Table 1.
Tests for selection on IGF2 in teleosts
| Model | Model comparison | Foreground branches | 2Δl | df | P value | ω* | Positively selected sites† |
|---|---|---|---|---|---|---|---|
| Site models | M1a vs. M2a | NA | 0 | 2 | 1 | 1 | 139 |
| M7 vs. M8 | NA | 11.82 | 2 | 0.0027 | 2.63 | 139 | |
| Branch-site models | Test 1/Test 2 | Poeciliidae | 28.27/3.26 | 2 | 7.26 × 10−7/0.0712 | 2.07 | 139, 146 |
| Test 1/Test 2 | Extensive matrotrophs | 24.26/7.81 | 2 | 5.40 × 10−6/0.0052 | 4.11 | 84, 86 | |
| Test 1/Test 2 | Extensive matrotrophs with P. lucida and P. prolifica | 21.85/8.64 | 2 | 1.80 × 10−5/0.0033 | 6.69 | 83, 86 |
Likelihood values are generated by using PAML 3.14b and are analyzed by a likelihood ratio test (2Δl) applied to a χ2 distribution with df = 1 − number of free parameters for each model. ″Extensive matrotrophs″ means that all species with extensive matrotophy (MI > 2), shown in red in Fig. 2, are designated as foreground lineages; ″P. prolifica and P. lucida″ means P. prolifica, P. lucida are included as foreground. NA, not applicable.
*ω values are presented as estimated from the data (ω2; see text). Values in bold are those significantly supported (P < 0.05).ω2 for branch/site models are shown for foreground branches as listed.
†Positively selected codon sites as determined by Bayes Empirical Bayes (BEB) analysis. Plain text indicates >95% confidence, and bold text indicates >99% confidence.