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Oldest Human DNA Contains Clues To Mysterious Species

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."

93 comments

  1. Denisovans? by Anonymous Coward · · Score: 0, Offtopic

    OK, OK, still better than Kardashians, I guess.

    1. Re:Denisovans? by Spy+Handler · · Score: 0, Redundant

      What we call the Denisovans were actually direct descendants of Pak breeders, who lost the ability to advance to the protector stage due to the lack of thallium in earth's soil.

    2. Re:Denisovans? by MightyMartian · · Score: 1

      I love a log of Niven's writing, and try very very hard to ignore the whole Pak Protector aspects of his stories, though it is awfully bloody hard with the Ring World material.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    3. Re:Denisovans? by Anonymous Coward · · Score: 0

      I love a log of Niven's writing

      What does this mean, please?

    4. Re:Denisovans? by Anonymous Coward · · Score: 0

      You throw a few of Nivens books in the blender together with some milk, strawberries or bananas and rolled oats, and blend it well. Drink this delicious concoction and dome 24-48 hours late you'll have a "log" of Niven's writing.

    5. Re:Denisovans? by Anonymous Coward · · Score: 0

      Log in and he'll tell you, dummy.

    6. Re:Denisovans? by cyberchondriac · · Score: 1

      Pssthpok, I say..

      --

      Look back up at my post, now look back down, you're on the Internet. Now look back up. I'm a signature.
  2. Very interesting, but by ColdWetDog · · Score: 5, Interesting

    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.

    --
    Faster! Faster! Faster would be better!
    1. Re:Very interesting, but by ColdWetDog · · Score: 4, Interesting

      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 into the chain is repaired by a specific enzyme. Does the Thymine naturally degrade to Uracil over time?

      --
      Faster! Faster! Faster would be better!
    2. Re:Very interesting, but by Anonymous Coward · · Score: 0

      1. I am not sure and not an expert at all but isn't it the lab do clean out contamination first? If the sample is already contaminated before arriving to the lab..

    3. Re:Very interesting, but by HiChris! · · Score: 5, Informative

      No, but Cytosine does - the amine group gets hydrolyzed, leaving a Uracil nucleobase. (Also Thymine is a modified Uracil, it's also know as 5-methyl uracil)

    4. Re:Very interesting, but by Concerned+Onlooker · · Score: 2

      "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 up being more tricky and costly than you think, not to mention the treatment the specimen got before it got to the lab.

      --
      http://www.rootstrikers.org/
    5. Re:Very interesting, but by Anonymous Coward · · Score: 1

      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.

    6. Re:Very interesting, but by Jane+Q.+Public · · Score: 2

      "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 mitochondrial DNA may have been the best preserved, because it's inside walled micro-structures in the cell.

      "4. It's only one person."

      Bingo.

    7. Re:Very interesting, but by wbr1 · · Score: 1

      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.

      --
      Silence is a state of mime.
    8. Re:Very interesting, but by sackbut · · Score: 1
      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.

    9. Re:Very interesting, but by Anonymous Coward · · Score: 1

      So *that's* how people feel when I speak code or maths...

      Interesing :-)

    10. Re:Very interesting, but by Anonymous Coward · · Score: 0

      Not to mention if it was contaminated from modern human piss (or other modern human sources) they would have found a different result, like the intitutive one where neanderthals and modern humans share the common ancester heidelbergenesis.

  3. science writer knows nothing of science by Anonymous Coward · · Score: 0

    film at 11...

    sounds like this "journalist" never even heard of Denisovans before now. So what exactly is the "clues" that have been gained?

    1. Re:science writer knows nothing of science by Curunir_wolf · · Score: 1

      sounds like this "journalist" never even heard of Denisovans before now.

      Yea, well, neither have I. But then I'm not a professional that is expected to know anything about it.

      So what exactly is the "clues" that have been gained?

      are

      --
      "Somebody has to do something. It's just incredibly pathetic it has to be us."
      --- Jerry Garcia
    2. Re:science writer knows nothing of science by wonkey_monkey · · Score: 3, Funny

      So what exactly is the "clues" that have been gained?

      are

      Sorry.

      So what exactly is the "clues" that are been gained?

