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New genetic analysis of archaic hominids binds us closely together


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An endogenous retrovirus or ERV is a genetic scar produced by a failed viral infection. Geneticists can tell its of viral origin because it will contain base pairs associated exclusively with viruses. If the ERV happens to insert in a portion of a cell genome that goes onto contribute to an egg or sperm that creates a new person, and if that same stretch of DNA containing the ERV is part if an allele that ultimately gets selected for widely, eventually the entire population will share it. If the population then splits over time, both descendant groups will have it in the same place. If you and a stranger have a unique ERV occupying the exact same segment in both your respective genomes, it is powerful evidence you are closely related.

Humans and chimps share a number of ERVs, which is more than just a smoking gun that we share a relatively recent common ancestor, it’s a video tape of evolution pulling the trigger. So it was with great interest that a new study comparing ERVs in anatomically modern humans to Neandertal DNA as well as poorly understood contemporary referred to as Denisovans has been released:

In this latest study, the researchers compared genetic data from fossils of Neanderthals and another group of human ancestors called Denisovans to data from modern-day cancer patients. In the end, they found evidence of Neanderthal and Denisovan viruses in the modern human DNA. This suggested that the viruses originated in our common ancestors more than half a million years ago. Currently, the scientists are looking to further investigate these ancient viruses, which belong to the HML2 family of viruses, for possible links with cancer and HIV. More specifically, they’re looking at whether these ancient viruses affect a person’s risk of developing diseases such as cancer.

I’ve already seen a couple of articles pop up with the “scientists baffled” undertone that new evidence shows we are related to neanders and denisovans. Scientists aren’t baffled at that. Finding multiples identical typos in two old copies of War and Peace would make a good case they were printed by the same publisher at the same time. But there would be little doubt they were written by the same author before that. What is fascinating is there was a time, not that long ago in evolutionary scales, when the hominid population was more like Middle Earth, with many different kinds of humans, and less like modern Earth with just the one clade.

Whether or not we could interbreed and produce fertile offspring is also a fascinating debate. The smart money says not only could we, but that we probably did, and may still carry traces of those ancient, now extinct humans deep in our modern DNA.


  1. colnago80 says

    In this latest study, the researchers compared genetic data from fossils of Neanderthals and another group of human ancestors called Denisovans to data from modern-day cancer patients.

    Apparently the folks who wrote this have been reading articles by Milton Wolpoff. Just to correct the record, Neanderthals and Denisovans are not, repeat not ancestors of Homo sapiens. As correctly stated by Darksyde, they have a common ancestor, probably Homo Erectus, with Homo sapiens.

  2. says

    Sayeth my friend the anthropologist when I showed her this –

    I’m trying to figure out whether this is the “Neanderthal/Denisovan DNA in living humans is due to shared ancestry before Neanderthal/Denisovan divergence” hypothesis, or just a broad statement of ultimately common deep ancestry. The hypothesis has been disproved, because there is a large population of living humans (Subsaharan Africans) that are both at the base of existing Y-chromosome and mtDNA lineages (ancestral to everyone) and lacking Neanderthal/Denisovan DNA.

    The only scientists who are baffled are those who insist on labelling these groups as separate species. And they are dreadfully baffled, poor things.

    But the Middle-Earth analogy holds, since Tolkien tells us Men and Elves interbreed, and implies that there was at least one fertile Hobbit-”Fairy” (Elf?) cross.

  3. otrame says

    Andrew, dear, I have to say that

    which is more than just a smoking gun that we share a relatively recent common ancestor, it’s a video tape of evolution pulling the trigger.


    Finding multiples identical typos in two old copies of War and Peace would make a good case they were printed by the same publisher at the same time. But there would be little doubt they were written by the same author before that.

    are two of the best analogies for teaching “why we know evolution happens” I’ve run across in recent years. Thanks for adding to my toolbox.

  4. otrame says

    Now if I can figure out why I put Andrew instead of Steven, I might be getting somewhere. Sorry. Old lady syndrome, I guess.

  5. Ysidro says

    @Kevin, 友好火猫 (Friendly Fire Cat) ,

    I’m glad I wasn’t the only one! I’m still a bit frightened at the idea!

