Details on alignments and markers used in our study as well as often-used markers at three taxonomic levels.

Marker structure refers to structure of amplified fragment (e = exon, i = one intron in the fragment, ii = two introns in the fragment, iii = three introns in the fragment). Sequencing success is the percentage of obtained, readable sequences. PIC refers to number of parsimony-informative characters in an alignment. PIC % shows the percentage of parsimony-informative sites within alignments. Substitution model refers to the applied substitution model for phylogenetic inference; values in brackets refer to alternative substitution model used in RAxML. Asterisk indicates that information is based on TAIR10.Details on alignments and markers used in our study as well as often-used markers at three taxonomic levels.