      --
      systemd is Roko's Basilisk.
    3. Re:science writer knows nothing of science by Anonymous Coward · · Score: 0

      lol, you should win a prize, that was actually one of the more laugh-inducing comments I have read here in a looooooong time :D

  4. Hominin? by rossdee · · Score: 1

    "400,000-year-old hominin"

    I thought they were hominids

    1. Re:Hominin? by Anonymous Coward · · Score: 1

      From the Repository of Knowledge:

      http://en.wikipedia.org/wiki/Hominin

    2. Re:Hominin? by camperdave · · Score: 0

      Ah! So these hominini are the monkey's uncle we keep hearing about?

      --
      When our name is on the back of your car, we're behind you all the way!
    3. Re:Hominin? by a_n_d_e_r_s · · Score: 4, Informative

      Hominin a subtribe of homonids

      Homonids is great apes thus humans gorillas chimpanzea orangutans

      Homonin are all those related closer to humans than chimpanzees thus neantherthals etc

      --
      Just saying it like it are.
    4. Re:Hominin? by wbr1 · · Score: 1

      You could have replied and used ad-hominem, you lazy lout.

      --
      Silence is a state of mime.
    5. Re:Hominin? by Nerdfest · · Score: 4, Funny

      ... because hominem is a homonym of hominim.

  5. mitochondrial dna! by schlachter · · Score: 2

    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

    --
    My God can beat up your God. Just kidding...don't take offense. I know there's no God.
    1. Re:mitochondrial dna! by MightyMartian · · Score: 1

      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.

      --
      The world's burning. Moped Jesus spotted on I50. Details at 11.
    2. Re:mitochondrial dna! by Anonymous Coward · · Score: 0

      I think the mystery is less the absence of neanderthal dna and more the presence of a dna signature thus far only seen in asian sources (siberia and china) at the extreme western edge of europe, over 4,000 miles distant from the previous location.

      (captha: "marches" - presumably for a very long time!)

    3. Re:mitochondrial dna! by Dcnjoe60 · · Score: 1

      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.

  6. underground cave... by Kaenneth · · Score: 2

    "underground cave" is there another kind?

    1. Re:underground cave... by Nkwe · · Score: 5, Informative

      "underground cave" is there another kind?

      Man Cave

    2. Re:underground cave... by gspira · · Score: 1

      underwater cave?

    3. Re:underground cave... by Kaenneth · · Score: 1

      I'll give you that, you're also likely to find unknown species there as well.

    4. Re:underground cave... by Anonymous Coward · · Score: 1
    5. Re:underground cave... by a_n_d_e_r_s · · Score: 1

      Well the cave could technically be in an mountain. Over ground level and inside the mountain thus making it a mountain cave.

      --
      Just saying it like it are.
    6. Re:underground cave... by Anonymous Coward · · Score: 0

      So if you were standing on top of that mountain what would you say you were standing on? Something other than the ground? :-P

    7. Re:underground cave... by Anonymous Coward · · Score: 0

      Technically, yes. Underwater, uncovered.

    8. Re:underground cave... by camperdave · · Score: 2

      "underground cave" is there another kind?

      Yes, that annoys me too. However, there are snow caves and ice caves

      --
      When our name is on the back of your car, we're behind you all the way!
    9. Re:underground cave... by camperdave · · Score: 1

      Mountain caves are still underground. The key being that if there is ground above you, you are underground.

      --
      When our name is on the back of your car, we're behind you all the way!
    10. Re:underground cave... by M.+Baranczak · · Score: 3, Funny

      Nick Cave. Does he still count as "underground"?

    11. Re:underground cave... by Anonymous Coward · · Score: 0

      The mountain could be underwater. Below sea level.

      However it would still be underground. If your cave is above ground, we can use another word like tent, house, clearing, or 747.

    12. Re:underground cave... by Anonymous Coward · · Score: 0

      At last, we have discovered Captain Obvious' real identity!

    13. Re:underground cave... by Anonymous Coward · · Score: 0

      As a retired caver, we called them Alpine caves.

    14. Re:underground cave... by slashmojo · · Score: 2

      Does he still count as "underground"?

      Not since the duet with Kylie Minogue..

    15. Re:underground cave... by dgatwood · · Score: 1

      Yeah, but they're all varieties of mold, mostly in the mini fridge.

