Neanderthal genes are everywhere

by Matthew Cobb

[EDIT: IN JANUARY 2016, KEY POINTS OF THE STUDY DESCRIBED BELOW WERE DISCOVERED TO BE UNTRUE. Read this to see why.]

As regular readers will know, some of the most astonishing discoveries in the whole of science that have occurred over the last few years have been with regard to our understanding of recent human evolution.

In the last five years we have not only sequenced the genome of an extinct form of human, generally known as Neanderthal man, we have also used genomics to prove the existence of another human population, called the Denisovans after the name of the cave in Siberia where one tooth and a little girl’s finger bone – our only physical traces of this type of human – were found.

Studies of these genomes, using the kind of analysis we talked about yesterday, have revealed the amazing fact that our human ancestors mated with both Neanderthals and Denisovans. We know this because we can find traces of the genomes of both these extinct types in modern humans.

For example, it turns out that the gene that helps Tibetans live at high altitude was obtained from the Denisovans! There are only 95 genetic differences between humans and Neanderthals that would produce a difference in an amino acid (the building blocks of proteins), out of the 3 billion genetic bases in our genome.

This exchange of genes between humans and Neanderthals and Denisovans proves that, from a biological point of view, we were all part of the same species, whatever differences there may have been in our morphology (Neanderthals were generally stockier and stronger – their skeletons show many signs of fractures; we know nothing at all about Denisovan morphology beyond that tooth and finger).

Modern reconstructions of Neanderthals tend to look less like a cartoon caveman, and more like this:

Neanderthal reconstruction: Fabio Fogliazza/Human Evolution Museum (MEH)-Junta de Castilla y León (Spain)

These interactions with our extinct cousins may have gone one quite extensively. In spring this year the genome from a human skeleton from 40,000 years ago was analysed, showing that this person – who lived in what is now Romania – had as much Nenaderthal DNA as if he had had a great-great-grandparent who was a Neanderthal…

Up until last week, it was argued that all modern populations outside of Africa contained DNA from the encounters between the humans who left Africa around 60,000 years ago, and then met the Neanderthals in Europe and the Middle East. Those humans who migrated out through Asia towards the far East, Australia, and Oceania, also mated with the Denisovans.

Modern Africans, it was argued, had no Neanderthal DNA, for the simple reason that their African ancestors did not leave the continent, and so did not encounter our Neanderthal cousins. Intriguingly, there are hints that African DNA may contain unique signs of mating with yet another, completely unknown, form of human, in Africa. These DNA sequences are apparently not shared by modern people from outside Africa.

The story has now become even more complicated, following the publication of an article last week studying the DNA from a man who lived in what is now Ethiopia, around 4,500 years ago. This man, who the scientists called Mota, is the first ancient DNA to have been isolated from Africa – most skeletal remains from the continent have been too degraded by bacteria to be useful. So researchers deliberately sought a skeleton in arid mountainous conditions, hoping it would be in a good state to be analysed.

Apart from the technical prowess involved (and the promise of future studies of other, older African skeletons), analysis of Mota’s genome provided a big surprise.

It had long been known from archaeological data that people from Middle East had migrated into Africa around 3,000 years ago, in what is known as ‘back-flow’. So the researchers expected that Mota, who predated this migration, should not have had any genetic connection with Europe. But it turned out that his closest relatives would have come from Sardinia, off the coast of Italy. This suggested that the ‘back-flow’ from West Eurasia into Africa was of far greater duration and extent than archaeologists had previously suspected.

When they compared Mota’s DNA with those of modern African populations, they found that the European sequences he carried were also present deep in the continent, even amongst the Pygmies of the Congo. Even ‘reference’ African genomes, such as those from the Yoruba and Mtubi peoples, which were thought not to have been affected by interbreeding with Europeans, turned out to have around 6% of their DNA from European DNA, like Mota.

This indicates that there was substantial migration into Africa by people from Europe and the Middle East, and that their offspring – and their DNA sequences – mixed deep into the Continent. It should be noted that most of that DNA probably did not code for proteins (only 5% of our DNA does this) but will either have been regulatory DNA that controls gene expression or, more, like, the other 85% of our genome, which apparently does nothing and is ‘junk DNA’.

