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Was Charles Darwin Wrong About Speciation?
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Citation:,/b> Tree of life reveals clock-like speciation and diversification

Citation: Tree of life reveals clock-like speciation and diversification

speciation Perhaps Charles Darwin was wrong about how species originated? This shouldn’t be so surprising. If you read The Origin of Species you’ll be struck by how much Darwin got wrong, and, how much he got right. As a fully grown adult with some knowledge of evolution re-reading Darwin in the original confirmed for me what a genius he was. The man was writing over 150 years ago in a pre-genetic era. Not only did he not have molecular phylogenetics, but he didn’t even have a proper theory of inheritance! It’s a miracle Charles Darwin got so much right. It’s no sin that he missed the mark even on the big questions.

simonconway05_16 With that I have to admit it’s awkward when people ask me about big picture evolutionary questions (as opposed to, for example, the rate of new mutations in humans), as unfortunately I’m not very well versed in macroevolution. Much of what I know about speciation in particular I know from Jerry Coyne and H. Allen Orr’s mid-2000s book Speciation. It’s true that both are population geneticists by training, so that might give me a biased view, so I’ve also read Stephen Jay Gould’s books (e.g, The Structure of Evolutionary Theory). But with Gould it’s hard to tell when he’s transmitting consensus, and when’s presenting his own heterodox views, unless you engage in very close reading. Simon Conway Morris wrote The Crucible of Creation specifically to rebut what he felt were Gould’s misrepresentation of his research in Wonderful Life (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable).

A new open access paper in MBE, Tree of Life Reveals Clock-Like Speciation and Diversification, concludes that speciation is a clocklike and neutral process. As you can see from the figure above it looks as if ~2 million years is some major peak when it comes to the point at which lineages which are species converge in terms of their last ancestral populations. First, it seems clear that they’re using the biological species concept. Second, their mechanism is totally unoriginal. Rather than positive selection due to exogenous natural pressures (think Darwin’s finches, though he himself gave a lot of thought to sexual selection as the driver of speciation) the authors indicate that neutral mutational differences between diverged populations eventually lead to genetic incompabilities. This was an idea that was part of the neo-Darwinian Synthesis, so we’re talking about modulating weights, not overturning of the established order. This is an active area of research in population genetics today, see Emergent speciation by multiple Dobzhansky-Muller incompatibilities. It’s not crazy on the face of it as a hypothesis.

But it’s a whole different thing to generalize about the tree of life. Quanta Magazine has a collection of responses from researchers in the field, A Surprise for Evolution in Giant Tree of Life: Researchers build the world’s largest evolutionary tree and conclude that species arise because of chance mutations — not natural selection. I think the title is misleading for the general audience, as this isn’t a novel thesis at all, but the piece itself is more evenhanded. As noted within phylogenetics is a highly statistical enterprise. Leibniz’s famous injunction “let us calculate” is a bit more complicated when you have biased data to put into your inference generation machine. Obviously the authors couldn’t sample extinct lineages, as noted by some in the Quanta piece. They try to account for this, but the devil is in the details. Overall a ~2 million year figure invariant across arthropods and vertebrates strikes me as strange, and likely a statistical artifact if I had to put money on it (or perhaps low effective population size lineages exhibit more build up of neutral alleles producing genetic incompabilities, while large Ne groups are more impacted by positive diversifying selection, when it comes to speciation?).

Time will tell. This is not the final answer, and my passing acquaintance with this field suggests that a “first look” often does not hold up because people are missing part of this very big picture. The whole tree of life is a big thing to tackle when it comes to generalization. But, I am optimistic that this generation shall not pass before we have enough sequence across the tips of the tree and computational power to analyze it to come to more robust conclusions.

Citation: S. Blair Hedges, Julie Marin, Michael Suleski, Madeline Paymer, and Sudhir Kumar, Tree of Life Reveals Clock-Like Speciation and Diversification, Mol Biol Evol (2015) 32 (4): 835-845 first published online March 3, 2015 doi:10.1093/molbev/msv037

Addendum: I should note also that natural selection itself is somewhat stochastic over short enough time intervals. Don’t know if that would produce neutrality in speciation over the long term.

 
• Category: Science • Tags: Evolution 
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  1. Jim W says:

    Your post reminds me of a question that’s been in the back of my mind for a while. I hope it’s not too off-topic. Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels. On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren’t for environmental changes. He specifically thought that catastrophic changes (such as meteor strike 65m years ago) were important, in how they unsettled things and set the evolution of various species off on new paths.

