This set includes two NEXUS alignments. Ppygmaeum_nuc_7379_10039.nex is the partial concatenation of the 7379 (positions 1-301) and 10039 (positions 302-456) nuclear regions from the bait set publised in https://doi.org/10.5061/dryad.8rq9465. Ppygmaeum_plast_4loci.nex is the concatenarion of loci atpB-rbcL (positions 1-729), psbA-trnH (730-1167), rps4 (1168-1810), and trnL-F (1811-2319). Taxon names and accession numbers are referenced to herbarium vouchers in the publication.