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Science

The Incredible Shrinking Genome 113

Posted by Soulskill
from the hey-it's-cold-alright dept.
Shipud writes "Mammalian genomes have been shrinking for about 65 million years, roughly since the dinosaur extinction. Why? And why were ancient mammalian genomes three times larger than they are today? A new article in Genome Biology and Evolution tries to explain this bizarre finding, and why the genomes of mammals (but not of other living groups) are still shrinking. 'Once [the dinosaurs] were gone, mammals started to radiate, fill those niches, and a whole new level of competition arose. The selective advantage of not having a genome encumbered by potentially damaging mobile DNA elements has probably become critical at this "be ye fruitful and multiply; bring forth abundantly in the earth, and multiply therein" stage. In effect, the genomes of mammals has been shrinking by removing mobile DNA elements, just after the KT boundary. And according to the model presented in this study, this process is still ongoing: mammalian genomes are not at an equilibrium size. Unlike flies, mammals are still cleaning up.'"
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The Incredible Shrinking Genome

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  • by Anonymous Coward

    bigger genome.... bigger mammals! that's it. The woolly mammoth was big because his dna was big! guess size does matter.

  • refactoring (Score:5, Funny)

    by farker haiku (883529) on Wednesday July 01, 2009 @10:39AM (#28542251) Journal

    I blame it on increased use of design patterns and better tools for refactoring ;)

    • I was going to make a similar joke.

      No coincidence that I'm halfway through Fowler's book at the moment.

    • by MindKata (957167)
      "I blame it on increased use of design patterns and better tools for refactoring"

      So its taken us 65 million years to become more optimal?!.

      Still it helps explains politicians, they must be running an earlier version?

      So if its taken us 65 million years, then I can't wait for Windows 6502009 !

      (My old programmer brain just threw an interrupt when I wrote down the numbers 6502 ... ahh ... memories ... maybe it means Windows will be so optimal by then, that it'll run on a 6502!).
      • by HTH NE1 (675604)

        (My old programmer brain just threw an interrupt when I wrote down the numbers 6502 ... ahh ... memories ... maybe it means Windows will be so optimal by then, that it'll run on a 6502!).

        If it's good enough for a T-800....

  • God is a computer programmer who made the many species by writing in some high level language which is ultimately compiled into DNA. The similarities in DNA among different species are a result of code re-use, and mammals are his (her?) "flagship product." He's currently refactoring the code, to make it more efficient.
    • by ruin20 (1242396)
      Everyone knows god programed in perl :) [xkcd.com]
    • by Artifakt (700173)

      Or we should all become polytheists, because God has open-sourced the project, and it's getting small and streamlined because of the 'many eyes' effect.

  • by Absolut187 (816431) on Wednesday July 01, 2009 @10:44AM (#28542303) Homepage

    Mammals genomes are getting smaller, primarily by cleaning out viral DNA.
    This "house cleaning" seems to have started about the time of the massive KT extinction that killed the dinosaurs. Nobody knows for sure how or why the cleaning is occuring, although some hypotheses are set forth. Nobody knows whether it has anything to do with the KT extinction..

    • Eventually some outcompete the others by allowing their replication machines to replicate more successfully. The ones which don't, also die off because their replication machines are unable to reproduce.

      The result is an averaging out of gene noise, leaving only the successful signal for a particular niche.

  • by sadtrev (61519) on Wednesday July 01, 2009 @10:45AM (#28542315) Homepage

    Body temperature control is very effective in reducing the number of different enzymes that need to be coded for.
    Frogs, for example have ~8x more genes than humans - partly because they have lots of different enzymes that do the same thing but at different temperature.

    • maybe global warming is the cause?

      does that mean that heat is shrinking out genes?

      • by mcvos (645701)

        Do I need to point this out?

        Global warming is very recent. Also, the amazing shrinking genome is about mammals in particular, and mammals can control their own temperature, which means environmental temperature has little or no effect on genes. It's possible that warmbloodedness is shrinking our genome, though (which is what the GP is suggesting).

