Recombination in Drosophila

Description of the data and file structure This dataset contains ancestry-probability outputs generated using a hidden Markov model (HMM) to reconstruct parental ancestry along chromosomes in Drosophila crosses. The HMM evaluates ordered genetic markers and estimates support for two parental ancestry states at each marker. Changes in inferred ancestry state between adjacent markers identify candidate recombination intervals bounded by two flanking marker positions. These files are intermediate, marker-level HMM outputs. They document the ancestry reconstruction used in the downstream recombination analyses. They are not the final recombination maps or recombination-rate summaries. Species abbreviations: Dsim: Drosophila simulans Dyak: Drosophila yakuba Dtei: Drosophila teissieri Chromosome labels are 2L, 2R, 3L, 3R, and X. The labels par1 and par2 identify the two parental ancestry states used by the HMM. All 38 files are compressed .tsv.zip archives. Each archive contains a tab-separated .tsv file. Files Dsim 2022 cross outputs 2022_ancestry-probs-par1_2L.tsv.zip 2022_ancestry-probs-par1_2R.tsv.zip 2022_ancestry-probs-par1_3L.tsv.zip 2022_ancestry-probs-par1_3R.tsv.zip 2022_ancestry-probs-par1_X.tsv.zip 2022_ancestry-probs-par2_2L.tsv.zip 2022_ancestry-probs-par2_2R.tsv.zip 2022_ancestry-probs-par2_3L.tsv.zip 2022_ancestry-probs-par2_3R.tsv.zip 2022_ancestry-probs-par2_X.tsv.zip PE_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip PE_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip SE_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip SE_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dtei cross outputs Dtei_L2_L3_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip Dtei_L2_L3_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dtei_pilot_L1_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip Dtei_pilot_L1_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dtei TUZ35 × CT04 cross outputs TUZ35_CT04_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip TUZ35_CT04_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dyak cross outputs Dyak_ancestry-probs-par1_2L.tsv.zip Dyak_ancestry-probs-par1_2R.tsv.zip Dyak_ancestry-probs-par1_3L.tsv.zip Dyak_ancestry-probs-par1_3R.tsv.zip Dyak_ancestry-probs-par1_X.tsv.zip Dyak_ancestry-probs-par2_2L.tsv.zip Dyak_ancestry-probs-par2_2R.tsv.zip Dyak_ancestry-probs-par2_3L.tsv.zip Dyak_ancestry-probs-par2_3R.tsv.zip Dyak_ancestry-probs-par2_X.tsv.zip Parental-panel outputs Dsim MD221: md221ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip md221ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dsim w501: w501ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip w501ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dtei TUZ: TUZ_parent_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip TUZ_parent_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Dtei Yun: Dtei_YUN_ancestry-probs-par1_2L_2R_3L_3R_X.tsv.zip Dtei_YUN_ancestry-probs-par2_2L_2R_3L_3R_X.tsv.zip Variables The output tables contain the following information: Sample identifier: identifier for the offspring Chromosome or chromosome arm: chromosome arm analyzed. In arm-specific files, this may be indicated only by the filename. Position: marker coordinate in base pairs on the reference assembly used for the analysis. Ancestry probability or posterior support: HMM support for assignment to the specified parental ancestry state. For downstream recombination analyses, candidate transitions are bounded by two flanking marker positions. When marker1 and marker2 are available, the interval midpoint can be calculated as: midpoint_bp = (marker1 + marker2) / 2 The midpoint is an inferred position within the marker interval. Code and software The HMM outputs were generated using the ancestryinfer pipeline. The scripts, configuration files, installation instructions, and user manuals are available at the ancestryinfer GitHub repository. Additional documentation is available in the ancestryinfer README and the ancestryinfer user manual.