The Unz Review: An Alternative Media Selection
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
 TeasersGene Expression Blog
Revenge of the Drift
🔊 Listen RSS
Email This Page to Someone

 Remember My Information



=>

Bookmark Toggle AllToCAdd to LibraryRemove from Library • BShow CommentNext New CommentNext New ReplyRead More
ReplyAgree/Disagree/Etc. More... This Commenter This Thread Hide Thread Display All Comments
AgreeDisagreeLOLTroll
These buttons register your public Agreement, Disagreement, Troll, or LOL with the selected comment. They are ONLY available to recent, frequent commenters who have saved their Name+Email using the 'Remember My Information' checkbox, and may also ONLY be used once per hour.
Ignore Commenter Follow Commenter
Search Text Case Sensitive  Exact Words  Include Comments
List of Bookmarks

coop

As longtime readers know the role of selection and drift in shaping evolutionary processes have long been at issue within the field. Even as early as Charles Darwin’s time there were some, including his famous bulldog Thomas H. Huxely, who were skeptical that natural selection was a primary engine of evolutionary change (Darwin had convince him about the reality of common descent with modification though). The the decades around 1900 saw what Peter J. Bowler has described as the “eclipse of Darwinism.” All intellectuals understood and accepted evolution, but many were skeptical of the framework and arguments of Darwin. This eclipse receded with the integration of genetics into evolutionary theory, which gave rise to population genetics, and birthed the Neo-Darwinian Synthesis by ~1950.

51tQuYMf7gL._SY344_BO1,204,203,200_ One might argue that this marked the high-tide of adaptationism and acceptance for the role of selection in shaping all the picayune details of biological phenomena. But even then there were those who were more cautious (there are arguments over whether Sewall Wright, one of the fathers of population genetics, did or did not argue for a strong role for stochasticity in his metaphor for evolutionary process, the shifting balance across the adaptive landscape).

In the 1960s the dialogue between empirical results which reported high degrees of realized polymorphism in the field of molecular evolution and the formal models promoted by thinkers such as Motoo Kimura which eventually came under the heading “neutral theory” induced a revolution in our thinking about evolution. Though many might argue for the primacy of selection constraining and shaping morphological variation (or phenotypic traits on a coarser scale more generally), a null hypothesis on the molecular scale was that most variation was the outcome of neutral process. That is, even if most new mutations were deleterious (this may not even be the case in most of the genome of some organisms), the ones which attained high frequency to generate polymorphism did so usually by chance, not because they were favored.

This debate was surprisingly vociferous for several decades. When I first encountered it in the mid-1990s it had cooled off, but there did not seem to be a final resolution (though my impression is that among evolutionary geneticists a form of neutralism seemed to be widely accepted as a default model in any sort of hypothesis testing).

41qS+5MyBmL._SX331_BO1,204,203,200_ In general I am not a believer that genomics has “changed everything” when it comes to evolutionary biology. Rather, evolutionary genomics literally stands on the shoulders of giants (well, mostly dead white men). But I do think genomics offers up the possibility to obtain greater empirical clarity on the relative role of neutral stochastic forces and selection in shaping variation on the molecular level. A full genome sequence (or enough to gain an appreciable sense of patterns in the genome) is invaluable information. It is in relation to the patterns of DNA arguably all the information (at some point in the future long reads will capture structural variants and epigenomics will also advance).

Last spring I wrote about a fascinating new paper, Natural Selection Constrains Neutral Diversity across A Wide Range of Species, in the post Selectionism Strikes Back! The title says it all. Using a wide range of genomes the authors argue that two forms of natural selection, the background selection which constrains the emergence of deleterious alleles at high frequency, and selection of positive alleles which allow for linked regions of the genome to sweep at high frequency and eliminate variation (and so generate haplotype blocks), can help resolve what has been termed “Lewontin’s paradox”. The paradox is simple: neutral theory predicts that population size will dictate the amount of variation one sees within a species. Large populations have many mutations traversing the frequency range from ~0 to 1, while small populations will have far less diversity because of the power of drift in fixing mutants rather quickly. The manner in which some have resolved this paradox is that large populations are subject to powerful selection dynamics which constrain the neutral variation; in particular, positive sweeps (producing “genetic draft”) and negative constraints homogenize large regions of the genome. Since the above paper is open access I recommend you read it. They found that selection did seem to impact species with different population sizes in the direction in which the selectionist resolution would imply (those species which have large population sizes should have more polymorphism, but selection constraints variation much more).

But Graham Coop has posted a note on bioRxiv, Does linked selection explain the narrow range of genetic diversity across species?, which suggests that though the qualitative results match the selectionist narrative, the magnitude of the effect is simply not what one might expect if selection was dominant over stochastic forces driven by variation in demographics. That is, just because Drosophila has a huge census size today does not mean that it had a huge census size over the course of its history, and genetic diversity is strongly sensitive to the smallest population size over a temporal window (this is when most of the diversity can get expunged by drift forces). The figure above shows Coop’s reanalysis of the results in the above paper using their model. He suggests that quantitatively the magnitude of the effect of linked selection seems far more modest. From the preprint:

To understand the contributions of the two explanations to levels of diversity, it is helpful to distinguish between the average observed level of neutral polymorphism in the genome (π) and that expected in the absence of linked selection (π0 ). Our idealized neutral level of variation in which π0 ≈ 4Ne μ, reflects the effective size of the population (Ne ) in the absence of linked selection ( here Ne is not estimated simply from putatively neutral diversity levels genome-wide). To illustrate this point, take the extreme scenario in which linked selection explains nearly all of the deficit in variation in species with large census sizes, with fluctuations in population size playing a minor role. In these species, π should be orders of magnitude smaller than π0 , and Ne should be roughly the same order of magnitude as the census size. In contrast, if fluctuations in population size explain most of the deficit, then π should be close to π0 for all species, while Ne would be many orders of magnitude lower than census population sizes for species with large population sizes.

Coop does observe that patterns of variation within the genome may be strongly shaped by linked selection, and, that a thorough understanding of linked selection is essential to generating a proper model which captures natural dynamics. But at the end of the day he seems to reject the thesis that it’s “all selection, all the time.” His argument is broadly persuasive to me, but I think the authors above have work that will follow up the original paper.

Both the original paper and the preprint that responds to it should be read closely. I do not believe this will be a decades long debate. Yes, there are many badly assembled draft genomes out there, but in the next ten years we’ll have the data to actually test robustly these competing theses as to the power of different evolutionary forces in shaping variation. At least on the scale of the sequence….

 
• Category: Science • Tags: Neutralism 
Hide 10 CommentsLeave a Comment
10 Comments to "Revenge of the Drift"
Commenters to Ignore...to FollowEndorsed Only
Trim Comments?
  1. They found that selection did seem to impact species with different population sizes in the direction in which the selectionist resolution would imply (those species which have large population sizes should have more polymorphism, but selection constraints variation much more).

    Doesn’t selectionism imply that species formation should be easily observable in experiments with Drosophila?

    • Replies: @Razib Khan
    Doesn’t selectionism imply that species formation should be easily observable in experiments with Drosophila?


    that's not what selectionism is about. also, most people don't talk as if they are selectionists or neutralists anymore that i know of in academia. you are stuck in the 1980s....
  2. I may not understand the argument properly but seems to me

    1) randomness creates a fail-safe – if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)

    however might there be an optimum population size for selection and might that square the circle?

    So say

    selection > randomness when pop size is x
    randomness > selection when pop size is 10x

    • Replies: @Wizard of Oz
    Vice versa?
    , @Razib Khan
    1) randomness creates a fail-safe – if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)


    you're getting at arguments for sex. also, you are alluding to some of the debates around fitness landscapes.
  3. @notanon
    I may not understand the argument properly but seems to me

    1) randomness creates a fail-safe - if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)

    however might there be an optimum population size for selection and might that square the circle?

    So say

    selection > randomness when pop size is x
    randomness > selection when pop size is 10x

    Vice versa?

    • Replies: @notanon
    quite possible - i can't say i've actually thought about it really

    just struck by how if mutation is proportional to effective population size then that creates the logical possibility of effective population size being too small or too big for the rest of the mechanism - especially if the mechanism developed for much smaller populations.

  4. @Wizard of Oz
    Vice versa?

    quite possible – i can’t say i’ve actually thought about it really

    just struck by how if mutation is proportional to effective population size then that creates the logical possibility of effective population size being too small or too big for the rest of the mechanism – especially if the mechanism developed for much smaller populations.

    • Replies: @Wizard of Oz
    Indeed I see the logical possibility but can't comment with the necessary expertise on the facts and I don't understand Razib's reply which is too cryptic for me.
    , @Wizard of Oz
    See #8. I'm doing this with one thumb typing so won't repeat.
  5. @Sean

    They found that selection did seem to impact species with different population sizes in the direction in which the selectionist resolution would imply (those species which have large population sizes should have more polymorphism, but selection constraints variation much more).
     
