Data and resources on the population history of the harlequin fly

This dataset contains phased vcf files of Chironomus riparius, ouput files of RepeatMasker, RepeatOBserver and MSMC2, such as supporting files. For further details also check the GitHub page: https://github.com/lpettrich/Crip_PopulationHistory_Centromere_2025 phased-vcfs: Artificially phased vcf-files of five populations with four individuals each. Needed to generate multihetsep files. Input files for iSMC. Hesse in Germany = MG Rhône-Alpes in France = MF Lorraine in France = NMF Piemont in Italy = SI Andalusia in Spain = SS multihetsep-files: Created with msmc-tools. Input files for MSMC2. RepeatMasker: Raw output of RepeatMasker run and summary file. RepeatOBserver: Summary files on centromere predictions based on histograms and Shannon Diversity from RepeatOBserver. Genome-wise Shannon Diversity per chromosome included. MSMC2: Raw ouput of combined cross-coalescence and mean values if MSMC2 per populations. Calculate tMRCA: Steps to repeat calculations for tMRCA input-files figures: Supporting files needed to create figures.