Browsing by Author "Cavedon, Maria"
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- ItemOpen AccessDesign and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)(2022-10-05) Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, ClaudeAbstract 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.
- ItemOpen AccessEcological genomics and conservation of caribou in Western North America(2020-09-09) Cavedon, Maria; Musiani, Marco; VonHoldt, Bridgett M.; Mariani, Stefano; Hebblewhite, Mark; Darimont, Chris T.; Ruckstuhl, Kathreen E.Selection can favor different phenotypes along environmental clines. Clines are also compatible with balancing forces, which maintain phenotypic polymorphisms within populations -for example, migratory or sedentary behaviour in caribou. The use of genomics is fundamental to evaluate such evolutionary processes and, in conjunction with ecological information, has also been advocated for to inform conservation planning for endangered caribou. I examined Single Nucleotide Polymorphisms (SNPs) across caribou populations from western North America. I detected population structure and genes under selection within each caribou group. I also analysed seasonal movements and habitat selection using GPS telemetry, and morphological information gathered at capture. Some of the genes under selection in my study were linked to morphological characteristics, migratory behavior, habitat selection and climatic and environmental factors. These findings suggest that exclusive mutations, resulting in different phenotypes, are maintained within caribou groups. Moreover, I detected a signal of balancing selection, a genetic force that maintains genetic polymorphisms within populations. I suggest that this force has a fundamental role in maintaining multiple haplotypes and phenotypes within caribou populations, also including partial migration. In this thesis, I identified genes under selection and patterns of population structure that should be considered in conservation planning and management of caribou populations. Habitats and climate are dramatically changing worldwide, and the genetic aspects of selectivity, that I described, could indicate that caribou may be challenged in their ability to adapt to certain changes. For example, my results indicate a specialization of caribou for cold climates and seasonal foraging in pristine environments, with genes linked to these specializations. In addition, as part of conservation planning, caribou breeding programs have been proposed. A fundamental aspect of these programs is deciding the best source animals, from wild populations, to be used to found captive populations. My population structure results could help inform these programs, as I “practically” suggested for the Southern Canadian Rockies region. Overall, I used an integrative and innovative approach to investigate the link between movement ecology, morphology, genomics, with applications to caribou conservation and conservation of other species, in which genetic traits may also influence behaviour, and limit resilience to changing habitats and climates.
- ItemOpen AccessSeasonal movements in caribou ecotypes of Western Canada(2022-03-10) Theoret, Jessica; Cavedon, Maria; Hegel, Troy; Hervieux, Dave; Schwantje, Helen; Steenweg, Robin; Watters, Megan; Musiani, MarcoAbstract 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.