Code, data and vectorised figures associated with the publication on the evolutionary origin of the Lake Victoria cichlid radiation

Initial data preparation

LSF job submission script to align the reads to the reference genome: BashPipelines/00_alignToBam.lsf
LSF job submission script to use GATK Haplotype Caller to get gvcf files of each sample: BashPipelines/00_runHaplotypeCaller.lsf
LSF job submission script to get a vcf file per chromosome and apply some basic filters: BashPipelines/00_runGenotypeGVCF_filter.sh
Remove sites with too high sequencing depth, indicative of paralogous regions collapsed in the reference: BashPipelines/00_removeTooHighDepthSites.sh

Generate the nuclear phylogeny: BashPipelines/01_iqtree2.sh
for file conversion: BashPipelines/01_vcf2phylip.py
Plot nuclear phylogenies as fan trees for Fig 3 and Figure S2: Rscripts/Fig3_FigS2_giantPhylogenies.R
Generate the mitochondrial phylogeny: BashPipelines/01_iqtree2.sh
Make co-phyloplots of quartet tree vs iqtree2: Rscripts/FigS14_cophyloplot_quartets_iqtree.R
Co-phyloplot of nuclear vs mitochondrial phylogenies for Aux Fig. 1 Rscripts/AuxFig1_cophyloplot_mtDNA-nuc.R

Compute MDS with different combinations of individuals: Rscripts/FigS3_FigS8_MDS.R

Compute genomic variation explained by ecomorph or genus across the Victoria Radiation: BashPipelines/02_amova.sh

Compute D statistics with ADMIXTOOLS: BashPipelines/Dstatistics.sh
Example of Fbranch script, here for all LVRS and outgroups: BashPipelines/03_fbranch.sh
Plotting f4 values of ecomorph pairs across lakes: Rscripts/Fig5B_f4values.R
Plotting Dstats of Upper Nile ancestry in the LVRS and Western Lakes in the Victoria Radiation: RScripts/FigS4_FigS7_Dstats.R
Compute DFOIL to test the direction of gene flow between Har. squamipinnis (Edward piscivore) and Victoria piscivores: BashPipelines/FigS6_computeDfoil.sh which requires BashPipelines/FigS6_runDfoil.sh
Compute fdM to test for correlations between ancestries (example of dwarf predators): FigS13_fdM_dwarfPredators.sh

Get allele frequencies for each ecomorph and group: BashPipelines/Fig5_FigS10-S12_getFrqs.lsf
Get sites with at least 0.9 allele frequency difference between ecomorph and all other Victoria Radiation cichlids: BashPipelines/Fig5_FigS10-S12_getDiffSites.lsf
Fig 5 plot: Rscripts/Fig5_ancestry_proportions.R Note, the data is found in Data/Fig5_ancestry_proportions.csv
Fig S10-S12 plots: RScripts/FigS10-S12_alleleFrequencies_ecogroups.R

Get the file with all sites of piscivores and paedophages (one sample per species): FigS9_runGenotypeGVCF.lsf
Compute DXY: FigS9_computeDXY.sh
Plot DXY: RScripts/FigS9_dxy_sympatric_vs_allopatric.pdf

Requires these scripts: