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Science

Evolution Can Occur Much Faster Than Previously Thought (ox.ac.uk) 208

Posted by samzenpus from the getting-better-faster dept.
An anonymous reader writes: An Oxford study on chickens discovered that evolution can make significant changes to a genome in as little as 15 years. "For a long time scientists have believed that the rate of change in the mitochondrial genome was never faster than about 2% per million years. The identification of these mutations shows that the rate of evolution in this pedigree is in fact 15 times faster." Professor Greger Larson, senior author on the study, said, "Our observations reveal that evolution is always moving quickly but we tend not to see it because we typically measure it over longer time periods."
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Evolution Can Occur Much Faster Than Previously Thought More

Evolution Can Occur Much Faster Than Previously Thought

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  • Old (Score:3, Funny)

    by Smiddi ( 1241326 ) on Wednesday October 28, 2015 @06:42PM (#50821225)
    See the Earth is only 4,000yrs old :)

  • The long term changes in DNA didn't always get there in a straight line. So measuring over a shorter time would indicate a faster rate of change. But interesting nonetheless.

    • Re:Not a huge surprise (Score:5, Informative)

      by Michael Woodhams ( 112247 ) on Wednesday October 28, 2015 @10:14PM (#50822395) Journal

      There are two issues here. One is that a single DNA site could mutate several times. If we only see the end points, it looks like only one mutation has occurred (or even zero, if it mutates back to where it started.) This is pretty easy to correct for. E.g. if you compare two sequences and they differ in 10% of sites, it is reasonable to think that 1% of sites have actually mutated twice. (That is a little oversimplified, but not by much.)

      The other issue is that a DNA mutation can spread through part of the population, but then go extinct. If you measure over short time periods, you see these mutations, but over long time periods you don't. There are mathematical reasons to think this does not affect your measured mutation rates if the mutations are neutral (neither helpful nor harmful.) Look up "neutral theory of molecular evolution" for details. However, if they mutations are slightly deleterious, this can be an issue, but there are limits to what you can achieve with this mechanism. (I wrote a paper on that once.)

      • Re: (Score:3, Insightful)

        by Mr Z ( 6791 )

        Let me see if I understand. By measuring over a long period, we're measuring the long term rate of mutation survival after applying selection pressure, and that could be noticeably different than the raw rate of mutation. Is that a correct summary?

        Please go slowly with me. I'm an engineer, not a biologist, and I admit biology is not my strongest subject. I am actually curious, though.

        I remember hearing that there are large sections of DNA in many living things that are effectively "junk DNA," or at least

        • Re:Not a huge surprise (Score:5, Informative)

          by Michael Woodhams ( 112247 ) on Thursday October 29, 2015 @12:13AM (#50822847) Journal

          Let me see if I understand. By measuring over a long period, we're measuring the long term rate of mutation survival after applying selection pressure, and that could be noticeably different than the raw rate of mutation. Is that a correct summary?

          Yes, that is correct. The technical term for 'mutation survival' is 'fixation'. A mutation is 'fixed' once the entire population carries it. It is 'extinct' (unsurprisingly) when it no longer exists in the population. When it exists in part of the population it is 'segregating'.

          There are huge amounts of DNA that have no known purpose and appear to be junk. This is over 98% in humans, but varies a lot between organisms. The junkness of this is under debate. My feeling is that much of it really is junk, but some of it has a function we don't yet understand. (Also, sometimes the function is simply "we need a certain amount of space between these two bits of non-junk". This has a clear purpose, but is 'junk' in that the DNA letters don't matter.)

          This particular experiment is about mitochondrial DNA which has very little 'junk', and that which it does have probably at minimum has something like 'need this amount of space' function.

          Yes, scientists do like using 'junk' DNA for phylogeny (making family trees of organisms) because it is (we think) not subject to selection. On the other hand, you need to find the corresponding junk regions in all your critters and sequence them. It is easier to identify corresponding genes, and often someone else (who cared about the genes themselves) has done the sequencing work for you. Often the choice is doing phylogeny on genes using only a computer, when phylogeny on junk DNA requires samples and a molecular biology lab. Another issue is time scale: the junk DNA mutates faster, so it is good for closely related species (e.g. 'apes') but for distantly related species (e.g. 'vertebrates') you need highly conserved sequences (genes). The junk DNA will have mutated so much that it is all noise, no signal.

          Is there a way to measure the mutation rates for different sites in the overall genome of a given organism, so that: (a) we can determine if some regions are actually junk because mutations to them do not affect organism fitness

          Yes, if we have diverse organisms and a good alignment of their DNA, we can look for 'junk' regions by how much mutation occurs where. (Actually it tends to be the other way around - we see islands of conserved sequence, and deduce therefore that they have a function. This isn't how genes are detected, as there are more sensitive gene-specific ways of doing this.)

          and (b) can distinguish between the rate of mutation and the rate of mutation survival?

          Only I think by comparing mutation rates over pedigree time scales (a few generations) with mutation rates over long time scales - which is what this paper addresses.

