DOI: 10.5061/dryad.4f4qrfjhf
title: Semipermeable species boundaries create opportunities for gene flow and adaptive potential

description: Hybridisation and gene flow can have both deleterious and adaptive
 consequences for natural populations and species. To better understand the
 extent of hybridisation in nature and the balance between its beneficial
 and deleterious outcomes in a changing environment, information on
 naturally hybridising non-model organisms is needed. This requires the
 characterisation of the structure and extent of natural hybrid zones. Here
 we study natural populations of five keystone mound-building wood ant
 species in the Formica rufa group across Finland. No genomic studies
 across the species group exist, and the extent of hybridisation and
 genomic differentiation in sympatry is unknown. Combining genome-wide and
 morphological data, we demonstrate more extensive hybridisation than was
 previously detected between all five species in Finland. Specifically, we
 reveal a mosaic hybrid zone between F. aquilonia, F. rufa and F.
 polyctena, comprising further generation hybrid populations. Despite this,
 we find that Formica rufa, F. aquilonia, F. lugubris, and F. pratensis
 form distinct gene pools in Finland. We also find that hybrids occupy
 warmer microhabitats than the non-admixed populations of cold-adapted F.
 aquilonia, and suggest that warm winters and springs, in particular, may
 benefit hybrids over F. aquilonia, the most abundant F. rufa group species
 in Finland. In summary, our results indicate that extensive hybridisation
 may create adaptive potential that could promote wood ant persistence in a
 changing climate. Additionally, they highlight the potentially significant
 ecological and evolutionary consequences of extensive mosaic hybrid zones,
 within which independent hybrid populations face an array of ecological
 and intrinsic selection pressures.
description: 1) Whole-genome (separate nuclear and mitochondrial) filtered SNP
 data (VCF files) from 89 Formica rufa group wood ant individuals, both
 non-admixed and hybrid samples from species <em>F. aquilonia, F.
 polyctena, F. rufa, F. lugubris, </em>and<em> F.
 pratensis</em>. Scripts for producing the VCF files from raw
 whole-genome sequencing data are included, and description of the pipeline
 can be found in the Materials and Methods section of Satokangas et al.
 2023 (DOI: 10.1111/mec.16992).<br><br>2) Climate data
 (temperature and precipitation) for 33 Finnish <em>F.
 aquilonia</em> and hybrid nest sites for broadscale temperature and precipitation
 modelling in Satokangas et al. 2023 (DOI:
 10.1111/mec.16992). The
 nest site coordinates in the deposited files are rounded. The
 data was extracted from digital rasters
 of daily mean air temperature and daily precipitation sum (sourced from
 the Finnish Meteorological Institute ClimGrid gridded daily climatology at
 a 10 km spatial resolution; (Aalto et al., 2016)) based on the nest site
 coordinates. Scripts for the climatic modelling performed in Satokangas et
 al. 2023 are included, and description of the analysis can be found in the
 Materials and Methods section of the mentioned
 publication.<br><br>3) Within-nest and ambient temperatures for five
 Finnish <em>F. aquilonia</em> and hybrid populations for
 temperature modelling performed in Satokangas et al. 2023 (DOI:
 10.1111/mec.16992). The daily mean
 ambient temperatures are extracted for each population based on the mean
 coordinates of nests within that population from the ClimGrid gridded
 daily climatology rasters at a 1 km spatial resolution (Aalto
 et al., 2016). Scripts for the within-nest and ambient temperature
 modelling performed in Satokangas et al. 2023 are included, and
 description of the analysis can be found in the Materials and Methods
 section of the mentioned publication.
description: 1) '<strong>VCF_files</strong>': This
 folder contains two compressed VCF files, one for nuclear, and one for
 mitochondrial SNP data.
 '<strong>Raw_reads_to_SNPs_scripts</strong>'
 (Zenodo): This folder contains scripts used to process raw whole-genome
 sequencing data into both nuclear and mitochondrial SNP data that are used
 in the genomic analyses of this manuscript.  2)
 '<strong>Broadscale_climate</strong>': This folder
 contains an input data table for the broadscale temperature and
 precipitation modelling and a metadata table that is used to extract the
 climatic information in the input data file.
 '<strong>Broadscale_climate_scripts</strong>'
 (Zenodo): This folder contains scripts for the broadscale temperature and
 precipitation modelling of 33 Finnish <em>Formica
 aquilonia</em> and hybrid nest sites covering steps from data
 extraction to modelling and plotting.  3)
 '<strong>Within_nest_temp</strong>': This folder
 contains an input data table for the within-nest and ambient temperature
 modelling.
 '<strong>Within_nest_temp_scripts</strong>' (Zenodo): This folder contains a script ('<strong>NestTemperatures.Rmd</strong>') for the within-nest and ambient temperature modelling for five Finnish <em>F. aquilonia</em> and hybrid populations.