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Oldest Human Genome Reveals When Our Ancestors Mixed With Neanderthals 128

sciencehabit writes DNA recovered from a femur bone in Siberia belongs to a man who lived 45,000 years ago, according to a new study. His DNA was so well preserved that scientists were able to sequence his entire genome, making his the oldest complete modern human genome on record. Like present-day Europeans and Asians, the man has about 2% Neanderthal DNA. But his Neanderthal genes are clumped together in long strings, as opposed to chopped up into fragments, indicating that he lived not long after the two groups swapped genetic material. The man likely lived 7000 to 13,000 years after modern humans and Neanderthals mated, dating the mixing to 52,000 to 58,000 years ago, the researchers conclude. That's a much smaller window than the previous best estimate of 37,000 to 86,000 years ago.
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Oldest Human Genome Reveals When Our Ancestors Mixed With Neanderthals

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  • Yeah but ... (Score:5, Informative)

    by ve3oat ( 884827 ) on Wednesday October 22, 2014 @09:30PM (#48209269)
    The same tests on DNA from another man from the same era and locale but from a different Y-haplogroup (and different mt-haplogroup) might show a completely different proportion of genetic mixing and time to most recent mating. Don't draw too many conclusions from a sample of just one.
    • Re:Yeah but ... (Score:5, Insightful)

      by Doubting Sapien ( 2448658 ) on Wednesday October 22, 2014 @10:59PM (#48209741)
      Mod parent up. The article as written is dumbed down and misleading in many ways. Against my usual temperament I'm going to make a sociological/anthropological argument that someone reading the article will draw very wrong conclusions about the nature of prehistoric Neanderthal-modern human interaction. Genetic inheritance or progeny happens to be the only evidence we have right now about early Neanderthal-modern human interaction. But it does not say anything useful about when we "first had sex with" them as the article claims. Consider the following: Archaeological evidence suggests that large scale violence we would consider warfare was a part of human life as far as 7,500 [wikipedia.org] or possibly 14,000 [wikipedia.org] years ago. Does that mean ancient society was all about peace and love before that time? No. There is too little information to make such sweeping conclusions. To return to the subject at hand, not all sexual encounters with Neanderthals are going to leave evidence for us to conveniently find. What we *DO* know at this point is that at least one such encounter resulted in a pregnancy that was carried to term and the resulting offspring lived long enough to have children of his/her own who continued to survive. That's ALL we know. Put another way, imagine the young men and women of ancient communities playing a game of "fuck, marry, or kill" that included their funny looking neighbors. The visual may not be pleasant, but any earlier incidents of war-rape and deliberate infanticide due to parental rejection will leave little to no evidence behind for us. And barring extreme luck, there is almost NO WAY we can know if/when such incidents occurred. Who really knows when Neanderthals and us *FIRST* had sex?
      • Re: (Score:3, Funny)

        by pastafazou ( 648001 )
        Well I don't know about you, but I know when I first had sex with a Neanderthal...and that's all I'm willing to say about it....
      • by radtea ( 464814 )

        This is a general problem with the way people infer origin dates from sparsely sampled distributions: http://www.tjradcliffe.com/?p=... [tjradcliffe.com]

        The earliest anatomically modern human fossils date from about 195,000 years ago, and people often say on this basis that anatomically modern humans appeared about 200,000 years ago, which is statistically illiterate at best.

        Maybe people in the field know better, but I've seen an awful lot of claims like this and even in the semi-professional literature there seems to be a s

    • by globaljustin ( 574257 ) on Thursday October 23, 2014 @01:02AM (#48210227) Journal

      We've got to stop with the Neanderthal nonsense...

      Neanderthals are *not* the magical missing link, nor does proving/disproving the existence of God or the truth of the theory of Evolution...none of this is in play

      This is about legacy academia and how century-old academia wars are burdening good research today.

      Another example: Clovis Culture http://www.examiner.com/articl... [examiner.com]

      Clovis Culture theory has been the bane of anthropologists and archaeologists for decades...the only reason it was so entrenched is b/c of flaws in academia.

      Neanderthals are the same. The whole notion of "Neanderthals" being a separate thing is just a miscategorization of traits that modern humans have. Maybe they are rare, and have become less attractive over the millenia, but not any different than any other trait.

      Look at Russian boxer Nikolai Valuev [google.com]

      The traits we collectively call "Neanderthal" are a distinction without a difference.

      It's a failure of science that some ideas are irrationally difficult to disprove. Usually it is because people are using the research wrongly to prove a non-science point.

      Again...Neanderthals can be variations on modern humans and it **does not disprove evolution!!!**

      • We've got to stop with the Neanderthal nonsense...

        Right we do. There are just a few pieces of evidence now, but it may be that Neanderthal is actually a distant race that falls within our human specie. If their whole genome diverged from the branch of modern humans ~600,000YA and yet --- if there is additional evidence of interbreeding up to ~50,000YA, and humans from ~50,000YA could interbreed with us today (which I believe is true) --- then I consider it extremely likely that a Neanderthal could breed with a modern human.

