Figure 6

Phylogenetic distribution of stop codon mutations in sampled Pinus accessions. Exon names given above boxes, amino acid shift relative to stop codon position in outgroups given below boxes. Polarity of events determined by comparison to most distant outgroups; "+" signifies extension of coding region due to stop codon mutation, "-" signifies shortening. The value of zero for the psbH- and psaM-associated events corresponds to events that alter the original stop codon without altering the total number of codons in the locus. Events for only the first copy of psaM are reported. Diagonal line represents a putative reversal in psaJ of P. parviflora. Branching order of tree corresponds to RAxML analysis of complete alignment. * 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).