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Molecular clocks and "living fossils"

L.A. Moran lamoran at gpu.utcs.utoronto.ca
Mon Jun 22 09:58:32 EST 1992

Andrew Clifton asked some questions about the Molecular Clock. 
One of them was;


      If, as the molecular clock hypothesis asserts, sequence variations
      between two organisms are dependend only on the time which has
      elapsed since they separated from their common ancestor, one would
      expect that in species which have survived for a remarkably long
      period of time, such as the lungfish, coelocoanths and horse-shoe
      crabs, there would be much more intra-specific sequence variation
      than there is in more recently evolved species.  Is there any data
      on the amount of intra-specific variation in these species, as
      compared to, say, homo sapiens?"

First let me congratulate you for putting "living fossils" in quotation marks.
This suggests that you understand how silly it is to pretend that any living
species has stopped evolving. For the benefit of others I want to point out 
that the lack of obvious morphological change over time is not the same as
the lack of evolution. In the case of the coelacanth the rate of evolution
at the molecular level has been studied and found to be normal. The same is
true of lungfish and horseshoe crabs.

It is worth bearing in mind that it is POPULATIONS that evolve. Mutations
arise in individuals and then they either spread through the interbreeding
population (fixed) or they are lost. The mechanisms of fixation or loss are
usually natural selection or genetic drift. The rate at which mutations become
fixed in a population depends on the mutation rate and on how easy it is for
the mutation to "take over". Since, at the molecular level we are usually
dealing with neutral mutations, then the rate of fixation depends mostly on
genetic drift. This in turn depends on the population size.

In small populations there is much interbreeding and individuals are mostly
homozygous (as in inbred colonies of mice or some human communities). In 
this case a new allele can become fixed, by chance, in a short period of
time. However, because the population is small there are not very many new
mutations arising each year.

By contrast, in a large population there can be many new mutations each year
since there are many more "targets". But because the population is large it
is very difficult for a new mutation to "take over" or become fixed in the
population. (Imagine how long it would take for every human to become
homozygous for a new blood type allele.) This trade-off between the rate
of mutation and the probability of fixation is well known to population
biologists. It turns out that the two effects cancel each other so that for
a given population the rate of substitution of an allele is equal to the
mutation rate. (For example, if the mutation rate at a locus is .000001
per gamete per generation then the rate at which a new allele becomes fixed
is also .000001 per generation. In a population of one million individuals
there will be a new mutation every generation but only every million 
generations will one of these become fixed.)

Heterozygosity can be viewed as fixation in progress, or evolution in action.
When there are several alleles present in a population (such as human blood
types) it is likely that one of them will become fixed and the other(s)
disappear. (There are some exceptions where heterozygosity is favored.) At
any point in time the population will be in a dynamic state as new alleles
are created by mutation and lost by genetic drift. 

Some populations have less variation than others because they are small or
because they have recently come through a stage where the population was
very small. Such bottlenecks tend to reduce heterozygosity for many
generations. Some SPECIES exhibit a large amount of variation because they
are divided into many smaller inbreeding POPULATIONS (or demes) and different
allels can become fixed in the smaller groups. In the jargon of population
genetics these species are not panmitic. Humans are an example.

Now to answer the question. There is no reason to postulate that the current
population of lungfish has any more variation than the current populations
of codfish or bluebirds. All three populations have evolved continuously
from an ancestral population that lived several hundred million years ago.
Over that period of time new alleles have arisen and been lost or fixed in
all three populations. The fact that some alleles have been selected and that
this results in striking morphological differences does not affect the vast
majority of neutral alleles that calibrate the molecular clock. 

Laurence A. Moran (Larry)
Dept. of Biochemistry

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