Genotypes in Arlequin format

Genotypes for all SNPs in Arlequin format (as in Figure 1c

Input file for the GPhoCS analysis.

Sequence data for 60 individuals of 6 capuchino species in GPhoCS format

Fst estimates for each locus

Species are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis

Restriction Site Associated DNA data

Compressed file containing quality-filtered and demultiplexed reads for each individual in the study. Files are identified by species name followed by sample number as shown in Table S1

Stacks output with identified variants in VCF format

Variants identified by Stacks. Assembly parameters M=n=5

Output from Stacks assembly

This folder contains the Stacks output from the RAD assembly (M=n=5). There are four files per sample (72 samples in total) plus three catalog files (291 files in total). Samples are identified by species name followed by collection number as indicated in Table S1

Genotypes in Arlequin format for the randomized dataset

Genotypes in Arlequin format for the randomized datase

Fst estimates for each locus - RANDOMIZED dataset

Species are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis

Fst estimates for each locus

Species are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis

Inter-species average PhiST matrix

Inter-species average PhiST matrix displayed in a Neighbor-joining tree built in PHYLIP (Figure 1a