USAGE NOTES ON DATA AND CODE FOR FELLER & SEEHAUSEN: "GENETIC ARCHITECTURE OF ADAPTIVE RADIATION ACROSS TWO TROPHIC LEVELS" PHENOTYPE DATA PROCESSING PNPxNOM_pheno_data_prep.R R-script used to prepare the phenotype data for QTL mapping Input: the files containing the morphological measurements / colour scores: • PNPxNOM_morphology_done_adj.csv (parental species individuals (last 25 lines) not used in manuscript) • PNPxNOM_teeth_done.csv (parental species individuals (last 20 lines) not used in manuscript) • PNPxNOM_guts_done.csv ‘gutlength’=intestine length; ‘fat’: qualitative score of amount of fat removed from around intestine (not used in manuscript); the parental species individuals (last 12 rows) were preserved differently and hence the measurements have to be interpreted with caution (not used in manuscript) • PNPxNOM_colourscores_done.csv 1=presence, 0=absence; Y=yellow, tg=transgressive; there was no variation in traits in columns W-Y; traits in columns T&W-Y were not mapped • PNPxNOM_7more_ids.txt List of all genotyped individuals with info on sex (0=females, 1=males) and family (this info is also embedded in the fastq sample names, but not complete for all samples) Intermediate file(s): • allPhenoMeans.csv Output: • allPhenos.csv PNPxNOM_morphological_comparison_with_wildcaught_males.R R-script used to compare phenotype distributions and trait correlations between F2s and parental species. Input: • "Pundamilia Python.txt" and "Neochromis Makobe.txt" from van Rijssel et al. 2018 PRSB: https://doi.org/10.5061/dryad.vk23f • allPhenoMeans.csv • allPhenos.csv SEQUENCE PROCESSING & LINKAGE MAP PNPxNOM_sequence_processing.txt Log file containing all code and scripts used to process the sequencing data from raw reads to the final vcf-file Output: • PNPxNOM_7more_f1_r1_f2_f3_homfixF1het.vcf (final vcf-file containing genotypes of 168 F2 individuals and the two grandparents (P) at SNPs that are reciprocally homozygous fixed between the two P and heterozygous in the F1s) PNPxNOM_vcfToJoinMap.R R-script used to produce the input file for JoinMap. Input: • PNPxNOM_7more_f1_r1_f2_f3_homfixF1het.vcf Output: • PNPxNOM_7more_JM_input.loc input file for JoinMap • PNPxNOM_7more_genos.txt this is the same file as the .loc file without the header and list of individuals PNPxNOM_7more_map_LGadj.txt The linkage map produced with JoinMap, linkage group numbers adjusted manually (known from alignment) QTL MAPPING PNPxNOM_rqtl_input.R R-script used to prepare input file for R/qtl Input: • PNPxNOM_7more_map_LGadj.txt • PNPxNOM_7more_ids.txt • PNPxNOM_7more_genos.txt • allPhenos.csv Intermediate files: • allGenotypes.csv • allPhenotypes.csv Output: • GenoPheno.csv PNPxNOM_QTLmapping.R QTL mapping analysis R-script. Input: GenoPheno.csv Output: QTL mapping results tables and plots. PNPxNOM_QTLmapping_bayesint_PVE_and_plots.R R-script used to extract Bayesian Confidence Intervals, calculate Percent Variance explained, and produce key QTL results Figure. Input: same as PNPxNOM_QTLmapping.R as well as the output from the latter script. QTL MAPPING 2 (2-QTL and multiple-QTL models) PNPxNOM_scantwo_on_cluster.R R-script used to run 2-QTL scans on HPC cluster PNPxNOM_2QTLpermruns1.sh PNPxNOM_2QTLpermruns1.txt PNPxNOM_2QTLpermruns1.R Example bash-/R-scripts and txt-file (here for the morphological traits with both covariates) used to run permutations or 2-QTL scans on HPC cluster in 4 x 250 batches per trait PNPxNOM_QTLmapping2QTLmodels.R QTL mapping analysis R-script for 2-QTL scans, i.e. processing the output from PNPxNOM_scantwo_on_cluster.R & PNPxNOM_2QTLpermruns1.R PNPxNOM_2QTLpermruns11.sh PNPxNOM_2QTLpermruns11.txt PNPxNOM_2QTLpermruns11.R Example bash-/R-scripts and txt-file (here for the morphological traits with both covariates) used to run permutations for multiple QTL scans on HPC cluster in 4 x 250 batches per trait PNPxNOM_QTLmappingMultipleQTLmodels.R QTL mapping analysis R-script for multiple QTL models (using stepwise qtl).(Permutations run on HPC cluster in 4 batches of 250 per trait with PNPxNOM_2QTLpermruns11.R.) -------------------------------------------------------------------------------------------------------------------------------------- PNP refers to Pundamilia sp. “nyererei-like”, NOM to Neochromis omnicaeruleus from Makobe Island.