DOI: 10.5061/dryad.9cnp5hqjt
title: Dataset 2 for Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly

description: Understanding factors influencing patterns of genetic diversity and the
 population genetic structure of species is of particular importance in the
 current era of global climate change and habitat loss. These factors
 include the evolutionary history of a species as well as heterogeneity in
 the environment it occupies, which in turn can change across time. Most
 studies investigating spatio-temporal genetic patterns have focused on
 patterns across wide geographical areas rather than local variation, but
 the latter can nevertheless be important particularly in topographically
 complex areas. Here we consider these issues in the Sooty Copper butterfly
 (Lycaena tityrus) from the European Alps, using genome-wide SNPs
 identified through RADseq. We found strong genetic differentiation within
 the Alps with four genetic clusters, indicating western, central, and
 eastern refuges, and a strong reduction of genetic diversity from west to
 east. This reduction in diversity may suggest that the southwestern refuge
 was the largest one in comparison to other refuges. Also, the high genetic
 diversity in the West may result from (1) admixture of different western
 refuges, (2) more recent demographic changes, or (3) introgression of
 lowland L. tityrus populations. At small spatial scales, populations were
 structured by several landscape features and especially by high mountain
 ridges and large river valleys. We detected 36 outlier loci likely under
 altitudinal selection, including several loci related to membranes and
 cellular processes. We suggest that efforts to preserve alpine L. tityrus
 should focus on the genetically diverse populations in the western Alps,
 and that the dolomite populations should be treated as genetically
 distinct management units, since they appear to be currently more
 threatened than others. This study demonstrates the usefulness of
 SNP-based approaches for understanding patterns of genetic diversity, gene
 flow and selection in a region that is expected to be particularly
 vulnerable to climate change.
description: From each male, we used head and thorax for the extraction of
 genomic DNA with the E.Z.N.A. ® Tissue DNA Kit (Omega bio-tek, Germany).
 We followed the manufacturers’ instructions but included an additional
 step of RNase A treatment. Afterwards, we applied double digest
 restriction-site associated DNA sequencing (ddRADseq) following Trense et
 al. (2021) and used the restriction enzymes NlaIII and MluCI. We pooled
 individuals into four libraries, each containing DNA fragments from
 individuals with different adapter pairs. Libraries were cleaned with 1.5x
 volume of Sera-Mag beads. We selected 250-400 base pair (bp) fragments
 using a 2% gel cassette and Pippin-Prep software 4.3 (Sage Science, USA).
 This was followed by a polymerase chain reaction (PCR) enrichment in a 10
 µL reaction with 1 µL of size selected DNA, 2 µL 5x Phusion ® HF Reaction
 Buffer, 0.2 µL dNTPs (10 mM), 0.1 µL (100 units) Phusion ® HF DNA
 Polymerase (New England BioLabs Inc, USA), nuclease free water, and 2 µL
 (10 µM) each of Illumina P1 and P2 primers (Peterson, Weber, Kay, Fisher,
 & Hoekstra, 2012). The profile of thermal cycling consisted of
 denaturation at 98°C for 30 sec, followed by 12 cycles with 10 sec at
 98°C, 30 sec at 65°C, and 70 sec at 72°C, and an extension for 5 min at
 72°C. For the final library, we used seven PCR reactions. The four
 libraries were sequenced on an Illumina Novaseq 6000 platform generating
 150 bp paired-end reads.
description: Possibly the coordinates of the collection points could be
 used.