The
ultimate objective of evolutionary biologists and ecologists is to find
answers to two general questions: how different species (including human
beings) have come into existence, and how they have come to live together
and interact with each other to form structured communities. Such answers
will not be forthcoming unless we can trace back the trail of life and reconstruct
the natural history that has spun hundreds of millions of years into the
remote past.
The
recent explosion of molecular data has resulted in a general realization
that natural history has been recorded in many subtle ways in the voluminous
book of DNA, written in the four-letter ATCG language. The field of molecular
ecology, evolution and phylogenetics is now advancing rapidly, leaving a
trail of dazzling achievements.
The
most spectacular success of molecular ecology and evolution is the discovery
of Archaebacteria by Carl Woese. Nowadays, one should be very pleased to
discover a single new species. But Woese discovered the whole new kingdom
of Archaebacteria, by phylogenetic analysis of rRNA genes. This perhaps
represents the best example in which biodiversity (bacterial diversity in
this case) has been staring at us for a long time begging to be recognized,
and only through a new lens did we appreciate its charm.
How
much of biodiversity remains invisible to us? Is that part of biodiversity
disappearing without us ever knowing its value? We all know that microscopes
have introduced scientists to a formerly unknown world, and that telescopes
have led scientists into a much deeper space. It is now the molecular probes
that will reveal to us new treasures hidden in nature.
The
use of molecular phylogenetics as an aid to ecological and evolutionary
studies has resulted in many surprises. For example, the Old World and New
World vultures are very similar in morphological and behavioural characters,
and traditionally have been grouped taxonomically with other diurnal raptors
into Falconiformes. However, recent DNA-DNA hybridization by Sibley and
Ahlquist demonstrated that New World vultures were related more closely
to storks, and had independently acquired morphological and behavioural
adaptations for a carrion-feeding life style. In other words, the similarity
in morphology and behaviour is due to convergent evolution, not due to inheritance
of ancestral characters. There are now many cases in which the age-old knot
intertwining homology and analogy has been cut with a single stroke of the
powerful molecular sword.
My
first contact with genes dates back to 1988 when 1 was studying the mating
system of the white-footed mouse, Peromyscus leucopus, in Ontario, Canada.
P. leucopus
was suspected to be monogamous. However, by bringing pregnant
females back into the laboratory, allowing them to give birth, and carrying
out electrophoresis on allozyme loci, we found clear evidence of multiple
paternity in single litters. For example, when the genotype of the mother
was AA, the genotypes of her offspring in the same litter were found to
be AA, AB, AC, which implies that the litter must have been sired by at
least two males. Such data allow us to calculate the proportion of litters
with multiple paternity in natural populations (Xia & Millar, 1991).
Similar methods have been used to quantify reproductive success in many
mammalian and avian species.
Investigation
of DNA molecules can also shed light on the intensity of purifying selection.
It has long been established that proteins are coded as triplet codons in
the DNA molecules. For example, glycine is coded by GGA, GGA, GGG and GGT.
The third codon site can be filled by any of the four nucleotides without
changing the meaning of the codon, whereas substitution of the guanine (G)
at either the first or the second codon site will result in a codon coding
for a different amino acid, i.e., a nonsynonymous change. Nonsynonymous
substitutions often disrupt the normal functioning of the protein molecule
and lead to adverse physiological effects; for example, sickle-cell anaemia
is caused by a single nonsynonymous substitution involving a change of the
triplet codon GAA (coding for glutamic acid) to GTA (coding for valine)
at the sixth amino acid site of the b chain of the haemoglobin molecule.
For this reason, the neutral theory of molecular evolution expects purifying
selection to select against nonsynonymous substitutions, but to tolerate
synonymous substitutions. Therefore, the stronger the purifying selection,
the fewer nonsynonymous substitutions relative to the number of synonymous
substitutions. Because the number of synonymous and nonsynonymous substitutions
can be estimated from the evolutionary history of protein genes, we can
devise a measurement of the intensity of purifying selection experienced
by various protein genes, or by various organisms, during their evolutionary
history (Xia et al., 1996).
Recently,
the optimality model, which has been a powerful tool for ecologists, has
also found its applications in molecular biology and evolution. There are
evolutionary advantages for organisms to accelerate their biosynthetic processes
to grow faster, and one optimality model of maximizing protein synthesis
predicts that gene duplication should occur more frequently in organisms
living in cold environments than in hot environments (Xia, 1995). This prediction
was supported by an analysis of the relationship between genome size of
salamanders and their ambient temperature, indicating a special kind of
thermal adaptation at the molecular level.
There
are also evolutionary advantages for organisms to increase the rate of transcription,
and an optimality model predicts that the most frequently used ribonucleotide
at the third codon sites in mRNA molecules should be the same as the most
abundant ribonucleotide in the cellular matrix where mRNA is transcribed.
For example, ATP is much more abundant in mitochondria than the other three
ribonucleotides, and we therefore expect ATP to be used much more frequently
in the third codon sites of protein-coding genes than alternative ribonucleotides
(Xia, 1996), which has been supported by empirical evidence.
There
is much uncertainty surrounding the life of a biologist, but I am certain
that 1 will follow the twisting trail of the everlasting DNA into the future.
And I am almost certain that I will have followers.
References
Xia,
X., 1995. Body temperature, rate of biosynthesis, and evolution of genome
size. Molecular
Biology
and Evolution 12, 834-842.
Xia,
X.,1996. Maximising transcription efficiency
causes codon usage bias. Genetics in press, November issue.
Xia,
X. & J.S. Millar, 1991. Genetic evidence of promiscuity in Peromyscus
leucopus. Behavioral Ecology and Sociobiology 28, 171-178.
Xia,
X., M.S. Hafner & P.D. Sudman, 1996. On transition bias in mitochondrial
genes of pocket gophers. Journal of Molecular Evolution 43, 32-40.
Xia
Huhua
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