Llorentefig1

Map showing the distribution of genetic similarities across the African continent, in comparison to Mota (Gallego Lllorente et al. in press)

Llorente-10-09-15 (1)

Map showing the proportion of West Eurasian component, λMota,LBK, across the African continent. (Gallego Lllorente et al. in press)

The final novelty came when the researchers looked at Neanderthal DNA. Mota carried that DNA, just like me, because his ancestors had mated with Neanderthals tens of thousands of years earlier.

And it turned out that some of those Neanderthal sequences could also now be detected in African populations, too. They were very dilute – around 0.5% – but they were clearly there. They do not indicate that there were Neanderthals in Africa, but rather that when the offspring of Mota and others carrying migratory European sequences spread their DNA into Africa, they also spread small amounts of Neanderthal DNA, too.

Those sequences had always been seen, but they had been misinterpreted – because they were present in Neanderthals, Europeans and Africans, researchers had assumed that they were ‘ancestral’, that is, traces of our deep common ancestry in Africa. Now we know that at least some of them were the consequence of distant matings with Neanderthals, carried into Africa by people migrating into the continent.

It is even possible that those rumours of strange DNA sequences in African populations may in fact relate to matings elsewhere in the world, the consequences of which were then carried back into Africa by migrants, leaving their traces in the DNA of today’s populations.

This is a momentous time in the study of human evolution. Sadly, I’m too late in my career to start over, but students should seize the moment and flock into this area. As Wordsworth said with regard to the French Revolution:

      Bliss was it in that dawn to be alive,
      But to be young was very heaven!

81 Comments

  1. GBJames
    Posted October 13, 2015 at 1:10 pm | Permalink

    Thanks, Matthew. Very, very interesting stuff.

  2. Mark Sturtevant
    Posted October 13, 2015 at 1:15 pm | Permalink

    Very cool. This is the stuff that keeps me coming back to WEIT several times a day. I come for the science. I stay for the cats and all the other stuff.

  3. Merilee
    Posted October 13, 2015 at 1:17 pm | Permalink

    Sub

  4. Billy Bl
    Posted October 13, 2015 at 1:20 pm | Permalink

    These are certainly interesting times we live in. Within my lifetime, we have gone from a few finds of Homo erectus to quite a large family. And our descent seems far from linear. Good article.

  5. Stephen Barnard
    Posted October 13, 2015 at 1:21 pm | Permalink

    The information we’re gleaning from genomics boggles my mind.

    That Neandertal reconstruction is the best I’ve seen, if not for accuracy (because who really knows?) then for artistic merit.

    I wonder if we’ll find evidence of mating between sapiens and erectus? The most recent erectus fossils at 70,000 years overlap out-of-Africa by quite a bit.

    And by the way, Matthew, I much enjoyed your book.

    • Frank
      Posted October 13, 2015 at 2:00 pm | Permalink

      When we look across large spans of time, species designations (and even the biological species concept) become quite nebulous. I find it difficult to believe that “Homo erectus” specimens from 70,000 years ago belong in the same category as African specimens from more than 1.5 million years ago (also called H. ergaster). There’s something to be said for wishy-washy designations like “late H. sapiens”, etc., since temporal change shows the artificiality of Latin binomials.

  6. reasonshark
    Posted October 13, 2015 at 1:23 pm | Permalink

    I think there’s a stereotype about the Out of Africa migration of humans; that it was like some single, one-way, intergenerational “great undertaking”. It’s refreshing to see that the reality is more complicated than that.

    This reminds me of the chapter in The Ancestor’s Tale about the migrations of different species of ape during the Neogene period, specifically the Orang Utan’s tale. It suggested that generations of apes as a whole have been bouncing between Asia and Africa over millions of years. And now it looks like our ancestors and distant cousins did the same on a much smaller scale! It’s like a fractal pattern of migrations within migrations. And this is just for a handful of taxa close to one species, Homo sapiens!

    I shudder to think of the astronomical sets of migrations hidden in the darkness of prehistory. The more we know, the more we realize we don’t know.

  7. darrelle
    Posted October 13, 2015 at 1:38 pm | Permalink

    Thank you for a fascinating article Matthew. I couldn’t agree more, that we live in exciting times regarding what science has revealed, and will continue to reveal, about our ancestory.

    Especially interesting are the hints of gene flow between early Africans and an unknown human subspecies. It shouldn’t really come as a surprise exactly, just very interesting. After all Africa is where all of our known Homo ancestors appear to have evolved. It is certainly plausible that there where periods of coexistence and interaction between one or more subspecies of humans in early Africa.

