Genotyping-by-sequencing based SNP discovery in a non-model rodent, the endangered hazel dormouse

Abstract

The hazel dormouse Muscardinus avellanarius presents an exemplary non-model species that is both locally threatened and whose genetic status is not fully understood owing to insufficient resolution of the currently available molecular tools. We performed normalized Genotyping-by-Sequencing (nGBS) on 48 hazel dormouse samples collected across the species European distribution, aiming at discovering useful single nucleotide polymorphism (SNP) markers for the assessment of population structure and genomic diversity. The analyses of > 24,000 SNPs showed a high divergence between the Eastern and Western lineage of the species with high rates of SNP allele fixation, consistent with previous studies suggesting the divergence of lineages occurred over 2 mya. These results indicate that investigating inter-lineage as well as within-lineage genetic composition will be a conclusive approach for identifying conservation strategies in the future. Results presented here indicate the highest genetic divergence in the Italian and Lithuanian populations. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism, potentially informing monitoring and conservation strategies.

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

“…Larger sampling efforts are required to substantiate these findings that are based on rather low sample numbers. A similar east-west pattern of differentiation has also been observed in the garden dormouses' spatially overlapping relative, the hazel dormouse (Muscardinus avellanarius), which is distributed as two separate lineages or 'partial ESUs', delineated along a similar geographic divide as the garden dormouse (Leyhausen et al 2022;Mouton et al 2017). Unlike the hazel dormouse, however, this east-west pattern of differentiation was not reflected by mtDNA in the garden dormouse (Perez et al 2013), indicating that the division among lineages may be a more recent phenomenon resulting from habitat fragmentation and/or demographic changes such as population declines.…”

“…Tissue samples for nGBS were extracted using the DNeasy Blood & Tissue Kit (Qiagen) with slight protocol modifications to increase yield of RNA-free genomic DNA as described in (Leyhausen et al 2022). Extracts were quantified with fluorometry (Qubit) and spectrophotometry (NanoDrop) and screened for DNA integrity using gel electrophoresis to identify samples of sufficient quality for NGS.…”

“…Selected samples (n = 100) with ≥ 300 ng of high molecular weight DNA were sent for nGBS at LGC Genomics GmbH (www.biosearchtech.com). Details on enzymatic digestion, library preparation and nGBS protocols can be found in (Leyhausen et al 2022;Arvidsson et al 2016).…”

Development of a microfluidic SNP assay for lineage discrimination in the endangered hazel dormouse

“…192 SNPs were initially chosen from a set of 24,903 SNPs obtained from a normalised Genotyping-by-Sequencing (nGBS) approach (Leyhausen et al 2022). Selected SNPs were ltered for bi-allelic state, single SNP per RAD locus, 40pb anking region on both ends, GC content ≤ 0.65, linkage r2 < 0.3, MAF > 0.1, missing data < 0.2, and Ho within sampled populations > 0.8.…”

“…The division of the hazel dormouse distribution in Europe into a highly divergent Western and Eastern cluster, potentially forming cryptic species, has been proposed on the basis of mitochondrial DNA analysis (Mouton et al 2017) and genome-wide SNP data (Leyhausen et al 2022). Regardless of the taxonomic status, those lineages represent evolutionary signi cant units and should thus be treated as separate conservation units following Moritz (1994).…”