Genomic population structure and inbreeding history of Lake Superior caribou

Abstract

Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), 1 of the 12 Designatable Units, has lost approximately half of its historic range in the last 150 years, particularly along the southern edge of its distribution. Despite this overall northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the continuous boreal caribou range in Ontario, along the coast and nearshore islands of Lake Superior. The population history of caribou along Lake Superior remains unclear. It appears that these caribou likely represent a remnant distribution at the trailing edge of the receding population of boreal caribou, but they may also exhibit local adaptation to the coastal environment. A better understanding of the population structure and history of caribou along Lake Superior is important for their conservation and management. Here, we use high-coverage whole genomes (N = 20) from boreal, eastern migratory, and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate population structure and inbreeding histories. We discovered that caribou from the Lake Superior range form a distinct group but also found some evidence of gene flow with the continuous boreal caribou range. Notably, caribou along Lake Superior demonstrated relatively high levels of inbreeding (measured as runs of homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between ranges. Despite inbreeding, caribou along Lake Superior retained high heterozygosity, particularly in genomic regions without ROH. These results suggest that they present distinct genomic characteristics but also some level of gene flow with the continuous range. Our study provides key insights into the genomics of the southernmost range of caribou in Ontario, beginning to unravel the evolutionary history of these small, isolated caribou populations.

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

“…The genetic erosion captured in the southern range boundaries, particularly in Alberta and the Lake Superior coastal population in Ontario, was further highlighted by lower node-based metric values (closeness centrality and MIW) which could again be indicative of increased fragmentation and isolation of caribou in those regions. These results align with recent genomic studies focusing on runs of homozygosity which found evidence of increased inbreeding in Ontario’s coastal populations (Solmundson et al 2023). The reduced levels of genetic diversity (and hence the associated reduced adaptive potential) in the southern range extent has important management implications for boreal caribou, particularly since some areas showing low genetic diversity are within LPUs (i.e.…”

“…The eastern portion of the range presented overall lower genetic diversity compared to the western portion of the range. The higher baseline genetic diversity in the west could be due to animals in the Northwest Territories being of Beringian-Eurasian Lineage (BEL) origin (Polfus et al 2017), in conjunction with overall higher levels of introgression into the North American Lineages (NAL) in the west – considering that genetic diversity and historical effective population sizes in the Beringian refugia during the Pleistocene were larger (Klütsch et al 2016; Taylor et al 2021; Solmundson et al 2023). By incorporating the first hierarchical community detection partition from the CIP network, we were able to control for the overall variation of genetic diversity between the eastern and western portions of the range and create interpolated raster surfaces that revealed genetic erosion occurring along the southern range periphery in both the east and west.…”

“…We apply this framework to an extensive dataset (4911 unique genotypes) of two woodland caribou ( Rangifer tarandus caribou ) ecotypes occupying the Canadian boreal forest (i.e., boreal and eastern migratory caribou; COSEWIC 2011). Caribou occupying this region present a largely continuous distribution and different phylogenetic origins shaped by past glacial cycles and patterns of introgression and divergence (Klütsch et al 2016; Polfus et al 2017; Taylor et al 2021; Solmundson et al 2023). Wide-ranging species with continuous distributions often have no obvious breaks in population genetic structure to use to a priori partition the dataset into nodes (Perez et al 2018).…”