  8. Posted October 13, 2015 at 1:38 pm | Permalink

    Mota had no Eurasian backflow. Rather by learning what the baseline genomics were prior to backflow, the authors learned that backflow later on was more prevalent than previously understood. And that it included more Neatherthal genetics than previously understood.

    http://www.sciencemag.org/content/350/6257/149.full

    “By comparing 250,000 base pairs from Mota’s genome with the same sites in individuals from 40 populations in Africa and 81 populations from Europe and Asia, the team found that Mota was most closely related to the Ari, an ethnic group that still lives nearby in the Ethiopian highlands. They zeroed in on the DNA that the Ari carry but Mota doesn’t, which was presumably added during the past 4500 years. They found that Mota lacks about 4% to 7% of the DNA found in the Ari and all other Africans examined. This new DNA most closely matches that of modern Sardinians and a prehistoric farmer who lived in Germany. Hints of these early farmers’ DNA previously had turned up in some living Africans, but Mota helped researchers zero in on the farmer’s genetic signature in Africa, and to establish when it arrived.”

    • Mark Sturtevant
      Posted October 13, 2015 at 2:46 pm | Permalink

      This helps with my questions below. All I can say is that the backflow is not a big deal.

    • Matthew Cobb
      Posted October 13, 2015 at 2:58 pm | Permalink

      Thanks for the clarification!

  9. Heather Hastie
    Posted October 13, 2015 at 1:40 pm | Permalink

    This is absolutely fascinating!

  10. rickflick
    Posted October 13, 2015 at 1:44 pm | Permalink

    I’m very impressed with the recent progress in genomics. I look forward to more of the unfolding story.

  11. nickswearsky
    Posted October 13, 2015 at 1:46 pm | Permalink

    4,500 years ago the Nile Valley civilization had already existed for 6 centuries. A significant commercial and political state. I do not find it at all surprising that there was considerable admixture from the Mediterranean basin all the way down the Nile River and well into Sub-Saharan Africa. The Nile Valley civilization would have sent traders and others far and wide, and attracted even more. Some carried Neandertal genes (nobody is making the claim that Neandertals entered Africa in any significant way). From there, gene flow did it’s work. People tend to think of prehistoric Africa as a static, singular entity. It never was. As an Africanist, I am glad people are finally realizing this.

    • Mark Sturtevant
      Posted October 13, 2015 at 2:43 pm | Permalink

      You know, that seems obvious now that you point it out.

    • Posted October 15, 2015 at 3:57 pm | Permalink

      We tend to forget that African Nubians were a significant component of the Egyptian Empire for a very long time.

      The Queen of Sheba, who purportedly visited King Solomon, was thought to have been from Saaba from the far south of Africa. Saaba was a very highly developed civilization.

      Trading and warfare has mixed human genes throughout history. It’s good to be learning ever more precisely about how intertwined we all are.

  12. Joe Dickinson
    Posted October 13, 2015 at 1:54 pm | Permalink

    We always see such data interpreted in terms of “migrations”, but I wonder if the more neutral term “gene flow” might be preferable. Migration evokes images of people picking up and moving over considerable distances. Given the sparse sampling and long time intervals, it seems just as likely that we are just looking at the results of exchange of mating partners between bands a few miles distant. Over thousands of years, genes could flow between the most distant parts of Africa, Asia and Europe even if no individual ever moved more than 10 or 20 miles from his/her birthplace.

  13. Mark Sturtevant
    Posted October 13, 2015 at 1:54 pm | Permalink

    Two things. I guess they are questions.

    1. From the figures that I have seen showing the trees of genetic relationships involving H sapiens sapiens, H. sapiens neanderthalis, and the Denisovans, the different branch lengths on the trees seem to say that the Denisovans are a more ancient group, perhaps in the range of what we call H. heidelbergensis or H. erectus. I wonder if other people have wondered that.

    2. The key evidence that we interbred with neanderthals was that the genetic markers were shared between populations that lived together. We interbred with neanderthals mainly in Europe, and so Europeans have neanderthal genes (and also Asians, I guess b/c of later admixture between Europe and Asia). So finding evidence of backflow of non-African humans with their neanderthal DNA well into Africa sort of undercuts this whole elegant argument. So my question is how do we know that this backflow came later, and was not ancestral to all H. sapiens?

    • darrelle
      Posted October 13, 2015 at 2:21 pm | Permalink

      RE your 2, see Nathan Taylor’s clarifications of the study at comment 8 above.

