are unevenly distributed between the exons [364].
The chorion genes of Hawaiian Drosophila species show extremely high rates of evolution. The
amino acid exchange rate of 21 . 10- 9 per site per
year is the highest yet recorded (Table 4.12). The
rate of amino acid-exchanging substitutions is
twice that of synonymous substitutions [261].
Extremely high rates of synonymous substitution have been observed in vertebrate mtDNAs.
The mtDNAs of various mammals, with synonymous substitution rates of 35 . 10- 9 to 94 . 10- 9 ,
have a rate of evolution 10-20 times greater than
that of chromosomal DNA; similar results have
been obtained with the mtDNAs of different
Xenopus species [57,360]. There is, as yet, no
explanation for these differences in rates of synonymous substitution, except that in the vertebrates mtDNA possibly has a higher mutation rate
than chromosomal DNA. The results from vertebrates, however, may not be used as a basis for
generalization. In various Drosophila species, the
rate of mtDNA evolution is at most only twofold
higher than that of chromosomal DNA [332, 360,
373]; in some sea urchins, the mtDNA substitution rate is just as high as in the vertebrates but
that of single-copy DNA is also high, i.e. about
five times the rate of the mammals [422]. The
mtDNA of higher plants evolves very slowly, the
substitution rate being 100-times lower than that
of vertebrate mtDNA and three- to fourfold
lower than chloroplast DNA [312].
4.6.3 Is There a Molecular Clock?
Based on the random character of mutation,
Zuckerkandl and Pauling expressed, at the
beginning of the 1960s, the idea that the
sequence of amino acid exchanges in a line of
evolution must be so regular that it could be used
as a molecular clock. The sequence differences
between homologous polypeptides would then
allow conclusions to be drawn about the time
that has elapsed since their separation. This concept has subsequently been applied to evolutionary distance derived from data other than molecular data and has proved to be very profitable.
On the occasion of the 25th anniversary of the
idea, the Journal of Molecular Evolution devoted
the whole of a special issue to the molecular
clock [200, 236]. In order to apply the principle
of the clock, the relevant molecular data are used
to construct a phylogenetic tree, the branch
lengths of which reflect the evolutionary distance. Then, with the help of the fossil record,
4.6.3 Is There a Molecular Clock?
163
the time from at least one branch fork to the present is determined and related to the evolutionary distance. The molecular clock is thus calibrated, and all evolutionary distances in that particular tree can be converted to units of time.
This process includes two obvious and significant
sources of error. One is to be found in the separation time used for the calibration. Although the
age of fossils can now be determined with great
accuracy, it is usually the case that no available
fossil corresponds exactly to any branch point in
the tree being investigated. The second source of
error involves the problems, which have already
been mentioned, of the estimation of evolutionary distance and the construction of family trees
from molecular data. Clearly, only orthologous
and not paralogous sequences may be used for
age determination. Statistical methods may be
used to estimate the range of error for the branch
points of the tree [295]. In view of the variable
evolution rates determined within the mammalian phylogenetic tree, the question has been discussed of whether the number of generations,
rather than absolute time, should be used as the
time scale of evolution; in general, however,
molecular evolution is proportional to time
[102,440,447].
The largest amount of data, related to the
molecular clock, that has so far been analysed
consists of the thousands of immunological distances determined by micro complement fixation
of serum albumins. The calibration of the "albumin clock" gives 1.7-1.9 units of immunological
distance per million years [440]. Other sets of
molecular data obtained by other methods have
shown constant rates of evolution corresponding
to a molecular clock, e.g. immunological data
from turtles, crocodiles and other vertebrates,
and hybrid DNA melting points (i\Tm values)
from rodents [43, 88,303]. Convincing arguments
for the functioning of the molecular clock may be
found in evolutionary events that are clearly
defined in terms of time, as, for example, the
separation of sibling species between the Pacific
and Atlantic sides of the isthmus of Panama.
According to Nei, the genetic distance, calculated
from electrophoretic data, of such fish species,
had a value of 0.234; this would indicate a separation time of about 3.5 million years, which fits
quite well to the geologically determined age of
the isthmus. The mean immunological distances
for the serum albumins of 103 and 114 for marsupials and tree frogs, respectively, from South
America and Australia, given 1.7 units per million
years, suggest a separation time of 70 million
The chorion genes of Hawaiian Drosophila species show extremely high rates of evolution. The
amino acid exchange rate of 21 . 10- 9 per site per
year is the highest yet recorded (Table 4.12). The
rate of amino acid-exchanging substitutions is
twice that of synonymous substitutions [261].