    Doesn't selectionism imply that species formation should be easily observable in experiments with Drosophila?

    Doesn’t selectionism imply that species formation should be easily observable in experiments with Drosophila?

    that’s not what selectionism is about. also, most people don’t talk as if they are selectionists or neutralists anymore that i know of in academia. you are stuck in the 1980s….

  6. @notanon
    I may not understand the argument properly but seems to me

    1) randomness creates a fail-safe - if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)

    however might there be an optimum population size for selection and might that square the circle?

    So say

    selection > randomness when pop size is x
    randomness > selection when pop size is 10x

    1) randomness creates a fail-safe – if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)

    you’re getting at arguments for sex. also, you are alluding to some of the debates around fitness landscapes.

    • Replies: @Wizard of Oz
    Too cryptic for me Razib. I wouldn't ask for a "For Dummies" version but it would help those of us who, having taken the trouble to understand something technical which is way outside our own expertise, forget the necessary detail after a few weeks were to be provided with a quick access button to a comprehensive Glossary of words and concepts.

    When I answered notanon with "vice versa?" I was of course questioning what I took him to be saying with his formulae
    Selection > Randomness when pop size X
    Randomness > Selection when pop size 10X

    I understood him to be saying that the effect of Randomness (BTW is that identical with Genetic Drift in this context?) would be greater in the larger population - in the sense presumably of being the most likely cause of any largescale genotype changes - but that you had been saying the opposite. Have I misunderstood one or both of you?

  7. @notanon
    quite possible - i can't say i've actually thought about it really

    just struck by how if mutation is proportional to effective population size then that creates the logical possibility of effective population size being too small or too big for the rest of the mechanism - especially if the mechanism developed for much smaller populations.

    Indeed I see the logical possibility but can’t comment with the necessary expertise on the facts and I don’t understand Razib’s reply which is too cryptic for me.

  8. @Razib Khan
    1) randomness creates a fail-safe – if selection is too efficient it might lead to dead ends
    2) selection towards an optimum for a particular environment makes too much sense not to be at least partially true (imo)


    you're getting at arguments for sex. also, you are alluding to some of the debates around fitness landscapes.

    Too cryptic for me Razib. I wouldn’t ask for a “For Dummies” version but it would help those of us who, having taken the trouble to understand something technical which is way outside our own expertise, forget the necessary detail after a few weeks were to be provided with a quick access button to a comprehensive Glossary of words and concepts.

    When I answered notanon with “vice versa?” I was of course questioning what I took him to be saying with his formulae
    Selection > Randomness when pop size X
    Randomness > Selection when pop size 10X

    I understood him to be saying that the effect of Randomness (BTW is that identical with Genetic Drift in this context?) would be greater in the larger population – in the sense presumably of being the most likely cause of any largescale genotype changes – but that you had been saying the opposite. Have I misunderstood one or both of you?

  9. @notanon
    quite possible - i can't say i've actually thought about it really

    just struck by how if mutation is proportional to effective population size then that creates the logical possibility of effective population size being too small or too big for the rest of the mechanism - especially if the mechanism developed for much smaller populations.

    See #8. I’m doing this with one thumb typing so won’t repeat.

    • Replies: @notanon
    I think I just restated the post at a tabloid level as a way of digesting it.

    I understood him to be saying that the effect of Randomness would be greater in the larger population – but that you had been saying the opposite.
     
    I don't think there's a disagreement, one paper said x then another said y so they basically cancelled out in the middle which is where it was previously.

    Kinda like selection itself is under balanced selection - pop size gets too big and evolution says come back to me when half of you have died from a random brain pox.

    The other thing i was thinking is this might imply species do a lot of their selecting when they are / were at an optimal pop size (whatever that might be).

    These are just random thoughts though - not arguments.

  10. @Wizard of Oz
    See #8. I'm doing this with one thumb typing so won't repeat.

    I think I just restated the post at a tabloid level as a way of digesting it.

    I understood him to be saying that the effect of Randomness would be greater in the larger population – but that you had been saying the opposite.

    I don’t think there’s a disagreement, one paper said x then another said y so they basically cancelled out in the middle which is where it was previously.

    Kinda like selection itself is under balanced selection – pop size gets too big and evolution says come back to me when half of you have died from a random brain pox.

    The other thing i was thinking is this might imply species do a lot of their selecting when they are / were at an optimal pop size (whatever that might be).

    These are just random thoughts though – not arguments.

Comments are closed.

Subscribe to All Razib Khan Comments via RSS