each of the studied subspecies and ecotypes. However, seasonal ranges overlap (an index of sedentary behaviour) varied, with proportions of clear migrants (0 overlap) of 40.94% for Barren-ground caribou and 23.34% for Woodland caribou, and of 32.95%, 54.87%, and 8.86% for its Northern Mountain, Central Mountain, and Boreal ecotype, respectively. Plastic switches of individuals were also detected between migratory, resident, dispersing, and nomadic seasonal movements performed across years. CONCLUSIONS: Our unexpected findings of marked seasonal movement plasticity in caribou indicate that this phenomenon should be better studied to understand the resilience of this endangered species to habitat and climatic changes. Our results that a substantial proportion of individuals engaged in seasonal migration in all studied ecotypes indicate that caribou conservation plans should account for critical habitat in both summer and winter ranges. Accordingly, conservation strategies are being devised for the Woodland subspecies and its ecotypes, which were found to be at least partially migratory in this study. Our findings that migration is detectable with both planar and altitudinal analyses of seasonal displacement provide a tool to better define seasonal ranges, also in mountainous and hilly environments, and protect habitat there.

Selection of both habitat and genes in specialized and endangered caribou.

Genetic mechanisms determining habitat selection and specialization of individuals within species have been hypothesized, but not tested at the appropriate individual level in nature. In this work, we analyzed habitat selection for 139 GPS-collared caribou belonging to three declining ecotypes sampled throughout Northwestern Canada. We used Resource Selection Functions (RSFs) comparing resources at used and available locations. We found that the three caribou ecotypes differed in their use of habitat suggesting specialization. On expected grounds, we also found differences in habitat selection between summer and winter, but also, originally, among the individuals within an ecotype. We next obtained Single Nucleotide Polymorphisms (SNPs) for the same caribou individuals, we detected those associated to habitat selection, and then identified genes linked to these SNPs. These genes had functions related in other organisms to habitat and dietary specializations, and climatic adaptations. We therefore suggest that individual variation in habitat selection was based on genotypic variation in the SNPs of individual caribou, indicating that genetic forces underlie habitat and diet selection in the species. We also suggest that the associations between habitat and genes that we detected may lead to lack of resilience in the species, thus contributing to caribou endangerment. Our work emphasizes that similar mechanisms may exist for other specialized, endangered species. This article is protected by copyright. All rights reserved.

Genomic legacy of migration in endangered caribou.

Wide-ranging animals, including migratory species, are significantly threatened by the effects of habitat fragmentation and habitat loss. In the case of terrestrial mammals, this results in nearly a quarter of species being at risk of extinction. Caribou are one such example of a wide-ranging, migratory, terrestrial, and endangered mammal. In populations of caribou, the proportion of individuals considered as "migrants" can vary dramatically. There is therefore a possibility that, under the condition that migratory behavior is genetically determined, those individuals or populations that are migratory will be further impacted by humans, and this impact could result in the permanent loss of the migratory trait in some populations. However, genetic determination of migration has not previously been studied in an endangered terrestrial mammal. We examined migratory behavior of 139 GPS-collared endangered caribou in western North America and carried out genomic scans for the same individuals. Here we determine a genetic subdivision of caribou into a Northern and a Southern genetic cluster. We also detect >50 SNPs associated with migratory behavior, which are in genes with hypothesized roles in determining migration in other organisms. Furthermore, we determine that propensity to migrate depends upon the proportion of ancestry in individual caribou, and thus on the evolutionary history of its migratory and sedentary subspecies. If, as we report, migratory behavior is influenced by genes, caribou could be further impacted by the loss of the migratory trait in some isolated populations already at low numbers. Our results indicating an ancestral genetic component also suggest that the migratory trait and their associated genetic mutations could not be easily re-established when lost in a population.

Genomics, environment and balancing selection in behaviourally bimodal populations: The caribou case.

Selection forces that favour different phenotypes in different environments can change frequencies of genes between populations along environmental clines. Clines are also compatible with balancing forces, such as negative frequency-dependent selection (NFDS), which maintains phenotypic polymorphisms within populations. For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioural trait prominent in species where only a fraction of the population seasonally migrates. Overall, NFDS is believed to be a common phenomenon in nature, yet a scarcity of studies were published linking naturally occurring allelic variation with bimodal or multimodal phenotypes and balancing selection. We applied a Pool-seq approach and detected selection on alleles associated with environmental variables along a North-South gradient in western North American caribou, a species displaying partially migratory behaviour. On 51 loci, we found a signature of balancing selection, which could be related to NFDS and ultimately the maintenance of the phenotypic polymorphisms known within these populations. Yet, remarkably, we detected directional selection on a locus when our sample was divided into two behaviourally distinctive groups regardless of geographic provenance (a subset of GPS-collared migratory or sedentary individuals), indicating that, within populations, phenotypically homogeneous groups were genetically distinctive. Loci under selection were linked to functional genes involved in oxidative stress response, body development and taste perception. Overall, results indicated genetic differentiation along an environmental gradient of caribou populations, which we found characterized by genes potentially undergoing balancing selection. We suggest that the underlining balancing force, NFDS, plays a strong role within populations harbouring multiple haplotypes and phenotypes, as it is the norm in animals, plants and humans too.

High prevalence of prion protein genotype associated with resistance to chronic wasting disease in one Alberta woodland caribou population.

Chronic wasting disease (CWD) is a prion disease found in deer, elk and moose in North America and since recently, wild reindeer in Norway. Caribou are at-risk to encounter CWD in areas such as Alberta, Canada, where the disease spreads toward caribou habitats. CWD susceptibility is modulated by species-specific polymorphisms in the prion protein gene (Prnp). We sequenced Prnp of woodland caribou from 9 Albertan populations. In one population (Chinchaga) a significantly higher frequency of the 138N allele linked to reduced CWD susceptibility was observed. These data are relevant for developing CWD management strategies including conservation of threatened caribou populations.