Genomic islands of heterozygosity maintained across caribou populations despite inbreeding

Solmundson, Kirsten; Bowman, Jeff; Wilson, Paul J.; Taylor, Rebecca S.; Horn, Rebekah L.; Keobouasone, Sonesinh; Manseau, Micheline

doi:10.1101/2020.12.29.424772

Cited by 4 publications

(2 citation statements)

References 38 publications

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“…Whole genome sequences of 46 individual used in this study have been previously published and are available on the National Centre for Biotechnology (NCBI) under BioProject Accession numbers PRJNA634908, PRJNA694662, and PRJNA754521 (electronic supplementary material, table S1; 23,44,50,51]. For this study, we sequenced 20 new genomes (electronic supplementary material, table S1; figure 1) using the same protocols as before (23,44).…”

Section: (B) Re-sequenced Whole Genome Sequencesmentioning

confidence: 99%

High genetic load without purging in a diverse species-at-risk

Taylor

Manseau

Keobouasone

et al. 2022

Preprint

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Intra-specific diversification in the northern hemisphere is a recent phenomenon, particularly for vertebrates, due to climatic oscillations during the Quaternary. Caribou (Rangifer tarandus) are a recently diversified, keystone species in North America with a continental-wide distribution and a large amount of phenotypic variation. We assess patterns of intra-specific genetic variation and adaptive divergence, which are of critical interest to the fields of evolutionary biology and conservation. We characterized the relationship among caribou ecotypes and rapidly evolving genes among intra-specific lineages using phylogenomic analyses and a newly assembled chromosome-scale reference genome and 66 high-coverage genomes. Nine phylogenomic lineages showed different levels of introgression, with some lineages highly introgressed. Despite this, dN/dS ratios of all genes in the caribou genome (>30,000) identified 700-800 genes with significant signatures of positive selection in each lineage. These genes function in diverse pathways ranging from immune responses to circulatory systems, with the most enriched molecular pathways found in lineages with high levels of introgression. Glacial cycles and repeated introgression events between caribou lineages likely inflated both neutral and adaptive genetic variation: findings that are particularly timely given the importance of intra-specific diversity and adaptive variation in wild species for resilience to global change.

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Section: (B) Re-sequenced Whole Genome Sequencesmentioning

confidence: 99%

High genetic load without purging in a diverse species-at-risk

Taylor

Manseau

Keobouasone

et al. 2022

Preprint

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“…Interestingly, F ROH varies only slightly between populations; increased ROH are expected in smaller, isolated populations, that have undergone the most recent bottlenecks (e.g. Palkopoulou et al, 2015 ; Solmundson et al, 2020 ). It is possible that the ROH detected in the larger populations might actually be under selection (e.g.…”

Section: Discussionmentioning

confidence: 99%

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

Dedato

Robert

Taillon

et al. 2022

Evolutionary Applications

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The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision‐making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re‐sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θπ and estimated the coalescent or ancestral effective population size (Ne), which ranged from 12,030 to 15,513. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. In contrast, values of contemporary Ne, estimated from linkage‐disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral Ne and Tajima's D into management decisions.

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Genomics of founders for conservation breeding: the Jasper caribou case

et al. 2023

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Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species.

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Genomic islands of heterozygosity maintained across caribou populations despite inbreeding

Cited by 4 publications

References 38 publications

High genetic load without purging in a diverse species-at-risk

High genetic load without purging in a diverse species-at-risk

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

Genomics of founders for conservation breeding: the Jasper caribou case

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