  14. Matt
    Posted October 13, 2015 at 2:18 pm | Permalink

    Proves my theory that homo sapiens are the sluttiest species ever. Even before alcohol.

    • Torbjörn Larsson
      Posted October 14, 2015 at 3:47 am | Permalink

      Alcohol use (from fermented fruit admittedly) is old in apes. I am more surprised that the genes doesn’t turn up in monkeys, as I remember it.

      Cross mating is common in mammals and, I think, fairly common in some crustaceans (or at least the insect subclade).

      It is nature that is slutty. Blame the contingency of evolution. 😉

      • Posted October 15, 2015 at 4:11 pm | Permalink

        Use of alcohol from fermented fruit is also old in elephants and birds, among others. In
        Palo Alto, we used to enjoy watching the birds get smashed on fermenting Pyracantha berries. Such acrobatics!

        I’m pretty sure that with or without the influence of alcohol, when the urge hits, any port in the storm becomes the objective. If progeny happens to be produced, the gene pool allowed it and more potential inherited characteristics become available to be spread
        further. If the participants weren’t compatible, no progeny results and it was
        just a good time, maybe.

  15. Posted October 13, 2015 at 2:22 pm | Permalink

    Interesting stuff, great read

  16. Jeffery
    Posted October 13, 2015 at 2:29 pm | Permalink

    People must have gotten along better then than they do now…..

    • Mark Sturtevant
      Posted October 13, 2015 at 2:51 pm | Permalink

      Well, maybe not. I like to point out that as more advanced kinds of humans appeared, with their bigger brains and fancy new kinds of stone tools, the earlier kinds of humans disappeared. I do not think that the older cultures asked them to leave, if the known history of our species is any guide.

    • Gregory Kusnick
      Posted October 13, 2015 at 3:26 pm | Permalink

      This tells us there was sex between various human populations. It doesn’t tell us whether it was consensual.

      • Posted October 14, 2015 at 8:41 am | Permalink

        Yes. Due to slavery in the USA, most American blacks have about 25% European DNA.

  17. Posted October 13, 2015 at 2:52 pm | Permalink

    Enjoyed the post.

    As someone commented above, 4500 years ago seems pretty late in the day. We were already well into Egypt rising and all the trading and movement of people that such should have entailed.

    A couple of questions for anyone:

    Can we not take good DNA samples from mummies?

    How confident are we in the denisovan story?

    • darrelle
      Posted October 13, 2015 at 3:08 pm | Permalink

      DNA samples from mummies has been done, but I don’t know the details off hand. I imagine that, as with any old sources, that reliably accounting for contamination is a thorny problem.

      • Torbjörn Larsson
        Posted October 14, 2015 at 3:52 am | Permalink

        Pääbo started out with mummies IIRC. But I don’t think they were very old (~2 kyrs).

  18. Michael Michaels
    Posted October 13, 2015 at 3:04 pm | Permalink

    I went looking to find how much difference in DNA there is between humans, chimpanzees and neanderthals, this is what I found (in case anyone else is interested):

    The Neanderthal mtDNA sequences were substantially different from modern human mtDNA (Krings et al. 1997, 1999). Researchers compared the Neanderthal to modern human and chimpanzee sequences. Most human sequences differ from each other by on average 8.0 substitutions, while the human and chimpanzee sequences differ by about 55.0 substitutions. The Neanderthal and modern human sequences differed by approximately 27.2 substitutions. Using this mtDNA information, the last common ancestor of Neanderthals and modern humans dates to approximately 550,000 to 690,000 years ago, which is about four times older than the modern human mtDNA pool. This is consistent with the idea that Neanderthals did not contribute substantially to modern human genome.

    http://humanorigins.si.edu/evidence/genetics/ancient-dna-and-neanderthals/neanderthal-mitochondrial-dna

    “A substitution is a mutation that exchanges one base for another (i.e., a change in a single “chemical letter” such as switching an A to a G). Such a substitution could: change a codon to one that encodes a different amino acid and cause a small change in the protein produced.”
    (Google search definition)

    • Matthew Cobb
      Posted October 13, 2015 at 3:17 pm | Permalink

      This refers to our mitochondrial DNA, which is about 26,000 base pairs and is involved in producing energy. The Neanderthal DNA we are referring to here is the 3 billion base pairs of our nuclear DNA which helps determine what we look like etc. We were exchanging that DNA with Nesnderthals, mixing it up, right till the Neanderthals died out about 30,000 years ago. As far as we know, the last of them lived in caves on Gibraltar, looking over the plains below the Rock, with the sea far in the distance.

