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Oldest Human Genome Reveals When Our Ancestors Mixed With Neanderthals

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.

20 of 128 comments (clear)

  1. Yeah but ... by ve3oat · · Score: 5, Informative

    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.

    1. Re:Yeah but ... by Doubting+Sapien · · Score: 5, Insightful

      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 or possibly 14,000 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?

      --
      ========== "Hello World" in my programming language of choice: ATG - LET THERE BE LIFE - TAG ==========
    2. Re:Yeah but ... by K.+S.+Kyosuke · · Score: 2

      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?

      --
      Ezekiel 23:20
    3. Re:Yeah but ... by pastafazou · · Score: 3, Funny

      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....

  2. One sample by wbr1 · · Score: 3, Insightful

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

    --
    Silence is a state of mime.
    1. Re:One sample by jc42 · · Score: 2

      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".

      --
      Those who do study history are doomed to stand helplessly by while everyone else repeats it.
  3. Re: Exinction by saloomy · · Score: 2

    My guess is that the fact that no organisms exist with a Neanderthal genome defines them as extinct. Where one draws the line is more art than science I guess. There is a species of Galapagos tortoise that was biologically extinct since there was until recently just one male member (lonesome George). I know that there are some genetics in us (like the HMG group of proteins) that are ancient, but work so well that we still retain them. That doesn't mean the first species to have evolved them isn't extict, it just means we evolved from them.

  4. Re:Never fails... by Anonymous Coward · · Score: 2, Informative

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

  5. Title seems a bit racist by Parafilmus · · Score: 4, Insightful

    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."

  6. Re:First? by Anonymous Coward · · Score: 3, Funny

    I belong to the group having two to four percent Neanderthal in me and I still haven't scored with a pure blooded homo sapiens, you insensitive clod!

  7. Question for sequencing expert. by tloh · · Score: 4, Interesting

    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?

    --
    Stay sentient. Don't drink bad milk.
    1. Re:Question for sequencing expert. by kinko · · Score: 3, Informative

      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.

  8. Re: Bone a Neanderthal by bill_mcgonigle · · Score: 3, Informative

    it couldn't be measured if it weren't a distinct genotype. That says nothing about speciation, of course.

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  9. Re: Exinction by jc42 · · Score: 5, Insightful

    My guess is that the fact that no organisms exist with a Neanderthal genome defines them as extinct. Where one draws the line is more art than science I guess ... I know that there are some genetics in us (like the HMG group of proteins) that are ancient, but work so well that we still retain them. That doesn't mean the first species to have evolved them isn't extinct, it just means we evolved from them.

    Well, I don't think that quite matches the scientific concept of "species". By your definition, almost all species who were alive 50,000 years ago would be considered extinct, but hardly any biologists would agree with that. It's true that no humans alive today have 100% Neanderthal genes, but it's also nearly certain that there are no living humans with 100% Cro-Magnon genes, either. What happened would be considered a mixing of several human sub-species after migrations of one or more African groups into Eurasia. The Cro-Magnon sub-species disappeared, too, and modern human Caucasian and Asian sub-species are the results of that mixing. This sort of thing happens in species all the time, when conditions allow such genetic mixing, and the result is rarely considered a new species.

    The fact is that modern humans are all one species. We can and do interbreed when groups mingle, and there are no groups of modern humans that are genetically incompatible. If sub-species "disappear" by genetic mixing, that is usually not called an extinction event. It's just the routine and normal mingling of subspecies.

    An interesting contrast is that most North American duck species are known to hybridize occasionally, and the offspring are usually fertile. Does this mean they're really all one species? No, because they all mingle a lot, but interbreeding is rare. They have "behavioral" species-separation features, mostly based on female mate choice. The females are mostly all mottled brown (protective coloring), and the males often approach females of other species (because they can't tell them apart either ;-). But the females usually only accept males that have the "right" color markings; the others are ugly to them. This suffices to keep the species separate, though there is probably a very low level of genetic interchange between many of the species.

    But humans aren't like this. Even if we do generally prefer mates in our own subspecies, most of us do find many members of other subspecies physically attractive, and we'll mate with them given the opportunity. This means that we really are all the same species. We now have good evidence that the Neandertals were merely another subspecies, because when they had the opportunity, they did interbreed with those slender, dark-skinned folks who migrated into their territory. They did so often enough to produce a new subspecies that's physically distinct from either of the earlier two (or three or more).

    --
    Those who do study history are doomed to stand helplessly by while everyone else repeats it.
  10. Africans. by Truth_Quark · · Score: 2

    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.

  11. Neanderthals are 'modern' humans by globaljustin · · Score: 3, Insightful

    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...

    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

    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!!!**

    --
    Thank you Dave Raggett
  12. 52,000 to 58,000 years ago? by Vinegar+Joe · · Score: 3, Insightful

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

    --
    "The average reporter we talk to is 27 years old......They literally know nothing." - Ben Rhodes
  13. Re: Exinction by radtea · · Score: 2

    Well, I don't think that quite matches the scientific concept of "species".

    There is no generally-agreed-upon "scientific concept of species". The "Biological Species Concept" is a well-know and highly contentious artifact. It is clearly useful, but how it is defined varies enormously from person to person and across sub-fields.

    This variation doesn't matter much in practice, but it gives philosophers who for some unfathomable reason want there to be just one BSC fits. They seem unaware that concepts are tools used by knowing subjects to understand objective reality, so different subjects with different purposes will tweak the tool as appropriate, much the way a carpenter and a plumber are apt to use different types of hammer.

    --
    Blasphemy is a human right. Blasphemophobia kills.
  14. Re: Bone a Neanderthal by K.+S.+Kyosuke · · Score: 2

    If we could breed with it and the offspring was fertile, I guess there's a reason why some people still insist on calling them Homo sapiens neanderthalensis instead of just Homo neanderthalensis.

    --
    Ezekiel 23:20
  15. Re: Exinction by HiThere · · Score: 2

    What's a Neanderthal? What's a Cro Magnon?

    Basically, these are names assigned to groups of fossils with similar bones. Sufficiently similar, for some nearly arbitrary value of sufficiently.

    FWIW, it is my belief that they typical Neanderthal woman had a pelvic girdle to tight to pass a Cro Magnon baby. (The adults definitely had very differently shaped heads, though what that means is subject to doubt.) This explains nicely the lack of Neanderthal mitochondria in our genome. And it means that while Neanderthal males could successfully mate with Cro Magnon women, the converse didn't work out. As a result heads shaped like the Neanderthal disappeared from the gene pool, and any genes for producing them, and any genes that were tightly coupled with them.

    OTOH, I haven't heard anything about the shape of the heads of the Denisovians. Some people have some of their genes, too.

    It is my belief that Cro Magnon/Neanderthal/Denisovian is all one species, and that splitting them into separate species is an error, one fostered througout palentology, not just in this case, because it is much more important to discover a new species than to discover a new population with some unusual features.

    OTOH, please note that species boundaries are nowhere near as absolute as normally thought. Often there will be diverse populations of a single species clustered in a spread out area, with the populations at the extremes of the area either unable or unwilling to interbreed, even though there is a continual flow of genes throughout the cluster, i.e., every adjacent population is willing to breed with its neighbors.

    --

    I think we've pushed this "anyone can grow up to be president" thing too far.