theoretical population genetics - The evolutionary force of great environmental change

[Geert]

Dear all,

This is my theory http://www.geert.com/The_evolutionary_force_of_great_environmental_change.htm. Can all the theoretical population geneticists please give me some scientific feedback / criticism?

 

Many thanks in advance,

 

Geert

 

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The evolutionary force of great environmental change

 

Highlights

- The Cambrian explosion and Darwin's dilemma explained.
- Adaptive mutation is a viable mechanism (current theory proven to be incorrect).
- The level of environmental change and the optimum mutation rate are linked.
- Evolution's high speed, and the emergence of fundamental mechanisms, explained.

 

Keywords
adaptive mutation - Cambrian explosion - Darwin's dilemma - explosive period - extinction - optimum mutation rate - phyletic gradualism - speciation - still period

 

ABSTRACT
In the period just after a great environmental change, all individuals of most species are seriously maladapted. So many new resources are left under-exploited. In this situation radical mutations are less deleterious while their potential benefits are greater. In part because the first proto-species, which evolves enough to dominate the exploitation of a new resource, effectively wins the race and becomes a new species (speciation). While the losers face extinction. So higher mutation rates for radical mutations are advantageous within this period. In the subsequent non-eventful period the situation is reversed. All the species are well adapted and the quality of the competition for the available resources is very high. This leads to a self-enforcing cycle in which ever higher levels of fine-tuning lead to ever lower mutation rates. As great environmental changes occur regularly in the history of the earth, it is reasonable to assume that the resulting cycle between the two types of periods is a major factor in explaining the high speed of evolution on earth.

 

1. Introduction
Currently there is renewed debate about the Cambrian explosion as there is now strong evidence that evolutionary rates were significantly higher than normal 1 during the Cambrian period. Another study of the fossil record has even shown that, in the aftermath of a mass extinction, many of the initially surviving species still go extinct at a later time due to unexplained after effects from the original mass extinction 2.

Once again 'Darwin's dilemma' determines the debate. For Darwin had noted that the higher evolutionary speed during the Cambrian period seemed to contradict his prediction of a slow and constant evolutionary speed. The extreme imperfection of the geological record 3 p.280 was Darwin's explanation, but this argument is no longer valid in light of the new evidence. It is obvious that something much more significant is going on here.

One part of the Darwin & Wallace theory of evolution has been largely ignored until now. Darwin wrote in his famous 'On the origin of species' that 'Though nature grants vast periods of time for the work of natural selection, she does not grant an indefinite period; for as all organic beings are striving, it may be said, to seize on each place in the economy of nature, if any one species does not become modified and improved in a corresponding degree with its competitors, it will soon be exterminated.' 3 p.102. This idea of Darwin, in combination with the aftermath of a great environmental change, forms the conceptual starting point of this article. This approach has proved to be very fruitful.

The science of population genetics is very good in testing evolutionary theory. It distils any theory into a clear and well defined form, and then tests it for all possible scenarios. Many previously popular theories were found to be wanting when the science of population genetics was first established. However, any error in the process can have serious consequences down the line. It can block scientific progress and it can distort publications on interesting field-findings. This article exposes just such an error. An error that actually contradicts the extract from Darwin's 'On the origin of species' that I just cited above 3 p.102. In order to clarify this point by example, as well as to demonstrate what my theory is capable of, I will therefore also present an explanation for the Cambrian explosion in this article.

There has long since been a possible explanation for the Cambrian explosion know as 'adaptive mutation'. This is a mechanism that can adjust mutation rates to the optimum rate. But adaptive mutation is generally considered to be an unviable mechanism because theoretical models prove that mutation rates will always evolve to become as small as is practically possible.

So much has been written on the subject of 'adaptive mutation' since Darwin that it is impractical to list all the references. So I will only list a few who best explain the origins of the current line of thought 4,5,6 and a few interesting ones who dispute it to some extent 7,8,9,10,11. I suggest these as a starting point for anyone who wishes to delve deeper into this age old debate.

