Table 2.

Datasets

Dataset	Strategies that use the dataset	Number of strategies	Description
${\mathcal{D}}_s$	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.