Table 1 in Using RADseq to resolve species boundaries in a morphologically complex group of yellow-flowered shrubs (Geleznowia, Rutaceae)

Table 1. Summary of filtering parameters and the resulting SNP datasets used for downstream genomic analyses of Geleznowia and outgroups. DatasetAnalysisSamplingNumber of samplesMinimum sample cover (%)Minimum minor allele countSNPs per locusSNPsMissing per sample (%)Average depth per site1PCA, STRIngroup84903116832.2 (0.8 – 4.3)58.9 (19 – 100)2DISTIngroup842511739240.8 (23.4 – 54.9)42.6 (17 – 100)3CONCATPhylo97501all22 92923.3 (9.2– 73.6)51.7 (17 – 100)4SVDPhylo975011333824.9 (8.2 – 82.3)51.3 (17 – 100) PCA, principal-component analysis; STR, Structure; DIST, distance-based SplitsTree 4 network; CONCAT, concatenated maximum-likelihood phylogenetic analysis; SVD, SVDquartets coalescent phylogenetic analysis. Sampling included all populations of Geleznowia (ingroup) and all populations of Geleznowia plus Drummondita ericoides and Philotheca sericea, excluding putative hybrid individuals (phylo).