Table 4.
100,000 simulations are ran to track frame-disrupting features in case of CDS region derived from PSMD4, CDS region derived from PIP5K1A and the complete CDS of PIPSL, respectively.
| Locus | Ancestor ReconstructionA | Na/Nsobs | PNaNsB | #Nonsenseobs | #indelsobs | PdisC |
| PSMD4 | PAML | 2.53 | 0.417 | 1 | 1 | 0.00071D |
| Dnapars | 0.402 | 0.00093 | ||||
| PIP5K1A | PAML | 1.50 | 0.00045 | 2 | 0 | <10-5 |
| Dnapars | 0.00044 | <10-5 | ||||
| Complete-Gene | PAML | 1.91 | 0.01016 | 3 | 1 | <10-5 |
| Dnapars | 0.00879 | <10-5 |
A. We used two distinct methods to reconstruct the ancestral sequence, PAML and Dnapars of Phylip package (Maximum-parsimony based inference). In all cases, there results are similar between each other.
B. PNaNs is defined as the proportion of simulated datasets that show a Na/Ns ratio smaller or equal to the observation. Here, Na and Ns indicates the number of nonsynonymous mutations and that of synonymous mutations, respetively.
C. Pdis corresponds to the percentage of simulated datasets that demonstrates a number of frame-disrupting mutations (stop codons and frameshifts) smaller or equal to the observed number. Out of all lineages of interest, human, chimp, orangutan and gibbon, only three stop codons and one indel are observed and those only in the gibbon genome. Specifically, two nonsense substitutions occur in the PIP5K1A-derived region, while the other one nonsense substitution and one indel situate in the PSMD4-derived region.