Supplemental Material for Sendell-Price et al., 2020

Supplementary tables and figures for Sendell-Price et al. (2020) The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis)

Pairwise_VCFs.zip
Contains individual population comparison VCF files used for PCAdapt outlier detection (~403K LD filtered biallelic SNPs per file).

ZFified_Filtered_MinGQ30_MinDP8_MaxMissing0.7_NonVariant_plus_Biallelic.150Indv.15MSites.vcf.gz
VCF file containing ~15million loci assigned to zebra finch chromosomes based on output from satsuma synteny (used for pairwise FST/dxy calculations).

ZFified_BiallalicOnly_MaxMissing0.3_Chr5_46853SNPs.vcf.gz
SNP subset used for simulations (contains ~46K biallelic SNPs from chromosome 5 only).

Reorder_ZLat_VCF_Files.R
R script used to reorder VCF files so that loci have zebra finch chromosomal positions - based on output from Satsuma Synteny.

Detect_Islands_Valleys_BiomartQuery.R
R script used for detection of genomic islands and genomic valleys and identification of zebra finch genes contained within identified islands/valleys (requires Island_Detecting_Functions.R and windowed FST/DXY statistics).

PCAdapt_Loop.R
R script used for detection of outlier SNPs via PCAdapt (requires pairwise VCF files and satsuma Synteny output for calculating genomic positions relative to the zebra finch genome).

SamplesInPops.txt
Text file assigning samples to relevant populations.

ZLat_scaffold_order_from_ZFinch.csv
File specifying mean location and orientation of Z. lateralis scaffolds on zebra finch chromosomes. This file is based on output from Satsuma Synteny.

Zost_Scaffold_Lengths.txt
File specifying Z. lateralis scaffold lengths (required when orientating VCF files to zebra finch chromosomes).