    The analogy to search problems is obvious: you can see evolution (genetic algorithms) as a type of search engine, which can settle into a local minima in the energy landscape. Consistent with the biologist’s view, it is only environmental change which prevents the system from getting stuck. The most dramatic case is something like an asteriod strike, but there are also local changes that are important, such as a drier climate that caused our ancestors to move out of the trees.

    So, I’m wondering what you think would happen in evolution (before humans) if the environment were held constant: would it stabilize into a fixed set of species that remain unchanging throughout eternity, consistent with the biologist’s view? Or, would the power of nonzero interactions produce ever-increasing levels of complexity?

    • Replies: @Razib Khan
    i agree with wright. life itself is an environmental pressure, so it's always just a metastable equilibrium even in fixed environmental conditions. there may be an ultimate minima in the search space, but it would probably take too long to find in the history of the universe (foreseeable). in the meantime local stochastic perturbations are going to destabilize. but the searching is not random over the long term. life is getting more complex and changing on a trend line.
    , @marcel proust

    (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable)
     

    Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels.
     
    My favorite SJGould book is Full House: The Spread of Excellence from Plato to Darwin, with some previously published popsci essays lightly rewritten as book chapters, and newly worked up ideas that he had presented differently previously. It changed the way I thought about the world to a much more statistical point of view, focused on 2nd moments (variation) as much first (means, medians, etc.).*

    Anyway, as I recall, the largest section of the book argues that there is no bias toward complexity in evolution. Rather, that since life had to start at the most simple level possible, the maximum level of complexity at anyone time is bound to rise over time. However, now, as always, the modal form of life remains unicelled, and perhaps (I don't recall) not even eukaryotes, just prokaryotes. Because it takes time for complexity to evolve, it appears that life is becoming ever more complex if one is not looking at the whole distribution but only at those life forms that are maximally complex among their contemporaries. But the average, as measured by the mode, has never changed at least since the development of eukaryotes. This struck me then and now as eminently plausible (but I admit that I have not sought out counter-arguments).

    *As for the rest of his books, I think I agree with RK. I have tried on occasion to read several of the actual books as opposed to collected essays, and never made it past a chapter or two.
    , @notanon

    On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren’t for environmental changes.
     
    Seems to me randomness creates a fail-safe. If a species in a range is solely selected by the environment then what happens if the environment changes suddenly? Much better if a mixture of selection and randomness creates a bunch of sub-species in the same range with different neutral DNA so if the environment changes maybe some of that varied selection of neutral DNA is by chance positive DNA in the new environment.

    Spare tyre DNA?
  2. Is there a version of Origin of Species which has footnotes or commentary to point out where he erred, and where the current consensus differs with the original text? Like a secular Tasofot.

    • Replies: @Razib Khan
    if you read it in the kindle you can see comments.
  3. @AshTon
    Is there a version of Origin of Species which has footnotes or commentary to point out where he erred, and where the current consensus differs with the original text? Like a secular Tasofot.

    if you read it in the kindle you can see comments.

  4. @Jim W
    Your post reminds me of a question that's been in the back of my mind for a while. I hope it's not too off-topic. Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels. On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren't for environmental changes. He specifically thought that catastrophic changes (such as meteor strike 65m years ago) were important, in how they unsettled things and set the evolution of various species off on new paths.

    The analogy to search problems is obvious: you can see evolution (genetic algorithms) as a type of search engine, which can settle into a local minima in the energy landscape. Consistent with the biologist's view, it is only environmental change which prevents the system from getting stuck. The most dramatic case is something like an asteriod strike, but there are also local changes that are important, such as a drier climate that caused our ancestors to move out of the trees.

    So, I'm wondering what you think would happen in evolution (before humans) if the environment were held constant: would it stabilize into a fixed set of species that remain unchanging throughout eternity, consistent with the biologist's view? Or, would the power of nonzero interactions produce ever-increasing levels of complexity?

    i agree with wright. life itself is an environmental pressure, so it’s always just a metastable equilibrium even in fixed environmental conditions. there may be an ultimate minima in the search space, but it would probably take too long to find in the history of the universe (foreseeable). in the meantime local stochastic perturbations are going to destabilize. but the searching is not random over the long term. life is getting more complex and changing on a trend line.

