Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics DOI Creative Commons

Si Lok,

Timothy N H Lau,

Brett Trost

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 16, 2024

The muskox (Ovibos moschatus), an integral component and iconic symbol of arctic biocultural diversity, is under threat by rapid environmental disruptions from climate change. We report a chromosomal-level haploid genome assembly Banks Island in the Canadian Arctic Archipelago. has contig N50 44.7 Mbp, scaffold 112.3 complete representation (100%) BUSCO v5.2.2 set 9225 mammalian marker genes anchored to 24 chromosomes muskox. Tabulation heterozygous single nucleotide variants our specimen revealed very low level genetic which consistent with recent reports having lowest genome-wide heterozygosity among ungulates. While populations are currently showing no overt signs inbreeding depression, expected strain genomic resilience species. One notable impact change spread emerging infectious parasitic diseases muskox, as exemplified range expansion lungworms, fatal outbreaks Erysipelothrix rhusiopathiae, pathogen normally associated domestic swine poultry. As genomics resource for conservation management against existing disease modalities, we annotated major histocompatibility complex on chromosome 2 performed initial assessment diversity this complex. This further supported annotation principal innate immunity system, that rapidly evolving positive selection adaptations, socioeconomic benefits communities such wool (qiviut) attributes. These annotations will benefit conservation.

Language: Английский

A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies DOI Creative Commons
Fabian L. Kellner, Mathilde Le Moullec, Martin R. Ellegaard

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(5)

Published: Jan. 27, 2024

Overharvest can severely reduce the abundance and distribution of a species thereby impact its genetic diversity threaten future viability. remains an ongoing issue for Arctic mammals, which due to climate change now also confront one fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic Svalbard, experienced harvest-induced demographic bottleneck that occurred during 17-20th centuries. Here, we investigate changes in diversity, population structure, gene-specific differentiation after this overharvesting event. Using whole-genome shotgun sequencing, generated first ancient historical nuclear (n = 11) mitochondrial 18) genomes from (up 4000 BP) integrated these data with large collection modern genome sequences 90) infer temporal changes. We show hunting resulted major restructuring populations. Near-extirpation followed by pronounced drift has altered allele frequencies important genes contributing diverse biological functions. Median heterozygosity was reduced 26%, while only limited extent, likely already low pre-harvest complex post-harvest recolonization process. Such genomic erosion isolation populations past anthropogenic disturbance will play role metapopulation dynamics (i.e., extirpation, recolonization) under further change. Our results case study therefore emphasize need understand long-term interplay past, current, stressors wildlife conservation.

Language: Английский

Citations

4
Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos DOI Creative Commons

Katharina Hold,

Edana Lord, Jaelle C. Brealey

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Feb. 20, 2024

Climate warming at the end of last glacial period had profound effects on distribution cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about routes and timing colonisation. At ice age, reindeer/caribou (Rangifer tarandus) expanded Holarctic region colonised archipelagos Svalbard Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from Eurasian mainland or Canada via Greenland. Here, we used 174 ancient, historical modern mitogenomes reconstruct phylogeny reindeer across its whole infer route Our data shows a close affinity among Svalbard, Land Novaya Zemlya reindeer. We also found tentative evidence for positive selection in mitochondrial gene ND4, which possibly associated with increased heat production. results thus support provide some insights into evolutionary history adaptation species High habitat.

Language: Английский

Citations

4
Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population DOI Creative Commons
Nicolás Dussex, Ingela Jansson, Tom van der Valk

et al.

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 21, 2025

Abstract Small, isolated populations are at greater risk of genome erosion than larger populations. Successful conservation efforts may lead to demographic recovery and mitigate the negative genetic effects bottlenecks. However, constrained gene flow can hamper genomic recovery. Here, we use population analyses forward simulations assess impacts near extinction in Ngorongoro Crater lion ( Panthera leo ) sub-population. We show that 200 years quasi-isolation recent epizootic 1962 resulted a two-fold increase inbreeding an excess frequency highly deleterious mutations relative other Greater Serengeti. There was little evidence for purging load. Furthermore, indicate higher from outside is needed prevent future population, with minimum one five effective male migrants per decade required reduce long-term depression reduction diversity. Our results suggest spite rapid post-epizootic since 1970s, continued isolation driven by habitat fragmentation potentially territoriality, exacerbate erosion.

