Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.

Howie JM, Mazzucco R, Taus T, Nolte V, Schlötterer C

Date Published: April 16, 2019

DOI: https://doi.org/10.5061/dryad.744p394

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Title 1_recombination_maps_csv_ZIP
Downloaded 2 times
Description Recombination 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.
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Title 2_recombination_maps_mimicrEE_ZIP
Downloaded 4 times
Description Recombination 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.
Download 2_recombination_maps_mimicrEE_ZIP.zip (11.48 Mb)
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Title 3_dmel-fimo_ZIP.tsv
Downloaded 1 time
Description Motif 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.
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Title 4-dsim-fimo_ZIP.tsv
Downloaded 2 times
Description Motif 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.
Download 4-dsim-fimo_ZIP.tsv.zip (4.622 Mb)
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Title 5_figures+mapfiles
Downloaded 1 time
Description R-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.
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Title 6_PrepareFasta_X
Downloaded 1 time
Description Phased 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.
Download PrepareFasta_X.tar.gz (2.511 Gb)
Download README.rtf (1.464 Kb)
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Title 7_PrepareFasta
Downloaded 1 time
Description Phased 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.
Download PrepareFasta.tar.gz (5.795 Gb)
Download README.rtf (1.324 Kb)
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When using this data, please cite the original publication:

Howie JM, Mazzucco R, Taus T, Nolte V, Schlötterer C (2019) DNA motifs are not general predictors of recombination in two Drosophila sister species. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evz082

Additionally, please cite the Dryad data package:

Howie JM, Mazzucco R, Taus T, Nolte V, Schlötterer C (2019) Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species. Dryad Digital Repository. https://doi.org/10.5061/dryad.744p394
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