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700,000-Year-Old Horse Becomes Oldest Creature With Sequenced Genome

Posted by samzenpus on from the old-gray-sequenced-mare dept.

sciencehabit writes "Scientists have sequenced the oldest genome to date—and shaken up the horse family tree in the process. Ancient DNA derived from a horse fossil that's between 560,000 and 780,000 years old suggests that all living equids—members of the family that includes horses, donkeys, and zebras—shared a common ancestor that lived at least 4 million years ago, approximately 2 million years earlier than most previous estimates. The discovery offers new insights into equine evolution and raises the prospect of recovering and exploring older DNA than previously thought possible."

13 of 69 comments (clear)

  1. Welcome to Pliocene Park by plover · · Score: 5, Funny

    We may never get a dinosaur theme park, but we've got a decent shot at a carousel full of ancient horses, saber-tooth tigers, and wooly mammoths. What could possibly go wrong?

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    John
  2. World's Oldest and First Ass by danbert8 · · Score: 4, Funny

    I'm glad we now understand the genetic base of the jackass. Maybe with this knowledge medical science can remove those genes from human DNA.

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    Yes it's an anecdote! Were you expecting original research in a Slashdot comment?
  3. Is the science repeatable? by cold+fjord · · Score: 4, Interesting

    I've read some articles on attempts to extract and sequence old DNA in this sort of range, and I'm surprised they've been able to do this given the half-life of DNA.

    I wonder how many other researchers are making claims of extracting DNA this old? It seems improbable, but maybe the state of the art has greatly improved.

    DNA has a 521-year half-life

    The team predicts that even in a bone at an ideal preservation temperature of 5 C, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.

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    much of left-wing thought is a kind of playing with fire by people who don't even know that fire is hot - George Orwell
    1. Re:Is the science repeatable? by cold+fjord · · Score: 4, Informative

      You have to not only recover it, but to read it as well. And the fine article from the post indicates they were able to actually conduct genetic analysis on it. That pulls the maximum viability date in quite a bit. The jump in age over previous finds in which they've been able to extract viable information is pretty significant, going from 130,000 years to between 560,000 and 780,000. And note that the figures I show from the story I quoted were under ideal preservation. Maybe it is all correct, but it seems a bit of a longshot to pull that information from such an old bone. I suppose they could just have been lucky.

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      much of left-wing thought is a kind of playing with fire by people who don't even know that fire is hot - George Orwell
    2. Re:Is the science repeatable? by csirac · · Score: 4, Interesting

      To cut a long story short, at "6.8 mllion years old" I assume they mean "the longest read (maximum number of consecutive GATC 'letters' in a row) you're possibly going to get is one". Imagine having a pile of letters which were once arranged into the collective works of William Shakespeare: could you re-assemble the original work? No. But what if you had 4-letter fragments? You might be able to learn something about the english language, indirectly, but you probably won't be able to reverse-engineer the complete original work. Now what if you had slightly longer fragments? That would help. What if the garbled pile of letters/fragments actually consisted of multiple, similarly (randomly!) shredded copies of Shakespeare? Well, as long as they're randomly fragmented in different ways - you can imagine that where we guess two fragments might join each other, if we have a fragment from that same region from another copy wich spans that join - we can become more and more confident about forming a plausible assembly. So we can take advantage of this redundancy and randomized fragmentation to attempt recovery of the original work.

      In other words, the more degraded the DNA, the shorter the fragments and the harder it is to come up with an assembly. At some point the fragmentation might be so bad that the only way you can attempt to achieve anything is to try to use a relevant, well understood reference sequence from a modern day specimen/consensus for comparison (or clues, or to fill-in-the-blanks)... if one exists. I'm no geneticist, but I think in those circumstances the confidence in the results start to go from "hey, that's cool!" to "interesting" to, eventually, an artist's rendition of what an ancient genome might have looked like - drawing from long lost cousins which are still alive today.

