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Response to Non-Darwinian Evolution
The initial response to the non-Darwinian evolution or the neutral theory was caused by the lack of
understandings among researchers of different fields. Evolution and population genetics people were accustomed
to think in terms of neo-Darwinian model. To them, any mutations were either advantageous or deleterious, and
no intermediate class existed. On the contrary, biochemistry people did not know population genetics and did not
care how natural selection worked. They used the term"natural selection" vaguely. So most oppositions to the
neutral theory were from evolution and population genetics people.
-- Tomoko Ohta, October 31, 2001
The neutral theory
I was most interested in the proposal of the neutral theory
when Kimura's paper came out in 1968. It seemed to me at
the time to be a very bold theory, in that over many years
neutrality had often been claimed for specific alleles (eg
in the ABO system), only to be shown later that selection
prevailed for those alleles. Indeed Dobzhansky had reglarly
made derisive comements on those who claimed neutrality for
the alleles at this or that locus, over the years.
However Kimura was clearly too clever to fall into this
trap, and his theory had to be taken seriously.
As a statistician/mathematician, perhaps my main interest
was in the theory leading to the neutrality claim, together
with the obvious thought: how can we test this theory,
given gene frequency data?
On the theoretical support for the theory, I felt then, and
feel just as strongly now, that the "substitutional load"
argument for the theory was total nonsense, and derived
from extremely poor modeling on Kimura's part. I have give
the reasons for this view, in detail, in my 1979 book
"Mathematical Population Genetics" and elsewhere, and there
is no point in repeating the details here. I am happy
however to discuss them with anyone who wants to.
The "truth or otherwise" (whatever that can mean) of the
neutral theory, however, does not depend on load arguments,
so in my view it is a pity that these were ever advanced.
On the point of testing for neutrality, I started to think
hard about this two or three years after Kimura's paper
came out, and this resulted in my 1972 paper "The sampling
theory of selectively neutral alleles". This gave, in a
very simplified evolutionary model, the null hypothesis
(i.e. neutrality) distribution of a sample of genes, under
the infinitely-many alleles model. This could then be used
as a basis for a test of neutrality.
After a year or two I came to think that testing for
neutrality would be very difficult, because of the very low
power that any test one could think about at the time would
have. I still think that this is largely true - one has to
make many(and to me probably unrealistic) assumptions to
get a test with much power.
On the other hand, the sampling theory in part led Kingman
to the idea of the coalescent, and that is something that
has proved very useful in data analysis. So I don't feel
that my efforts were wasted.
-- Warren Ewens, November 1, 2001
Structural Reduction
I well remember the appearance of the King and Jukes paper
and the papers by Motoo Kimura. I had already published a
prediction concerning the consequences of the mose likely
mutation based on the same appraisal of the molecular
control of heredity. That was entitled "Structural
reduction in evolution" and it appeared in the American
Naturalist in 1963 (vo. 97, pp. 39-49). That had provoked a
reaction by Sewall Wright himself the next year ("Pleiotropy
in the evolution of dominance," vol. 98, pp. 65-69). I had
suggested that his term "mutation pressure" would better be
called the "probable mutation effect" and would generally
interfere with the development of the phenotypica
manifestation which it controlled. If selection were
suspended, then the structure would reduce over time.
What had gotten me started on that gambit was reading
Christian B. Anfinsen's work The Molecular Basis of
Evolution (1959). When the King and Jukes paper appeared I
regarded it as
support for what I had proposed. I did not then and do not
now
regard it as opposed to a Darwinian interpretation of
evolution
but just an extension of it. Darwin had observed the
reductions that follow disuse, and it seemed to me that this
was the mechanism at the molecular level that could account
for the phenomenon. As a student of human evolution, I felt
that it cold account for a series of reductions that had
occurred by which "modern" form emerged from the more robust
Pleistocene hominids who were the only people present from
a million years ago until about 50,000 years ago. In regard
to the "neutralist" approach, my take has been very much
that of Francisco Ayala et al. in the PNAS in July of 1974
(91:687-6794). "The neutralist theory may . . . be
considered
a modification or extension of the synthetic theory of
evolution" (1974:6793). My own attempt to harness a portion
of it to explain particular aspects of human evolution has
met with thunderous silence and outright opposition in the
realm of anthropology. With two co-authors I did get an
application of it published in Evolution in 1987 ("Gradual
change in human tooth size in the laate Pleistocene and
post-Pleistocene" 41[4]:705-720), but my attempt to expand
on the approach was rejected twice by anthropological
journals
over the last year. Recently, however, molecular genetics
has emerged as a major segment of biological anthropology,
and I suspect that there may yet be a change in views as the
molecular perspective becomes part of the general outlook.
