Figure 5. Neutrality plots (GC1,2 vs.
GC3) for Hsp60 genes from 17 phyla. The
GC1,2 values represent the average GC content at the
first and second positions of codon (GC1 and
GC2), while GC3 values represent the GC
content at the third synonymous codon position. The solid line
represents the linear regression of GC1,2 versus
GC3, the correlation of which is described by the
regression coefficient R and its p-value. The correlation coefficient R
reflects the strength of the impact of GC3 on
GC1,2. The p-value characterizes the significance of R.
Changes in GC3 values actually affect the
GC1,2 values when the p-value of R is less than 0.05. In
turn, changes in GC3 are considered random, and the R
coefficient is not irrelevant when the p-value is greater than 0.05,
i.e. GC3 and GC1,2 values are not
correlated. The slope ε of the regression line indicates the
neutrality of the codon usage. Neutrality values were determined by
equation [ε × 100, %]. Slope values ranging from 0 to 1 were
calculated using the least-squares regression analysis. The dashed line
is a complete neutrality plot, which reflects the complete equilibrium
of the nucleotide composition of the gene/genome with directional
mutation pressure. The equilibrium point Ep was
defined as the intersection point of the neutrality plot (regression
line) and the complete neutrality plot. The Epvalue reflects the GC3 content of the gene/genome when
the mutation frequencies (AT→GC and GC→AT) are equal. The direction of
the mutational pressure, indicating an imbalance in the frequencies of
the AT→GC and GC→AT mutations, was determined in accordance with the
following conditions: the average GC content value less than theEp value reflects the AT mutational pressure; the
average GC content value greater than the Ep value reflects the GC mutational pressure. Phyla were sorted by
average total GC content of Hsp60 genes.
The results of the neutrality analysis reflect statistically significant
correlations between the GC1,2 and GC3values of the Hsp60 genes from 15 phyla (Figure 5). Taking into account
the results of neutrality analysis and difference between the average
GC3 values and the corresponding values at equilibrium
points, 17 phyla were divided into three groups according to the
direction of mutational pressure (Table 2).
Table 2. The results of neutrality plot analysis