Biology Reference
In-Depth Information
by two groups of mammals, the ruminant artiodactyls and the leaf-eating colobine
monkeys (Prager, 1996; Stewart
et al
., 1987). Both groups are able to ferment plant
material in the foregut and possess stomachs that contain high levels of lysozyme.
Advanced ruminants such as cows, sheep and deer possess ~10 lysozyme genes as
a result of gene amplification events which occurred after the divergence from the
pig lineage. Sequence comparison of the lysozyme genes from human (
LY Z
; chro-
mosome 12) and other primates has indicated a k
s
/k
a
ratio significantly less than
unity in both the colobine and hominoid lineages (Messier and Stewart, 1997),
indicative of the action of positive selection for amino acid replacements.
Interestingly, several of the amino acid replacements noted in the colobine lin-
eage also occurred in parallel or convergently in the ruminant artiodactyls
(Messier and Stewart, 1997; Stewart
et al
., 1987; Swanson
et al
., 1991). Comparison
of the nucleotide sequences of the coding regions of the lysozyme genes of
advanced ruminants and pigs revealed no difference in the rate of synonymous
substitution consistent with the view that it was a change in selective pressure
rather than the mutation rate that was responsible for changes in the rate of stom-
ach lysozyme evolution (Yu and Irwin, 1996). The reasons for positive selection
for lysozyme amino acid replacements in hominoids are at present unclear but
Messier and Stewart (1997) suggested that it might have been associated with the
increased neutrophil expression of lysozyme in hominoids as compared with
other catarrhines.
Since synonymous substitutions are likely to be neutral with respect to selec-
tion, they have been employed in numerous attempts to calibrate
molecular clocks
(Easteal
et al
., 1995 Fitch and Ayala, 1994; Li, 1997). However, substitution rates
can vary quite widely between orthologous gene sequences in different taxonomic
groups or lineages, as well as between different genes in the same species (Britten,
1986; Easteal, 1988; Easteal and Collet, 1994; Gibbs and Dugaiczyk, 1994; Li
et
al
., 1990; Li
et al
., 1996; Ohta and Ina, 1995). The speed of the molecular clock
appears to vary according to the lineage. In order to estimate the relative rates of
nucleotide substitutions in two lineages leading to extant species A and B, a
rela-
tive rate test
is employed. This involves the use of a third (reference) species, C,
which is known to have branched off prior to the divergence of A and B. Pairwise
comparisons of orthologues in A and C, and in B and C, are used to calculate the
k
value, the number of substitutions per 100 sites. The
k
AC
and
k
BC
values then
provide a measure of the relative rates of mutation in the lineages leading to
species A and B, respectively. Such calculations have suggested that the substitu-
tion rates in the lineages leading to mouse and rat are approximately equal (~7.9
× 10
-9
(3.9-11.8); Li and Graur, 1991; O'hUigin
et al
., 1992; Wolfe and Sharpe,
1993) whereas comparable estimates for humans and Old World monkeys (~2.2 ×
10
-9
(1.8-2.8)) and humans and chimpanzees [~1.3 × 10
-9
(0.9-1.9)] are consider-
ably lower. This is held to be indicative of a slowdown in the substitution rate in
primates which appears to be at its greatest in hominoids (Bailey
et al
., 1991;
Ellsworth
et al
., 1993; Gu and Li, 1992; Koop
et al
., 1986; Li and Graur, 1991; Li
and Tanimura, 1987; Li
et al
., 1996; Seino
et al
., 1992). Despite these data, the
hominoid slowdown
is not a universal phenomenon in primate evolution since it is
not apparent with some gene sequences (Easteal, 1991; Kawamura
et al
., 1991;
Shaw
et al
., 1989).