At the moment, however, the majority of the business is
still
reacting the way the biological world did to Kind and Jukes
when they first published.
C. Loring Brace, Museum of
Anthropology, University of Michigan, Ann Arbor, Mi.
clbrace@umich.edu
-- C. Loring Brace, November 5, 2001
Dismay and disbelief
As quoted on this site, James Crow stated that the initial
reaction was one of dismay and disbelief. I wonder if the
contributors so far, who seem by contrast to have been
interested, feel that their interest was unusual at the
time?
-- Arne Hessenbruch, November 24, 2001
The neutral theory - a further comment
I would like to respond to the request that those who have
contributed so far respond to Jim Crow's comment that the
neutral theory was greeted with dismay.
There certainly was an element of that - after all, we were
all convinced Darwinians at the time, meaning in this
context that it was felt that the vast bulk of the
variation observed in natural populations was selection-
based.
On the other hand, for those (such as myself) who were
interested in the mathematical aspects, the neutral theory
opened up many lines of research, simply because the math
for the theory was much simpler than that for selectively-
based theory. What I find myself constantly fighting
against is biasing my view of the neutral theory as a
scientific theory just because of the enjoyment of the math
that it led to.
I want to emphasize again that it is meaningless to me to
say that the neutral theory is true or not true. It comes
down to a question of proportions, of asking whether one is
asking if the alleles at a locus are selectively neutral
now or have been for millions of years, of whether one
argues at the DNA or protein level, and so on.
-- Warren Ewens, November 26, 2001
Response to Biology vs. statistics
Contrary to Ewens statement, the intention of both Kimura
and King/Jukes was to show that drift was the
main force of molecular evolution. Mathematical developent
of the neutral theory was of course very important,
but the main interest had been on the evolutionary aspect of
the neutral theory. Kimura and King/Jukes did
not make any statements on the relationship between the
evolutionary change of molecules and that at the
phenotypic level. Their theory was solely on molecular
evolution. Many evolution people misunderstood this
point, and thought that the neutral theory was applicable to
both molecules and phenotypes. So, many criticisms
were based on the misunderstanding. To clarify the
mechanisms of molecular evolution is a most important
purpose of evolutionary studies at the molecular level. The
Ewens sampling theory and other statistics are
very useful for the purpose.
-- Tomoko Ohta, November 28, 2001
From the biochemical side...
I was very surprised to get an e-mail suggesting that I
was "one of the first botanists to comment on the neutral
theory"! I cited the papers by King and Jukes, Nei (1969)
and Kimura because they provided estimates of mutation
rates. I was trying to explain why the %GC of moss and fern
DNAs fell in a rather narrow distribution with about the
same mean as angiosperms. Using a rough average of these
estimates and others, I calculated that there hadn't been
enough time in the 400 million years since divergence from a
common ancestor for the %GC to have changed very much.(BBA
254:402-406, 1971; BBA 277: 29-34, 1972).
Dr. Ohta is quite correct in what he says about
biochemists. I did my Ph.D. in Biochemistry at the Univ. of
Washington (1965), and the idea that most mutations had no
effect seemed quite sensible to us. It still does. Take a
look at the molecular models of the amino acids in Stryer or
any other biochem text. It is obvious that some of them are
going to "pack" in the same spaces. By that time, there were
enough sequences of hemoglobins so it was clear that oxygen
was carried quite efficiently by molecules with a variety of
substitutions, especially on the surface of the protein. If
you are being chased by an annoyed elephant, it will be
pretty clear that your hemoglobin sequence and his are not
going to be the deciding factor in the race!
We were taught that selection acts on the whole organism,
generally by affecting the relative reproductive success of
individuals in a population. Unless a mutation is quite
deleterious, there will be other factors, e.g. behavioural,
that will swamp out any small effect due to a small change
in a protein molecule. Also, by 1965, Jacob and Monod's
paper on the regulation of the lac operon had appeared, and
there were a number of examples of negative feedback
regulation in metabolic pathways. So, even if a given enzyme
doesn't operate quite as efficiently, the steady state level
of end-product will be the same, because it depends on
feedback regulation.