          • Re: (Score:2)

            by Mr Z ( 6791 )

            Thank you for the thoughtful and detailed response. I think I have a better understanding. (But, I'll always stay mindful of the Dunning-Krueger effect... ;-) )

            BTW, this statement captures something I was trying to express more clearly than I stated it:

            (Actually it tends to be the other way around - we see islands of conserved sequence, and deduce therefore that they have a function. This isn't how genes are detected, as there are more sensitive gene-specific ways of doing this.)

            What I was trying to get

            • Re:Not a huge surprise (Score:5, Informative)

              by Michael Woodhams ( 112247 ) on Thursday October 29, 2015 @01:51AM (#50823063) Journal

              What I was trying to get at was that if a section of DNA performs some useful function, even if we don't know what it is, it'll tend to be preserved...

              Yes.

              Would such cyclic shifts meaningfully affect the assumptions underlying the multiple mutation rate?

              I'd expect it to be a very minor effect. I'm not aware of anyone getting worried about this. It is a matter of statistics: if you're comparing 100,000 DNA sites, you don't care much if 50 of them behave weirdly in some fashion. If you successfully target 'junk' DNA for the comparison, it is not an issue.

              A related effect is convergent evolution. Say two species of bacteria each colonize high temperature environment. Then certain mutations which are favoured in high temperature will likely occur in both of them. When we compare their DNA, this can make it look like they are more closely related than they really are. This is more of an issue in morphology (Darwin's finches, for example, or cormorants, which look very similar all around the world but turn out often not to be closely related) but it can happen at the DNA level too.

              • Re: (Score:2)

                by Mr Z ( 6791 )

                I'd expect it to be a very minor effect. I'm not aware of anyone getting worried about this.

                Got it. With everything else you've explained, that makes sense.

                A related effect is convergent evolution. Say two species of bacteria each colonize high temperature environment. Then certain mutations which are favoured in high temperature will likely occur in both of them. When we compare their DNA, this can make it look like they are more closely related than they really are.

                Ah, that also makes sense.

                I thank yo

                • Re: (Score:3, Interesting)

                  by Michael Woodhams ( 112247 )

                  I could have spent the effort debating the creationists. This was much more fun.

                  • Great discussion. I don't want to over-complicate, but we would be remiss if we didn't bring up the fact that some "junk" DNA is not junk at all, even if it is "non-coding" (does not encode for a protein product). The original concept of genes is that they have "exons" and "introns", where the exons code for parts of a protein product, and the introns get snipped out during the process of generating RNA from DNA. But some of the so-called junk DNA generates different kinds of RNA rather than standard "messe

                    • In addition, some DNA that doesn't make RNA at all (as far as we know, anyway) is important for regulating other pieces of DNA, which can be pretty far away.

  • Fossils (Score:4, Insightful)

    by The Evil Atheist ( 2484676 ) on Wednesday October 28, 2015 @06:44PM (#50821239)
    Well considering that for the longest time, fossils were our main source of viewing evolution through time, of course it would seem to be slow. Who knows how many speciation events happen and die off before being able to leave a mark in the fossil record.

    • Fossils are not relevant here. The methodology of this study, and of the studies over long time periods it is comparing to, are both from DNA sequencing, not fossils.

      • Try reading again:

        Senior author Professor Greger Larson said: 'Our observations reveal that evolution is always moving quickly but we tend not to see it because we typically measure it over longer time periods. Our study shows that evolution can move much faster in the short term than we had believed from fossil-based estimates. Previously, estimates put the rate of change in a mitochondrial genome at about 2% per million years. At this pace, we should not have been able to spot a single mutation in just 50 years, but in fact we spotted two.'

        The reason why mitchondrial measurements used long time frames was because of the mindset carried over from fossil estimates. The senior author himself says so in this quote from the article.

  • Nobody has thought for decades that evolution is a slow continuous process. Rather that it has periods where nothing much happens, then there's a spurt of changes, then another period of calm.

    Pick the right time interval and duration and you can see either one or the other, as you want. Great way to make data fit your favorite theory :-)

    • I think you're talking about punctuated equilibrium, which is about phenotypic change (change in body shape/size/colour/function etc.) I think punctuated equilibrium is somewhere between controversial and discredited, but it is not my field so I'm not sure.

      In this case, we are talking about evolution at the level of DNA, which is commonly thought to be a continuous process with rate being nearly constant. https://en.wikipedia.org/wiki/... [wikipedia.org]
      The limitations of the molecular clock are what are being argued about

      • Any change that doesn't result in a "change of body shape/size/colour/function etc" isn't going to be selected for or against unless and until the environment changes. Then it may prove to be either beneficial, detrimental, a bit of both, or neutral. Even then, it's a crapshoot. Blue eyes are a recent recessive mutation that carries with it a three-fold increased risk of glaucoma, as well as other diseases. Being left-handed comes with its' own problems, such as increased risk of ptsd and psychosis (weird f

  • This needed proving? (Score:5, Insightful)

    by Dereck1701 ( 1922824 ) on Wednesday October 28, 2015 @07:08PM (#50821353)

    Domesticated animals have changed significantly in the past few few decades let alone the past few thousand years. Modern broilers (meat chickens) can't even self procreate due to the changes but also grow from chicks to food in a couple months. Dairy cattle are another example, Today 9.3 Million dairy cattle produce 59% more milk than 25.6 Million cattle produced in the 40s. This isn't limited to animals, grain producing plants have significantly changed since the 30s, corn specifically has went from around 25 bushels per acre in the 30s to over 140 bushels per acre today. Anyone with even a passing knowledge of farming could have told you this. It should be noted though that while these plants/animals work well for modern farming, most would almost certainly go extinct after a few years without human care due to their extreme specialization (grain production, milk production, meat production, egg production etc).