    • Replies: @CupOfCanada
    Hrm. How do you feel that meshes with the Rare Earth Hypothesis? Do you think increasing complexity would generally lead to intelligence of a kind or...?
  5. Anonymous • Disclaimer says: • Website

    Shortly after its appearance I posted the following comment on the Hedges paper in PubMed Commons. It draws attention to the late nineteenth century view of Darwin’s research associate that adaptation was decoupled from speciation. This can be interpreted in the modern era as the non-adaptive ticking of the GC% clock that generates GC% differences sufficient to impair meiotic pairing (hybrid sterility):

    ADAPTATION DECOUPLED FROM SPECIATION. This fine new paper presents an impressive synthesis of phylogenetic data aiming to “explore how it bears on evolutionary hypotheses and mechanisms of speciation and diversification.” In keeping with the results of Venditti et al. (2010) that are cited, the major conclusion is that “if adaptation is largely decoupled from speciation, we should not expect it to be a driver of speciation.” Indeed, “Cases where the phenotype has changed little (e.g. cryptic species) … are interpreted here as evidence of uncoupling.” There is reference to geographic isolation as “the major model,” but it is noted that “time constraints should be similar with ecological speciation, and other models exist.”

    One of these “other models” is considered by Venditti et al. (2008 Biologist 55, 140-146), who note:

    “There is a growing appreciation amongst evolutionary biologists that rapid reproductive isolation is more common than previously thought and is often associated with what is known as sympatric speciation, or speciation between populations which share the same geographic range.”

    The idea of a non-geographic decoupling of adaptation from speciation was advanced by Darwin’s research associate George Romanes in 1886. As with Venditti et al. (2010), the present results nicely support Romanes, whose work is the major focus of my speciation text (The Origin of Species, Revisited, McGill-Queen’s University Press, 2001). There is further elaboration both in our biography of the geneticist William Bateson (Treasure Your Exceptions, Springer, New York, 2008) and in my textbook Evolutionary Bioinformatics (Springer, New York, 2011).

  6. 2 million years for all species seems peculiar, given different life expectancies (and metabolic rates) and average number of offspring. I’d think, at least at a minimum, that number of generations would be more likely.

  7. @Jim W
    Your post reminds me of a question that's been in the back of my mind for a while. I hope it's not too off-topic. Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels. On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren't for environmental changes. He specifically thought that catastrophic changes (such as meteor strike 65m years ago) were important, in how they unsettled things and set the evolution of various species off on new paths.

    The analogy to search problems is obvious: you can see evolution (genetic algorithms) as a type of search engine, which can settle into a local minima in the energy landscape. Consistent with the biologist's view, it is only environmental change which prevents the system from getting stuck. The most dramatic case is something like an asteriod strike, but there are also local changes that are important, such as a drier climate that caused our ancestors to move out of the trees.

    So, I'm wondering what you think would happen in evolution (before humans) if the environment were held constant: would it stabilize into a fixed set of species that remain unchanging throughout eternity, consistent with the biologist's view? Or, would the power of nonzero interactions produce ever-increasing levels of complexity?

    (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable)

    Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels.

    My favorite SJGould book is Full House: The Spread of Excellence from Plato to Darwin, with some previously published popsci essays lightly rewritten as book chapters, and newly worked up ideas that he had presented differently previously. It changed the way I thought about the world to a much more statistical point of view, focused on 2nd moments (variation) as much first (means, medians, etc.).*

    Anyway, as I recall, the largest section of the book argues that there is no bias toward complexity in evolution. Rather, that since life had to start at the most simple level possible, the maximum level of complexity at anyone time is bound to rise over time. However, now, as always, the modal form of life remains unicelled, and perhaps (I don’t recall) not even eukaryotes, just prokaryotes. Because it takes time for complexity to evolve, it appears that life is becoming ever more complex if one is not looking at the whole distribution but only at those life forms that are maximally complex among their contemporaries. But the average, as measured by the mode, has never changed at least since the development of eukaryotes. This struck me then and now as eminently plausible (but I admit that I have not sought out counter-arguments).

    *As for the rest of his books, I think I agree with RK. I have tried on occasion to read several of the actual books as opposed to collected essays, and never made it past a chapter or two.

    • Replies: @Jim W
    My impression is that the random-walk diffusion view of complexity that Gould espoused is more mainstream than what Wright argued for in Nonzero. Shouldn't there be a way to test between the two?

    I think the Cambrian explosion argues for something more nonlinear. With the incredible development of eukaryotic cells, it suddenly became possible to evolve higher levels of complexity as seen in multicellular life forms. It's sort of analogous to a child trying to build structures from rocks versus legos.