My work on families of chlorophyll-binding proteins leads
me to the view that there is quite a large degree of
adaptability in protein structure (see the attached
Commentary on "Molecular Opportunism" in PNAS
98:2119-2121,Feb27, 2001. One of my students once commented
that "evolution is the survival of the adequate". He had a
point.
-- Beverley R. Green, November 28, 2001
Attachment: PNAScomment.pdf
Response to More again
I would like to add one word to Tomoko Ohta'a comment.
Tomoko implies that there is some contradiction, in my
previous comments, to what Kimura and others were doing, by
pointing out that Kimura's main focus and emphasis was
biological.
I have never questioned this, or said anything to the
contrary. What I said was the MY OWN INTEREST was in the
statistics relevant to this, and in how one could test the
theory by statistical methods. I agre that this is a narow
focus, but it was nevertheless my focus at the time.
-- Warren Ewens, November 29, 2001
Kimura and Jukes-King papers
This is response to the question of my initial reaction to
the Kimura and King and Jukes papers.
Kimura sent me a copy of his manuscript, but I didn't get
around to studying it, so he went ahead and published it. It
is probably just as well, for I didn't like his use of the
Haldane cost of evolution argument along the assumption that
all the DNA is genic. Sewall Wright received a copy at the
same time and commented rather adversely, although I have
forgotten what he said.
Science sent me a copy of the King and Jukes paper. I
believe it had originally been rejected and I participated in
the second round of reviewers. In any case I liked the paper
and recommended publication. Whether my review was
influential or not I don't know, but the paper was published
as everyone knows.
I spent part of the summer of 1968 in Mishima with Kimura.
Of course we talked a great deal about the neutral theory.
By this time Kimura had much stronger arguments and these,
along with those of King and Jukes made what I thought was a
convincing case. I was also aware of the earlier work by
Sueoka and Freese reaching the same conclusion from quite a
different direction. By the end of the summer I was
convinced that the theory had a great deal of merit. I had
been invited to give the closing address at the International
Congress of Genetics in Tokyo, and took the opportunity to
say nice things about the neutral theory. This is published
in the Proceedings of the XII International Congress of
Genetics, Vol III, p. 105-113.
Although Kimura and I had worked together a great deal, I
want to make clear that the neutral theory was entirely his.
I had participated in the development of the "infinite allele
model". The history of this is summarized in Genetics 121:
631-634, 1989.
-- James F. Crow, December 1, 2001
Questions for Tomoko Ohta
I think that Tomoko could add further information on the
origins of Kimura's paper, since she did some of the
background work for it. Also I think she may remember better
than I the conversations that took place in Mishima in the
summer of 1968.
-- James F. Crow, December 2, 2001
Dismay and disbelief
I don't recall saying this, but I have said a lot and don't
doubt that I said this at some time. In any case I think it
is a fair description of the way the neutral theory was
initially regarded by most biologists, especially
evolutionists. Some of these were simply knee-jerk reactions,
but later there were thoughtful objections, too (e.g.
Gillespie, Kreitman).
-- James F. Crow, December 3, 2001
Wilson Lab and Stony Brook
I left Alan Wilson's lab in August,1968 to take a position
in Biochemistry at SUNY Stony Brook. The Wilson Lab was very
happy with the neutral model as I recall. Alan and Vince
Sarich's attempt to date the Chimp-human split rested on the
protein sequence data suggesting constant rates of protein
evolution. The Kimura and King and Jukes papers provided a
firm genetic foundation for this observation.
After both papers came out I tried to test the neutral
model. I recruited Charles Taylor who was then a graduate
student in the Ecology and Evolution Department to help with
the neutral theory. We published a test of the model in
Nature (Arnheim and Taylor 1969 Nature 223:900-903) three
months after the King and Jukes paper came out.
The crux of the proposed method was to compare the number of
segregating neutral amino acid substitutions in each of two
proteins in the same population. If both proteins evolved at
the neutral rate, the theory at that time suggested that the
number of segregating neutral amino acid substitutions at
each locus should be the same. No estimate of Ne was needed
since it will be the same for both loci.