      • Torbjörn Larsson
        Posted October 14, 2015 at 3:57 am | Permalink

        Re lost mitochondrial lineages, which is one reason besides higher mutational frequency of the old image of no interbreeding:

        I also seem to remember that one Neanderthal nuclear genome sequencing show that individual didn’t contribute to today’s gene pool.

      • Torbjörn Larsson
        Posted October 14, 2015 at 3:59 am | Permalink

        But – I remember now – he (it was a male) had ancestors that had recently interbred with our subspecies. So fairly frequent mating has happened, but also extinctions.

        • Michael Michaels
          Posted October 14, 2015 at 11:12 am | Permalink

          Thank you for clearing up my misconception.

          Do you know how the mitochondrial DNA got passed on, but not nuclear DNA? Is that just the luck of the draw, or not known?

          I don’t suppose you recall the article?

          I obviously need to read up on this again if I made such an obvious error.

  19. nickswearsky
    Posted October 13, 2015 at 3:26 pm | Permalink

    The evidence for gene flow from Asia into Africa long ago is also abundant when you look at cattle. Nearly 10,000 years ago, people were living as cattle pastoralists in what is now the Sahara (then, a rather pleasant grassland). Although there is some debate, those cattle came from SW Asia, as did sheep and goats, which are not native to Africa. Those animals did not come by themselves! They are indicative of substantial interaction between Africa and the outside world in the prehistoric past — well before 4,500 years ago.

    • tinwoman
      Posted October 13, 2015 at 3:54 pm | Permalink

      African, European, and Asian cattle all belong to different species and were domesticated separately. African cattle have no relationship to the humped Zebus of India, and there are only many Zebus in Africa now because they were brought there in modern times. Similarly European cattle, descended from the Aurochs, have close relationship to either African or Asian species of cattle. All can mate with each other and produce fertile offspring; that is also true of yaks, water buffalo, and bison both American and European. Domestic cattle have many branches and there were different domestication events, something which isn’t true for all livestock. It’s complicated.

    • tinwoman
      Posted October 13, 2015 at 3:55 pm | Permalink

      Excuse me, that should read “no close relationship”

    • tinwoman
      Posted October 13, 2015 at 3:57 pm | Permalink

      Some more precise and detailed information and species names here: http://archaeology.about.com/od/domestications/qt/cattle.htm

  20. Posted October 13, 2015 at 4:24 pm | Permalink

    Great stuff! We are all sapiens now.

    • Stephen
      Posted October 13, 2015 at 5:20 pm | Permalink

      If only we were all sapient.

  21. John Harshman
    Posted October 13, 2015 at 4:25 pm | Permalink

    This exchange of genes between humans and Neanderthals and Denisovans proves that, from a biological point of view, we were all part of the same species

    Beg to differ. It would be very convenient if species were that clearly demarcated, but they just aren’t in many taxa, including lots of birds and mammals. Of course that’s what we expect from evolution as long as speciation isn’t a saltational event.

    Anyway, I and many others would not consider a small amount of introgression to be a conclusive argument against separate species status, though it might be suggestive. How strong was pre-mating isolation between populations? What were the comparative population sizes? How long did they live in sympatry? Was there selection favoring some of the genomic regions that introgressed? “Were they the same species?” seems a less interesting question to me than those.

    • Petu W.
      Posted October 14, 2015 at 1:55 am | Permalink

      I agree. There is still no reason to think that sapiens and neanderthalensis are the same species. Anymore than coyotes & wolves or grizzlies & polar bears.

      Anyways, I just finished Matthew’s book and it was great!

    • Posted October 14, 2015 at 2:50 am | Permalink

      I think the key point is that the genetic data undermine the paleoanthropological definition of neanderthalis and sapiens as two different species on the basis of morphology.

      They may well have generally been isolated – by environment, by social mores or other factors – but the extent of the introgression we can now detect shows that sexual encounters took place both ways, and have left traces wherever they look. Our two populations (species, if you prefer, but I don’t), overlapped for around 5,000 years it seems.

