Table 1. NDPS results for B. forskalii ORFs and URFs.

These π and πN/πS values were measured using biopython’s cal dn ds function, and πN/πS was measured using the NG method (Nei & Gojobori, 1986). The Monte-Carlo p-value is estimated from the Nucleotide Diversity Permutation Simulation and measures the probability that this locus is evolving neutrally. This Monte-Carlo p-value was calculated by counting the number of simulated πN/πS less than the observed πN/πS that also had πS values greater than zero, and dividing by the number of simulations for which πS was greater than zero. All loci, including the URFs, appear to be evolving under negative selective pressure. The ND4L locus’ high MC p-value is likely an artifact of the short sequence length.

Sequence	π	πN/πS	MC p-value
COX1	0.0094	0.0124	0.0000
COX2	0.0032	0.0000	0.0000
COX3	0.0027	0.0650	0.0000
CYTB	0.0085	0.0120	0.0000
ND1	0.0050	0.0122	0.0000
ND2	0.0075	0.0267	0.0000
ND3	0.0048	0.0285	0.0000
ND4	0.0058	0.0353	0.0000
ND4L	0.0040	0.4329	0.4191
ND5	0.0044	0.0710	0.0000
ND6	0.0066	0.0410	0.0000
URF1	0.0055	0.3497	0.0120
URF2	0.0214	0.2477	0.0000