For the test we used the 84 known amino acid variants at the
human alpha and beta chain hemoglobin loci. The criteria for
a neutral amino acid substitution was biochemical. We used a
paper by Perutz and Lehman (Nature 1968, 219:902) who
predicted from haemoglobin's three dimensional structure
whether any of the known variant amino acids would have an
effect on the function of the haemoglobin tetramer.
-- Norman Arnheim, December 3, 2001
Response to Dr. Crow
I joined the Kimura laboratory in the spring of 1967, and I remember the atmosphere when Kimura proposed
the neutral theory. I helped, or confirmed the calculation on the rate of mutant substitution of hemoglobin,
cytochrome c and another protein based on the reports in Evolving Genes and Proteins by Bryson and Vogel.
Kimura and myself were much impressed by the Zuckerkandl and Pauling paper in this volume, which was the
first to propose the molecular clock. In the next year Dr. Crow visited us and we had many lively discussions.
Through these discussions, I noted Crow's comment that if the number of genes was much smaller than the
total DNA amount suggested, protein evolution was in accord with the load concept. I remember also what
Kimura told me about Wright's comment. Wright wrote to him that the pattern of protein evolution was not
incompatible with the shifting balance theory of evolution.
-- Tomoko Ohta, December 3, 2001
Response to Comment on King and Jukes
About King and Jukes
You asked me to comment on my response to the 1969 paper by
King and Jukes.
Initially I thought that their arguments were so obviously
wrong that the paper would sink into decent obscurity, but a
year later there were authors declaring, "As King and Jukes
have shown", and the like. A reply seemed to be needed.
Rollin Richmond must have felt the same, because he, too,
published a critique in 1970 (Nature 225: 1025-1028).
Thirty-one years later, most of the criticisms still stand,
and some are greatly strengthened. We have clear evidence of
selection on codon use, and of differences between lineages
in the evolutionary rates of single proteins, but we remain
ignorant about the importance, or otherwise, of three-
dimensional structures in messenger RNAs. Statistical
evidence of selection on amino acid sequences continues to
accumulate, even though the tests have very low power.
Experimental evidence of selection on protein polymorphisms
also accumulates, particularly through differential
susceptibilities to disease.
Where does this leave the neutral theory? The answer may
depend on the kind of variation. The original argument was
about amino acid replacements. It is reasonable (though not
yet obligatory) to suppose that the majority of such
replacements have been driven by selection. This does not
deny the existence, or indeed the importance, of random
genetic drift. It is theoretically possible, as Fisher
pointed out in 1930, for most evolutionary replacements to
be selected while most polymorphisms are neutral. It is much
more difficult to imagine a world in which replacements are
neutral while polymorphisms are selected.
In some proteins, virtually all amino acid replacements must
have been selected. It is hardly credible to suppose that
histone 4, in which a single amino acid has been replaced
since the common ancestor of the pea and the cow, arrived at
its initial state by random drift.
When we consider non-coding nucleotide replacements, the
assumption of neutrality can be more plausible, but often it
may just reflect our ignorance about the activity or
function of the region concerned.
The neutral theory was appealing because it overcame two
apparent difficulties of selection, the problem of high
genetic loads when many loci are changing, and the problem
that the evolutionary rates of individual proteins seemed to
be constant. Both difficulties have turned out to be
illusory. Truncation selection, epistasis, density
dependence and other factors can minimise loads (as Warren
Ewens has remarked), and evolutionary rates are not
constant.
Another advantage of the neutral theory was that it simply
and quantitatively explained both evolutionary replacements
and polymorphisms. Nowadays the simplicity has gone. To
accommodate known facts, the theory must accept varying
degrees of purifying selection, the widespread substitution
of mildly deleterious genes, generation-time effects,
variable mutation rates, background selection, and
associations with selective sweeps. In these circumstances,
it seems quixotic to deny, on the grounds of economy, an
important role for directional selection in driving
replacements.
You enquired why, in responding to King and Jukes, I
described myself as a classical evolutionist. Their paper
had made slighting remarks about such people, showing more
than a hint of molecular triumphalism. I took the term
classical evolutionist to mean someone who had been
educated in a relatively molecule-free environment. My first
degree was in zoology, which in those days meant comparative
anatomy, evolution, ecology, behaviour. palaeontology and
physiology (most of which I missed). My doctorate was in
ecological genetics, and my job at the time was to teach
ecology. This history seemed to fit King and Jukes
designation pretty well, though it must be admitted that I
was already interested in molecular biology, and had avidly
read Bryson and Vogels Evolving Genes and Proteins.
