Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection

This dataset contains VCF files, morphological data and custom scripts required to repeat analyses conducted in Sendell-Price et al. (in press). Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection. Heredity. ZLat_Orientated_SNZ_FP_FullFiltered_63849SNPs.vcf Full dataset VCF file (63,849 SNPs) mapped to the Zosterops lateralis melanops reference genome. ZLat_Orientated_SNZ_FP_LD_Filtered_5414SNPs.vcf SNP dataset filtered to remove one of every pair of SNPs with r2 > 0 within 100kb sliding windows and SNPs with missing data. This VCF file was used for admixture analysis. ZLat_Orientated_SNZ_FP_MaxMissingZero_LD_Filtered_1587SNPs.vcf SNP dataset filtered to remove one of every pair of SNPs with r2 > 0 within 100kb sliding windows and SNPs with missing data. This VCF file was used when producing SFS for demographic analysis. GWAS The following files were used when preforming GWAS in GEMMA. SNZ_FP_75indv.bbgeno.gz SNZ_FP_75indv.pheno ZF_Pos_Map.txt gemma_bslmm.sh - script to perform analyses gemma_relmatrix.sh - script to produce relatedness matrix Pairwise_VCFs Contains VCF files used for outlier detection using PCAdapt. Each VCF contains samples from the New Zealand population plus one French Polynesian island. VCF files have been re-ordered relative to the zebra finch genome (based on output from satsuma synteny). Reorder_VCF Custom scripts (plus required files) used to re-order VCF files into zebra finch chromosomes. Calculating_Landes_Statistic.xlsx Excel spreadsheet containing morphological data for French Polynesian and New Zealand silvereyes. Also contains calculations of Lande’s statistic Ne* for each morphological trait. Fastsimcoal The following directory contains scripts and SFS required to repreform demopgraphic inference using fastsimcoal. This directory contains two sub-directories (1 per model tested). Files ending .tpl - describe the model to be tested Files ending .est - details prior estimates for parameters Files ending .obs - 2D site frequency spectra Launch_PointEstimate_Runs.sh - script used to run fastsimcoal for given model.