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.

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 F. aquilonia, F. polyctena, F. rufa, F. lugubris, and F. pratensis. 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).

2) Climate data (temperature and precipitation) for 33 Finnish F. aquilonia 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.

3) Within-nest and ambient temperatures for five Finnish F. aquilonia 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.

1) 'VCF_files': This folder contains two compressed VCF files, one for nuclear, and one for mitochondrial SNP data. 'Raw_reads_to_SNPs_scripts' (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) 'Broadscale_climate': 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. 'Broadscale_climate_scripts' (Zenodo): This folder contains scripts for the broadscale temperature and precipitation modelling of 33 Finnish Formica aquilonia and hybrid nest sites covering steps from data extraction to modelling and plotting. 

3) 'Within_nest_temp': This folder contains an input data table for the within-nest and ambient temperature modelling. 'Within_nest_temp_scripts' (Zenodo): This folder contains a script ('NestTemperatures.Rmd') for the within-nest and ambient temperature modelling for five Finnish F. aquilonia and hybrid populations.