Table 1.

PAML-Based Tests for Positive Selection on Goddard.

Data From Six Species of the melanogaster Subgroup:

Model M0 (uniform ω): ω = 0.25, ln L = −882.10, np = 11

Model M7 (10 site classes, each with 0 ≤ ω ≤ 1): ln L  = −879.18, np = 12

Model M8 (10 site classes as in M7, and 1 class with ω ≥ 1): ln L  = −879.18, np = 14, ω for extra class of sites = 1.00 (0.0% of sites)

Model M8a (10 site classes as in M7, and 1 class with ω = 1): ln L  = −879.18, np = 13

M7 vs. M8 LRT: χ2 = 0, df = 2, P = 1.00

M8 vs. M8a LRT: χ2 = 0, df = 1, P = 1.00

Data From 16 Species of the melanogaster Group:

Model M0 (uniform ω): ω = 0.21, ln L  = −3038.97, np = 31

Model M7 (10 site classes, each with 0 ≤ ω ≤ 1): ln L  = −2979.22, np = 32

Model M8 (10 site classes as in M7, and 1 class with ω ≥ 1): ln L  = −2979.03, np = 34, ω for extra class of sites = 2.20 (0.7% of sites)

Model M8a (10 site classes as in M7, and 1 class with ω = 1): ln L  = −2979.19, np = 33

M7 vs. M8 LRT: χ2 = 0.38, df = 2, P = 0.83

M8 vs. M8a LRT: χ2 = 0.32, df = 1, P = 0.57

NOTE.—ln L , log likelihood; LRT, likelihood ratio test; np, number of parameters.