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 con...
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ftdoajarticles:oai:doaj.org/article:ef113184c2e948258749bbc69700aa17 2023-05-15T18:04:17+02:00 Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec Morgan N. Dedato Claude Robert Joëlle Taillon Aaron B. A. Shafer Steeve D. Côté 2022-12-01T00:00:00Z https://doi.org/10.1111/eva.13495 https://doaj.org/article/ef113184c2e948258749bbc69700aa17 EN eng Wiley https://doi.org/10.1111/eva.13495 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13495 https://doaj.org/article/ef113184c2e948258749bbc69700aa17 Evolutionary Applications, Vol 15, Iss 12, Pp 2043-2053 (2022) ancestral varaiation effective population size genetic diversity threatened ungulates Evolution QH359-425 article 2022 ftdoajarticles https://doi.org/10.1111/eva.13495 2022-12-30T20:05:17Z 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, 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. Article in Journal/Newspaper Rangifer tarandus Directory of Open Access Journals: DOAJ Articles Canada Evolutionary Applications 15 12 2043 2053 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
ancestral varaiation effective population size genetic diversity threatened ungulates Evolution QH359-425 |
spellingShingle |
ancestral varaiation effective population size genetic diversity threatened ungulates Evolution QH359-425 Morgan N. Dedato Claude Robert Joëlle Taillon Aaron B. A. Shafer Steeve D. Côté Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec |
topic_facet |
ancestral varaiation effective population size genetic diversity threatened ungulates Evolution QH359-425 |
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, 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. |
format |
Article in Journal/Newspaper |
author |
Morgan N. Dedato Claude Robert Joëlle Taillon Aaron B. A. Shafer Steeve D. Côté |
author_facet |
Morgan N. Dedato Claude Robert Joëlle Taillon Aaron B. A. Shafer Steeve D. Côté |
author_sort |
Morgan N. Dedato |
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 |
https://doi.org/10.1111/eva.13495 https://doaj.org/article/ef113184c2e948258749bbc69700aa17 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Rangifer tarandus |
genre_facet |
Rangifer tarandus |
op_source |
Evolutionary Applications, Vol 15, Iss 12, Pp 2043-2053 (2022) |
op_relation |
https://doi.org/10.1111/eva.13495 https://doaj.org/toc/1752-4571 1752-4571 doi:10.1111/eva.13495 https://doaj.org/article/ef113184c2e948258749bbc69700aa17 |
op_doi |
https://doi.org/10.1111/eva.13495 |
container_title |
Evolutionary Applications |
container_volume |
15 |
container_issue |
12 |
container_start_page |
2043 |
op_container_end_page |
2053 |
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1766175605537112064 |