The logic behind the generally accepted position, that adaptive mutation is impossible because mutation rates will always evolve to become as small as is practically possible, is based on the fact that most mutations are either neutral or deleterious. Therefore, the off chance of a modifier gene (a gene that raises the overall mutation rate) causing a beneficial mutation, cannot compensate for the many deleterious mutations that it would also cause. So on average a modifier gene would cause more harm than good and it would therefore die out. For asexually reproducing species there is an exception to this logic if the modifier gene is by chance linked to one of the beneficial genes that it caused. But this is considered to be only a temporary reprieve as the link, between the modifier gene and the beneficial gene it caused, will inevitably be cut at some point in time. Within sexually reproducing species any link would quickly be terminated due to meioses. So for sexually reproducing species there is not even a temporary exception.

This generally accepted logic on adaptive mutation is based on work done with theoretical models. And a quintessential part of all these models is a small set of implicit assumptions. Namely: that one may ignore the influence of other species, that all the species inhabiting the environment are well adapted to it, and that there are no un- or under-exploited new resources. These assumptions allow for a great simplification of the theoretical models and are probably correct for most evolutionary processes. However, I believe them to be incorrect regarding the period just after a great environmental change. A period, which might only be short (like the start of the Cambrian), but which I will show to be essential in the process of evolution.

For the purpose of discussion I would therefore like to propose an addition to the Darwin & Wallace theory of evolution. Whether or not this addition is plausible, and to what extent it is generally applicable, I leave to the subsequent debate.

I am aware that there have been countless publications, and even whole movements in the biological sciences, which have covered the same ground to some extent. But these were all proven wrong by the science of population genetics. This article is different because it is completely in line with the science of population genetics. Many interesting field-findings can now (finally) be theoretically explained, and many old theories can now be re-evaluated.

 

2. The underlying forces
Within this article I will define a niche as; 'the set of opportunities used by a species within its environment to survive and prosper'. A 'proto-species' as 'a group of members of an existing species that could potentially evolve into a new species'. A 'period just after a great environmental change' as an 'explosive period'. And a 'period of little change' as a 'still period'.

In the text these periods are described as real periods. But it is good to realise that, on a deeper level, they are more like forces pulling in different directions. So any real situation is always somewhere in-between these theoretical extremes.

The accepted term 'optimum mutation rate' (the best possible mutation rate in regard to its potential costs and benefits) is a bit ambiguous in the context of this article. A graph, showing the optimum mutation rate in relation to the level of effect that it results in, would be more accurate. However, as the shape of such a graph would be subject to quite a lot of speculation, I will only focus on radical and non-radical mutations. It is also important to realise that within the context of this article, an increased mutation rate for radical mutations, might simply mean that genes might be more likely to be made dormant or might mean some other genetic change that affects the gene regulatory system.

 

2.1 General outline
Environments can remain unchanged for over long periods of time, change slowly, change cyclically between several stages or change greatly in only a short period of time. This level of change directly affects the level at which all the individuals are adapted to survive within their environment. For it takes all the inhabiting species time to adapt to a new or changed niche.

 

2.2 Still periods
In still periods (periods of little change), evolution will have taken its course, and all the species will be well adapted for the environments and niches in which they live. So the competition, between all the species for all the available opportunities, will be fierce and of high quality. A radical mutation could enable a species to exploit an opportunity outside its niche. But radical mutations initially come with harmful side effects which need to be fine-tuned away over time by other non-radical mutations. And, as the competing species for that opportunity would be fine-tuned to perfection, this initial lack of quality would instantly force the mutation to go extinct before fine-tuning could ever take place (the same logic holds true within a species and its niche). So in still periods, ever higher levels of fine-tuning result in ever lower levels of mutation rates for ever less radical mutations, being advantageous (and if one assumes adaptive mutation then this is equates to a self-enforcing cycle).

