IlluminaContaminants

List of possible Illumina adaptor contaminants used in read trimming

snp_table_deserticola

List of SNPs for H.deserticola. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individua

coverage_per_gene_individuals

Coverage (Number of reads aligned) per individuals and per gene

snp_table_anomalus

List of SNPs for H.anomalus. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individua

bol_exi_fst_map_dnds

Contains list of all polymorphic genes in H. exilis - H. bolanderi species pairs and dn, ds, dn/ds values

deb_pet_fst_map_dnds

Contains list of all polymorphic genes in H. debilis - H. petiolaris species pairs and dn, ds, dn/ds values

deb_pet_fst_map_cluster_nonoverlapping_windows

Contains list for H. debilis - H. petiolaris of all unique positions in the genetic map, linkage groups, associated fst valuse, and other various statistics (not used in this study, but part of the original script)

deb_pet_fst_map

Contains: all SNPs kept in the H. debilis - H. petiolaris comparison, name of reference gene, position of SNP in gene, genotypes of all individuals, Fst, Fit, Fis, name, linkage group, position in centimorgan, unique position on map, number of nucleotides in gene, boolean value whether SNP is in the top5% most divergent

unique_genes

Contains list of all unique polymorphic genes found in either of the three species pairs, and the fst value for all three species pairs

ann_arg_fst_map_dnds.out

Contains list of all polymorphic genes in H. annuus - H. argophyllus species pairs and dn, ds, dn/ds values