Water vole genome will help boost conservation of one of UK's most endangered mammals

The water vole genome is published as part of the Darwin Tree of Life Project to assemble the genomes of 70,000 animal, plant, fungal and protist species across Britain and Ireland

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A new tool to help conserve one of the UK’s most threatened mammals has been released today, with the publication of the first high-quality reference genome for the European water vole. The genome was generated by scientists at the Wellcome Sanger Institute, in collaboration with animal conservation charity the Wildwood Trust, as part of the Darwin Tree of Life Project.

The genome, published today (24 June) through Wellcome Open Research, is openly available as a reference for researchers seeking to assess water vole population genetics, better understand how the species has evolved and to manage reintroduction efforts.

The European water vole (Arvicola amphibius) is a small semi-aquatic mammal that lives on the banks of freshwater habitats and in wetlands. The species is native to Europe, west Asia, Russia and Kazakhstan. While the water vole’s conservation status is ‘least concern’ worldwide1, populations in the United Kingdom have declined to such an extent that the species is considered nationally endangered. Habitat loss and predation by the American mink, an invasive alien species, have reduced the UK population from 7.3 million in 1990 to an estimated 132,000 in 20182.

Water voles gained full legal protection in the UK in 2008. There have been a number of conservation projects in the UK aimed at supporting water vole populations, including efforts at habitat restoration and to control the population of American mink. There are also efforts to reintroduce the water vole in a number of restored urban and wild habitats, as well as mitigate the impact of new development3.

European water voles returned to Britain from ice-free refuges in Iberia and Eastern Europe after the last ice age, with these two clades contributing to genetic diversity in UK populations. This diversity may be apparent in certain traits, such as the black fur of Scottish water voles, which is distinct from those in England that tend to have brown fur. But the full wealth of genetic diversity cannot be estimated by appearance alone. It is also unknown how much diversity has been lost as a result of the recent population crash.

“Water voles are amazing animals and we don’t fully understand what ecosystems lose without them. They are industrious habitat managers, almost like miniature beavers in the way they fell stems, make burrows and alter the landscape. We suspect that some water vole populations have become inbred in recent decades owing to shrinking numbers and the fragmentation of populations through habitat loss. The reference genome offers us a way to better understand genetic diversity for reintroductions and consider mixing individuals to ensure populations have the best chance to thrive.”

Hazel Ryan, Senior Conservation Officer at the Wildwood Trust

To sequence the European water vole reference genome, a blood sample was taken from a live male A. amphibius individual that was part of the captive breeding population of the Wildwood Trust in Kent, UK. DNA was extracted from this sample and sequenced by scientists at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL I and Illumina HiSeq X instruments.

“Understanding the genetic diversity and structure of water vole populations is an important aspect of their conservation in the UK, and is central to international guidelines on the movement of wildlife for conservation management. The release of the water vole genome provides a comprehensive set of genetic tools to support the future sustainability of the species in the UK.”

Professor Rob Ogden, Director of Conservation Science at the University of Edinburgh

The water vole genome is published as part of the Darwin Tree of Life Project, which will see partner organisations sequence and assemble the genomes of 70,000 animal, plant, fungal and protist species across Britain and Ireland.

“The European water vole is a prime example of a British species whose genetic diversity we’re in danger of losing before we’ve had chance to fully record it. This high-quality Arvicola amphibius reference genome will allow us to do that, as well as support ongoing conservation efforts to preserve existing populations and reintroduce new ones in a way that ensures these populations are genetically robust.”

Professor Mark Blaxter, Programme Lead for the Darwin Tree of Life project at the Wellcome Sanger Institute

More information

1 IUCN Red List of Threatened Species

2 Population estimate by Natural England

3 For more information, visit the Wildwood Trust website


Angus I. Carpenter, Michelle Smith and Craig Corton. (2021). The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758. Wellcome Open Research. DOI:


The Darwin Tree of Life Project is funded by Wellcome.