About amino acid replacements
In the early days of the neutral theory, Motoo Kimura
proposed that about 50% of mutations were disadvantageous,
and the remainder neutral. I plotted Sneaths measure of the
chemical difference between each pair of amino acids against
the frequency, in a range of proteins, of evolutionary
replacements between the members of the pair. The analysis
included only pairs whose codons were one mutational step
apart. There was a clear negative correlation. By
extrapolating to a chemical difference of zero, one could
estimate the average rate of replacement for completely
neutral changes. Comparing this value to the overall average
rate gave an estimate of the minimum proportion of mutations
that were disadvantageous. This was about 90%. Kimura
accepted this value.
Interpreting the negative correlation was more contentious.
Kimura, King and Jukes regarded it as evidence of the
neutral theory (to them, fast rates represented neutral
evolution, slow rates represented the elimination of large
chemical changes by purifying selection). I pointed out that
the selective theory made exactly the same prediction.
Fisher had shown, by a geometrical argument, that the larger
the phenotypic effect of a mutation, the less likely it is
to be advantageous. Therefore we should expect a negative
relation between the size of the chemical difference and the
evolutionary rate. Kimuras reply, in his book, was somewhat
disingenuous. He emphasised, quite correctly, that the
magnitude of the disadvantage and the slowness of the
evolutionary rate are not the same thing. Making some
plausible assumptions, he obtained an expected relation
between the size of phenotypic effect and the evolutionary
rate. The relation was a curve with a positive slope when
the phenotypic effects were very small, but a negative slope
when they were larger. He implied that this invalidated my
argument. However, if you observe the part of the curve
where 90% of the mutations are disadvantageous, the slope is
very clearly negative.
General Remarks
Those who favour the overriding importance of random drift
in evolution have shifted attention from replacements in
amino acids, where their case has weakened, to replacements
in non-coding nucleotides, where the issue is still unclear.
The debate between neutralists and selectionists has
been quiet for decades, not because there has been a clear
resolution, but because people got tired of the battle.
Meanwhile, for many purposes there has been comfort in
assuming neutrality because it is mathematically tidy, and
because it absolves one from having to do difficult
experiments. There is still a lot of territory between the
tenable extremes. Recent developments, particularly in
analysing DNA and studying microbial populations, are likely
to narrow the available range of argument.
-- Bryan Clarke, December 10, 2001
hemoglobin variability
Unusual to be asked about an article which I have written 30
years ago! But indeed we were sequencing hemoglobins at that
time in the MPI in Munich and wondered about the variability
it displayed in different species. To sum up what is known
today, only 2 of the about 150 amino acid residues are
invariant in this protein family. Thus the papers by M.
Kimura (1968) and J. King and Th. Jukes (1969) gave an
elegant and quantitative explanation but unfortunately
bothered us with the term `Non-Darwinian Evolution` and even
today in your e-mail outline I read that the theory lead to
`a powerful new critique of Darwinism`. I think, that is not
true: It has been shown, that already Darwin has discussed
the matter of neutral changes in his ``The Origin if
Species....``(1859) including the possibility of them being
established by chance (Arnheim, 1973). Neutral variation is
well in the concept of (Neo-)Darwinism; an extension of the
theory, as it may come up in science when a new level of
investigation-in this case the molecular- has been reached.
Another aspect behind the Neutral Theory, however, has not
gained much attention: the dependence of the variability of
nucleic acids/proteins from the general structure of these
informative macromolecules. The elements of both are built
from stabile backbones, providing the
phospho-ribosyl/peptidyl-connections, which are not subject
of the normal variation (pointmutation) but conserve the
conformation and thus prevent destructive all-or-non effects
of mutations, enabling a spectrum of variation
(substitution), including the nearly neutral, and thus open
a variety of possible adaptations in a population.
