Thursday, July 31, 2008

Species Diversity

 
Some of you might recall my series of postings last year on the top Science questions. One of them was What Causes Species Diversity?. This is an important unanswered question in evolutionary biology even if it's conflated with speciation. We don't really have a good handle on what causes speciation.

That doesn't mean that we are completely ignorant. There are several candidates that, singly or in combination, account for much of what we understand about speciation and diversity. I'd like to quote Richard Dawkins from Unweaving the Rainbow since, as an admitted adaptationist, his view carries much more weight than that of a pluralist. (The reason will become apparent.) Here's how Dawkins describes the problem ...

The standard neo-Darwinian view of the evolution of diversity is that a species splits into two when two populations become sufficiently unalike that they can no longer interbreed. Often the populations begin diverging when they chance to be geographically separated. The separation means that they no longer mix their genes sexually and this permits them to evolve in different directions. The divergent evolution might be driven by natural selection (which is likely to push in different direction because of different conditions in the two geographical areas). Or it might consist of random evolutionary drift (since the two populations are not genetically held together by sexual mixing, there is nothing to stop them drifting apart). In either case, when they have evolved sufficiently far apart that they no longer interbreed even if they were geographically united again, they are defined as belonging to separate species.
Either, or both, of the two main mechanisms of evolution—natural selection and random genetic drift—can lead to speciation and diversity.

One could also argue that diversity depends ultimately on mutation. In this case, the main role of natural selection and random genetic drift is to reduce diversity by eliminating unfit and neutral alleles.

This has always been similar to my understanding of speciation and diversity. I was surprised, therefore to learn that one of my colleagues at the University of Toronto, Spencer Barrett, doesn't think random genetic drift plays a role in speciation [see Darwinism at the ROM]. Barrett is one of the featured presenters in a video at the Darwin exhibit at the Royal Ontario Museum.

In a display on the evolution/creation controversy, I copied down the following statement ...
Darwin's Theory of Evolution by Natural Selection is the only scientific explanation for the spectacular diversity of life on Earth.
So, here's the question of the day. Do you agree with that statement? Do you agree that natural selection is the only scientific explanation of diversity? Spencer Barrett seems to agree. Richard Dawkins would not agree. What do you think?1


1. If you disagree with the statement then please try and explain why it is featured so prominently in the Darwin exhibit. Is this an example of framing, or ignorance?

14 comments :

  1. Parsimony?

    I believe that mutation + drift + selection explains the diversity of life, and that "selection" is more than Darwin's theory. That said, "Darwin's theory" is useful when trying to talk to people who have come to believe that there is an "alternative" theory of evolution (ID, "scientific" creationism, etc.)

    That said, I think you can make a case for selection as being the force that generates diversity, since one could argue that mutation and drift cannot generate diversity in the absence of selection, while selection can (kinda) do so without the other two.

    Not a great argument, not an argument I'd make...but not totally indefensible.

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  2. Hmmm, it is impossible to be precise when speaking to the public in general.

    I'd say that "naturalistic evolution" is the only scientific theory that explains the diversity of life on earth".

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  3. I think you're being overly exact for a lay museum. And missing the gestalt of the statement by a wide margin.

    I believe the author is saying that Evolution, as opposed to divine origin, or spontaneous generation, or anything else of the sort, is responsible for diversity. To use that one statement as an argument for `selection alone` is getting rather pedantic.

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  4. "Darwin's Theory of Evolution by Natural Selection is the only scientific explanation for the spectacular diversity of life on Earth."

    Not technically correct, but not really wrong because non-Darwinian scientific explanations like the neutral theory and new mutation theory does at least allow for negative and purifying selection, so it is impossible to completely tease them apart.

    Having said that, I believe that us molecular-level biologists will tend to focus more on mutationism rather than natural selection, since we can never tell exactly what sort of environmental pressures resulted in the genotype today.

    The only concrete thing we have is sequence information. Whether it was selection pressure or random drift, phenotypic diversity occurred due to specific base changes.

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  5. This nearly falls into the category of "This isn't right. It isn't even wrong." Avoiding speciation is like staying in touch with an old friend. After forty years it's nearly miraculous that you can do it at all, and the odds are that you won't recognize them at the reunion.
    rt.

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  6. Something I'm not sure of: In the following sentence, are you saying that random genetic drift contributes independently to reducing diversity, or only in concert with natural selection?

    In this case, the main role of natural selection and random genetic drift is to reduce diversity by eliminating unfit and neutral alleles.