      Happily, re-assembling short, fragmented DNA happens to be how commodoty high-speed, high-throughput, low-cost sequencing works these days - DNA is split into small lengths, Eg. 500-ish basepairs, and then depending on the experiment/purpose/targets etc. it's all (or partially) re-assembled by finding enough overlapping bits (hopefully beginning and ending with proprietary markers used in the splitting process) with statistical tricks to qualify if the data is sufficient, which areas are problematic in coverage/confidence etc... and it helps enormously if you're working on an organism that's already been sequenced to death for comparison.

      So there are many well advanced tools for coming up with contiguous DNA from a pile of short reads.

      IIRC, the other trick with ancient DNA is - first of all, extracting enough useful material to begin with, without damage. As reads get shorter, increased redundancy helps - more randomly overlapping regions can ease the task of re-assembly - but very short reads might mean that a number of different assemblages are possible. Not to mention delicate amplification methods which might increase the noise as well as the signal...

    3. Re:Is the science repeatable? by julesh · · Score: 2

      You have to not only recover it, but to read it as well. And the fine article from the post indicates they were able to actually conduct genetic analysis on it. That pulls the maximum viability date in quite a bit.

      Which is why the article you cited goes on to state "[t]he DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information." Given that 1.5Myear figure, why is 700Kyear surprising? It's not like they're expecting a technological breakthrough to make that 1.5My figure possible: we can already sequence pretty-much any single DNA strand we want, and reconstruction from short fragments is also an existing and thoroughly-developed technology.

    4. Re:Is the science repeatable? by only_human · · Score: 2

      It looks like it was a difficult accomplishment:
      They also combined DNA sequencing techniques to get maximum DNA coverage — using routine next-generation sequencing with single-molecule sequencing in which a machine directly reads the DNA without the need to amplify it up which can lose some DNA sequences. [1]
      Such genetic puzzle assembly generally includes multiple samples from each part of the genome, sometimes as many as five or 10. In this case, the so-called coverage was just 1.12. [2]
      "We sequenced 12 billion DNA molecules, of which 40 million [were of] horse origin," said Orlando. "There was a bit of horse DNA in an ocean of microbial DNA." [3]
      [1]http://www.nature.com/news/first-horses-arose-4-million-years-ago-1.13261
      [2]http://www.latimes.com/news/science/la-sci-ancient-horse-genome-20130627,0,2514595.story
      [3]http://news.nationalgeographic.com/news/2013/06/130626-ancient-dna-oldest-sequenced-horse-paleontology-science/

  4. Source material by antifoidulus · · Score: 4, Funny

    So they sequenced a 700,000 year old horse? In other words, a Tesco hamburger?*rimshot*

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    Monstar L
  5. Re:Bible is truth not false science by Barsteward · · Score: 2, Informative

    " You don't have to be stupid to be a creationist unfortunately"

    You do....

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    "The hands that help are better far than lips that pray." - Robert Ingersoll (1833-1899)
  6. Ancient DNA NOT derived from a horse fossil? by K.+S.+Kyosuke · · Score: 2

    If there's DNA inside, how can that be a fossil? I always thought that this would make it a subfossil, by definition.

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    Ezekiel 23:20
    1. Re:Ancient DNA NOT derived from a horse fossil? by IndustrialComplex · · Score: 2

      Do you really care if someone calls Pluto a planet instead of the more precise term dwarf planet?

      Nature doesn't have to organize itself into neat little boxes for easy categorization. If the message is understood, even with non-precise language, the message is still understood.

      Also with regard to your concern for definition:

      http://science.howstuffworks.com/environmental/earth/geology/soft-tissue-dinosaur-fossil.htm

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      Out of modpoints but really liked a post? 1BDkF6TtmmeZ3yqXbz9yhdYVqRYnwFoXDj
  7. No: Welcome to PLEISTOCENE Park by Dr+La · · Score: 2

    Pleistocene Park, not Pliocene Park.

    The Plio-Pleistocene boundary is at 2.6 million years ago. With 700 000 yrs, this Horse is Middle Pleistocene (the Lower-Middle Pleistocene boundar is at 780 000 yrs ago).

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    Ceterum censeo Carthaginem delendam esse
    1. Re:No: Welcome to PLEISTOCENE Park by plover · · Score: 2

      Philistine.

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      John