EcoGenomics students and postdoctoral fellows presented their recent findings at the North American Caribou Workshop (NACW) earlier this month. The NACW is held every two years and is a central event for sharing Indigenous knowledge, science and lessons learned, reporting on caribou status and discussing approaches to address key challenges to caribou conservation, management and recovery.
Dr. Rebecca Taylor
EcoGenomics Postdoctoral Fellow
Presentation: Demographic history reconstruction in Western Canada reveals major diversification, divergent histories and genetic structure within mountain caribou
Abstract: Pleistocene glacial cycles influenced the diversification of high-latitude wildlife species, such as caribou. There has been a lot of research on the demographic history of caribou since the Last Glacial Maximum (LGM) and the consequences on contemporary genetic structure and Designatable Units (DUs) for conservation. However, glacial cycles before the LGM also likely impacted contemporary genetic patterns. We investigate diversification and the introgressive history of caribou (Rangifer tarandus) in western Canada, including caribou from northern mountain, southern mountain, central mountain, boreal, and barren-ground DUs, using 33 high-coverage whole genomes coupled with ~1,700 mitochondrial DNA sequences. We found that a major diversification of caribou occurred around 110 kya, the start of the last glacial period, with effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals. We found genetic divergence and different demographic histories even within DUs, especially within the northern mountain caribou DU. Mitochondrial DNA dated introgression events prior to the LGM, even as ancient as 60 kya, coinciding with colder periods with extensive ice coverage. We highlight the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of caribou diversity. Differences in demographic history and genetic variation within DUs suggest that current DUs insufficiently capture evolutionary histories and natural genetic diversity. However, the genetic variation that was shaped by different glacial periods may be of importance for caribou facing climate change. Our reconstruction of the origins, differential introgressive history, and genetic structuring of the mountain caribou DUs thus has implications for their conservation.
EcoGenomics PhD student
Presentation: Genomic regions of high variation maintained across caribou populations despite inbreeding
Abstract: Caribou populations are declining across their range in Canada and becoming increasingly isolated; thus, understanding the effects of inbreeding on genetic potential is pertinent for conservation. Typically emerging in small and isolated populations, inbreeding increases the proportion of homozygous sites across the genome, which can be quantified as runs of homozygosity (ROH). We quantified ROH in high-coverage whole genomes of boreal caribou from small, isolated populations in Ontario, Canada, in comparison to caribou from the continuous range of Ontario, other caribou ecotypes in Canada, and western Greenland. The populations we sampled present divergent evolutionary histories, differing population sizes, and extents of isolation. We conducted BLAST searches across regions of elevated heterozygosity to identify genes that have maintained variation despite inbreeding. As predicted, caribou from recently declined populations in Ontario had a large proportion of their genome in long ROH. We observed even larger proportions but shorter ROH in western Greenland, indicating inbreeding has occurred over a longer period in comparison to other populations. We observed the least inbreeding in barren-ground and eastern migratory caribou, which occur in larger population sizes than boreal caribou. Despite vastly different inbreeding extents, we found regions of high heterozygosity maintained across all populations. Within these islands of heterozygosity, we identified genes associated with cellular processes, biological regulation, metabolism, stimulus response, signaling, and immunity. In this study, we confirm inbreeding in isolated populations of caribou in Ontario and Greenland but uncover high variation in some genes maintained across divergent populations despite inbreeding, suggesting strong balancing selection.
EcoGenomics Technologist and Advisor
Poster: The Caribou Genomics Applications and Technology (CGAT) Database: a web portal to support data access and analysis
Abstract: As interest in non-invasive genetic sampling increases, it is imperative to develop efficient data organizational methods to streamline workflow and ensure that standardized methods are applied when generating data. To accomplish this, we developed two main web-based platforms that store and process large datasets and keep track of field records and associated protocols.