Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Drake, Christine; Manseau, Micheline; Klütsch, Cornelya F. C.; Priadka, Pauline; Wilson, Paul J.; Kingston, S. David; Carr, Natasha L.

doi:10.7557/2.38.1.4124

Cited by 4 publications

(10 citation statements)

References 19 publications

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“…This dataset was assembled primarily from caribou fecal samples collected during winters of 2005-2011. Island populations (i.e., Slate Islands, Michipicoten Island, and Pic Island) were not included in this study as they are isolated, disjoint from the continuous mainland distribution and experiencing genetic drift (Drake et al, 2018). Fecal samples collected during the winter generally produced relatively high yields of DNA (Ball et al, 2007), which minimized genotyping error rates (see Hettinga et al, 2012).…”

Section: Study Area and Samplingmentioning

confidence: 99%

“…Fecal samples collected during the winter generally produced relatively high yields of DNA (Ball et al, 2007), which minimized genotyping error rates (see Hettinga et al, 2012). Island populations (i.e., Slate Islands, Michipicoten Island, and Pic Island) were not included in this study as they are isolated, disjoint from the continuous mainland distribution and experiencing genetic drift (Drake et al, 2018).…”

Section: Study Area and Samplingmentioning

confidence: 99%

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Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

Thompson

Klütsch

Manseau

et al. 2019

Ecology and Evolution

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With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on RST and FST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the RST network. The FST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.

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Section: Study Area and Samplingmentioning

confidence: 99%

Section: Study Area and Samplingmentioning

confidence: 99%

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

Thompson

Klütsch

Manseau

et al. 2019

Ecology and Evolution

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“…Notably, the caribou from Cochrane has undergone less inbreeding than the other Ontario boreal caribou sampled and had the least IBD ROH with the Michipicoten Island caribou. Previous research based on microsatellite data suggested Michipicoten Island and Pukaskwa National Park belong to a different genetic cluster than the nearby boreal caribou from Cochrane (Drake et al, 2018).…”

Section: Inbreeding Historiesmentioning

confidence: 90%

“…Caribou disappeared from the park in 2011, and reappeared in 2015, perhaps due to colonization from one of the Lake Superior islands. One of the last caribou captured on wildlife cameras deployed in Pukaskwa National Park had small, malformed antlers, which was suggested to be a sign of inbreeding (Drake et al, 2018). Currently, there are no caribou in the park and the population is considered potentially extirpated.…”

Section: Caribou Samplingmentioning

confidence: 99%

“…We sampled caribou from populations that differed in evolutionary history, demographic history and extent of isolation. We predicted to find a large proportion of genomic ROH in boreal caribou from the southern range of Ontario (Figure 1), where recent range contraction has resulted in small and isolated populations (Drake et al, 2018;Schaefer, 2003). We expected to detect lower levels of inbreeding, quantified as ROH, in boreal caribou from the continuous range of Ontario and Manitoba, as well as in the eastern migratory caribou from Ontario and Quebec; populations that have experienced recent declines but are not as small and isolated as the southern range of Ontario (COSEWIC, 2014a(COSEWIC, , 2017a).…”

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confidence: 96%

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Genomic islands of heterozygosity maintained across caribou populations despite inbreeding

Solmundson

Bowman

Wilson

et al. 2020

Preprint

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Small, isolated populations are prone to inbreeding, increasing the proportion of homozygous sites across the genome that can be quantified as runs of homozygosity (ROH). Caribou (Rangifer tarandus) are declining across their range in Canada; thus, understanding the effects of inbreeding on genetic potential is pertinent for conserving small, isolated populations. We quantified ROH in high-coverage whole genomes of boreal caribou from small, isolated populations in southern Ontario, Canada, in comparison to caribou from the continuous range of Ontario, other caribou ecotypes in Canada, and western Greenland. Sampled populations presented 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. We found caribou from recently isolated 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 that 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 immunity, signaling regulation, nucleotide binding, toxin elimination, and feeding behaviour regulation. In this study, we confirm inbreeding in isolated populations of a species at risk, but also uncover high variation in some genes maintained across divergent populations despite inbreeding, suggesting strong balancing selection.

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Genomic population structure and inbreeding history of Lake Superior caribou

Solmundson

Bowman

Manseau

et al. 2023

Ecology and Evolution

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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.

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Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Cited by 4 publications

References 19 publications

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

Genomic islands of heterozygosity maintained across caribou populations despite inbreeding

Genomic population structure and inbreeding history of Lake Superior caribou

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