    The fact that the mode of the distribution remains centered on less complex forms is consistent with both views, as those environmental niches still need to be filled.
  8. @Jim W
    Your post reminds me of a question that's been in the back of my mind for a while. I hope it's not too off-topic. Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels. On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren't for environmental changes. He specifically thought that catastrophic changes (such as meteor strike 65m years ago) were important, in how they unsettled things and set the evolution of various species off on new paths.

    The analogy to search problems is obvious: you can see evolution (genetic algorithms) as a type of search engine, which can settle into a local minima in the energy landscape. Consistent with the biologist's view, it is only environmental change which prevents the system from getting stuck. The most dramatic case is something like an asteriod strike, but there are also local changes that are important, such as a drier climate that caused our ancestors to move out of the trees.

    So, I'm wondering what you think would happen in evolution (before humans) if the environment were held constant: would it stabilize into a fixed set of species that remain unchanging throughout eternity, consistent with the biologist's view? Or, would the power of nonzero interactions produce ever-increasing levels of complexity?

    On the other hand, an eminent biologist (I forget his name) gave a lecture at my institution a few years ago, and he argued that evolution would settle into a stable state if it weren’t for environmental changes.

    Seems to me randomness creates a fail-safe. If a species in a range is solely selected by the environment then what happens if the environment changes suddenly? Much better if a mixture of selection and randomness creates a bunch of sub-species in the same range with different neutral DNA so if the environment changes maybe some of that varied selection of neutral DNA is by chance positive DNA in the new environment.

    Spare tyre DNA?

  9. Jim W says:
    @marcel proust

    (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable)
     

    Robert Wright argued in his book Nonzero that there is a bias in evolution toward the development of greater and greater complexity, basically due to the benefits of cooperation at multiple levels.
     
    My favorite SJGould book is Full House: The Spread of Excellence from Plato to Darwin, with some previously published popsci essays lightly rewritten as book chapters, and newly worked up ideas that he had presented differently previously. It changed the way I thought about the world to a much more statistical point of view, focused on 2nd moments (variation) as much first (means, medians, etc.).*

    Anyway, as I recall, the largest section of the book argues that there is no bias toward complexity in evolution. Rather, that since life had to start at the most simple level possible, the maximum level of complexity at anyone time is bound to rise over time. However, now, as always, the modal form of life remains unicelled, and perhaps (I don't recall) not even eukaryotes, just prokaryotes. Because it takes time for complexity to evolve, it appears that life is becoming ever more complex if one is not looking at the whole distribution but only at those life forms that are maximally complex among their contemporaries. But the average, as measured by the mode, has never changed at least since the development of eukaryotes. This struck me then and now as eminently plausible (but I admit that I have not sought out counter-arguments).

    *As for the rest of his books, I think I agree with RK. I have tried on occasion to read several of the actual books as opposed to collected essays, and never made it past a chapter or two.

    My impression is that the random-walk diffusion view of complexity that Gould espoused is more mainstream than what Wright argued for in Nonzero. Shouldn’t there be a way to test between the two?

    I think the Cambrian explosion argues for something more nonlinear. With the incredible development of eukaryotic cells, it suddenly became possible to evolve higher levels of complexity as seen in multicellular life forms. It’s sort of analogous to a child trying to build structures from rocks versus legos.

    The fact that the mode of the distribution remains centered on less complex forms is consistent with both views, as those environmental niches still need to be filled.

    • Replies: @Razib Khan
    gould's views that were mainstrehttp://www.pkarchive.org/theory/evolute.htmlam were not notable. his notable views were not mainstream.

    http://www.pkarchive.org/theory/evolute.html
  10. Clearly it is not true that species arise only or mostly by genetic incompatibilities. There are many genera of plants with hundreds of species with overlapping habitats that can interbreed freely using artificial pollination. The speciation process must have been a result of pollinator switching or timing of flowering.

  11. @myself

    A possible human example of this is r/K in humans – assuming there’s a bunch of traits involved in defining those behaviors and in reality individuals are a composite mix of this set of r behaviors and K behaviors and a society is a product of the balance of those r/K percentages among all the individuals that make up the society i.e.where the individuals within a society are mostly K the society will be mostly K and vice versa along a sliding scale.

    For example in an industrial working class society K behaviors gradually get selected for so eventually the “provider” male species whose reproductive psychology revolves around providing a nest become the dominant majority. It’s not total though as there’s always a percentage of r behaviors under the surface. When mass unemployment hits it’s effectively an extinction event – psychologically speaking – for the provider males which doesn’t effect the slackest males at all i.e. the men with the highest percentage of r behaviors.

