DNA assembly method
Sequence assembly methods (probe versus contig) yielded important
differences across analyses. Notably, in the probe dataset, we observed
systematically higher differences in heterozygous/homozygous allele
calls between capture and RADseq replicates than between capture-based
replicates (Table 2; Fig. 3) but we did not observe this pattern in the
contig dataset. We also inferred higher rates of heterozygosity in the
probe dataset (Fig. S4). Further, only by using the contig dataset
pruned to SNPs within the coordinates of the original RADseq loci were
we able to accurately place all four technical replicates together in
phylogenetic analyses (Fig. 4; S6). As such, we present results in the
main manuscript for only the contig dataset (pruned to SNPs within the
coordinates of the original RADseq loci) and present results for the
probe dataset in the Supporting Information. See the Discussion for more
on this subject.