    • The article is about mitochondrial DNA, which to use a computer analogy, is closer to the operating system than features of software as you describe.

  • The mechanisms for Evolution itself should also be under selective pressure. I would expect that traits, that allow for a quicker adaption to a changed environment, are a huge improvement of fitness. One example seems to be sexual reproduction as this allows for mixing of different sets of traits and allows sexual selection. But there should be other mechanisms as well. Random mutation seem to be quite ineffective, mechanisms that cause more specific mutations with a higher likelihood of increasing the fit

  • Wrong measure (Score:5, Insightful)

    by AK Marc ( 707885 ) on Wednesday October 28, 2015 @07:43PM (#50821553)
    There's a common misconception that fear can cause your hair to turn white. It's wrong, but true. What happens is that your hair us going white. It's 10% white, and nobody notices. 30% white and people can see it clearly, but don't point it out. But when you are at 30% white and have a strong fear event, you can have some hair fall out. The hair that falls out is disproportionately non-white. So it gives the appearance of a sudden whitening of your hair, caused by fear.

    And my first thought on this was the same thing. Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for. There is no "evolution", but a selection pressure that reveals the previous mutation as a preferential trait, making it appear to happen suddenly and revealed by the "cause" but not actually caused by the "cause".
    • That's a great analogy!

    • And my first thought on this was the same thing. Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for.

      Based on that logic, the elephant statue was already in the marble block before Leonardo began carving, and he just removed everything that wasn't elephant.

    • Random mutation is long-term. But when a selection event happens, the "hidden" trait isn't created, but selected for. There is no "evolution", but a selection pressure that reveals the previous mutation as a preferential trait

      That IS evolution. What else do you think is meant by evolution by natural selection?

      • Re: (Score:2)

        by AK Marc ( 707885 )
        Most people speak about it like the new mutation dominates much quicker. Why would they say that they are finding evolution happens faster than they thought if they already thought what you assert?
  • Their understanding of this phenomenon is slowly... well, you know.

  • Background information, link to paper. (Score:5, Informative)

    by Michael Woodhams ( 112247 ) on Wednesday October 28, 2015 @09:33PM (#50822209) Journal

    The paper is here [royalsocie...ishing.org] but it is probably paywalled. (I have institutional access, so I'm not sure what that link will do to people who don't.)

    This is part of an ongoing debate about rates of evolution. To a large extent it was kicked off by a 2005 paper by Simon Ho et al. (Ho is second author on this paper.) They observed that estimates of mutation rates derived from studies over short time periods are much higher than mutation rates derived from studies over long time periods. Short time periods are up to a few thousand years, e.g. comparing populations that have been separated by for a few thousand years, or ancient DNA compared to modern DNA in the same species, or multigenerational studies over a few years or decades such as this one. Long time periods are from comparing species whose common ancestor is typically millions of years ago.

    This apparent acceleration in mutation rates is controversial.

    I'm going to read the paper now, so I may have more to say later.

    • I've read the (mercifully short) paper now.

      A long-running experiment started with a single population of chickens, and has been selectively breeding half for high body weight and the other half for low body weight. The full pedigree is known (mothers and fathers) over 40-50 generations. In addition, the two populations have been cross bred, for 8 generations.

      Two mitochondrial mutations were detected in the low weight half of the population, both in one maternal lineage out of four major maternal lineages in

    • Re: (Score:2)

      by RichMan ( 8097 )

      Have they factored in epigenetics into this? Where the gene is there but not expressed. Seems to me a lot of generation to generation adaptation can be explained by epigenetics and simply brining out already present factors.

      The whole "15 years" thing in the summary should be in generations. That is like forever in botfly generations, yet nothing in land tortoise generations.

      • No, the paper has nothing about epigenetics. They are looking only at mitochondria which I believe is not affected by epigenetics. I don't think mitochondria can function without all of their genes. They are actually looking directly at the DNA - the mutations really did happen, because they are observing them at the most fundamental level. There is nowhere for them to 'hide'.

        The experiment covers about 50 generations. (Or, more accurately, they are piggybacking off an existing experiment that has been runn

    • I'm going to read the paper now, so I may have more to say later.

      Pontificating without reading the paper with a mere cursory glance at the title and guessing what the paper ought to say based on my prior biases produces very interesting threads of conversation.

  • We have already observed recent mitochondrial evolution in the human population, with a few mutations specific to Polynesian populations that must have arisen during radiative settlement a few hundred years ago:

    http://dx.doi.org/10.1371/jour... [doi.org]

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