  6. jakc says

    Call me old school on this but the most recent evidence is that moderns, Neandertals and Denisovans are a Claude. The impetus for splitting Neandertals from H sapien was the Out of Africa/Recent African Origin claims from about 25 years ago that Neandertals were an evolutionary dead end, based on the then best genetic evidence available. That claim was wrong. Prior to ROA, Neandertals were considered a subspecies. Cladistically, and I think cladistics are the only legit classification system for evolutionary relationships, modern humans can’t be aligned with H sapiens from 20,000 and then split off from Neandertals and Denisovans. I am surprised to see the continuing effort by people like Chris Stringer, an anthropologist who championed the geneticists, still try to maintain a multiple homo species classification. That’s really a Linnaean approach. Sure, Newton still works if you want to go to the moon, but you need Einstein to make GPS work. In that manner, Stringer and others insist on classifying species on the basis of comparative anatomy. That doesn’t work very well anymore and we shouldn’t use it when we can supplant it with genetic information.

    We are pretty sure at this point of an initial divergence in homo lineages (say 350K ago) followed by later admixture. (The latest evidence doesn’t support the idea that the genetic differences we identify as Neandertal and Denisovan occurred in Africa prior to these groups leaving). The insistence by some on using classifications not based on cladistics leads to an unnecessary profusion of groups – heidelbergenis, habilis, register and so forth and real misunderstandings about evolution. Why do people think that the monkey/human question (why are there monkeys ….) is a good question? Because they don’t understand that when you have an ancestral group and two descendent groups, you can have three species or one species or whatever evolutionary grade you’re using). Stringer and the ROA people use the profusion of species to cover up the weakness of their classification system but sometimes … Stringer suggests that h sap and h erectus may have hybridized in SE Asia, similar to the claim of h sapiens and Neandertals “hybridizing”. It is a ridiculous argument – Erectus cannot give rise to H sap and then later hybridize The two groups would be equally descended from H Erectus. The fact that one group looks more “like” Erectus is beside the point, and shows the danger of using comparative anatomy to define species.

    Whoo. Just finished reading Lone Survivors and needed to get that off my chest.

  7. Holms says

    But the Middle-Earth analogy holds, since Tolkien tells us Men and Elves interbreed, and implies that there was at least one fertile Hobbit-”Fairy” (Elf?) cross.

    WHAT! Who, and when? I’m currently in the middle of my sort-of-regular rereading of The Silmarillion ==> LoTR ==> The Hobbit (+ Unfinished tales alongside each age), which has happened almost yearly since I discovered Tolkein in primary school… and hobbit-on-elf action has not a single mention. Is it in one of those labyrinthine extended notes series?

  8. says

    I am not sure why the idea that there might be multiple Homo species is tough for some… to me it seems more likely than not… based on genetics or other means… for example, erectus could indeed give rise to sapiens, by having a splinter group become isolated and form a new species, and then at a later date, having that new species, sapiens, come back into contact with the still extant erectus, and then have them hybridize… there is nothing illogical about this, and nothing that we have3 not seen in many other species…

