Table 3

Summary of the analyses of selective pressures on ago-1 and dcr-1 with PAML
Branch models Site models Branch-site models
ago-1 Region 1 (726 nt) one-ratio:two-ratio P<0.0001
one-ratio:free-ratio P<0.0001
two-ratio:free-ratio P=0.6706 M7:M8 P<0.0001 MAof:MAoe P=0.0285
ωago1a=0.0001 ωago1b=0.8621 4 sites with P>0.95 52 sites with P>0.95
ago-1 Region 2 (909 nt) one-ratio:two-ratio P<0.0001
one-ratio:free-ratio P<0.0001
two-ratio:free-ratio P=0.0506 M7:M8 P<0.0001 MAof:MAoe P=0.0218
ωago1a=0.0001 ωago1b=0.6236 5 sites with P>0.95 74 sites with P>0.95
ago-1 Region 3 (276 nt) one-ratio:two-ratio P<0.0001
one-ratio:free-ratio P<0.0001
two-ratio:free-ratio P=0.4675 M7:M8 P=0.9802 MAof:MAoe P=1
ωago1a=0.0039 ωago1b=0.2476 No positively selected sites No positively selected sites
dcr-1 (957 nt) one-ratio:two-ratio P=0.0002
one-ratio:free-ratio P=0.0515
two-ratio:free-ratio P=0.6424 M7:M8 P=0.4677 MAof:MAoe P=1
ωdcr-1/1a=0.1247 ωdcr-1b=0.3577 No positively selected sites No positively selected sites

For branch models, the best overall model is highlighted (two-ratio model for all the alignments) with its corresponding ω values. For site and branch-site models, the best model is highlighted as well as the number of positively selected sites when relevant. MAof: model MA with omega fixed to 1; MAoe: model MA with omega estimated. See text for further explanations about the models.

Ortiz-Rivas et al.

Ortiz-Rivas et al. BMC Evolutionary Biology 2012 12:216   doi:10.1186/1471-2148-12-216

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