Genome-wide data
The samples included in the 3RAD data set had from 75193 to 1007069
reads, and the generated matrices contained 986–7094 loci (Table S2).
The outgroup employed for this data set, E. tuberculatum , shared
between 375 and 1322 loci with the ingroup. The matrices derived from
the unphased UCE data varied from 642 to 2196 loci and from 508859 to
1,817,455 characters (100% and 75% taxon occupancy matrices,
respectively; Table S3). The phased UCE matrices had considerably fewer
loci than those with unphased data (737 and 390 loci for the 85 and
100% taxon occupancy matrices, respectively), though the unphased data
contained more parsimoniously informative sites (Table S3). SNP
codification as a binary matrix for the UCE data showed the presence of
heterozygous loci in the male samples which are also present in the
nucleotide alignments.