This repository contains important intermediate result data and custom scripts supporting the work "Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution" by Hongxin Xie, Hans Recknagel, Chao Li, Maria Capstick, Olivier Guillaume, Maureen M. Bain, Jean Clobert, & Kathryn R. Elmer

01_reference_geneome_and_annotation: the new reference genome and its annotations generated in this study.
	Eovi.ref.V1.19Chr.soft.masked.fa: fasta file of the genome (soft masked)
	Eovi.ref.V1.19Chr.gff: gene structure annotation result in gff format
	Eovi.ref.V1.19Chr.cds.fa: CDS sequecnes for annotated genes
	Eovi.ref.V1.19Chr.protein.fa: protein sequences for annotated genes
	Eggnog.mapper.annotations.txt: functional annotation result of all genes obtained from eggNOG-mapper

02_Mitochondrial_genome_alignment_15375bp.fasta: the alignment file for mitochondrial genomes for all samples sequenced in this study. The highly variant D-loop region in the alignment was removed

03_genotype_vcf_files: the raw genotyping result obtained for all samples sequenced in this study
	Zootoca_vivipara_101_samples_raw_p(1-5).vcf.gz: all genomic variants for 101 Zootoca samples called assuming diploid genome. The five parts (p1-p5) contains variants for different chromosomes (p1: Chr1,Chr2; p2: Chr3,Chr4,Chr5; p3: Chr6,Chr7,Chr8; p4: Chr9,Chr10,Chr11,Chr12; p5: Chr13,Chr14,Chr15,Chr16,Chr17,ChrZ,Chrw)
	Zootoca_vivipara_101_samples_raw_ChrZW.vcf.gz: variants called for sex chromosomes for 101 Zootoca samples setting ploidy information according to the sex of samples and Z/W sex determination system
	Lacerta_agilis_ELT07096.raw.allSites.vcf.gz: all genotype result (including variant and invariant) for the outgroup sample (Lacerta agilis) for the whole genome assuming diploid genome
	Lacerta_agilis_ELT07096.raw.allSites_ChrZW.vcf.gz: all genotype result (including variant and invariant) for the outgroup sample (Lacerta agilis) for sex chromosmes according to the sex of the sample (female) and Z/W sex determination system
	Podarcis_muralis_ELT12115.raw.allSites.vcf.gz: all genotype result (including variant and invariant) for the outgroup sample (Podarcis muralis) for the whole genome assuming diploid genome
	Podarcis_muralis_ELT12115.raw.allSites_ChrZW.vcf.gz: all genotype result (including variant and invariant) for the outgroup sample (Podarcis muralis) for sex chromosomes according to the sex of the sample (female) and Z/W sex determination system

04_custom_data_processing_scripts: main custom scripts generated in this study for data processing
	01-Gphocs_input.sh: custom shell script for generating the input neutral loci for Gphocs analysis
	02-filter_fixed_variants.py: custom python script to find fixed variants between oviparity and viviparity for core viviparity genes.
	03-Go_enrichment_analysis_23candidates.R: custom R script to do GO enrichment of a candidate gene list (here the 23 viviparity-concordant barrier genes) using eggnog-mapper result and the TopGO package.
	04_TajimaD_calculation_R_script: includes custom R scripts to calculate Tajima's D for viviparity regions (100% topology1) and other extreme topology regions (100% topology2 and 100% topology3) and the autosome background. Intermediate input and output files are also included