Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)

Corey Kirkland,Marta Farré

doi:10.3390/genes12020138

Abstract

The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.

Highlights

Rodents are one of the most speciose orders within the mammalian kingdom, containing around 2552 species and 513 genera [1]
All 13 mitochondrial DNA (mtDNA) protein-coding gene alignments were concatenated and PartitionFinder was used with two partitions grouping first and second codon position independently to third codon position, with generalised time reversible (GTR) + G + I chosen as the best substitution model for both partitions
When comparing a declining species in Britain (A. amphibius) with a species with stable numbers in Britain (M. glareolus), we found a similarity in haplotype diversity, with a difference of 0.004 in the mtDNA control region, whilst nucleotide diversity was lower in bank voles by 0.01

Summary

Introduction

Rodents (order Rodentia) are one of the most speciose orders within the mammalian kingdom, containing around 2552 species and 513 genera [1]. Phylogenetic studies sequenced and analysed the mitochondrial cytochrome b (Cytb) gene but found rapid, near-simultaneous radiations when using this marker (reviewed in [3]). This led to the hypothesis that substitution saturation had occurred in this gene in Arvicolinae, reducing its value as a phylogenetic marker. Later studies validated this claim and found that genetic saturation occurred at both transitions and transversions of the Cytb gene in arvicoline species [4]

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Results

Discussion

Conclusion