XDH
The rate of amino acid replacement is fairly regular. The rates are 32.6× 10 −^10 /site per
year between Drosophila groups, 31.6 between Drosophila subgenera, and 34.2 between
drosophilid genera, acceptable as sample variation of the same stochastic clock. The
average of these three rates is ≈32.8× 10 −^10 , similar to the rate between dipteran families
(see Table 1.2 and Figure 1.2).
Global rates of evolution of six genesThe best description of the amino acid substitution process of GPDH, G6PD, PGD,
SOD, TPI, and XDH is provided by the JTT-F+dG model (see Table 1.1). However, the
among-site rate variation along GPDH, SOD, and XDH is much less than for the
dipterans (i.e. α values are larger; a similar comparison of α values between dipterans
and global is not feasible for G6PD, PGD, and TPI, because the available dipteran
sequences from these three proteins are too few). Amino acid rate variation from site to
site decreases least for SOD, with α=0.57 (0.22 for dipterans), and most for GPDH,
α=0.82 (0.06 for dipterans), nearly equal to that of XDH, α=0.84 (0.45 for dipterans).
The increase in α from dipterans to global is expected because the proportion of
invariable positions decreases with the enlarged timescale (i.e. 1000 myr versus 100 myr
since the split of the three dipteran families); but also because the variable positions of one
lineage are not the same as those of another (i.e. the proteins evolve in non-stationary fashion
with regard to the among-site rate variation). Fungi show significantly larger a (0.94±0.
20) than dipterans (0.06±0.02) and mammals (0.21±0.14) for GPDH, and than dipterans
(0.22±0.05) for SOD; and dipterans show a greater a (0.45±0.04) than mammals (0.34
±0.09) for XDH (normal deviate tests with standard errors computed by the curvature
method of Yang 2000).
The results of the pairwise distance analysis conducted with the models and estimates
of the among-site rate variation obtained above (see Table 1.1) are summarized in
Table 1.3 and Figure 1.3. The rates change erratically among genes from one level of
taxonomic comparison to another. The GPDH rate of amino acid replacement is ≤2.
0 × 10 –10/site per year between Drosophila species, but 40.0 between fungi, and ~13
between animal phyla or between kingdoms. For G6PD, the rate between Drosophila
species is 44.1, but ~12 between animal phyla or between kingdoms. The rate is
substantially larger between animal phyla than between kingdoms for SOD and XDH (19.
2 versus 12.6 and 19.2 versus 11.5, respectively), but very nearly the same for GPDH and
G6PD (as noted), and TPI. Fungi exhibit much faster rates of evolution than most other
comparisons for GPDH, G6PD, and TPI, but slower than most for PGD and XDH. For
the three levels of comparison highlighted in Figure 1.3, we see that Drosophila exhibits
the slowest rate for GPDH, the highest for G6PD, PGD, and XDH, and intermediate for
SOD and TPI. Specific comments about individual genes follow.
GPDH
We have noted earlier (Ayala et al. 1996; Ayala 1997), that the rate of amino acid
replacement is highly erratic, very slow within the genus Drosophila (≤2.0× 10 −^10 /site per
16 FRANCISCO RODRÍGUEZ-TRELLES ET AL.