Figure 2

Schematic for creating the four subsets${\mathcal{D}}_{\mathit{s}}$,${\mathcal{D}}_{\mathit{s}\mathbf{,}\mathbf{0}}$,${\mathcal{D}}_{\mathit{p}}$, and${\mathcal{D}}_{\mathit{p}\mathbf{,}\mathbf{0}}$ from dataset. For the matrices of datasets , ${\mathcal{D}}_s$, ${\mathcal{D}}_{s,0}$, ${\mathcal{D}}_p$, and ${\mathcal{D}}_{p,0}$ (see Table 2), each row is an individual and each column is a locus. Thick black lines in these matrices separate the individuals in different species. Gray boxes indicate missing sequences. (A) At each locus, a single sequence from each species (indicated in red) is selected from dataset . These selected sequences are used to create ${\mathcal{D}}_s$ such that there exists a single sequence sampled per species at each locus. Sequences from a subset of loci in ${\mathcal{D}}_s$ (indicated in yellow) are used to create dataset ${\mathcal{D}}_{s,0}$ such that each locus has at least one nucleotide difference between each distinct pair of species other than pairs from distinct outgroups. (B) Dataset ${\mathcal{D}}_p$ is the full starting dataset . At each locus ℓ, a distance matrix is created according to eq. 2. Sequences from a subset of loci (indicated in red) in ${\mathcal{D}}_p$ are used to create dataset ${\mathcal{D}}_{p,0}$ such that each locus has a nonzero p-distance between each distinct pair of species other than pairs from distinct outgroups. Observe that the ${\mathcal{D}}_{p,0}$ matrix includes loci 3 and 7, which are not included in the ${\mathcal{D}}_{s,0}$ matrix. Loci 3 and 7 are included in ${\mathcal{D}}_{p,0}$ but not in ${\mathcal{D}}_{s,0}$ because in ${\mathcal{D}}_{p,0}$, pairs of species contain at least one pair of individuals with different sequences, whereas in ${\mathcal{D}}_{s,0}$, at least one pair of the 11 selected individuals have identical sequences. Therefore, the set of loci in ${\mathcal{D}}_{p,0}$ is a superset of the set of loci in ${\mathcal{D}}_{s,0}$, and the number of loci in ${\mathcal{D}}_{p,0}$ is always greater than or equal to the number of loci in ${\mathcal{D}}_{s,0}$.