Relationships between haplotypes of nine individuals, including distinct head and body sequences for four marker genes, including two pairs of paralogous sequences: (a) L36 form 1; (b) L36 form 2; (c) L40 form 1; (d) L40 form 2. The indels are plotted onto the branches (green lines). Noticeably, some individuals display mixed sequences from different haplotypes, which is explained by recombination events between alleles (purple star). The substitutions occurring between copies of the same allele in the head and body of individuals (blue branches) are assumed to be somatic mutations. These neighbor-joining trees were inferred assuming kimura 2 parameter distances from Additional data files 7-10. Boostrap proportions are indicated for selected nodes.