      --

      Check out my sci-fi/humor trilogy at PatriotsBooks.

    16. Re:underground cave... by BottleCup · · Score: 1

      "underground cave" is there another kind?

      gruffalo cave

    17. Re:underground cave... by Anonymous Coward · · Score: 0

      Sure, the underwater cave

    18. Re:underground cave... by maxwell+demon · · Score: 1

      Ice cave?

      --
      The Tao of math: The numbers you can count are not the real numbers.
    19. Re:underground cave... by wbr1 · · Score: 1

      Underwater cave

      --
      Silence is a state of mime.
    20. Re:underground cave... by Paradise+Pete · · Score: 1

      The key being that if there is ground above you, you are underground.

      That also explains why this coffee tastes like mud today. Turns out it was ground this morning.

    21. Re:underground cave... by Anonymous Coward · · Score: 0

      Love Cave

  7. Re:"Prometheus" was not fiction, it was history .. by Anonymous Coward · · Score: 0

    That was me. Please give me your address so I can pick up the turd.

  8. So where is the Alien DNA? by bussdriver · · Score: 1

    We all know aliens have a problem with abducting and then "probing" farm animals and humans - we probably inherited some of that behavior from them... (some of us more than others.)

  9. Bingo? by dutchwhizzman · · Score: 1

    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 in the corner would have left a little DNA/RNA, but that would be limited to single cells on or near the surface, not being protected by bone structure or surrounding cells. The chance of that DNA/RNA surviving is way lower than the DNA/RNA inside the bones, so most likely, we're only dealing with the handling of the bones since the 1980s.

    Yes, this one person could still be a freak occurrence. However, if you were to see that as a valid argument, our entire theory of the origin of modern humans is based on a few freak occurrences we just happen to have found scattered around the planet.

    --
    I was promised a flying car. Where is my flying car?
    1. Re:Bingo? by Jane+Q.+Public · · Score: 1

      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.

    2. Re:Bingo? by Jane+Q.+Public · · Score: 1

      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.

  10. Re:Modern Denisovans and survivalinternational.org by EvilAlphonso · · Score: 1

    It makes me wonder how the Jomon and associated cultures fit in the picture.

  11. Sima de los Huesos = Pit of THE Bones by Anonymous Coward · · Score: 0

    ... not "pit of bones".
    "el"/"la"/"los"/"las" == "the".
    Omitting it in English when there is a "el/la/los/las" in Spanish is not optional. Don't do it.
    Adding a "el/la/los/las" in Spanish when there is no "the" in English is wrong aswell.

    In lots of American movies and TV shows I see this mistake over and over.
    i.e. In a Simpons episode we see the Bumblebee Man with a paper that says "El Divorcio". Why adding "El" here?. It's just "Divorcio".
    You probably see the article added to every word in Spanish class, but that's just so you can learn the word genre (masculine/femenine) and so you can use the correct article _if_ needed. Stop this nonsense please.

    1. Re: Sima de los Huesos = Pit of THE Bones by Anonymous Coward · · Score: 0

      just because you speak gutter spanish, doesn't mean the rest of us have to.

    2. Re:Sima de los Huesos = Pit of THE Bones by Anonymous Coward · · Score: 0

      Chinga tu puta madre, su mierda. Vama, gnomo.

  12. Simple Explaination by Anonymous Coward · · Score: 0

    Humans have always shagged anything that was on two legs. Its not surprising that there's a lot of cross-sharing of DNA material between the various Homo branches. Its just that thanks to our superior societal norms, that we're more uptight about the fact than Bonobono chimps are......

    Thank God for that?

    Hmmmm....

  13. Re:Whites evolved from blacks... by Paradise+Pete · · Score: 1

    Look at that. An actual example of begging the question.

  14. Oldest Human DNA?? by Dcnjoe60 · · Score: 1

    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.

    1. Re:Oldest Human DNA?? by Anonymous Coward · · Score: 0

      'Human' is quite conventionally used to refer to the entire Homo genus which has existed a good deal longer than 200000 years. The typical usage for Homo Sapiens is 'modern humans.'

    2. Re:Oldest Human DNA?? by Anonymous Coward · · Score: 0

      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.