 

2.3 Explosive periods
In explosive periods (periods just after a great environmental change) the situation is very different. These periods are basically the zero-hour moment in evolution.

All the inhabiting species find themselves in an environment that is (very) different to the one they evolved in. And, as they are therefore all badly adapted for their new environment, the quality of the competition for the newly available opportunities by all the inhabitant species is quite poor. This, in turn, leads to many of the new opportunities being un- or under-exploited. So, in explosive periods, the badly adapted individuals survive by the lack of serious competition for the new opportunities and by exploiting the new opportunities as best they can.

There will probably be several proto-species within the new environment that could potentially evolve to exclusively exploit part, or all, of its new opportunities. Which sets of opportunities will become the new niches in the new environment, will be determined by how quickly the different proto-species can adapt to exploit the new opportunities. For once a proto-species becomes superior in exploiting an opportunity, and it benefits enough from it to survive and multiply, this opportunity effectively becomes sealed off from the other proto-species and a niche's border has been set (speciation) (the availability of the opportunity becomes to low for the other proto-species to exploit it sufficiently). It has basically won the race while the other contenders for this opportunity will probably go extinct (extinction). In this way new species and new niches are formed. So we can conclude that a proto-species chance of survival is substantially dependent on how fast the proto-species can evolve in order to out compete its competitors.

Radical mutations have the potential benefit of enabling great leaps in design (breaking evolutionary stale-mates) which could prove decisive in winning the race. However, radical mutations are generally bad for the individuals concerned as they initially come with harmful side effects. So mutation rates for radical mutations are normally (in still periods) as low as possible. But, in explosive periods, a radical mutation could unlock an unexploited opportunity for its first carriers and, if so, they would therefore do well despite the harmful side effects. Once, the radical mutation then got more widespread and the opportunity became more exploited, the harmful side effects would be fine tuned away by other (non-radical) mutations as competition, between the carriers of the radical mutation, increased.

The severity of the harmful side effects of radical mutations, during explosive periods, is less than during still periods.
Simply because part of the harmful side effects are normally (in still periods) due to the fact that radical mutations offset the fine tuning that was done to adapt a species to its niche. But in an explosive period, the fine-tuning that was done to adapt a species to its old niche, is no longer valid as that old niche no longer exits.

Mutations which are only beneficial (and therefore prosper) when they are rare in the population, result in a more divers gene pool as they can never become dominant. This in turn aids in the chaotic search for the set of breakthrough mutations that are required for winning the race. For it increases the number of possible combinations as well as the number of possible mutations.

 

2.4 Conclusions on the underlying forces
These factors make that, within explosive periods, higher mutation rates for radical mutations are advantageous. While within each subsequent still period, continuous and ever more precise fine-tuning by non-radical mutations, makes, ever lower mutation rates for ever less radical mutations, advantageous. So, the level of environmental change and the optimum mutation rate, are linked.

 

3. Adaptive mutation / Cambrian explosion
So far I have shown that a mechanism, which could change the mutation rates in response to an organism's living conditions, would be beneficial. Such a mechanism is called 'adaptive mutation' and adaptive mutation is generally considered not to be a viable mechanism.

However, the proof for this has come from theoretical models which are all based on the set of implicit assumptions that I already listed in the introduction. And from what we have discussed so far it is clear that these only hold true for still periods. They are obviously incorrect for explosive periods. So adaptive mutation is a viable mechanism for changing mutation rates in both sexually and asexually reproducing species.

Now, with the new insights described in this article, the explanation for the Cambrian explosion is actually quite simple. It is well known that there was a great environmental change (and possibly more than one) at the beginning the Cambrian. So the start of the Cambrian was an explosive period. And the predicted effects, of an explosive period combined with the assumption that adaptive mutation actually exists, perfectly match those which define the Cambrian explosion 1,2. So ultimately 'Darwin's dilemma' did not contradict the theory of evolution, but only his prediction of a slow and constant evolutionary speed (phyletic gradualism). Interestingly, he did write that breeding programs often start-off from some half-monstrous form 3 p.83, which does suggests that he might have been closer to the solution than one might expect.

