RT Journal
A1 Byerly, Paige A.
A1 von Thaden, Alina
A1 Leushkin, Evgeny
A1 Hilgers, Leon
A1 Liu, Shenglin
A1 Winter, Sven
A1 Schell, Tilman
A1 Gerheim, Charlotte
A1 Ben Hamadou, 
Alexander
A1 Greve, Carola
A1 Betz, Christian
A1 Bolz, Hanno J.
A1 Büchner, Sven
A1 Lang, Johannes
A1 Meinig, Holger
A1 Famira-Parcsetich, Evax Marie
A1 Stubbe, 
Sarah P.
A1 Mouton, Alice
A1 Bertolino, Sandro
A1 Verbeylen, Goedele
A1 Briner, Thomas
A1 Freixas, Lídia
A1 Vinciguerra, Lorenzo
A1 Mueller, Sarah A.
A1 Nowak, Carsten
A1 Hiller, Michael
T1 Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
JF Genome Research 
JO Genome Research 
YR 2024 
FD November 01 
VO 34 
IS 11 
SP 2094 
OP 2107 
DO 10.1101/gr.279066.124 
UL http://genome.cshlp.org/content/34/11/2094.abstract 
AB Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (Eliomys quercinus) 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.