Gerhard Buse, Aachen, Germany
-- Dr. Buse Gerhard, December 17, 2001
King and Jukes
King and Jukes seemed to be spoiling our chances of seeing
evolution in action in the metabolic enzymes of hybridizing
house mice in Denmark. I was there doing field work in 1969
when Robert Selander sent me the K-J article. Our intention
was to find alleles that differed across the narrow hybrid
zone and to reveal natural selection in their patterns of
introgression. The idea that selection might not
distinguish among those still hypothetical genes was
depressing, and even when striking interlocus differences
in introgression did emerge a few months and a few hundred
gels later, we wondered how big a part chance (especially
linkage effects) had played with the distribution of those
alleles. Were they coadapted parts in two fine watches
(corresponding to the two mouse semispecies), or were those
alleles just generic equivalents in a sea of ho-hum
variation? The clincher was our discovery of five new
alleles associated with the hybrid zone. The obvious
explanation was that tight coadapted structure
characterized the two parental gene pools, but faltered
within the area of mixing (Hunt and Selander, Heredity
31:11-33).
-- Grainger Hunt, January 6, 2002
Response to The neutral theory - comment
Molecular Evolution and the Neutral Theory
When Kimura wrote his Nature paper, I had a rather
close contact with him. I was a visiting researcher in his
laboratory around that time and used to visit him in
Mishima once in about two months. (At that time I was
employed in the National Institute of Radiological
Sciences, Chiba, Japan.) In my recollection, his original
motivation of writing the Nature paper was to defend the
classical (mutation-selection balance) theory of
maintenance of genetic variability against the balance
(overdominance) theory (Dobzhansky, Cold Spring Harbor
Symp. Quant. Biol. 20:1-20, 1955). Around 1960 there was a
fierce debate between the ?classical? camp and
the ?balance? camp of population geneticists. The leaders
of the former camp were James Crow and Motoo Kimura,
whereas Theodosius Dobzhansky and Bruce Wallace were the
leaders of the latter camp. Around 1966 when
electrophoretic studies uncovered extensive protein
polymorphisms in human and fruitfly populations,
the ?balance? camp appeared to have won the battle because
the balance theory had predicted a large amount of
polymorphisms. However, there was a lingering problem
annoying the balance camp; it was the unbearably high
genetic load that is required to maintain polymorphism by
overdominant selection.
There were two ways out of this dilemma. One was
to assume that natural selection eliminates individuals
homozygous for many loci disproportionately (truncation
selection). The other one was simply to assume that the
majority of allelic polymorphisms are more or less neutral
and therefore do not produce any significant genetic load.
This latter idea was apparently conceived independently by
Alan Robertson and James Crow. I heard of this idea from
the late Terumi Mukai (who was working in Crow?s
laboratory), when I visited him in Madison in the summer of
1966. As soon as I returned to Japan, I told the story to
Kimura. I do not remember whether he knew of it or not,
but he seemed to be pleased with it. Now the problem was
how to convince fellow evolutionists who now seemed to be
sympathetic with the balance theory.
For Kimura, it was to compute the rate of
nucleotide substitution from protein sequence data and
argue that if all nucleotide substitutions in a mammalian
genome (about 4 billion base pairs) were caused by natural
selection the cost of natural selection as formulated by
J.B.S. Haldane would become unbearably high for most
mammalian species. This was soon challenged by John Sved
and John Maynard Smith, who argued that the Haldane cost
could be reduced substantially if natural selection
operates in the form of truncation selection. For a number
of reasons, I did not think that truncation selection
applies to natural selection, but Crow (Haldane and Modern
Biology, ed. K. R. Droniamraju, pp. 165-178, 1968) studied
the same problem independently using genes (10,000 genes)
as units of selection and reached the conclusion that the
rate of amino acid substitution observed in hemoglobins,
cytochrome c, etc. is compatible with the Haldane cost
argument. Later, I also showed that mammalian species can
tolerate a considerably higher level of cost than Haldane?s
suggestion by changing the assumptions slightly (Nei,
Molecular Population Genetics and Evolution, Elsevier,
1975).
Kimura sent me a copy of his Nature manuscript on
the day he sent it to Nature. I did not think about his
cost argument very carefully, but his final conclusion
appeared to be correct, because by that time a substantial
amount of molecular data supporting the idea of neutral
evolution had been published (see the papers by Zucherhandl
and Pauling, Margoliash and Smith, Freese and Yoshida,
Sueoka, and others in ?Evolving Genes and Proteins? edited
by Bryson and Vogel, 1965). This view was reinforced when
King and Jukes (1969) published their Science paper,
examining all available molecular data systematically.
