DOI: 10.5061/dryad.744p394
title: Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.

description: Meiotic recombination is crucial for chromosomal segregation, and
 facilitates the spread of beneficial and removal of deleterious mutations.
 Recombination rates frequently vary along chromosomes and Drosophila
 melanogaster exhibits a remarkable pattern. Recombination rates gradually
 decrease towards centromeres and telomeres, with a dramatic impact on
 levels of variation in natural populations. Two close sister species, D.
 simulans and D. mauritiana do not only have higher recombination rates,
 but also exhibit a much more homogeneous recombination rate that only
 drops sharply very close to centromeres and telomeres. Because certain
 sequence motifs are associated with recombination rate variation in D.
 melanogaster, we tested whether the difference in recombination landscape
 between D. melanogaster and D. simulans can be explained by the genomic
 distribution of recombination-rate associated sequence motifs. We
 constructed the first high-resolution recombination map for D. simulans
 based on 189 haplotypes from a natural D. simulans population, and
 searched for short sequence motifs linked with higher than average
 recombination in both sister species. We identified five consensus motifs
 significantly associated with higher than average chromosome-wide
 recombination rates in at least one species and present in both. Testing
 fine resolution associations between motif density and recombination, we
 found strong and positive associations genome-wide over a range of scales
 in D. melanogaster, while the results were equivocal in D. simulans.
 Despite the strong association in D. melanogaster, we did not find a
 decreasing density of these short-repeat motifs towards centromeres and
 telomeres. We conclude that the density of recombination-associated repeat
 motifs cannot explain the large-scale recombination landscape in D.
 melanogaster, nor the differences to D. simulans. The strong association
 seen for the sequence motifs in D. melanogaster likely reflects their
 impact influencing local differences in recombination rates along the
 genome.
description: 1_recombination_maps_csv_ZIPRecombination map files for D. simulans and D. melanogaster, at different smoothing resolutions. We provide moving median and LOESS smoothed maps. For Dsim, the moving median files are provided at the following resolutions: 5, 25, 101, 501, and 2501 kb. For Dmel, the moving median files are provided at the following resolutions: 501, and 2501 kb, due to a lower resolution initial map. For Dsim the LOESS files are provided with the LOESS smoothing parameter set at the following levels: 0.001, 0.005, 0.02, 0.10. These levels are equivalent to moving median windows of 25, 101, 501, and 2501 kb. For Dmel, the LOESS smoothing parameter is set at: 0.02, 0.10. Finally, a raw unsmoothed recombination map is provided for Dsim, in 1 kb windows, and for Dmel at 101 kb. Details for how this raw Dsim map was produced are in our paper, Howie et et al. 2019. The R script used to produce differently smoothed recombination maps for both species is also provided as an R-Markdown file.2_recombination_maps_mimicrEE_ZIPRecombination map files for D. simulans and D. melanogaster, at different smoothing resolutions. This set of files is the same as the CSV files, except that they formatted for use with MimicrEE simulation software. Also, we provide “Dsim_recombination_map_LOESS_100kb_1.txt”, in which LOESS smoothing equivalent to 100 kb windows is applied through an alternative R algorithm. The standard files provided are, again, the moving median and LOESS smoothed maps. For Dsim, moving median files are provided at resolutions: 5, 25, 101, 501, and 2501 kb. For Dmel, the moving median files are provided at resolutions: 501, and 2501 kb, due to a lower resolution initial map. For Dsim the LOESS files are at 0.001, 0.005, 0.02, 0.10. These levels are equivalent to moving median windows of 25, 101, 501, and 2501 kb. For Dmel, the LOESS smoothing parameter is set at: 0.02, 0.10. A raw recombination map is provided for Dsim, in 1 kb windows and for Dmel in 101 kb windows. Details for how this raw map was produced can be found in our paper, Howie et et al. 2019. The R script used to produce differently smoothed recombination maps is provided as an R-Markdown file.3_dmel-fimo_ZIP.tsvMotif density files for D. melanogaster, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file.4-dsim-fimo_ZIP.tsvMotif density files for D. simulans, which are output from FIMO. These can be used to plot motif density along the genome or, in combination with the recombination maps, to test the relationship between recombination rates and motif density. The script is provided in the R Markdown file.5_figures+mapfilesR-Markdown file. This contains the in house scripts used to process raw data files and run all downstream analyses reported in our paper. The script includes code to smooth recombination maps, generate motif density files, test correlations and and fit linear models to examine the relationship between motif density and recombination rate, at different smoothing scales, in Dmel and Dsim. Details can be found in our paper.6_PrepareFasta_XPhased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the X chromosome. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the X chromosome. This is essentially information about SNPs and their genomic positions.PrepareFasta_X.tar.gz7_PrepareFastaPhased Haplotypes - that is, SNP and genomic location - used to produce the Dsim Recombination Map, for the main autosomes, 2L, 2R, 3L, 3R. We crossed focal males from 189 isofemale lines, from Florida, to virgin “reference” females, and then individually sequenced the F1 progeny. From the raw BAM files, we produced phased haplotype files, in which reference alleles are removed and SNPs called. This was done in FreeBayes: segment size 1kb, alpha 0.05, theta 0.04. Full details are provided in our paper. Here, we provide 189 phased haplotypes for the autosome arms 2L, 2R, 3L, 3R. This is essentially information about SNPs and their genomic positions.PrepareFasta.tar.gz