biostudies-literaturePoikela NFinnish Cultural FoundationJenny and Antti Wihuri FoundationAcademy of Finland projectEuropean Research CouncilNatural Environmental Research Council (NERC)Natural Environmental Research CouncilNatural Environment Research Councilevae024https://www.ebi.ac.uk/biostudies/studies/S-EPMC10972691biostudies-literatureUnknown16(3)Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana toGenome biology and evolutionChromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana.PMC10972691NE/L011522/1322980757648Hoikkala VLohse KKankare MPoikela NLaetsch DRfalseChromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana.Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to2024-01-01T00:00:00Z2024 Mar2026-04-08T15:10:47.096Z2025-04-05T23:16:09.816ZS-EPMC109726913848269810.1093/gbe/evae024