biostudies-literaturePortinha BAcademy of FinlandSocietas pro Fauna et Flora Fennica3416-3431https://www.ebi.ac.uk/biostudies/studies/S-EPMC9320829biostudies-literatureUnknown31(12)The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across tMolecular ecologyWhole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges.PMC9320829309580Portinha BSeifert BHelantera HKulmuni JMonaghan JNouhaud PAvril ABernasconi CSousa VCfalseWhole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges.The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across t2022-01-01T00:00:00Z2022 Jun2026-05-28T05:03:53.872Z2022-08-02T22:31:20.382ZS-EPMC93208293546031110.1111/mec.16481