  9. jakc says

    @Paul Silver
    These are reasonable questions and I will do my best to deal with them. First though, a bit of background on the issue of hominid evolution. In the 1970’s, anthropologists generally considered Neandertal to be a subspecies: that is H Sapiens Neandertalis and H Sapiens Sapiens. In the 1980’s, with the advent of genetic analysis, geneticists and some anthropologists developed the “out-of-Arica”/Recent African origin theory: that H Sapiens arose in Africa and then replaced all other humans in the world. In their view then, Neandertals were an evolutionary dead end, and based on comparative anatomy, should be viewed as a separate species. What is wrong with this approach, you ask?
    It is needlessly complex and when not done carefully, violates the principles of cladistics. In cladistics, organisms are grouped in clades, based on the last common ancestor. Now initially, it didn’t appear to do so: the OOA theory put the last common ancestor of modern HS at about 200,000, and the last common ancestor of HS & HN at about 400,000 years ago, so you could group HS alone as a valid clade, and HN & HS as a larger clade. The OOA theorists also called the ancestor to HS and HN Homo Heidelbergensis in keeping with cladistics. Why does the ancestor have to have a different name? Because both HN and HS are equally descended from the parent group (Heidelbergensis). That is, take HN and HS at say 50,000 years ago. Both have been evolving from HH for 350,000 years. It may be, that relying on comparative anatomy, an anthropologist might regard HS as closer to HH than HN to HS. That’s a mistake. Both descendant groups are equally related to the ancestral group. Why favor one over the other? As it turns out, Neandertals are in the line of descent for modern humans, and so the premise of that the African group and modern humans form a clade is wrong. The most recent genetic work on humans now clearly shows that Neandertals contributed to our genetic make-up. We have Neandertal ancestors. Clades must include all the descendants from the common ancestral group. African hominids from 150,000 years ago, and modern humans are no longer a valid clade: that clade must include Neandertals. Calling the group from 150,000 years ago H Sapiens, and modern humans H Sapiens, largely on the basis of comparative anatomy, implies thde wrong relationship that Neandertals have with modern humans.
    It matters in a whole series of ways. Take the “if humans evolved from monkeys, why are there still monkeys” question that many people who are unfamiliar with evolution regard as a good question. Humans and old world monkeys are more closely related to each other than either group is to new world monkeys. In very rough figures, new world monkeys diverged from us 30 million years ago; old world monkeys diverged from us 25 million years ago (these are very rough numbers, and still subject to revision). Someone looking at the anatomy of monkeys might decide that a spider monkey is more like a vervet than a vervet is like a human, but that’s like saying your third cousin is more closely related to you than your second cousin because the third cousin “looks” more like you. That is the basic problem with using comparative anatomy for groupings, especially when studying evolution, instead of using cladistics (lines of descent). Different people, by emphasizing different features, can come to different judgments as to which groups are most alike. Cladistics requires determining lines of descent, but once done, the resulting relationships are easily understood in a cladogram and not subject to human judgments about relatedness. If we use comparative anatomy, most people would look at the common ancestor and say monkey, giving rise to odd ideas about “more evolved” and “less evolved”. However, applying cladistics, we understand that if we call that common ancestor of the spider monkey and humans a monkey, then both are monkeys. Both groups have been evolving from that common ancestor for an equal amount of time; and are roughly equally related to the common ancestor (given the length of human generations (we are in fact likely a bit closer in terms of the numbers of generations to that monkey-looking common ancestor than the spider monkey).
    In short, cladistics will let you have an ancestral species and two daughter species (or families or orders or whatever rank you wish to put in there), or an ancestor and two subspecies. You can’t have two species – that is, an ancestor and continuation of that line, and then a new species. Prof. Stringer generally follows this convention but near the end of the Lone Survivors suggests the Erectus-Sapiens “hybrid”. The book is not a scientific paper, so it may be in the literature, he would name the group as a species distinct from Erectus, but Erectus is the ancestor of both the groups. Alternatively, they could both be subspecies of Erectus. Calling one group Erectus, and the other H Sapiens, implies that one group is more related to Erectus than the other, something that is clearly wrong.
    Cladistics doesn’t require the use of a single human species, but I would argue that limiting the number of species is a simpler approach that emphasizes the real evolutionary history. Under a comparative anatomy approach, species are artificial categories, as much art as science, a judgment about relatedness. This is the old Linnaean system, a fine system in its time that helped pave the way for the theory of evolution. It made for real breakthroughs in understanding that life had common relations – after all, if all creatures are specially created, then why are some – cats and dogs for example, more closely related than others, cats and tuna, for example? The commonalities noted by Linnaeus eventually helped us understand that reason that some creatures seem more alike than others is due to more recent common descent. The problem with continuing to use this approach is that it leads to gross misunderstandings. If you look at Wikipedia for example, you’ll see sharks, tuna, lungfish and coelacanths all called fish. And yet, you are more closely related to the lungfish and coelacanth, and they to you, than any of the three are related to a tuna. You are more closely related to a tuna, and it to you, than either is to a shark. We distinguish dolphins from tuna because of their various anatomical differences, yet a dolphin and a tuna are more closely related to each other than to a shark, which gets lumped in with tuna as a fish. If you saw this information as a cladogram, you would see that lungfish, coelacanths and humans forms a clade, that those three groups form a larger clade with tuna, and that those four groups form an even larger clade with sharks. When we do not do classifications cladistically, how can we expect people to properly understand evolutionary relationships?
    To finish the point about multiple human species. First, simpler is better. Second, if we have multiple Homo species – Neandertals, Sapiens, Denisovians and perhaps others – then we need to add one more for modern humans, who are a hybrid of at least these three groups. Failing to do so give people the wrong ideas about our evolutionary history and violates cladistics principles.
    I hope this rambling post answers some of your questions about my earlier post. I have BA in anthropology but outside of some limited field work, and a continuing interest in the subject, have not pursued it professionally. I have however fairly recently come to the conclusion that cladistics is too often ignored in evolutionary studies and in taxonomy. In any event, I appreciated your response, and would be happy to continue this conversation. (I’ll try to be briefer in any future response).

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