        And give your children superpow

        • I checked it out...seems interesting

          I kind of wish we could just ditch "neanderthal" and "cro-magnon" from the lexicon entirely...Cro-Mags are "AMH" and IMHO all the evidence shows that Neanderthals are AMH as well...so let's start from scratch with the genomic comparisons and make a new nomenclature

          Back to Earth's Children....from reading the wikipedia, it seems like it might be similar to the film "Clan of the Cave Bear"

      • Neanderthals are the same. The whole notion of "Neanderthals" being a separate thing is just a miscategorization of traits that modern humans have. Maybe they are rare, and have become less attractive over the millenia, but not any different than any other trait.

        Look at Russian boxer Nikolai Valuev [google.com]

        The traits we collectively call "Neanderthal" are a distinction without a difference.

        If you were complaining about the "Cro Magnon" concept you would be on solid ground. That turned out to be an imaginary construct. Neanderthals and Denisovans though definitely form a genetically defined group much more divergent from modern human populations than are found between the most divergent populations among modern humans (defined roughly by the San on one hand and everyone who is not African on the other). That said there is only 0.3% variation across the entire Neanderthal-Denisovan-Modern Human

    • Uh, excuse me, but what do Y-haplogroups have to do with this? Weren't the co-located genes in question observed on the autosomes?
    • by HiThere ( 15173 )

      What they are is an existence proof. And since there is crossover happening with every sperm or egg, this puts a limit on the probable number of generations...though I do need to include "probable".

      P.S.: This wasn't a survey of the Y chromosome.

      OTOH, since the amount was only about 2%, that indicates that the hybridization must have occurred several generations ago, perhaps 50.
      (2% is the modern count, so you can't just say around 5 generations, as some of it is clearly being conserved).

      OTOH, since we shar

    • The same tests on DNA from another man from the same era and locale but from a different Y-haplogroup

      Where's the sample?

      In archaeology (and palaeontology in general), you play the hand you're dealt. (Though you can try to stack the deck a little by choosing where to dig.)

  • by Anonymous Coward

    This can't be right. The world is only 2014 years old!

  • Humanity always fall for the trailer trash around the corner.
    • Re: (Score:2, Informative)

      by Anonymous Coward

      Realize that 80% of the human population lives in abject poverty. The "trailer trash" are already above the average human condition.

  • One sample (Score:4, Insightful)

    by wbr1 ( 2538558 ) on Wednesday October 22, 2014 @09:42PM (#48209339)
    Does not conclusively prove. Mixing could have occurred at many times and locations. While useful, more data needed.
    • by aralin ( 107264 )

      What you say makes no sense. If there were multiple mixings over large periods (we talk thousands of years) there would be uneven chopping of the DNA. Parts would be chopped more than other parts. Also if there were two mixings, but the two resulting groups never met, as your hypothesis assumes, than the second group that didn't result into modern humans is irrelevant. But good try at sounding smart. :)

      • by wbr1 ( 2538558 )
        What if he is descending from one wandering group that ran into and and interbred once in their history. There would be no genetic fragmentation with this individual, however yet another find could be from a different group that interbred at a different time or times. This would result in many different, geographically isolated, groups of humans with different genetic histories of interbreeding with neanderthals.
        • by aralin ( 107264 )

          But this would show either in the way neanderthal DNA fragments in the present day humans. If these fragmentations occurred at different times, the present day DNA would be fragmented differently in different present day samples. Since that is not the case, either it happened in one period or the second case never merged again with the current lines, rendering that irrelevant to present day humans.

          • by Muros ( 1167213 )
            Now who's trying to sound smart. The fragmentation of neanderthal DNA strings in modern genomes is chaotic, because of repeated mixture of genomes with differing amounts of aforementioned genes, and with varying numbers of generations since it's introduction. The article even states that the timeframe for the introduction of neanderthal genes into this individuals genetic makeup is more accurately defineable than is possible for modern humans.
          • by HiThere ( 15173 )

            I'm sure that in present populations DNA traced to Neanderthals has been split every which way. You get crossovers in (nearly) random places everytime a sperm or egg is made.

            What's unusual here is that there haven't been many crossovers. This implies that the hybridization was recent.

            My problem with this is that I'm not convinced that the populations were ever distinct enough that most genes could be traced to one species or another. So what they're saying is that 2% of our genes can be traced to Neander

            • by aralin ( 107264 )

              That simply sounds like some journalist does not understand that there could be a world of difference between 1.7% and 1.9% for example and rounds both to 2%.

              • by HiThere ( 15173 )

                No, I don't think it's that simple. I think they're figuring the percentage against different baselines. Say the difference from chimpanzees was figured against the protein coding genes and the difference from Neanderthals was figured from a baseline of "common differences from chimpanzees". That would make it plausible. But there clearly isn't much time between the first different ancestor between humans and neanderthals, so a large difference is just implausible, even if we don't consider the evidence

    • by jc42 ( 318812 )

      Does not conclusively prove. Mixing could have occurred at many times and locations. While useful, more data needed.