      Human = "Homo", not "Homo Sapiens Sapiens". Homo Sapiens Sapiens is the only LIVING genus of human, but all extinct Homo species are considered "human" in taxonomy.

    3. Re:Oldest Human DNA?? by Anonymous Coward · · Score: 0

      Postmodern humans do date back. That's why these finds are important.

  15. Elvis lives by Anonymous Coward · · Score: 0

    Livid evil elvis genetic lost twin.

  16. Re: Whites evolved from blacks... by Anonymous Coward · · Score: 0

    people that resort to rules based argumentation tend to rely on not getting punched in the face.

  17. Re:Happy Wednesday from The Golden Girls! by Anonymous Coward · · Score: 0

    And yet your offtopic post was modded informative. Jesus H. Christ, what has happened to slashdot? Idiotic offtopic comments like yours being posted, and worse, idiot moderators modding them up. How much offtopic shit will I have to wade through to reach the actual topic today?

    As to the actual topic, human? We were human 100000 years ago? Weren't we human-LIKE way back then? I mean, denisovians and Neanderthals weren't human, were they?

  18. ^ mod up by globaljustin · · Score: 1

    let's do this more...

    if we must suffer AC trolls getting 'firsties' we can at least make lemons into lemonade & collectively mock all AC's...

    --
    Thank you Dave Raggett
    1. Re:^ mod up by Anonymous Coward · · Score: 0

      Anonymous Cowards are a bunch of faggots. There. Good?

  19. Stop It! by Anonymous Coward · · Score: 0

    Stop it right now. You are making me homorny!

  20. Overground coffee by Anonymous Coward · · Score: 0

    Sometimes coffee tastes muddy if it is overground and the smaller particles make it through the filter

    I prefer underground coffee where the grinds are fairly large chunks

  21. Re:Happy Wednesday from The Golden Girls! by werewolf1031 · · Score: 2

    If I understand the subject correctly: Humans, yes; homo sapiens, no.

    That is, 'human' encapsulates more than just us modern homo sapiens, and includes other species of the genus homo, such as homo neanderthalensis (or sub-species homo sapiens neanderthalensis, depending on where you're reading).

  22. Re:Modern Denisovans and survivalinternational.org by xupere · · Score: 1

    They look so kind! But, let us pray WWF and Greepeace doesn't get too involved in this. Or, in other words, How un-pc can this untangling get?

    The World Wrestling Federation and Greenpeace? Seems an unlikely combination but could be interesting ...

  23. Re:Happy Wednesday from The Golden Girls! by jc42 · · Score: 4, Informative

    We were human 100000 years ago? Weren't we human-LIKE way back then? I mean, denisovians and Neanderthals weren't human, were they?

    Well, if you're talking about the conventional usage of "human" in scientific circles, the answer is: Yes, they were; they just weren't modern humans.

    But "human" really isn't a technical term; For that you want something like "Homo" or "hominin", depending on how far back in the tree you want to describe. The term "human" is used informally to mean just about any critters later than the split from the Pan (chimpanzee) branch. It's used when you don't want to be too precise about such things.

    OTOH, "human" is widely used in common speech to refer to anyone "not like us". Sometimes it means "white people", especially in writings from before the 20th century. But you don't much hear such usages in scientific settings. You do see it a lot in media coverage of science, but then it means whatever the journalist thinks it means.

    --
    Those who do study history are doomed to stand helplessly by while everyone else repeats it.
  24. #bearcave by jfisherwa · · Score: 1

    *runs*

  25. Re:Happy Wednesday from The Golden Girls! by glitch23 · · Score: 1

    It's used when you don't want to be too precise about such things.

    It's used when you want to read more into something than you should (hint: there is only 1 kind of human, there is no "modern" vs "early" human) specifically for purposes of spreading doubt about Creation and facts (but not evidence) that attempt to explain a theory that has yet to take shape. There, I corrected that for you.

    Researchers extracted mitochondrial DNA from the femur of a 400,000-year-old hominin

    By the way, did anyone verify the measuring "stick" used to verify the 400,000 year age of this bone to ensure the measuring "stick" was itself accurate? I didn't think so. Carry on with your delusions and your faith in something that can't be proven by the best scientists that mankind can offer.

    --
    this nation, under God, shall have a new birth of freedom. -- Lincoln, Gettysburg Address