    Thanks in advance for the answer/clarification.

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  7. Masatoshi Nei argues against the importance of natural selection as a mechanism:

    Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

    http://www.pnas.org/content/104/30/12235.abstract?etoc

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  8. Damn, that's one very stripped down statement.

    Yes, NS can explain a lot of the observed species diversity, but there's also the factors involved with speciation, like drift and colonisation/gene-pool isolation events that shouldn't be left out. At least in the case of sexually reproducing organisms.

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  9. ollie says,

    Hmmm, it is impossible to be precise when speaking to the public in general.

    I'd say that "naturalistic evolution" is the only scientific theory that explains the diversity of life on earth".


    We really can't use the ignorance of the general public as an excuse to give them incorrect information about evolution. That's self-defeating.

    I agree with your alternative. There's nothing wrong with saying that "modern evolutionary theory, which includes Darwin's Theory of Natural Selection, is sufficient to explain species diversity."

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  10. Larry: “… random genetic drift—can lead to speciation and diversity.”

    I’ll focus just on the “diversity” part (since, that seems to be the topic of the bolded statement that we are asked to comment on, not speciation).

    Drift is unlikely to be a major factor in diversity, if only because its effects will be dwarfed by NS.

    Evolution that is restricted to the drift of neutral changes (i.e., mostly phenotypically silent changes, and, less commonly, changes that produce "fitness-equivalent" changes (as defined by reproductive success)) won't take you very far. It can build variation, and with that, coupled with changing circumstances (competition, changes in prey and predators, climate, environment, etc), NS will act to move that population in some direction.

    In the real world, populations are always under intense selection pressure, and as soon as a beneficial mutation arises, or the environment changes to now favor a preexisting variation, that’s when NS will drive that particular population off in some new area (and typically dragging a lot of neutral mutations with it).

    Consider a collection of bird species that evolved from a single founder species on a remote island group that each eke out a living by exploiting one of many ecological niches. To think that they got that way even primarily by drift is naïve. Particular secondary features (those not characteristic of how they exploit that niche) may be due to chance, locking in the variation in those individuals that happened to get the beneficial mutation, but it was nonetheless NS that got them there.

    I often get the sense that many people don’t truly understand genetic drift. It seems that some view it as a sort of magical process where a given neutral mutation, once it arises, has some sort of high probability of getting fixed merely by the operation of the laws of random chance. This is false. It is a very very rare neutral mutation that gets fixed by drift alone. Even in very small populations, the vast majority of new neutral mutations will get *eliminated* by drift, not fixed. (And even the beneficial ones mostly still have a tough row to hoe.)

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  11. Once again, there is no doubt that drift is responsible for the diversity of genotypes. I cannot conceive of how it would be otherwise.

    But the genotypes produced by drift are, themselves, selected for. Imagine a world in which only a single variant of a given gene was permissible for life. In this world, mutation would still occur, and these mutations could still be distributed randomly to offspring, thus producing distinct, diverse genotypes in the population.

    Unfortunately, the selection pressure in this hypothetical world only allows the survival of individuals who have a specific genotype. Thus, those mutations that became prevalent strictly by chance (i.e. drift) are still subject to selection.

    Thus, at the end of the day, selection still rules because, even in this world, the number of phenotypes that are compatible with life is much smaller than the number of possible genotypes that can be produced by drift.

    So I think it is fair to say that while drift can contribute to diversity, particularly to diversity of genotype, diversity of phenotype (and ultimately of speciation itself) is primarily the product of selection.

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  12. Mike, you are describing ordinary natural selection, not genetic drift.

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  13. divalent says,

    Drift is unlikely to be a major factor in diversity, if only because its effects will be dwarfed by NS.

    Hmmm ... let's see if you can defend that claim.

    Evolution that is restricted to the drift of neutral changes (i.e., mostly phenotypically silent changes, and, less commonly, changes that produce "fitness-equivalent" changes (as defined by reproductive success)) won't take you very far.

    Nobody says that nearly neutral changes are supposed to "take" you anywhere. They just are. Much of the diversity we see in populations is due to non-adaptive differences.

    It can build variation, and with that, coupled with changing circumstances (competition, changes in prey and predators, climate, environment, etc), NS will act to move that population in some direction.

    It's true that in some rare cases neutral alleles can become beneficial or detrimental if the environment changes. However, in most cases, the alleles that have become fixed by random genetic drift will not have been influenced by natural selection while they were becoming fixed.

    Furthermore, most of genetic diversity (e.g., protein variants, DNA fingerprints) has nothing to do with selection and never will.

