Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (<i>Eliomys quercinus</i>) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome reveal a sharp population decline since the last interglacial, indicating an association between colder climates and population declines before anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conduct the first population genomic analysis for this species. We find clear evidence for population structure across the species' core Central European range. Notably, our data show that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through the designation of ESUs.

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Journal
Genome Research
Published
2024-11-01
DOI
https://doi.org/10.1101/gr.279066.124
Citations
2
Primary Topic
Animal Ecology and Behavior Studies
Type
article

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article

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Alice Mouton, Sarah A. Mueller, Tilman Schell, Shenglin Liu et al.
2 citations
Genome Research
Animal Ecology and Behavior Studies
article

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Alice Mouton, Sarah A. Mueller, Tilman Schell, Shenglin Liu, Sandro Bertolino, Christian Stephan Betz, Lorenzo Vinciguerra, Evgeny V. Leushkin, Lídia Freixas, Alexander Ben Hamadou, Thomas Briner, Paige Byerly, Michael Hiller, Goedele Verbeylen, Holger Meinig, Sven Winter, Sven Büchner, Carola Greve, Alina von Thaden, Leon Hilgers, Carsten Nowak, Johannes Lang, Hanno J. Bolz, Sarah P. Stubbe, Charlotte Gerheim, Evax Marie Famira-Parcsetich
article en
2 citations

Abstract

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (<i>Eliomys quercinus</i>) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome reveal a sharp population decline since the last interglacial, indicating an association between colder climates and population declines before anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conduct the first population genomic analysis for this species. We find clear evidence for population structure across the species' core Central European range. Notably, our data show that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through the designation of ESUs.

Genome ResearchVol. 34(11)
Goethe University Frankfurt (DE), University of Veterinary Medicine Vienna (AT), Justus-Liebig-Universität Gießen (DE), University of St.Gallen (CH), Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE), LMU Klinikum (DE), Rode Kruis-Vlaanderen (BE), Hospital General de Granollers (ES), Senckenberg Biodiversity and Climate Research Centre (DE), LOEWE Centre for Translational Biodiversity Genomics (DE), Service Public Fédéral Économie (BE), University of Turin (IT), Ludwig-Maximilians-Universität München (DE)
Justus Liebig Universität Gießen, LOEWE Zentrum AdRIA, Hessisches Ministerium für Wissenschaft und Kunst, Bundesamt für Naturschutz, Bundesministerium für Umwelt, Naturschutz, nukleare Sicherheit und Verbraucherschutz
Life in Land
Animal Ecology and Behavior Studies
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