Phylogenetic relationship between LTR sequences. (A) Maximum-likelihood unrooted tree for solo LTRs and LTRs flanking full-length elements. Branches with bootstrap support higher than 95 are shown in yellow. LTR sequences associated with full-length elements are indicated with red points. Nomenclature of families follows Bowen et al. (2003) (Methods). (B) Number of flanking LTRs from full-length elements grouped by LTR family. Sequences without clear family membership are classified by the two most closely related families. (C) Pairwise divergence of LTR sequences belonging to the same family within syntenic clusters. Divergence between sequences is grouped by ancestral background: within ancestral background (Sp vs. Sp or Sk vs. Sk) or between ancestral backgrounds (Sp vs. Sk). Mean divergence per group is indicated by dashed vertical lines.