    In the real world, populations are always under intense selection pressure, and as soon as a beneficial mutation arises, or the environment changes to now favor a preexisting variation, that’s when NS will drive that particular population off in some new area (and typically dragging a lot of neutral mutations with it).

    There's no evidence that most populations are under "intense selection pressure." If that were the case then humans would be a lot more fit than they are.

    In addition, you promoted a blatantly false concept when you implied that as soon as a beneficial mutation arises it will sweep to fixation. The probability of fixation is directly dependent on the fitness coefficient. If an allele confers a 5% fitness advantage (a pretty high example) then 90% of the time it will be eliminated by drift before it ever becomes fixed.

    Consider a collection of bird species that evolved from a single founder species on a remote island group that each eke out a living by exploiting one of many ecological niches. To think that they got that way even primarily by drift is naïve.

    If you only focus on the adaptations, then obviously the differences are due to natural selection. That's what you are doing and it's a very naive view of evolution. You are ignoring all the other differences that have nothing to do with exploiting an ecological niche. Those differences are due to random genetic drift.

    Take the Galapagos finches, for example. They differ in hundreds of ways from the mainland finches and most of those differences are very likely due to founder effect and not natural selection. Similarly, the finches on different islands can be distinguished at the molecular level using many different assays. None of them are identified with adaptations.

    Particular secondary features (those not characteristic of how they exploit that niche) may be due to chance, locking in the variation in those individuals that happened to get the beneficial mutation, but it was nonetheless NS that got them there.

    You seem to understand the basic concept; namely, that non-adaptive differences exist. However, I do not understand why you claim that natural selection got them there. Surely you are not claiming that hitchhiking is responsible for fixing all neutral changes? That makes no sense.

    The regions involved in selective sweeps represent very small parts of a chromosome. In the human genome a centimorgan (1% recombination) only covers about 10 genes. After a hundred generations or so, the average beneficial mutations will be weakly linked to almost all of the variants in the near vicinity. When it becomes fixed, only the most tightly linked variants are carried along.

    I often get the sense that many people don’t truly understand genetic drift.

    I often get the same impression.

    It seems that some view it as a sort of magical process where a given neutral mutation, once it arises, has some sort of high probability of getting fixed merely by the operation of the laws of random chance. This is false. It is a very very rare neutral mutation that gets fixed by drift alone.

    That is correct. However, there are millions of nearly neutral mutations produced every generation and the rate of fixation is equal to the mutation rate. Thus, at every generation there are still many variants that become fixed in spite of the fact that the probability of fixing one particular mutations is slim [Random Genetic Drift and Population Size].

    The rate of fixation by natural selection is higher for any given allele that is beneficial but the number of beneficial alleles that arise in a population is only a small percentage of the total number of mutations.

    That's why most evolution is due to random genetic drift and not natural selection. It's why when you compare the nucleotide sequences of genes from different species you discover that almost all the differences are neutral.

    Most of the variation within a population is due to nearly neutral alleles that are in the process of being fixed or eliminated.

    Even in very small populations, the vast majority of new neutral mutations will get *eliminated* by drift, not fixed. (And even the beneficial ones mostly still have a tough row to hoe.)

    Yes. Most of the new neutral mutations will be lost before they become fixed. For any one new mutation the probability is only 1/2N (where N is the population size). In the human population there are about 10^11 new mutations every generation. Most of these are neutral. About 120 alleles become fixed every generation due to random genetic drift [Mutation Rates].

    How many alleles per generation become fixed by natural selection? More than 120?

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  14. Notwithstanding whether drift results in evolution (which it clearly does), one cannot overlook the tautology that alleles that are compatible with life (and, more specifically, with reproductive survival) are compatible with life; they are selected for.

    Mutations may arise, giving rise to new alleles, but whether those alleles can be passed on at all is still a function of selection.

    So even if drift is at play (which is surely is in small populations, and even in larger ones), you still have to conclude that only alleles that are compatible with life can exist; those that are incompatible with reproductive success (i.e. that produce individuals that cannot reproduce) will, by definition, be removed from the population.

    Thus, one could say that natural selection provides the raw material from which speciation can occur. Speciation itself can occur through either selection or drift, but in a world where not all alleles are allowable, only those which selection has deemed "valid" can contribute.

    So one cannot be completely divested from selection. This, I think, makes selection the most important force of speciation.

    I will, once again, state that I am but a humble cell biologist, but this is what my understanding of this issue tells me.

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