      Yup. But the fossil record tends to be rather sketchy, and has little concern for what we consider our "needs".

    • by u38cg ( 607297 )
      Would you mind outlining your qualifications in genetics that qualify you to make sweeping statements about peer-reviewed research?
  • by Parafilmus ( 107866 ) on Wednesday October 22, 2014 @09:56PM (#48209413) Homepage

    The author's cro-mag bias is showing.

    Her title implies that the neandertals in question are not also our ancestors.

    A better title might have been "...genome reveals when our Cro-Magnon ancestors had sex with our Neandertal ancestors."

    • by Anonymous Coward

      The author's cro-mag bias is showing.

      Her title implies that the neandertals in question are not also our ancestors.

      A better title might have been "...genome reveals when our Cro-Magnon ancestors had sex with our Neandertal ancestors."

      Yeah, I can't believe how many of my ancestors had sex with each other. Disgusting!

  • by tloh ( 451585 ) on Wednesday October 22, 2014 @10:03PM (#48209439)

    How accurate is it for the media to say a "complete" genome was sequenced? I know a little molecular biology and have been lead to believe that certain types of DNA, (centromeres, telomeres, other such regions with lots of repetitive sequences or "fragile sites") are very hard to sequence reliably. Are these "swept under the rug" in a "complete" sequence? Perhaps a related question, how are non-coding regulatory portions of chromosomes handled in whole genome analysis?

    • by kinko ( 82040 ) on Wednesday October 22, 2014 @10:45PM (#48209663)

      I don't know if ancient samples are processed differently, but for 'fresh' samples, the DNA gets broken up into small fragments (200-1000 base-pairs long), and then these fragments get sequenced. All bits of the genome have roughly even chance of getting sequenced, and with thousands or millions of copies of each fragment, you normally get reasonably even coverage over the whole genome.

      The problem is when you map your sequences back onto a reference genome (ie the currently known chr1, chr2, chrX, etc). The aligning software will have trouble deciding where to place a fragment that is part of a highly repetitive sequence (like centromeres or telomeres) , or is duplicated several/many times (eg large gene families that have large sections of the genes in common, or pseudogenes that look like copies of other genes). In addition, we don't even know the exact sequence for some of these regions, so our reference human genome is contantly being updated (currently up to version 38).

      For bioinformatics analysis, sometimes it is easier to sweep some of this under the rug. For example, some people use a reference genome that masks out the centromeres and telomeres (ie our reference sequence just has NNNNNNNNNNNN bases here, instead of As,Cs,Gs and Ts). Otherwise there are databases that list the regions containing repeated sequences or duplicated segments, so you can check any of your findings to make sure they aren't in a suspicious region.

    • by HiThere ( 15173 )

      I'd assume that the media is being quite "generous" in its interpretation. DNA tends to degrade fairly quickly, and I'd be really surprised if there was a good complete genome available to sequence. More probably several very long (unexpectedly long) sequences in several copies and nothing too corrupted.

      I don't think the problems will be restricted to "fragile sites", and I'd bet the problems with telomeres weren't even considered, as those grow and shrink even during a normal lifetime.

      If you're studying

  • The summary refers to the time when neanderthals and modern humans intermixed, but can we really call what came before the mixing modern humans? It seems that something about the combination sparked huge evolutionary changes that allowed us to rather rapidly (evolutionarily speaking) develop modern society. As far as I'm concerned, the history of modern humans starts with the mixing.

  • by Truth_Quark ( 219407 ) on Wednesday October 22, 2014 @11:45PM (#48209971) Journal
    I think that some of those Africans look a little bit more Homo Sapien than Europeans who have the Neanderthal Genes.

    A little bit more upright, less stooped, a little bit less hairy, a little mound of forebrain in their foreheads.

    There's a lot of genetic variation in Africa by comparison though. I'm thinking of those tall, really black-skinned, Sudanese looking people.
  • by Vinegar Joe ( 998110 ) on Thursday October 23, 2014 @01:53AM (#48210423)

    Strangely enough, beer was invented 57,999 years ago.

  • I can tell the same by looking at some of my neighbors

  • Judging by one of my coworkers I'd say it was still going on around sixty years ago.

  • This much older modern human has the same fraction of Neanderthal DNA as modern humans today.

    Think about it.

    We haven't seen any ancient Modern Humans that have a different degree of Neanderthal ancestry.

    When Modern Humans first bred with Neanderthals the offspring were 50/50. If these F1s bred with each other predominantly from then on you would end up with a new breeding population that was roughly 50/50 in heritage. If the F1s predominantly bred with Modern Humans, then the Neanderthan portion would be c

  • The latest big finding on Neanderthals: Some 20% of caveman DNA made its way into the human genome thanks to mating between humans and Neanderthals, though people today typically have only 1% or 2% of the stuff. (People have different parts of the DNA, which collectively represent what's left of the Neanderthal genome.) The results come compliments of two studies. Standout details: In one study of 1,004 people, Harvard researchers wanted to determine which populations have the most Neanderthal DNA; East As

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