Extremely high rates of synonymous substitution have been observed in vertebrate mtDNAs.
The mtDNAs of various mammals, with synonymous substitution rates of 35 . 10- 9 to 94 . 10- 9 ,
have a rate of evolution 10-20 times greater than
that of chromosomal DNA; similar results have
been obtained with the mtDNAs of different
Xenopus species [57,360]. There is, as yet, no
explanation for these differences in rates of synonymous substitution, except that in the vertebrates mtDNA possibly has a higher mutation rate
than chromosomal DNA. The results from vertebrates, however, may not be used as a basis for
generalization. In various Drosophila species, the
rate of mtDNA evolution is at most only twofold
higher than that of chromosomal DNA [332, 360,
373]; in some sea urchins, the mtDNA substitution rate is just as high as in the vertebrates but
that of single-copy DNA is also high, i.e. about
five times the rate of the mammals [422]. The
mtDNA of higher plants evolves very slowly, the
substitution rate being 100-times lower than that
of vertebrate mtDNA and three- to fourfold
lower than chloroplast DNA [312].
4.6.3 Is There a Molecular Clock?
Based on the random character of mutation,
Zuckerkandl and Pauling expressed, at the
beginning of the 1960s, the idea that the
sequence of amino acid exchanges in a line of
evolution must be so regular that it could be used
as a molecular clock. The sequence differences
between homologous polypeptides would then
allow conclusions to be drawn about the time
that has elapsed since their separation. This concept has subsequently been applied to evolutionary distance derived from data other than molecular data and has proved to be very profitable.
On the occasion of the 25th anniversary of the
idea, the Journal of Molecular Evolution devoted
the whole of a special issue to the molecular
clock [200, 236]. In order to apply the principle
of the clock, the relevant molecular data are used
to construct a phylogenetic tree, the branch
lengths of which reflect the evolutionary distance. Then, with the help of the fossil record,
4.6.3 Is There a Molecular Clock?
163
the time from at least one branch fork to the present is determined and related to the evolutionary distance. The molecular clock is thus calibrated, and all evolutionary distances in that particular tree can be converted to units of time.
This process includes two obvious and significant
sources of error. One is to be found in the separation time used for the calibration. Although the
age of fossils can now be determined with great
accuracy, it is usually the case that no available
fossil corresponds exactly to any branch point in
the tree being investigated. The second source of
error involves the problems, which have already
been mentioned, of the estimation of evolutionary distance and the construction of family trees
from molecular data. Clearly, only orthologous
and not paralogous sequences may be used for
age determination. Statistical methods may be
used to estimate the range of error for the branch
points of the tree [295]. In view of the variable
evolution rates determined within the mammalian phylogenetic tree, the question has been discussed of whether the number of generations,
rather than absolute time, should be used as the
time scale of evolution; in general, however,
molecular evolution is proportional to time
[102,440,447].
The largest amount of data, related to the
molecular clock, that has so far been analysed
consists of the thousands of immunological distances determined by micro complement fixation
of serum albumins. The calibration of the "albumin clock" gives 1.7-1.9 units of immunological
distance per million years [440]. Other sets of
molecular data obtained by other methods have
shown constant rates of evolution corresponding
to a molecular clock, e.g. immunological data
from turtles, crocodiles and other vertebrates,
and hybrid DNA melting points (i\Tm values)
from rodents [43, 88,303]. Convincing arguments
for the functioning of the molecular clock may be
found in evolutionary events that are clearly
defined in terms of time, as, for example, the
separation of sibling species between the Pacific
and Atlantic sides of the isthmus of Panama.
According to Nei, the genetic distance, calculated
from electrophoretic data, of such fish species,
had a value of 0.234; this would indicate a separation time of about 3.5 million years, which fits
quite well to the geologically determined age of
the isthmus. The mean immunological distances
for the serum albumins of 103 and 114 for marsupials and tree frogs, respectively, from South
America and Australia, given 1.7 units per million
years, suggest a separation time of 70 million