${\mathcal{D}}_{s}$

Concatenation or SMRT with ML, MP, or NJ

18

Consists of all 121 loci, with a single individual sampled from each of 11 species at each locus.

${\mathcal{D}}_{s,0}$

STEAC, STAR, RTC, or MDC with ML, MP, or NJ

36

Subset of ${\mathcal{D}}_{s}$ requiring that each locus has at least one sequence difference between each distinct pair of species, other than pairs from distinct outgroups.

${\mathcal{D}}_{p}$

Concatenation or SMRT with M

6

Consists of the full dataset , which contains all individuals and all loci.

${\mathcal{D}}_{p,0}$

STEAC, STAR, RTC, or MDC with M

12

Subset of ${\mathcal{D}}_{p}$ requiring that each locus has at least one sequence difference between each distinct pair of species, other than pairs from distinct outgroups.
