Signatures of host genomic and algal symbiont selection in the coral Porites harrisoni from the Persian/Arabian Gulf

Abstract

This repository contains the variant call files (VCFs) to generate the figures presented in Chapter 3 of the doctoral thesis: Fiesinger, A.: "Genomic signatures of adaptation in coral holobionts from the extreme thermal environment of the Persian/Arabian Gulf", submitted Dec 2025 Raw sequencing files are available at NCBI under BioProject PRJNA1191362 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1191362), and code to generate the VCF files as well as the figures is available on GitHub: https://github.com/afiesinger/UAE_PAG_WGS_PopGen. Files: Phar_SNPs_filt_noclones_POPGEN.vcf.gz: population genetic analyses specific filtered VCF file with clone mates removed for PCA, Fst, ADMIXTURE (Fig. 1) Phar_SNPs_filt_HOST-SYM.vcf.gz: population genetic analyses specific filtered VCF file before clone mate removal for host-symbiont genotype genotype association (Fig. 2) Phar_SNPs_filt_noclones_SWEEPS.vcf.gz: selective sweep analyses specific filtered VCF file with clone mates removed for genome-wide Fst, H-statistics, allele frequency calculations (Fig. 3 & Supplementary Figures) Phar_SNPs_filt_noclones_SWEEPS_pixy_invsites.vcf.gz: selective sweep analyses specific filtered VCF file with clone mates removed and including all sites (--include-non-variant-sites in GATK) for nucleotide diversity calculation (Supplementary Figures) Phar_SNPs_filt_POPGEN_forLD.vcf.gz: population genetic analyses specific filtered VCF file without LD pruning for LD decay analysis (Supplementary Figures)