10.25387/g3.12482000.v2
Ashley T. Sendell-Price
Ashley T.
Sendell-Price
Kristen C. Ruegg
Kristen C.
Ruegg
Eric C. Anderson
Eric C.
Anderson
Claudio S. Quilodrán
Claudio S.
Quilodrán
Benjamin M. Van Doren
Benjamin M. Van
Doren
Vinh L. Underwood
Vinh L.
Underwood
Tim Coulson
Tim
Coulson
Sonya M. Clegg
Sonya M.
Clegg
Supplemental Material for Sendell-Price et al., 2020
GSA Journals
2020
genomic heterogeneity
gene flow
genomic islands
genomic valleys
simulated divergence
RAD sequencing
genomic landscape
Population, Ecological and Evolutionary Genetics
2020-07-13 16:42:28
Figure
https://gsajournals.figshare.com/articles/figure/Supplemental_Material_for_Sendell-Price_et_al_2020/12482000
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)<div><br></div><div><div><b>Pairwise_VCFs.zip</b></div>Contains individual population comparison VCF files used for PCAdapt outlier detection (~403K LD filtered biallelic SNPs per file).<div><br></div><div><b>ZFified_Filtered_MinGQ30_MinDP8_MaxMissing0.7_NonVariant_plus_Biallelic.150Indv.15MSites.vcf.gz</b></div><div>VCF file containing ~15million loci assigned to zebra finch chromosomes based on output from satsuma synteny (used for pairwise FST/dxy calculations).<br></div><div><br></div><div><b>ZFified_BiallalicOnly_MaxMissing0.3_Chr5_46853SNPs.vcf.gz</b><br></div><div>SNP subset used for simulations (contains ~46K biallelic SNPs from chromosome 5 only).</div></div><div><br></div><div><div><b>Reorder_ZLat_VCF_Files.R</b><br></div><div>R script used to reorder VCF files so that loci have zebra finch chromosomal positions - based on output from Satsuma Synteny.</div><div><br></div><div><b>Detect_Islands_Valleys_BiomartQuery.R</b></div><div>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).</div><div><br></div><div><b>PCAdapt_Loop.R</b></div><div>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).</div><div><br></div><div><div><b>SamplesInPops.txt</b></div><div>Text file assigning samples to relevant populations.</div><div><br></div><div><b>ZLat_scaffold_order_from_ZFinch.csv</b></div><div>File specifying mean location and orientation of Z. lateralis scaffolds on zebra finch chromosomes. This file is based on output from Satsuma Synteny.</div><div><br></div><div><b>Zost_Scaffold_Lengths.txt</b></div><div>File specifying Z. lateralis scaffold lengths (required when orientating VCF files to zebra finch chromosomes).</div></div></div>