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

Abstract 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 c...

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Published in:Evolutionary Applications
Main Authors: Dedato, Morgan N., Robert, Claude, Taillon, Joëlle, Shafer, Aaron B. A., Côté, Steeve D.
Other Authors: Compute Canada, Genome Canada, Natural Sciences and Engineering Research Council of Canada
Format: Article in Journal/Newspaper
Language:English
Published: Wiley 2022
Subjects:
Online Access:http://dx.doi.org/10.1111/eva.13495
https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13495
https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13495
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spelling crwiley:10.1111/eva.13495 2024-09-15T18:31:45+00:00 Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec Dedato, Morgan N. Robert, Claude Taillon, Joëlle Shafer, Aaron B. A. Côté, Steeve D. Compute Canada Genome Canada Natural Sciences and Engineering Research Council of Canada 2022 http://dx.doi.org/10.1111/eva.13495 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13495 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13495 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Evolutionary Applications volume 15, issue 12, page 2043-2053 ISSN 1752-4571 1752-4571 journal-article 2022 crwiley https://doi.org/10.1111/eva.13495 2024-07-04T04:31:30Z Abstract 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, θ π and estimated the coalescent or ancestral effective population size ( N e ), which ranged from 12,030 to 15,513. When compared to the census size, N C , the endangered Gaspésie Mountain caribou population had the highest ancestral N e : N C ratio which is consistent with recent work suggesting high ancestral N e : N C is of conservation concern. In contrast, values of contemporary N e , estimated from linkage‐disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e : N C 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 N e and Tajima's D into management decisions. Article in Journal/Newspaper Rangifer tarandus Wiley Online Library Evolutionary Applications 15 12 2043 2053
institution Open Polar
collection Wiley Online Library
op_collection_id crwiley
language English
description Abstract 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, θ π and estimated the coalescent or ancestral effective population size ( N e ), which ranged from 12,030 to 15,513. When compared to the census size, N C , the endangered Gaspésie Mountain caribou population had the highest ancestral N e : N C ratio which is consistent with recent work suggesting high ancestral N e : N C is of conservation concern. In contrast, values of contemporary N e , estimated from linkage‐disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e : N C 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 N e and Tajima's D into management decisions.
author2 Compute Canada
Genome Canada
Natural Sciences and Engineering Research Council of Canada
format Article in Journal/Newspaper
author Dedato, Morgan N.
Robert, Claude
Taillon, Joëlle
Shafer, Aaron B. A.
Côté, Steeve D.
spellingShingle Dedato, Morgan N.
Robert, Claude
Taillon, Joëlle
Shafer, Aaron B. A.
Côté, Steeve D.
Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
author_facet Dedato, Morgan N.
Robert, Claude
Taillon, Joëlle
Shafer, Aaron B. A.
Côté, Steeve D.
author_sort Dedato, Morgan N.
title Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
title_short Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
title_full Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
title_fullStr Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
title_full_unstemmed Demographic history and conservation genomics of caribou ( Rangifer tarandus) in Québec
title_sort demographic history and conservation genomics of caribou ( rangifer tarandus) in québec
publisher Wiley
publishDate 2022
url http://dx.doi.org/10.1111/eva.13495
https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13495
https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.13495
genre Rangifer tarandus
genre_facet Rangifer tarandus
op_source Evolutionary Applications
volume 15, issue 12, page 2043-2053
ISSN 1752-4571 1752-4571
op_rights http://creativecommons.org/licenses/by/4.0/
op_doi https://doi.org/10.1111/eva.13495
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