        • genes = jeans

          it was not a serious post, but a badly worded attempt at a joke

    • Re: (Score:3, Interesting)

      by lavaforge (245529)

      Are we seeing the same tendency in other warm blooded creatures, such as birds?

      • Are we seeing the same tendency in other warm blooded creatures, such as birds?

        Since birds are dinosaurs, I'd expect not.

      • by jae471 (1102461)
        We should, if enzyme temperature range is a legitimate reason for the change.

        We should also expect to see less of an effect in monotreme mammals (the platypus and echidna genera). They don't exhibit as much thermal stability as plancentals and marsupials, so they should need a wider range of enzymes. But 3 living genera makes a poor sample size, and the fossil record for monotremes is very poor.

    • by Tablizer (95088)

      Body temperature control is very effective in reducing the number of different enzymes that need to be coded for. Frogs, for example have ~8x more genes than humans - partly because they have lots of different enzymes that do the same thing but at different temperature.

      But the downside is that mammals have to eat a lot more to maintain a constant temperature. Amphibians and reptiles can go a lot longer without food. This is partly why mammals have a bigger brain: we have to catch more food per hour, and thi

  • Design paterns? (Score:1, Redundant)

    by line-bundle (235965)

    Perhaps the genome is being optimized by design patterns instead of procedural programing.

  • Actual paper (Score:5, Informative)

    by drunken_boxer777 (985820) on Wednesday July 01, 2009 @10:56AM (#28542477)

    Here's [oxfordjournals.org] the actual scientific paper, rather than the blog.

  • by Anonymous Coward

    Sounds like some (open) source I hacked on years ago -- kept finding ways to take (stupid) things out without losing functionality.

  • by peter303 (12292) on Wednesday July 01, 2009 @11:04AM (#28542579)
    Some have over a hunred billion base pairs. There a tremendous amount of junk DNA and gene duplication.

    Size does not matter.
    • by Daimanta (1140543)

      "Size does not matter."

      That's what SHE said!

    • by MaXintosh (159753)
      Exactly. I have to wonder, if mammals' radiation is the cause of their shrinking genome, what powerful radiation did pufferfish undergo to shed so much of theirs? And where's all the left over diversity from that radiation?
      Every now and then people publish papers announcing they've solved the C-value paradox. I think it's like a bunch of undergrads who think they've solved the problem of induction the first time they hear about it. Except these guys have Ph.Ds, and get slashdot stories for their whole-lot-
  • It's interesting that the authors looked at the Fugu genome when determining 'shrinkage'. The Fugu genome has roughly the same number of genes as the human genome, but is only 1/8th the size, meaning it is quite 'cleaned up'.

    In fact, this is especially interesting because the Fugu genome isn't exactly representative of fish genomes in general, as most fish genomes are several times longer than the Fugu genome, and presumably don't contain a proportionate increase in the number of genes. There are other fish

  • Organisms can acquire DNA from other organisms by inserting bits of foreign DNA, known as mobile DNA, into the genome. One way this is done is by viral infections. Some viruses integrate genomic material of their own, and sometimes of other host organisms into the hosts they infect. If those viruses happen to also infect germ cells â" sperm or ova â" those insertions or retrotransposons would be passed on to subsequent generations. It is quite easy to identify these viral insertions: they are flanked by characteristic DNA stretches called Long Terminal Repeats or LTRs. During the infection and insertion process, LTRs serve as âoeinsertion hooksâ

    Easy to detect? wait till they start using polymorphism....

  • by presidenteloco (659168) on Wednesday July 01, 2009 @11:21AM (#28542825)

    As a thought experiment, imagine the genome to be a very big, very modular program, with lots of clusters of specialized subclasses of functionality that are occasionally or potentially useful.

    This program is represented by a coding sequence of molecules; at essence a copyable and readable bitstring.

    Time and living in a complex, energetic environment tend to break down complex structures which must be "binary-precise" to maintain their meaning. All else being equal, a longer program, a longer bitstring, has a higher probability of losing parts of itself to mutation. Longer programs; longer genomes, require cleverer techniques to preserve themselves over evolutionary time scales.

