The remaining sites (8.8%) were under neutral evolution with ω = 1, indicating the dominant role of purifying selection in the evolution of rbcL.
In model M2A, the majority of the sites (91.4%) were under purifying selection, 8.2% of the sites were under neutral evolution, and 0.4% of the sites experienced positive selection (ω = 11.494)(Table 1).
The nearly neutral model (M1a) assumes two classes of sites: one is under purifying selection with 0<ω0<1, the other is under neutral evolution with ω1 = 1, and was compared to the positive selection model (M2a) in which an additional ω parameter is included that allows positive selection where present (ω>1).
Our results showed that most sites are under purifying selection, while a small part is under neutral evolution.
In model M1, about 94% of the codons are under strict constraint (ω = 0.030), and the other 6% codons are under neutral evolution (ω = 1.0) (Table 3).
Because the majority (>95%) of the sites of human genome are under neutral evolution, the similarity of the pedigree-based rate with the interspecific rate appears to be due to the predominance of neutral mutations.
In this analysis, 156 of 249 codons (63%) in the alignment of DEF-like genes are under purifying selection with a P ≥ 0.95, whereas the rest of the codons are under neutral evolution (data not shown).
To see if the NMD-specific exons were under neutral evolution, we fixed the Ka/ Ks at one in the human NMD lineage under free ratio model [ 61], and compared this with a more general model (with Ka/ Ks free) to test if the neutral model could be rejected using likelihood ratio tests (calculated in R [ 78]).
However, this may not be true: Not all sequences are under neutral evolution; there may be differential rate of substitution among nucleotides as some regions may be important for transposition and there may be different rate of change in different genomic regions.
For numit rps13, 65% of the sites are under purifying selection with Ka/Ks less than one, 28% of sites are under neutral evolution with Ka/Ks close to one, and 7% of sites are under positive selection with Ka/Ks greater than one (Table 3) without statistical support by LRTs.
