DOI: 10.5061/dryad.5mkkwh7hk
title: Population structure of the endangered Siberian flying squirrel (Pteromys volans) revealed by genomic and mitochondrial data

description: The Siberian flying squirrel (Pteromys volans) is an arboreal rodent with
 a distribution range that covers large parts of the Eurasian taiga forest
 zone. However, extensive forestry has resulted in widespread local
 population declines and extinctions in recent decades. Even though it is
 widely distributed in Eurasia, almost nothing is known about its
 phylogeography. Here, we used genome-wide single nucleotide polymorphisms
 (SNPs) and mitochondrial DNA (mtDNA) to investigate population structure,
 connectivity, and genetic diversity in different sites throughout its
 distribution. Overall, the species shows low nucleotide diversity and
 heterozygosity. Locations in Finland, on the western edge of the
 distribution, had the lowest diversities in genomic SNPs and mtDNA, while
 individuals in the Far East (Sikhote-Alin, Russia) show the highest
 diversity. These findings fit with a rapid range expansion from the Far
 East to the west. We found a strong genetic differentiation between
 Sikhote-Alin and all other populations investigated, which might warrant a
 revision of their taxonomic classification. The inferred low genetic
 diversities at the western edge of their distribution are especially
 worrisome as they are currently experiencing strong population declines
 and major habitat changes, which can be especially detrimental when
 standing variation is low. Thus, there is a pressing need to revise the
 species' conservation status.
description: # Data S1 - *P. volans* population structure
 [https://doi.org/10.5061/dryad.3r2280grr](https://doi.org/10.5061/dryad.3r2280grr) ## Description of the data and file structure Samples were obtained from Finland and Russia during the years of 2006 and 202. In Finland, the samples were obtained from several locations and grouped into two subgroups: Western and Eastern Finland. In Russia, the Siberian flying squirrel was sampled in three regions: Tyumen, Baikal, and Sikhote-Alin. Genomic DNA was extracted from individual frozen tissue samples using the NucleoSpin tissue kit (Macherey-Nagel®) following the manufacturer’s protocol. All DNA stocks were quantified and normalized to 12 ng/µL to be used for molecular processing. Double-digestion RADseq libraries were prepared using an adapted protocol for low-concentration samples, with the restriction enzymes PstI-HF™ and BamHI. Sequencing was performed using Illumina Novaseq6000 over one lane with 150 paired-end reads. While two mitochondrial DNA markers were used to analyze the species' genetic diversity and structure: a fragment of 420 bp of the cytochrome B (CytB) gene, and 561 bp of the mitochondrial control region sequence (D-loop). The PCR reactions had a total volume of 10 µL, containing 5 µL of Phusion high-fidelity PCR master mix, 1 µM of each primer, 1 µL of extracted DNA (25-50 ng/µL), and 2 µL of mQ water. Following the program: activation step at 98°C for 10 s; 39 cycles of 98°C for 1 s, 55°C for 5 s and 72°C for 15 s; and a final extension step at 72°C for 2 min. Primers for both markers were selected based on Nummert et al. (2020): 5'-CGA TTC TTC GCA TTC CAT TT-3' and 5'-TAG TTG GCC GAT GAT GAT GA-3' for CytB; and 5'-TGC ACA GCC CCA TTA ATA CA-3' and 5'-GGG AGG GTT TCG AGT CAA AT-3' for D-loop. Positive reactions were purified and diluted 1:3, and then sequenced with ABI 3730 Genetic analyzer ### Files and variables #### File: Pvolans_scripts.txt **Description:** Complete scripts used to perform data cleaning, SNP calling and filtering. As well as for the population analyzes. #### File: Pvolans_mtDNA_cytb-dloop_fasta.txt **Description:** Concatenated sequences of CytB and D-loop in fasta format. ##### #### File: Pvolans_SNPs.vcf **Description:** Unfiltered SNPs called using Stacks denovo pipeline in vcf format.