Their main conclusion was that as long as the function of a
protein or RNA molecule remains the same most nucleotide
substitutions occurs by random fixation of nearly neutral
mutations. For me, this conclusion was easily acceptable,
and I believe it is still valid, though details of the King-
Jukes arguments have been modified.
Although I accepted the neutral theory without much
trouble (Nei, Nature 221:40-42, 1969), I was not very happy
about the fact that the neutral theory was powerless in
explaining the evolution of morphological and physiological
characters, in which most biologists were interested. I
also thought that if adaptive evolution ever occurs in
morphological or physiological characters it must be caused
ultimately by some nucleotide changes. I was then
interested in finding such evidence. I was therefore quite
happy when Austin Hughes and I were able to show that the
high degree of polymorphism in MHC loci is caused by
overdominant selection. One of the important implications
of the neutral theory was that protein and DNA molecules
could be used for clarifying evolutionary relationships of
different populations or species, and I then invested a
substantial amount of my time for this purpose.
I suppose this forum is not for arguing the
validity of the neutral theory. If we do this, we will
have to examine extensive literature. However, since Brian
Clarke strongly rejected the neutral theory, I would like
to add a few comments. A reader, who wants to know
detailed aspects of this issue, may refer to Li?s (1997)
book Ã?Â?Molecular Evolution.?
The first thing I want to emphasize here is that if
we are concerned with very minor fitness differences
between alleles, say s = 0.0001, it would be
extremely difficult to resolve the debate on neutrality.
However, is it important to identify alleles with very
small fitness differences? Early molecular evolutionists
were interested in knowing whether the function of a
protein is affected by amino acid substitutions or not. If
the function did not change appreciably, the alleles were
regarded as neutral. Examination of this problem was often
done by studying whether a protein from a species functions
normally with substrates from other species. We can now
use site-directed mutagenesis and gene-knockout experiments
for this purpose. Recent knock-out experiments have shown
that a surprisingly large number of genes are dispensable
in mice and yeast and that there are many different ways of
achieving a particular biological function such as host
defense from parasites. In my view this type of study is
more important than the identification of alleles with
minor fitness differences.
In recent years an extensive statistical study of
detecting selection among polymorphic alleles has been
done. The results indicate that it is generally difficult
to reject the null hypothesis of neutrality. However, a
substantial number of authors reported detection of
slightly deleterious mutations. These results are
interesting because they support the classical theory of
maintenance of genetic variability, which was discussed in
the 1950s and 1960s. However, these mutations would not be
very important in long-term evolution, because accumulation
of deleterious mutations in a gene is expected to result in
the deterioration or malfunctioning of the gene
eventually. Of course, if the fixation of slightly
deleterious mutations is followed by that of slightly
advantageous mutations, the function of the gene can be
maintained in long-term evolution. However, this is
essentially the same as the nearly neutral evolution as
envisaged by King and Jukes (1969). Similarly, background
selection may be important in understanding certain
patterns of genetic polymorphism, but it is unlikely to
play important roles in long-term evolution. It should
also be noted that purifying selection is allowed in the
neutral theory, and therefore the evolution of histone
genes is in accord with the neutral theory (Rooney,
Piontkivska, and Nei, Mol. Biol. Evol. 19:68-75, 2002).
Furthermore, selectively important amino acid substitutions
such as those for MHC loci have been identified in a number
of genes, but they are a minority of the total amino acid
substitutions.
Masatoshi Nei nxm2@psu.edu
-- Masatoshi Nei, January 8, 2002
Response to M. Nei
In general, my memories agree with Masatoshi's statements and
I appreciate his input. I had not known of his conversation
with Mukai, although I do remember his visit in Madison.
Although I entertained ideas about the possibility of neutral
evolution and neutral polymorphism in 1965 and 1966, I did
not, as I said earlier, participate in discussions with
Kimura immediately prior to his 1968 paper. Much of the time
we were in close contact if not in collaboration, but not in
this time period. His manuscript was new to me, and as I
said earlier, I didn't trust the Haldane argument for the
whole genome, although as both Nei and Ohta have said, the
difficulty disappears when the number of genes is considered
rather than tht number of nucleotides. I was receptive to
the neutral theory partly because of King and Jukes and
because of early familiarity with the work of Sueoka and
Freese.
