Corrections were based on the Kimura-2-parameter model taking invariable positions (+I) and varying substitution rates among sites (+G) into account.
Conserved nucleotides were unevenly distributed throughout the rrnL secondary structure, with highest level of invariable positions located on domain IV and lowest level observed in domains I-II.
One of the principal local factors which is particularly important in this respect is the invariable position of the algometer in relation to the examined structures.
Thus, invariable positions are all included in the first gamma rate category which encompasses the most sites for the three datasets, especially for the mitochondrial and exon genes (nearly 40% of sites).
Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.
From this dataset, a maximum likelihood tree was calculated by Phyml [ 81], using the HKY model of nucleotide evolution with an estimation of the transition/transversion ratio, including 4 rates of site heterogeneity, an estimated number of invariable positions, and an estimated alpha shape parameter.
Furthermore, 5 out of the 8 mutations in the head of the F protein are concentrated in a short invariable region at position 364 411, suggesting that the observed mutations are actually selected over time by the host immune responses.
In addition a single substitution was generated in which the invariable A at position 5 (relative to the beginning of the motif) that corresponds to the translation initiating AUG, was replaced by C (mut5).
The variability in the remaining 23%% of positions could stem from either selection pressure favouring a specific substitution (positive selection), or, on the contrary, from the lack of strong selection pressure to keep the position invariable (negative selection).
Additional studies will be required to determine whether this model also applies to SEPT9 or if this CGI is unusual, e.g., it is flanked by a position invariable methylation boundary.
Denoting the sequence length of replicators by N, the effective replication accuracy (Q e ) is obtained as by assuming that q and λ are uniform among the genotypes in x, that q is invariable over sequence positions, and that N is the same among the populations.
