No evidence of inbreeding depression in fast declining herds of migratory caribou

Gagnon, Marianne; Yannic, Glenn; Perrier, Charles; Côté, Steeve D.

doi:10.1111/jeb.13533

Cited by 10 publications

(19 citation statements)

References 90 publications

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“…As a result, a correlation between allelic diversity indices and performance would give support to the general effect hypothesis if other indices did not correlate with performance. We did not expect to observe such pattern, as we had previously shown that the caribou populations studied here do not suffer from inbreeding depression (Gagnon et al 2019). Instead, we predicted that direct effects were more likely to be involved in a potential correlation between MHC diversity and performance.…”

Section: Introductionmentioning

confidence: 62%

Adult survival in migratory caribou is negatively associated with MHC functional diversity

et al. 2020

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Genes of the major histocompatibility complex (MHC) are involved in acquired immunity in vertebrates. Only a few studies have investigated the fitness consequences of MHC gene diversity in wild populations. Here, we looked at the association between annual survival and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained from highthroughput sequencing, in two declining migratory caribou (Rangifer tarandus) herds. To disentangle the potential direct and general effects of MHC-DRB genetic diversity, we compared different indices of diversity that were either based on DNAsequence variation or on physicochemical divergence of the translated peptides, thereby covering a gradient of allelic-tofunctional diversity. We found that (1) body mass was not related to MHC-DRB diversity or genotype, and (2) adult survival probability was negatively associated with point accepted mutation distance, a corrected distance that considers the likelihood of each amino acid substitution to be accepted by natural selection. In addition, we found no evidence of fluctuating selection over time on MHC-DRB diversity. We concluded that direct effects were involved in the negative relationship between MHC functional diversity and survival, although the mechanism underlying this result remains unclear. A possible explanation could be that individuals with higher MHC diversity suffer higher costs of immunity (immunopathology). Our results suggest that genetic diversity is not always beneficial even in genes that are likely to be strongly shaped by balancing selection.

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Section: Introductionmentioning

confidence: 62%

Adult survival in migratory caribou is negatively associated with MHC functional diversity

et al. 2020

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“…In a recent study of two eastern migratory caribou populations, correlations between heterozygosity and fitness (HFCs) found no evidence of inbreeding depression (Gagnon et al, 2019). Notably, eastern migratory caribou from one of these population were also included in our study and had relatively low inbreeding estimates (FROH = 0.05-0.07).…”

Section: Islands Of Heterozygositymentioning

confidence: 86%

“…We selected two barren-ground caribou samples from the Qamanirijuaq population that ranges over northern Manitoba and Nunavut, a large population that was estimated to contain 264,661 individuals in 2014 and has not experienced dramatic historical or recent declines (COSEWIC, 2016). Within the eastern migratory ecotype, we included two samples from the George River population, Quebec, which has experienced a dramatic population decline over recent decades from approximately 823,000 individuals in 1993 (Couturier, Courtois, Crépeau, Rivest, & Luttich, 1996), to approximately 8,900 individuals in 2016 (Gagnon et al, 2019); our samples were obtained in 2008, after population declines had already occurred. We also included two eastern migratory caribou from the Pen Island population in northern Ontario, which was estimated to contain 16,638 individuals in 2011 (COSEWIC, 2017a).…”

Section: Caribou Samplingmentioning

confidence: 99%

“…Rapid declines in caribou range and population sizes have raised conservation concerns, as small and isolated populations are more prone to inbreeding and eventually may fall into an "extinction vortex" and become extirpated (Gagnon, Yannic, Perrier, & Côté, 2019;Gilpin & Soule, 1986). Yet, it remains unclear how inbreeding is affecting caribou, and whether inbreeding depression is a pertinent threat.…”

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confidence: 99%

“…Yet, it remains unclear how inbreeding is affecting caribou, and whether inbreeding depression is a pertinent threat. A recent study correlated heterozygosity and fitness in two rapidly declining eastern migratory caribou populations, and found no evidence of inbreeding depression (Gagnon et al, 2019). However, the two eastern migratory populations studied by Gagnon et al (2019) have historically experienced dramatic fluctuations in population size (COSEWIC, 2017a), which may have allowed for the purging of recessive deleterious alleles.…”

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confidence: 99%

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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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No evidence of inbreeding depression in fast declining herds of migratory caribou

Cited by 10 publications

References 90 publications

Adult survival in migratory caribou is negatively associated with MHC functional diversity

Adult survival in migratory caribou is negatively associated with MHC functional diversity

Genomic islands of heterozygosity maintained across caribou populations despite inbreeding

Genomic population structure and inbreeding history of Lake Superior caribou

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