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Science

Oldest Human DNA Contains Clues To Mysterious Species 93

Posted by samzenpus from the family-tree dept.
sciencehabit writes "Analysis of the oldest known genetic material ever to be recovered from an early human reveals an unexpected chapter in the story of human evolution. Researchers extracted mitochondrial DNA from the femur of a 400,000-year-old hominin found in the Sima de los Huesos ('pit of bones'), an underground cave in the Sierra de Atapuerca in northern Spain. Because the early hominins looked a little like Neanderthals, researchers expected their mitochondrial DNA to share a common ancestor. However, mitochondrial DNA from the Spanish hominin was found to share a common ancestor with an enigmatic eastern Eurasian sister group to the Neanderthals, the Denisovans."
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Oldest Human DNA Contains Clues To Mysterious Species More

Oldest Human DNA Contains Clues To Mysterious Species

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  • Very interesting, but (Score:5, Interesting)

    by ColdWetDog ( 752185 ) on Wednesday December 04, 2013 @10:40PM (#45604727) Homepage

    1. They had problems with modern human DNA contamination (not sure why they couldn't get everything clean but since they're the leading edge lab in this sort of thing, it must be a real issue).
    2. They had to limit analysis to fragment lengths around 45 base pairs to avoid this contamination. That's tiny compared to what one normally uses.
    3. They only had enough to sequence the mitochondrial DNA.
    4. It's only one person.

    So, it's confusing but it seems from the outside to be due to a limited data set. Now, this sort of thing is at the limit of our current technology and the lab is working to replicate and amplify the data (and work on the somatic genome). So stay confused and stay tuned.

    • Re:Very interesting, but (Score:5, Interesting)

      by ColdWetDog ( 752185 ) on Wednesday December 04, 2013 @10:47PM (#45604775) Homepage

      And one other thing, if anybody out there knows:

      They eliminated modern contaminating DNA by analyzing only DNA segments with uracil, a base usually found in RNA and a signature of older, degraded DNA.

      Uracil is a modified Thymine, in vivo DNA where uracil is incorporated [scienceinschool.org] into the chain is repaired by a specific enzyme. Does the Thymine naturally degrade to Uracil over time?

    • "1. They had problems with modern human DNA contamination (not sure why they couldn't get everything clean but since they're the leading edge lab in this sort of thing, it must be a real issue)."

      Just as an observation, I think this is going to be an increasing problem the more sensitive DNA testing gets. It is now possible for some DNA tests to detect a single cell's worth of evidence. Think about that. Then think about the trail of DNA evidence you leave behind everywhere. Getting a "clean" lab may end

    • Re: (Score:1)

      by Anonymous Coward

      1. They had problems with modern human DNA contamination (not sure why they couldn't get everything clean but since they're the leading edge lab in this sort of thing, it must be a real issue).

      I presume the site was contaminated. The cave it was found in was apparently discovered in the 1980s, and nobody at that time would have expected DNA to have survived, so no steps would have been taken to prevent contamination.

    • "1. They had problems with modern human DNA contamination (not sure why they couldn't get everything clean but since they're the leading edge lab in this sort of thing, it must be a real issue)."

      Unlikely that there were not later visitors to the cave. Pissing in the corner is eventually going to contaminate the DNA. This is one of the things the "DNA Forensics" folks like to play down: it is ridiculously easy to contaminate DNA evidence.

      "2. They had to limit analysis to fragment lengths around 45 base pairs to avoid this contamination. That's tiny compared to what one normally uses."

      See my point above. But also: time damages DNA as well. You get more accurate fragments if you limit the size of the fragments. (I.e., statistically, you're less likely to see a fractured or contaminated chemical bond, the smaller the sample you take.)

      "3. They only had enough to sequence the mitochondrial DNA."

      The mitochondr

      • They could have taken many samples of this one person to verify it's actually the true RNA. Given enough samples, you'd statistically eliminate the deterioration and contamination of individual samples quite drastically. You most certainly wouldn't be able to come up with the definitive complete RNA or DNA of this person, but the margin for error would be so low that even the most sceptical peer reviewer would be convinced.

        Contamination would most likely be limited to recent events. Ancient people peeing

        • Yes, what you say is all true but apparently (from what I understand of the situation) they were able to only obtain very small isolated samples at all. When it's in an area that was almost certainly contaminated with other DNA it's pretty hard to demonstrate much of anything.

          I wasn't trying to claim that they're wrong. I was simply pointing out some of the problems they face in trying to show something significant.
        • I was actually defending some of their methods: e.g. if you have long chains likely to be broken in places, you can often get better statistical results from studying shorter segments.

      • Re: (Score:2)

        by wbr1 ( 2538558 )
        Also RE Modern DNA contamination... I am certainly no expert, but chemical means are used to copy and 'amplify' weak or degraded DNA, both in this and in 'DNA forensics'. Regardless of 10000 years of piss in the corner of the cave, one modern skin cell floating in the air and landing in the sample will get amplified as much or more as the target sample. The replication and amplification process is not discriminatory IIRC.
        • The process is discriminatory in the sense that whatever there is a greater amount of to start with will be replicated/amplified at a faster (also) exponential rate.

          Also the samples are taken from the inside of bone/fossilized tissue that has undergone quite extensive cleaning prior to grinding/crushing and processing. It is possible though for contamination to occur at almost any point in the process.

  • "400,000-year-old hominin"

    I thought they were hominids

  • mitochondrial dna! (Score:3)

    by schlachter ( 862210 ) on Wednesday December 04, 2013 @11:00PM (#45604829)

    That's from the maternal line. It's the DNA that's directly passed down only from the mother. Just because no maternal Neanderthals DNA is present doesn't mean there isn't Neanderthals DNA present from Neanderthal fathers. I'm not arguing that this is the answer, only that the findings above don't prohibit this from being true.

    Besides, we all know those Neanderthals mean were the one's hitting our ancestral women on the heads, dragging them back their caves, and spreading their DNA. :P

    • Besides, we all know those Neanderthals mean were the one's hitting our ancestral women on the heads, dragging them back their caves, and spreading their DNA. :P

      I thought that was Congressman. Evolution is spool confusing.

    • That's from the maternal line. It's the DNA that's directly passed down only from the mother. Just because no maternal Neanderthals DNA is present doesn't mean there isn't Neanderthals DNA present from Neanderthal fathers. I'm not arguing that this is the answer, only that the findings above don't prohibit this from being true.

      Besides, we all know those Neanderthals mean were the one's hitting our ancestral women on the heads, dragging them back their caves, and spreading their DNA. :P

      What you say is true, but it doesn't mean anything. You could also just as validly state Just because no maternal Martian DNA is present doesn't mean there isn't Martian DNA present from Martian fathers. The point being that science should talk about what the data does show, not speculate about all of the possibilities that data doesn't support.

  • underground cave... (Score:3)

    by Kaenneth ( 82978 ) on Wednesday December 04, 2013 @11:05PM (#45604851) Journal

    "underground cave" is there another kind?

  • It's generally accepted that human beings (homo sapiens) are no more than 200,000 years old. So unless the researchers are proposing their data shows that humans are a lot older than originally thought, the title and summary are flawed. Not that the research isn't interesting, but one would hope that scientists would know the difference between the species involved and not misinform the public.

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