    There’s no need to suddenly evolve slack behaviors to suit the sudden change in environment because they already existe. What happens instead is the previously dominant behavioral “species” rapidly dies out (as provider males only reproduce properly when they can provide a nest) and the previously minority slack males become the majority.

    Maybe it’s the same with birds – momentum based sexual selection splitting species into multiple versions filling the same niche so if the environment changes one set of behaviors still works.

  12. @Jim W
    My impression is that the random-walk diffusion view of complexity that Gould espoused is more mainstream than what Wright argued for in Nonzero. Shouldn't there be a way to test between the two?

    I think the Cambrian explosion argues for something more nonlinear. With the incredible development of eukaryotic cells, it suddenly became possible to evolve higher levels of complexity as seen in multicellular life forms. It's sort of analogous to a child trying to build structures from rocks versus legos.

    The fact that the mode of the distribution remains centered on less complex forms is consistent with both views, as those environmental niches still need to be filled.

    gould’s views that were mainstrehttp://www.pkarchive.org/theory/evolute.htmlam were not notable. his notable views were not mainstream.

    http://www.pkarchive.org/theory/evolute.html

    • Replies: @Jim W
    Thank you for that. It's a hat trick:
    1. Krugman is one of my intellectual heroes
    2. I can't stand Gould
    3. I love chiastic put-downs
  13. @Razib Khan
    gould's views that were mainstrehttp://www.pkarchive.org/theory/evolute.htmlam were not notable. his notable views were not mainstream.

    http://www.pkarchive.org/theory/evolute.html

    Thank you for that. It’s a hat trick:
    1. Krugman is one of my intellectual heroes
    2. I can’t stand Gould
    3. I love chiastic put-downs

  14. @Razib Khan
    i agree with wright. life itself is an environmental pressure, so it's always just a metastable equilibrium even in fixed environmental conditions. there may be an ultimate minima in the search space, but it would probably take too long to find in the history of the universe (foreseeable). in the meantime local stochastic perturbations are going to destabilize. but the searching is not random over the long term. life is getting more complex and changing on a trend line.

    Hrm. How do you feel that meshes with the Rare Earth Hypothesis? Do you think increasing complexity would generally lead to intelligence of a kind or…?

  15. I am grateful for the introduction to the question. As an amateur of no great learning in biology I am moved to try my own simple analysis.

    It seems that speciation has two modes of genetic causation. One is mutations to genes sufficient to make it impossible for a zygote to develop (I leave aside the question of asexual reproduction for someone more knowledgeable) if the new allele was not paired. The other is mutations which preclude fertilisation or embryo formation by the existing method.

    Would it not be a very rare chance event for such mutations also to be ones that caused the bearers of it to multiply faster because of superior adaptation to the environment?

    If that is right it would seem to follow that speciation and natural selection causes would overlap but only very slightly.

  16. Regarding the complexity issue: What am I getting wrong in thinking that the “(George) Williams revolution” settled that question?

  17. AG says:

    Chance mutations provide the options. Natural selection provides result. Just think about immune epitopes. Random recombination created diversity of options for later use.

    As many scholars had pointed out that larger breeding population provide more chance mutations that correlate with more chance beneficial mutations that gives evolutionary edge over long period time.

    On the opposite side, smaller breeding population without exchange with outside have exact opposite effect. Higher chance of mutational meltdown and extinction.

    Promiscuity is biological beneficial to the population. Some small ethnic groups are famous for promiscuous behavior which serve as bridges with other populations, become part of larger effective breeding population.

  18. According to Darwin the flying squirrel tried and failed 1 billion times before one got a magical “random mutation” that gave some lift.

    • Replies: @CupOfCanada
    No. He didn't.

    Rather, he suggested that squirrels with slightly more aerodynamically optimized body shapes had a slight advantage of others.

    @Razib - I suppose this work supports your general view on the difference between modern humans and other

    Does anyone know if there's a reasonable estimate of what % Neanderthal us Out-Of-Africa folks would be had it not been for hybrid incompatibility?
  19. […] genetic events, not natural selection, play the main role in speciation.” – see also Was Charles Darwin Wrong About Speciation? from […]

  20. @Anonymous
    According to Darwin the flying squirrel tried and failed 1 billion times before one got a magical "random mutation" that gave some lift.

    No. He didn’t.

    Rather, he suggested that squirrels with slightly more aerodynamically optimized body shapes had a slight advantage of others.

    @Razib – I suppose this work supports your general view on the difference between modern humans and other

    Does anyone know if there’s a reasonable estimate of what % Neanderthal us Out-Of-Africa folks would be had it not been for hybrid incompatibility?

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