      Speciation is a process and it is always difficult to point to a single qualitative leap – Professor Ceiling Cat has written a fabulous book about this, exploring 8 recent definitions of species. I hope he will write something about this here! – MC

  22. Kevin
    Posted October 13, 2015 at 4:50 pm | Permalink

    Great post. I certainly have the feeling as an outsider to the field of human evolution that many great discoveries have occurred in a very short time. What a wonderful time to be delving deeper and deeper into our ancestors roots.

  23. Posted October 13, 2015 at 5:09 pm | Permalink

    Put the Neanderthal whose portrait is above in modern clothes and drop him in the middle of the city and nobody would bat an eye. Simply on a visceral level, it seems strange to call a group of people so similar to us a different species. There’s more superficial difference today between a modern native of Japan and Mexico than there is between this Neanderthal and somebody native to the Mediterranean.

    I bet the differences between Neanderthals and us were much more social and tribal than anything else.

    b&

    • Stephen Barnard
      Posted October 13, 2015 at 5:29 pm | Permalink

      The brow ridges, the nose, and the chin are extreme outliers on the sapiens scale. He might pass as a modern human, but he’d get some stares on a city bus.

      • Posted October 13, 2015 at 5:43 pm | Permalink

        I’m not so sure he would — especially not in a particularly cosmopolitan city.

        Here’re some of the “visually similar” matches Google came up with.

        Put the half-dozen of them together at the same bus stop and I don’t think anybody would give him any weirder looks than the others.

        b&

        • Petu W.
          Posted October 14, 2015 at 2:00 am | Permalink

          I’m not so sure. The difference between a slender sapiens female and a robust neanderthal female is quite clear.

      • Torbjörn Larsson
        Posted October 14, 2015 at 4:03 am | Permalink

        Another outlier would be Neanderthal large eyes as I have heard it. They were very visual hunter-gatherers, perhaps making up for the relative lack of technological progress.

  24. Art
    Posted October 13, 2015 at 5:45 pm | Permalink

    4% Neanderthal (Nat-Geo Genographic Project)and proud of it!

    • James Walker
      Posted October 13, 2015 at 6:13 pm | Permalink

      3% Neanderthal here (23andme)

    • GBJames
      Posted October 13, 2015 at 6:45 pm | Permalink

      3.5 here. And damned proud of my Neanderthal heritage!

      • Dave
        Posted October 13, 2015 at 8:10 pm | Permalink

        My daughter and I both had our genomes sequenced by Nat. Geo. 1.4% (N) and 1.9% (D) for me. It’s a fun thing to do and you are participating in mapping homo sapiens travels!

      • GBJames
        Posted October 13, 2015 at 8:42 pm | Permalink

        Oops. I misremembered. I’m only 3%. My daughter is 3.1%, so my wife is more Neanderthal than I.

    • willem
      Posted October 14, 2015 at 12:48 am | Permalink

      2.4% Neanderthal; 2.6% Denisovian as per Nat Genome 2. In South Africa, but came by ship 300yrs ago.

      • Posted October 14, 2015 at 7:34 am | Permalink

        1.3 % Neanderthal, but I don’t think it’s noticeable… 😉 No observable Denisovan.

        • nickswearsky
          Posted October 14, 2015 at 2:00 pm | Permalink

          1.8 percent Neanderthal and 1.2 percent Denisovan for me. Is it wrong that I feel somewhat disappointed it is not more?

  25. Diana MacPherson
    Posted October 13, 2015 at 6:38 pm | Permalink

    sub

  26. grasshopper
    Posted October 13, 2015 at 6:49 pm | Permalink

    It would be interesting to see if the inhabitants of the Spice Islands contain ancient Hungarian DNA. A dearth of condiments spurred the Hungarians to seek new sauces of spice, thereby giving rise to the “Out Of Paprika Theory” of human migration. There was plenty of thyme.

    • Torbjörn Larsson
      Posted October 14, 2015 at 4:06 am | Permalink

      Well, if that salt is what it comes to…

  27. ladyatheist
    Posted October 13, 2015 at 9:11 pm | Permalink

    I used to work with a lot of African immigrants. Ethiopians (& Eritreans – gotta be careful there) have a very different look from people from the rest of Africa. At the time I thought that they were the first humans and that both darker and lighter people were mutations over time. This woman looks typical of the people I met:

  28. Les Robertshaw
    Posted October 13, 2015 at 10:20 pm | Permalink

    Thank you for this article.

