Complete mitochondrial genome sequence of Aoluguya reindeer (
            <i>Rangifer tarandus</i>
            )

Ju, Yan; Liu, Huamiao; Min, Rong; Yang, Yumei; Hai-jun, Wei; Shao, Yuanchen; Chen, Xiumin; Xing, Xiumei

doi:10.3109/19401736.2014.984171

Cited by 6 publications

(3 citation statements)

References 2 publications

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“…The size and orientation of tRNA and rRNA genes are similar to those of other cervids [8, 12-13, 21, 25-27, 33, 35]. The lack of the ''DHU'' arm in tRNA Ser has been reported in other species of Cervidae [8,21,[25][26][27]35]. The non-coding control region contains conserved sequence blocks, and termination-associated sequences; and can be used for fine-scale population studies, since it is amongst the most rapidly evolving segments in the animal mtDNA [17,19,24,28].…”

Section: Discussionsupporting

confidence: 62%

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Frank¹,

Barta²,

Bana³

et al. 2016

Acta Biologica Hungarica

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Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes.We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used 'neighbor joining' and 'maximum likelihood' methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

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Section: Discussionsupporting

confidence: 62%

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Frank¹,

Barta²,

Bana³

et al. 2016

Acta Biologica Hungarica

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“…To analyse mtDNA haplotype diversity, we mapped our sequence data to a 16,357 bp reindeer mtDNA reference assembly (Ju et al, 2016 ). Then, we used the GATK 4.1.8.1 HaplotypeCaller (Depristo et al, 2011 ) to identify SNPs and call mtDNA haplotypes.…”

Section: Methodsmentioning

confidence: 99%

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high‐arctic wild reindeer

Burnett,

Bieker,

Le Moullec

et al. 2023

Evolutionary Applications

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Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high‐arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole‐genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome‐wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small‐scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

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“…To analyse mtDNA haplotype diversity, we mapped our sequence data to a 16,357 bp reindeer mtDNA reference assembly (Ju et al . 2016).…”

Section: Methodsmentioning

confidence: 99%

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

Burnett

Bieker

Moullec

et al. 2022

Preprint

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Anthropogenic reintroduction can supplement natural recolonisation in reestablishing a species’ distribution and abundance. However, both reintroductions and recolonisations can give rise to population bottlenecks that reduce genetic diversity and increase inbreeding, potentially causing accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonisations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonised populations without admixture possessed much lower heterozygosity, higher inbreeding, and longer runs of homozygosity, possibly caused by serial population bottlenecks and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonised populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonisation in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

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Complete mitochondrial genome sequence of Aoluguya reindeer ( Rangifer tarandus )

Cited by 6 publications

References 2 publications

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high‐arctic wild reindeer

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

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