Language: Английский

Citations

0
Assessing current visual tooth wear age estimation methods for Rangifer tarandus using a known age sample from Canada DOI Creative Commons
Grace Kohut, Robert J. Losey, Susan Kutz

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(4), P. e0301408 - e0301408

Published: April 2, 2024

Age estimation is crucial for investigating animal populations in the past and present. Visual examination of tooth wear eruption one most common ageing methods zooarchaeology, wildlife management, palaeontology, veterinary research. Such approaches are particularly advantageous because they non-destructive, can be completed using photographs, do not require specialized training. Several have been developed Rangifer tarandus , a widely distributed long-utilized species North. This paper evaluates practicality effectiveness three existing visual this large known-age sample from several caribou northern Canada (Bluenose East, Bluenose West, Dolphin-Union, Qamanirjuaq, Beverly herds). These evaluated based on: (1) amount error bias between estimated actual ages, (2) suitable interpretable results, (3) user-friendly unambiguous procedures, (4) which teeth features those used to record status. study finds that all variable errors biases, two show extensive biases when applied older individuals. Demographic data simpler generate more flexible report allow age as continuous or discrete variable, rather than ranges. The dentition samples by previously impact their applicability other . In method, individuals were unavailable some ranges leaving gaps assigning ages. For another -ageing population utilized was too distinct morphology diet with Canadian analyzed here. Additional refinement will benefit zooarchaeological research on reindeer remains.

Language: Английский

Citations

1
4200 Years of Mercury Variation in the Antlers of High-Arctic Wild Reindeer DOI
Tomasz M. Ciesielski, Saria Sato Bajracharya,

M. Le Moullec

et al.

Published: Jan. 1, 2024

Download This Paper Open PDF in Browser Add to My Library Share: Permalink Using these links will ensure access this page indefinitely Copy URL DOI

Language: Английский

Citations

0
Use of the Phylobone database for the annotation of bone extracellular matrix proteins in reindeer (Rangifer tarandus) DOI Creative Commons

Alba Sánchez-Reverté,

Margalida Fontcuberta-Rigo, Miho Nakamura

et al.

Science Progress, Journal Year: 2024, Volume and Issue: 107(2)

Published: April 1, 2024

Bone extracellular matrix (ECM) proteins play a key role in bone formation and regeneration, including structural regulatory functions. The Phylobone database consists of 255 ECM protein groups from 39 species can be used to support research. Here, we gathered reindeer ( Rangifer tarandus), member the Cervidae family. importance lies their ability regenerate antlers, both male female individuals. Protein sequences were extracted National Center for Biotechnology Information's repository selected by homology searches. We identified 215 corresponding functional domains, which are putatively present reindeer. sequence alignments have shown high degree conservation between R. tarandus other members This update expands shows that it is useful resource preliminary annotation novel proteomes.

Language: Английский

Citations

0
Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies DOI Creative Commons
Elif Bozlak, Kisun Pokharel, Melak Weldenegodguad

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(6)

Published: June 1, 2024

Abstract Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species ( Rangifer tarandus ). It survived Holocene thanks its immense adaptability successful coexistence with humans different forms of hunting herding cultures. Here, we examine paternal maternal history based on robust Y‐chromosomal mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest Svalbard Alaska caribou, woodland caribou. We first assembled contigs, 1.3 Mb single‐copy Y regions. Based 545 458 mtDNA SNPs defined 55 males, maximum parsimony were created. observed two well separated clades both phylogenies: “EuroBeringian clade” formed by animals from Arctic Islands, Eurasia, few America “North American only America. The time calibrated tree revealed an expansion dispersal lineages across continents after Last Glacial Maximum. show for unique reindeer reveal circumscribed haplogroup Fennoscandian reindeer. chromosome domesticated is markedly diverse indicating that several male have undergone domestication less intensive selection males. This study places R. onto list resolved phylogenies builds basis studies origin future.

Language: Английский

Citations

0
Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics DOI Creative Commons

Si Lok,

Timothy N H Lau,

Brett Trost

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 16, 2024

The muskox (Ovibos moschatus), an integral component and iconic symbol of arctic biocultural diversity, is under threat by rapid environmental disruptions from climate change. We report a chromosomal-level haploid genome assembly Banks Island in the Canadian Arctic Archipelago. has contig N50 44.7 Mbp, scaffold 112.3 complete representation (100%) BUSCO v5.2.2 set 9225 mammalian marker genes anchored to 24 chromosomes muskox. Tabulation heterozygous single nucleotide variants our specimen revealed very low level genetic which consistent with recent reports having lowest genome-wide heterozygosity among ungulates. While populations are currently showing no overt signs inbreeding depression, expected strain genomic resilience species. One notable impact change spread emerging infectious parasitic diseases muskox, as exemplified range expansion lungworms, fatal outbreaks Erysipelothrix rhusiopathiae, pathogen normally associated domestic swine poultry. As genomics resource for conservation management against existing disease modalities, we annotated major histocompatibility complex on chromosome 2 performed initial assessment diversity this complex. This further supported annotation principal innate immunity system, that rapidly evolving positive selection adaptations, socioeconomic benefits communities such wool (qiviut) attributes. These annotations will benefit conservation.

Language: Английский

Citations

0