Two alternative genealogies for simple sequence repeat (SSR) alleles containing the same number of repeats.

<p>SSR alleles are indicated by their number of repeats (n, n+1). The A/C letters indicate a SNP in the flanking regions. Red bars correspond to mutational events in the flanking region sequence or in the number of SSR repeats. (A) No sequence information: deduced genealogy of observed data (third line) groups alleles together according to their number of repeats and involves a single SSR mutation. Genealogy is recent. (B) Consideration of sequence information: deduced genealogy involves a SNP mutation and two SSR mutations (alternative topology will involve two identical and independent substitutions at the same nucleotide site and a unique SSR mutation, which is less likely). Genealogy is ancient and SSR alleles do not group according to their numbers of repeats.