  29. michael
    Posted October 13, 2015 at 11:02 pm | Permalink

    Excellent post! I just have one request/question if I may — I have some creationist family that often challenge me (as if I know everything there is to know about every field of science) and one thing that comes up is a sort of extreme skepticism that often leads to immature mocking or belittling of scientists for their claim that an entire reconstruction of an animal can be done with say a single tooth and a finger bone.

    Could someone please explain how this works and why a new species (like Denisovans) would be the conclusion rather than interpreting it as a deformed member of a previously known group like Australopithecus or H. Erectus. I realize those two were far older than the time frame we are discussing, but I bring them up as just an example.

    I also realize that if you have a complete or mostly complete skeleton, you certainly won’t confuse (for example) a Homo and an Australopithecine. But when it comes to a mere finger or tooth, how is it even known that the finger isn’t from one animal and the tooth of another? If the answer here is DNA, is there an age that DNA can no longer be used? I read something about the discovery of dinosaur red blood cells and soft tissue. If that is true, perhaps the way organisms decay is different than previously understood given the age of dinosaurs?

    Anyway,thanks in advance! I’m very interested in this process and hopefully will come to a greater understanding myself.

    • Posted October 14, 2015 at 3:03 am | Permalink

      The discovery of the molar in Denisova cave was enough to tell palaeontologists that there was something novel there – it wasn’t human or neanderthal. However, both the taxonomic status of the Denisovans and their morphology remain a mystery, and no one to my knowledge has made a reconstruction of them.

      The amazing thing was that their existence and phylogenetic position was proved by DNA extracted from the tooth and from the finger bone. That uncertainty is why they are called ‘Denisovans’ rather than by any latin binomial – we do not know if they were a separate species or not. A more precise (but inevitably contentious, IMHO) taxonomy will have to await more fossils.

      NB there is no number of DNA changes that prove that one population is a different species from another. It would all depend where those DNA changes were – it is conceivable that a single base change could lead to the isolation of two populations (the biological definition of a species).

      The oldest DNA that has been extracted is 700,000 years old, from a horse bone, but this did not lead to whole genome sequence as it was damaged. The key thing is the preservation conditions – needs to be dry and cold to stop bacteria munching their way through the DNA. That’s why we don’t (yet) have any DNA from ‘the hobbit’ – classified as Homo floresiensis, living on the island of Flores about 15,000 years ago. The preservation conditions were not conducive. We may be able to resolve those problems, in which case my bet would be that H. floresiensis would turn out to be no different from us that Neanderthals or Denisovans.

      Paleontologists can reconstruct whole dinosaurs from a couple of bones because of their distinctive shapes. They can often tell if it was from a sauropod or a theropod, and use other fossils to interpret it. It’s only a slightly artistic procedure, based on huge data sets of known fossils.

      MC

  30. Posted October 14, 2015 at 12:19 am | Permalink

    I always knew I was 4 percent Neanderthal. That’s why I spend 4 percent of my time dropping wheelies in my car, cat-calling women and vandalising letterboxes… Joking aside, the rehabilitation of these people has been a long time coming, and it’s about time. Whether the apparent hominin diaspora of the late Pleistocene (us, Neanderthals, Denisovans, Red Deer Cave people and perhaps another African type) represented speciation or merely a widely variable morphology across a single species is largely down to taxonomy. Perhaps all were really variants on the parent H. heidelbergensis stock, of which we’ve apparently found genetic traces. Things have moved fast of late, and have come SO far from the early ’80s when I was doing my undergrad degree on this stuff – back then, my lecturers were doing backflips to jam the evidence of our evolution and ancestry into the ‘multiregional’ hypothesis despite the fact that it was nonsensical even by the evolutionary mechanisms understood at that time.

  31. Tom
    Posted October 14, 2015 at 1:02 am | Permalink

    Marvelous piece on what it really means to be human ie a mongrel, as were all our ancestors.

  32. Posted October 14, 2015 at 3:43 am | Permalink

    Personally I think it was a mistake coming down from the trees! Vey interesting. I saw Svante Paabo at the RI a couple of years ago & he said there would be breakthroughs in ancient DNA. Now if only we had more of the Homo erectus pekinensis fossils…
    I did not realize they have four teeth of them in Uppsala!
    https://en.wikipedia.org/wiki/Paleontological_Museum_of_Uppsala_University

  33. Torbjörn Larsson
    Posted October 14, 2015 at 4:10 am | Permalink

    Thanks for the deep digest! I assume Mota came from the African Horn. I have heard of Twa before I believe. [ https://en.wikipedia.org/wiki/Congo_Pygmies ]

    It is even possible that those rumours of strange DNA sequences in African populations may in fact relate to matings elsewhere in the world, the consequences of which were then carried back into Africa by migrants, leaving their traces in the DNA of today’s populations.