    The cool thing is, longer programs are precisely those that have the capacity to implement cleverer strategies for keeping their own program information reliably preserved.

    That is the essential battle that life and evolution wage against entropy;
    More bits (longer genome) = more or better strategies for building bit-containers (organisms) and better strategies for taking advantage of environments or pacifying environments.
    But more bits = harder to preserve without critical errors breaking the program.

    The life bitstrings are in different states of adaptation to their environment as time passes and both environments and genomes change. In a dynamic environment (or a wide, general niche) more modules and subclasses (waiting in the wings, ready for activation if needed) is probably advantageous to a set of generations of the organism, whereas in a highly adapted state in a stable environment, and an environment with well established niches and in fact cross-supporting functions of those niches (a long-lived relatively stable ecosystem in relatively stable climate), the extra adaptability may carry costs of it being too difficult to retain that extra information reliably for the potential benefit it might have if things changed. The extra program bits can also be dangerous. Most organized variants of code-sections of the life-program are organism-killers, most of the time.

    In summary, a longer bitstring at the core of life can only be supported by evolution if it earns its keep in life-preserving strategy execution.

    I think life bitstrings (genomes) on Earth have GENERALLY been growing by 1 or 2 bits a year since life began (give or take an enormous waffle factor). But in some, relatively stable, organism-environment pairings, temporary program shortening trends may be advantageous prunings of the more wild-ass life mechanism "ideas".

    • by xenocide2 (231786)

      But you're missing a key point: DNA translates into protein in chunks of 3. Depending on where the translation starts, one chunk of DNA can translate into several different proteins. You don't actually need to grow the genome to increase the amount of proteins around, and it's probably the case that genomes will shrink over time as natural selection finds these random overlaps.

      To put it in computing terms, you can have two or three programs in one binary just by changing the word alignment. The only way I c

      • That might change things by a small and near-constant factor, but the essence of the argument remains; that you need more bits of information to encode more strategies and more complex strategies for organism construction and maintenance.

        Technically, the DNA is not encoding directly in binary anyway, it is something closer to base-4 with some symbols not useable. However, this is still very close to pure binary information representation, and is probably about as close as the requirements for chemical stabi

  • I suppose this could be because mammals have developed a better immune system that stops DNA insertions. Once the insertions stop of course then number will decrease as they are naturally cleanup up -- just as they are cleaned up in other animals.

    But don't worry something will come along that will figure out how to do DNA insertions in mammals eventually.

    • But don't worry something will come along that will figure out how to do DNA insertions in mammals eventually.

      Yes, I seem to recall having inserted my DNA into several mammals (which I was able to identify because they had mammaries) when I was younger....

  • Mitochrondia merged with eukaryote cells about a billion years ago. This allowed eukaryotes to increase metabolic power an order of magnitude over bacteria and evolve locomotive animal life.

    A mystery is why mitochondia kept enough DNA to code for about 10% of their proteins after all these eons. They get the other 90% of proteins from nuclear DNA of the host cells. Nick Lane [amazon.com] suggests in his mitochondria book this DNA codes for the most essential emzymes such as those that break down free-radical wast
    • by Anonymous Coward

      Presumably because there's no longer any selective pressure moving DNA from mitochondria to the nucleus. To make up a hypothesis, assume that if a mitochondrion has 100% of its "original" (ie, when it was still an independent, exogenous lifeform) then it is able to leave its host cell and resume independence, resulting in the host cell's death. This would select for those freak events involving transfer of mitochondrial DNA to the host cell (which, at this point in evolution, may or may not actually possess

      • by HiThere (15173)

        There is definite active pressure to move genes from the mitochondria to the nucleus. The environment inside the mitochondria is hostile to DNA because of the number of free radicals produced during the construction of ATP. (If I've got that bit wrong, during the release of energy.)

