# Data package

For the paper "Coadapted genomes and selection on hybrids: 
Fisher’s geometric model explains a variety of empirical patterns"
Simon A., N. Bierne and J. J. Welch
Evolution Letters, 2018

Original authors of used datasets not previously available online have
agreed to the inclusion in this repository. 

# Simulations

Source code used for the simulations of Figures S2 to S4 can be found
in the github repository
https://github.com/alxsimon/Hybrid_fitness_Fisher_geometric_model

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# File structure and description:

./README -> this file
./datasets_included.ods -> Spreadsheet to precise links to previously available data
./Drosophila_divergence -> Calculation of $g_X$ for the Drosophila species 
	/sum_CDS_lengths.R -> R script to calculate $g_X$
	/Drosophila_gX.ods -> Summary of the results for the different species
	/D.yakuba -> CDS length data for D. yakuba per chromosome
		/yakuba_2L.txt
		/yakuba_3L.txt
		/yakuba_2R.txt
		/yakuba_3R.txt
		/yakuba_X.txt
	/D.melanogaster -> CDS length data for D. melanogaster per chromosome
		/melanogaster_3L.txt
		/melanogaster_2L.txt
		/melanogaster_3R.txt
		/melanogaster_X.txt
		/melanogaster_2R.txt
	/D.pseudoobscura -> CDS length data for D. pseudoobscura per chromosome
		/dpse_merge.bed
		/dpse_cdf.gtf
		/command_lines.txt -> commands used to determine CDS lengths in pseudoobscura
		/dpse_sum_cds
		/dpse_cds_length
		/dpse-all-r3.04.gtf.gz
	/D.simulans -> CDS length data for D. simulans per chromosome
		/simulans_3L.txt
		/simulans_2L.txt
		/simulans_X.txt
		/simulans_3R.txt
		/simulans_2R.txt
./Mytilus_data -> Mytilus data analysis
	/Crosses_analysis_Dryad.Rmd -> Rmarkdown file to produce the html
	/Mytilus_crosses_genotypes.csv -> raw data for Mytilus including genotypes for crosses and reference populations
	/Crosses_analysis_Dryad.html -> html file presenting the analysis
	/Mytilus_markers_flanking_sequences.csv -> Flanking sequences for markers used
./Regression_models -> Fitting analyses for the section "Estimating the fitness surface" and "Predictions of Fisher’s geometric model with sex-specific inheritance" (Drosophila)
	/fitness_surface_fit.R -> fitting of the datasets for Figure 5, Tables S5 and S6
	/glms_table3.R -> fitting for Drosophila results in Table 3
	/data -> Datasets used in those regressions
		/BCsant.txt
		/BCpers.txt
		/BCyak.txt
		/BCsech.txt
		/BCpseu.txt
		/BCsim.txt
		/Turner.data.txt -> produced in ./Mus_musculus folder
		/White.data.txt -> produced in ./Mus_musculus folder
		/Chapman2016.csv -> produced in ./Senecio folder
		/Christe-q_q12_survivorship2015_GBS_Populus.txt
./Mus_musculus -> Formatting of the data for the Mus musculus model and calculation of $g_X$
	/White2011
		/White_raw_data.csv
		/White.data.txt -> final file
		/White_data_prep.R
	/Turner2014
		/snpAnnotation_Turner2014.csv
		/Turner2014_analysis.html -> Explanation of this preparation
		/Turner.data.txt -> final file
		/Turner2014_mus_fixed_recodeA.log
		/Turner2014_mus_fixed_recodeA.raw
		/Turner2014_analysis.Rmd -> Rmarkdown for the html file
		/Turner2014_mus_fixed_DMHcoded.csv
		/Determine_fixed_SNPs
			/sid_fixed_SNPs.txt
			/species_alleles_fixed.csv
			/fixed_SNPs.R
	/Mus_musculus_CDS_length -> data and analysis script to get $g_X$ for Mus musculus
		/mus_chr1.txt
		/mus_chr3.txt
		/mus_chr2.txt
		/mus_chr6.txt
		/mus_chr7.txt
		/mus_chr5.txt
		/mus_chr18.txt
		/mus_chr19.txt
		/mus_chr4.txt
		/Mus_CDS_lengths.ods
		/sum_prot_length.R
		/mus_chrMT.txt
		/mus_chrX.txt
		/mus_chr9.txt
		/mus_chr14.txt
		/mus_chr15.txt
		/mus_chr8.txt
		/mus_chrY.txt
		/mus_chr17.txt
		/mus_chr16.txt
		/mus_chr12.txt
		/mus_chr13.txt
		/mus_chr11.txt
		/mus_chr10.txt
./Senecio -> Preparation of Senecio data from Chapman et al. 2016
	/senecio_data_prep.R
	/RawGenotypesForDryad.csv -> raw data from Chapman et al. 2016
	/Chapman2016.csv