    Intriguing, though the increased likelihood subtracts a putative crossing. It could be this potential 4th group from sequencing an Altai Neanderthal. “The genome comparisons also show that Denisovans interbred with a mysterious, fourth group of early humans also living in Eurasia at the time.

    That group had split from the others more than a million years ago, and may have been the group of human ancestors known as Homo erectus, which fossils show was living in Europe and Asia a million or more years ago.” http://cdn4.sci-news.com/images/2013/12/image_1624_2-Neanderthals.jpg [ http://www.sci-news.com/othersciences/anthropology/science-neanderthal-genome-fourth-lineage-01624.html ; http://www.nature.com/nature/journal/v505/n7481/full/nature12886.html ]

    • Torbjörn Larsson
      Posted October 14, 2015 at 4:11 am | Permalink
  34. Ryan
    Posted October 14, 2015 at 4:32 am | Permalink

    Reblogged this on Endless Erring and commented:
    I’m always fascinated by human evolution and the genetic legacy of our ancestors. Now we know that modern humans may carry Neanderthal genes, which I find astonishing and a deeply moving reminder of our connection to other, now-extinct, humans.

  35. boggy
    Posted October 14, 2015 at 5:46 am | Permalink

    So,if we all walked out of Africa 100,000 years ago how is it that I, a white European have an average amount of Neanderthal genes but a black African does not?

    • Posted October 14, 2015 at 6:52 am | Permalink

      Because we didn’t *all* walk out of Africa. The ancestors of modern Africans stayed in Africa, and did not meet Neanderthals. My ancestors met and mated with Neanderthals, and some of that Neanderthal DNA made its way into my cells. The point of the post is that we now know that a small proportion of African DNA is also Neanderthal, because of the ‘backflow’ caused by people from West Eurasia moving back into contact with African populations and exchanging their DNA, the way we do. That effect was not as strong as mating with an actual Neanderthal – the offspring of a human-Neanderthal encounter would have had 50% Neanderthal DNA…

  36. Posted October 14, 2015 at 9:48 am | Permalink

    This is a great informative post and subsequent thread of comments from which I learned a lot. On a more romantic note, in a way we should not be surprised at genetic ‘back flow’ as it just validates that great human drive to ‘go home’, as it is now apparent that some of our human ancestors indeed did, returning to the African continent.

    • rickflick
      Posted October 14, 2015 at 3:09 pm | Permalink

      “…our human ancestors indeed did, returning to the African continent.”
      At least some of their genes did.

  37. Posted October 14, 2015 at 11:41 am | Permalink

    The “reconstruction” includes what I take to be makeup, not biological markings of the species. What is the basis for including this?

    • GBJames
      Posted October 14, 2015 at 11:43 am | Permalink

      Humans commonly paint and decorate themselves. They were human. It is entirely reasonable to show them that way.

      • Gregory Kusnick
        Posted October 14, 2015 at 12:54 pm | Permalink

        Modern humans commonly paint and decorate themselves today. Did Neanderthals do so 50,000 years ago? It’s a legitimate question.

        The earliest artifacts that can unequivocally be called art date from about the same era as the decline and extinction of the Neanderthals. Did Neanderthals share our aesthetic sensibilities, and can any of these art objects be attributed to them? I don’t know the answer, but in the absence of such archaeological evidence, I think we’d have to classify the body adornment in the image as artistic license.

        • GBJames
          Posted October 14, 2015 at 1:14 pm | Permalink

          Sure it is a legitimate question. (most questions are).

          We have evidence that Neanderthal folk used red ochre. It is not unreasonable to think that they, like other humans, decorated things with it, including their own bodies.

          We would need to classify all reconstructed images of prehistoric people with body decoration as artistic license except for those we have documented on actual bodies like that of Ötzi (the ice man). The question is whether it is reasonable to think of Neanderthals as having painted bodies. I think it is reasonable. Others may disagree but the research momentum seems to be behind the conclusion that they were more like “us” than not. Hell… they ARE us, at least at the 3% level in my case.


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