Genetic diversity of British water voles (Arvicola amphibius) and phylogenetics of the rodent subfamily Arvicolinae

The European water vole (Arvicola amphibius) has experienced rapid decline in Britain, resulting in numbers declining by approximately 90% in the last century, making them a conservation priority. Its phylogeny within the subfamily Arvicolinae, and its relationship to other taxa, remains debated. Additionally, the impact of captive breeding programs on the genetic diversity of water voles is unknown. We firstly optimise DNA extraction protocols for tail tissue, hair, faeces, buccal swabs, and cell culture to achieve high DNA yields and purity. We then sequence the mitochondrial control region for 17 captive water voles at Wildwood Trust using tissue, hair, and faecal samples collected at the park to assess their genetic diversity and population structure. Lastly, we use mitochondrial genomes and individual phylogenetic markers to construct the phylogeny of the subfamily Arvicolinae.Our study provides protocols for the extraction of DNA achieving high yields and improved purity, with cell culture resulting in the highest median yield, followed by buccal swabs and tail tissue. Our results reveal considerable genetic diversity in the mitochondrial control region ofcaptive water voles sampled at Wildwood Trust, with relatively high haplotype diversity. Similar haplotype diversity was also seen in natural populations in Britain. Captive water voles clustered closely with South East of England haplotypes, and were found within the English/Welsh clade. Additionally, we provided support for the phylogeny of several genera of Arvicolinae. Using mitogenomes provided the most resolved phylogenetic tree when compared with other genetic markers and approaches but lacked sequences for all genera to fully resolve phylogeny. The mitochondrial genome provides a useful marker to study both the conservation and population genetics of water voles, as well as the phylogenetics of the subfamily Arvicolinae. Our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation studies.