 

4. Geological long term
In the geological history of the earth, great environmental changes have occurred regularly, and each was followed by a long period with virtually no change (the geological time scale is less appropriate for bacteria and so, but the logic remains sound on a time scale more appropriate to them). This means that life continuously cycles from a short explosive period, in which radical mutations are more advantageous, to a long still period in which radical mutations are ever more disadvantageous.

It is therefore reasonable to propose that life will have evolved mechanisms that take advantage of this continuous cycling between explosive and still periods. These mechanisms probably come in one of two types. The first type raises the mutation rates for radical mutations when required. And the second type provides a structure wherein radical mutations are be more likely to be successful. So for example: regulation of mutation rates (adaptive mutation), structuring mutations into functional groups (genes) under the auspices of some controlling mechanism, allowing multiple variants of a gene to be carried within a single individual (for example: diploid), evolving sexual reproduction.

Therefore the continues cycling between explosive and still periods, and possibly in combination with these mechanisms, can potentially explain the high evolutionary speed of live on earth.

 

5. Acknowledgements
Thanks, to Odilia Drenth for her supportive criticisms and great kindness in dealing with unreadable texts, and to Franjo Weissing for teaching me the science of theoretical population genetics so well.

 

6. References
1. Lee M.S.Y., Soubrier J., Edgecombe G.D., 2013 Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion, Current Biology 23: 1-7, http://dx.doi.org/10.1016/j.cub.2013.07.055.
2. Jablonski D. 2002 Survival without recovery after mass extinctions, www.pnas.org - pnas.102163299, www.academia.edu/8104069.
3. Darwin C. 1859 On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, London: John Murray.
4. Futuyama D.J. 2005 Evolution. Sinauer Associates, Sunderland USA, p.417.
5. Sniegowski PD, Gerrish PJ, Johnson T, Shaver A. 2000 The evolution of mutation rates: separating causes from consequences. Bioessays. 22(12): 1057-1066.
6. Leigh E. G. Jr. 1973 The evolution of mutation rates. Genetics Suppl. 73: 1-18.
7. Gillespie J. H., 1981 Mutation modification in a random environment. Evolution 35: 468–476.
8. Gillespie J. H., 1981 Evolution of the mutation rate at a heterotic locus. Proc. Natl. Acad. Sci. USA 78: 2452-2454
9. Ishii K., H. Matsuda, Y. Iwasa and A. Sasaki, 1989 Evolutionarily stable mutation rate in a periodically changing environment. Genetics 121: 163–174.
10. Johnson T., 1999 Beneficial mutations, hitchhiking and the evolution of mutation rates in sexual populations. Genetics 151: 1621–1631.
11. King D.G. 2012 Indirect Selection of Implicit Mutation Protocols. Ann N.Y. Acad Sci. 1267: 45-52.

[Ken Fabian]

I'm not sure I have the background to give a capable critique. As an interested layperson I would note that I expect the opportunities for variant forms to survive would be greater in the 'recovery' period, regardless of mutation rates; less competition and less predation initially even if later on those would rise. It's distinguishing the greater variation from unchanged mutation rates in a changed environment with unexploited niches from greater variation from changed mutation rates that would seem to make or break this paper.

 

On a smaller scale this variation of mutation rate ought to be present locally and regionally wherever significant environmental change occurs - ie there ought to be observable examples.

 

I also wonder if it's actually the case that the surviving, initial mix of species can be considered poorly adapted; certainly they were better adapted to survive the crisis period and whilst some might have gotten here by scavenging on resources that won't be replenished others may thrive in the new environment even if it's absence of competition that gives them the opportunity. Those opportunists, successfully spreading in the presence of opportunity, seem most likely to be the progenitors of new species regardless of the potential for later variants to become their greatest competition.