Although Kimura was certainly associated with the classical
view, I thought that immediate antecedents of his 1968 paper
were molecular evolution rates rather than classical-balance
arguments. But Nei was in much closer contact with him at
this time than I was, as was Ohta. In any case, by the time
I spent several days in the summer of 1968 in Mishima the
neutral theory had taken on a life of its own.
I agreed with Nei at the time about truncation selection,
although I did mention Sved's analysis in my paper at the
Tokyo congress. My view changed later when Kimura and I
showed that a rather loose approximation to truncation had
rather similar consequences.
-- James F. Crow, January 9, 2002
Response to Dr. Nei
I would like to defend the nearly neutral theory. In the
early 1970s, I was hoping to find out the true processes or
the mechanisms of molecular evolution, because I could not
be satisfied by the neutral theory due to the
following three points.
1) Molecular clock. Why was the rate of molecular evolution
year dependent rather than
generation time dependent? I thought that the mutation rate
depended on generations.
2) Why was the heterozygosity measured by electrophoresis so
uniform among the species?
3) Mutants effects on fitness should be continuously
distributed around neutrality. Then one would expect
population size effects on the rate of
molecular evolution.
I was much puzzled by these questions. Then I realised that
the nearly neutral theory assuming the prevalence of
slightly deleterious mutations could explain these problems,
and published it. There were disagreements on the
significance of near neutrality between Kimura-Nei and
myself and we had many hot discussions. Dr. Crow agreed to
my idea to some extent but not quite, as I understood.
Jukes liked the idea and sent me Conglaturations when the
Nature (1973) paper was published, but he did not make any
statements until the last one. King completely agreed with
the near neutrality concept and we published the joint
paper(Genetics 79, 681-691). As to the relationship of
Mukai viability polygenes and nearly neutral mutations,
there should be overlap between the two classes. The mean
effect on fitness should be smaller for nearly neutral
mutations than for viability polygenes. The overlap is an
important problem for the future study. The effect of such
weakly selected mutations should not be constant for various
environmental conditions and genetic backgrounds, and
selection intensity in a local area is thought to be larger
than Nei's estimate. His value comes from molecular
evolution data which is the average effect. So nearly
neutral mutations are not totally noise, and may be related
to some quantitative characters. In any case, clarification
of interaction of drift and selection is important for
understanding mechanisms of molecular evolution.
-- Tomoko Ohta, January 10, 2002
A reply to Masatoshi Nei, and some comments
We cannot intelligently consider the King and Jukes paper
without discussing the value of their arguments. This may
not be the place for a full-blooded debate, but at least we
must state our own views clearly. Otherwise, this exchange
becomes just a set of pleasant reminiscences.
Many of the K-and-J arguments were silly, but Kimura's
neutral theory was not. Some nucleotide substitutions must
surely be neutral, or nearly so. However, the case that most
amino-acid substitutions are neutral is weak.
Of course histone 4 is subject to intense purifying
selection. It sits on a very sharp adaptive peak. The
question is how it got there. To suppose that it wandered
randomly over a flat landscape, and then a peak happened to
appear beneath it, stretches credulity.
In fairness, I should confess some failings of my paper
criticising King and Jukes (Science, 168, pp.1009-1011,
1970)
I wrote that the Treffers mutator (mut-T) allele would
probably be disadvantageous in natural circumstances. Since
then, the work of Cox and others has shown that it can
sometimes be favoured. In a changing environment, the
short-term advantage of producing beneficial mutations at
other loci can allow mut-T to spread by hitch-hiking,
despite its long-term disadvantages. Thus, selection on the
mutation rate is not always downwards, a fact that can
explain the pressure on GC ratios. The results of Sueoka do
not necessarily imply that the widespread changes in codons
have been neutral. There are two opposing selective forces.
I failed to point out that the natural selection of
synonymous codons to minimise mutational damage may be
effective only where just a few somatic mutations can
produce severe problems, as with oncogenes. Selection
against errors in translation is probably more common.
I argued for a selective interpretation of geographical
patterns in allozyme frequencies but did not discuss the
possible roles of historical events and gene flow. I should
have done so even though I felt that they had already
received too much emphasis. It is still true that selection
of molecular variants by ecological factors is rarely
tested, and often completely ignored. When a test is made,
evidence of selection is frequently found. There is still an
uncritical tendency to invent historical events a
posteriori as explanations of current geographical
patterns.
-- Bryan Clarke, January 17, 2002
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