Phylogenetic distribution of exon coding indel mutations in sampled Pinus accessions. Exon names given above boxes, size of indel (bp) and polarity ("+" = insertion, "-" = deletion) given below boxes. Polarity of events determined by comparison to most distant outgroups. Due to the apparent high rate of indel formation in ycf1 and ycf2, these loci were not able to be confidently scored for indels and are not included in this diagram. Events for only the first copy of psaM are reported. Branching order of tree corresponds to RAxML analysis of complete alignment. Diagonal lines represent putative reversals of indel events. * indicates missing data for one or more accessions of clade. Thin internal branches correspond to ML bootstrap support < 95% or topological difference in four largest data partitions (full alignment and exon nucleotides, with and without ycf1 and ycf2).