DOI: 10.5061/dryad.hmgqnk9jz
title: Effects of social organisation and elevation on spatial genetic structure in a montane ant

description: Studying patterns of population structure across the landscape sheds light
 on dispersal and demographic processes, which helps to inform conservation
 decisions. Here, we study how social organisation and landscape factors
 affect spatial patterns of genetic differentiation in an ant species
 living in mountainous regions. Using genome-wide SNP markers, we assess
 population structure in the Alpine silver ant, Formica selysi. This
 species has two social forms controlled by a supergene. The monogyne form
 has one queen per colony, while the polygyne form has multiple queens per
 colony. The two social forms co-occur in the same populations. For both
 social forms, we found a strong pattern of isolation-by-distance across
 the Alps. Within regions, genetic differentiation between populations was
 weaker for the monogyne form than for the polygyne form. We suggest that
 this pattern is due to higher dispersal and effective population sizes in
 the monogyne form. In addition, we found stronger isolation-by-distance
 and lower genetic diversity in high elevation populations, compared to
 lowland populations, suggesting that gene flow between F. selysi
 populations in the Alps occurs mostly through riparian corridors along
 lowland valleys. Overall, this survey highlights the need to consider
 intraspecific polymorphisms when assessing population connectivity and
 calls for special attention to the conservation of lowland habitats in
 mountain regions.
description: Sampling and
 genotyping <em>Formica selysi</em> lives in riverine ecosystems
 throughout the European
 Alps and the Pyrenees mountains (Seifert, 2002). J. Purcell and A.
 Brelsford sampled workers
 in 152 colonies from 13 localities ranging from 180 m to 1450 m in
 elevation (1-32 colonies per locality, Table S1). In each locality
 monogyne and/or polygyne colonies were sampled within a 1 km2 area (Table
 S1). The sampling localities were situated along the Rhine River or
 tributaries (3 localities, east Switzerland and west Austria), along the
 Upper Rhône River or tributaries (6 localities, west Switzerland) and
 along tributaries of the Lower Rhône River (4 localities, France; Figure
 1, Table S1). Each locality represents a separate
 population. We genotyped one worker per colony. We extracted
 DNA from the head and thorax of each worker using the Qiagen DNeasy Blood
 and Tissue kit, following the protocol for insect tissue. We obtained
 double-digest RAD sequence data by following the ddRAD-seq protocol
 described in Brelsford et
 al. (2016). In brief, we
 digested genomic DNA using restriction enzymes EcoRI and MseI, ligated
 inline barcoded adapters, removed DNA fragments shorter than 250 bp using
 AMPure magnetic beads, carried out PCR amplification of each individual in
 triplicate, during which we added a second unique adapter for each
 independent plate, and carried out a final size selection on the pooled
 libraries, to retain sequences in the 400-500 bp range. The resulting
 libraries were sequenced on the Illumina 2500 Hi Seq platform of the
 Lausanne Genomic Technologies Facility.
 Bioinformatics Demultiplexing and quality control of raw
 sequences were done with the <em>process_radtags</em> pipeline
 in STACKS v. 2.2 (Catchen
 <em>et al.</em>, 2013). Clean reads were aligned to an
 upgraded<em> </em>version<em> </em>of the
 reference genome of <em>Formica selysi</em> (Brelsford et al.
 2020, NCBI, GenBank accession number: GCA_009859135.1)<em>,
 </em>using BWA v. 0.7.17 (Li and Durbin, 2009). Single Nucleotide Polymorphisms (SNPs) and
 genotypes were called with the <em>ref_map</em> pipeline in
 STACKS, using default parameters. The initial consensus output catalogue
 from the <em>populations </em>program contained 628,232 RAD
 loci, with average length of 84.7 bp and average sample coverage of 28.9x.
 In total, 323,797 SNPs were retained, distributed across 99,299
 polymorphic RAD loci. Further SNP filtering was done using the
 VCFtools (Danecek
 <em>et al.</em>, 2011) and the “VcfR” <em>R</em> package
 (Knaus BJ,
 2017). Genotypes with
 quality score lower than 20 and sequencing depth lower than three-fold
 were considered missing data. We retained one random polymorphic site per
 RAD locus, to avoid bias due to linkage disequilibrium. We removed sites
 with heterozygosity higher than 0.70, to exclude merging paralogous loci
 (Paris, Stevens and
 Catchen, 2017). We only
 retained SNPs with minor allele frequency higher than 0.01 and mapping to
 one of the 27 chromosome-length scaffolds of the reference genome. We
 further removed individuals with more than 30% of missing data and
 selected SNPs present in 95% of the individuals retained. The resulting
 dataset had 13,421 SNPs, of which 923 were on chromosome 3, which contains
 the non-recombining social supergene (Purcell <em>et al.</em>,
 2014), and 12,498 were in
 the remaining 26 chromosomes.