        One result of this is that mitochondrial DNA evolves considerably faster than nuclear DNA. (Evolves here just means changes. I think it's usually neutral drift.) This may also be one of the reasons for aging. Too many cell

      • We actually know the reason for why mitochondria have DNA. It is because three proteins that are needed on the inner membrane (part of the electron transport chain) can't be transported from the cytoplasm by the mitochondria protein import system. These three proteins are too hydrophobic and get stuck in the import system. If they can't be imported then they have to be synthesized in the mitochondria and hence the need for mitochondrial gene expression and protein synthesis.
  • About the time of the KT extinction, mammals starting spreading and evolving into new niches.
    Around this same time, their genome expanded.
    Then, after they had spread into lots of niches, their genome switched from expanding to shrinking.

    And this is surprising?

  • by backwardMechanic (959818) on Wednesday July 01, 2009 @12:27PM (#28544123) Homepage
    "I made this letter longer than usual because I lack the time to make it short." Blaise Pascal, 1656.
    The watchmaker has had more time...
  • Does anyone know where they are getting 65 million year old mammal DNA? Can a full set of DNA really last that long? Are all the assumptions for the very long extrapolations of LTRs valid?
    • Does anyone know where they are getting 65 million year old mammal DNA?

      They aren't using 65 million year old DNA. The authors are drawing conclusions about the size of the genome 65 million years ago from calculations of the rate at which mobile DNA elements have changed.

      Can a full set of DNA really last that long?

      It's unlikely, but possible. There has been recovery of dinosaur DNA, but not an entire genome.

      Are all the assumptions for the very long extrapolations of LTRs valid?

      Yes and no. The authors compared their observations to two different models. The observations fit somewhere in between both models, indicating that rates of change in genome size are not constant. This means that dur

  • by naasking (94116) <naasking @ g m a il.com> on Wednesday July 01, 2009 @02:22PM (#28546491) Homepage

    The genome is shrinking because there is a selective advantage to a smaller genome when the environment is stable. Fewer errors can occur when copying for example. In unstable environments, having a larger genome with more adaptive mutations is a selective advantage. Shorter genomes marks species that are highly specialized to their environment.

    • by bar-agent (698856)

      The genome is shrinking because there is a selective advantage to a smaller genome when the environment is stable. Fewer errors can occur when copying for example.

      I should think that the number of errors, proportionally, would be the same in smaller genomes and larger genomes, e.g., cosmic rays cause 1 transcription errors per 1000 bases regardless of whether the genome is 1 million bases or 10 million bases. The smaller genome of one organism would have fewer errors than the larger genome of another organi

      • by naasking (94116)

        the more it seems that very little DNA can truly be considered junk.

        Exactly my original point. The DNA are or were likely latent adaptations that provide little advantage in a stable environment that do not trigger said sequences.

        The additional conservation in resources required to copy these smaller genomes is likely important in ensuring a selective advantage, such that an otherwise equally well-adapted species with a larger genome is at an inherent disadvantage since it would require more food. I think y

  • Was it ultimately because their DNA was incapable of radiating because it had lost so much of it's "junk DNA" that it couldn't have pulled any information out to help it adapt to changes?

  • "mammals started to radiate"

  • I recently watched a video where this was predicted.
    I did a Google Search to find it again just for you guys:

    YouTube - Polyworld: Using Evolution to Design Artificial Intelligence

    Anyway, the author had an interesting theory to why this happened in his simulation. He thought that once the peak of the DNA complexity was reached, evolution started removing the unnecessary parts. Weather this is called evolution or devolution is debateable.

  • Mammalian still refactoring [wikipedia.org] their code. And still practicing Extreme programming [wikipedia.org] too.
  • Energetic systems will always loose energy. Evolutionary Information systems will do likewise. Complexity does not mean more information, it means that the information is better structured and free from redundancy. I.e. Simpler is better. K.I.S.S. (?), hardly a surprise that all levels of reality comply. The Universe is Consistent when viewed as an Energetic Information System- not as balls of gas and stone strung along by gravity.

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