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

Johanna Leyhausen,Rimvydas Juškaitis,Hermann Ansorge,Sandro Bertolino,Sven Büchner,Maurice La Haye,Berardino Cocchiararo,Sarah A Mueller,Ruud Foppen,Alina Von Thaden,Joanna Fietz,Johan Michaux,Goedele Verbeylen,Carsten Nowak,Johannes Lang

doi:10.1007/s12686-022-01253-8

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.

Highlights

The hazel dormouse (Muscardinus avellanarius, linnaeus, 1758) is currently undergoing population decline in many areas of its European distribution
We provide a foundation for further genomic analyses on hazel dormouse populations, which will be able to be used for future developments in scientific assessment, monitoring and conservation, especially in regions where populations are currently declining
DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol with the following slight modifications: (i) to receive RNA-free genomic DNA, 4 μL of RNAse A were added during the lysis step at 56 °C, (ii) after the washing steps the spin columns were centrifuged for 3 min at 13,300xg and dried at 56 °C for 5–10 min, (iii) to increase the yield, DNA was eluted in two steps with 40 μL AE buffer each

Summary

Introduction

The hazel dormouse (Muscardinus avellanarius, linnaeus, 1758) is currently undergoing population decline in many areas of its European distribution. The hazel dormouse is a candidate species to benefit from NGS as this species is largely arboreal, nocturnal and generally remains at low population densities, making it challenging to detect and logistically prohibitive to monitor on a large scale (Goodwin et al 2017). Given these constraints, genetic solutions can inform applied conservation strategies for this elusive rodent

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