Sunday, February 12, 2012

Is "Out-of-Africa" Dead or Just Severely Wounded?

 
Here's a good summary from the New York Times [DNA Turning Human Story Into a Tell-All]. The story is written by Alanna Mitchell. John Hawks links to it [Denisova in the news], suggesting that he thinks it's pretty accurate.

The opening paragraphs of the New York Times story emphasize the controversy ...
The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.

The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.

Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.

Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,” Chris Stringer, a paleoanthropologist who is the research leader in human origins at the Natural History Museum in London, said in an interview.


[Image Credit: The map is from The Human Journey.]

34 comments :

  1. A thought occurred to me.

    Imagine that you're teaching an introductory anthropology course at one of the new teaching-only universities [How to Turn a University Into a Glorified High School]. How could you possibly keep up with stuff like this?

    ReplyDelete
  2. I don't understand why this would be the death of "out of Africa". Wouldn't this just mean that humans left Africa in 2 or 3 or more waves over a long period and then met up and hybridized eventually? The origin would still be Africa.

    ReplyDelete
    Replies
    1. AFAIK both of the major competing hypotheses have humans originating in Africa but differ in whether modern *Homo sapiens* originated in Africa and then swept out and supplanted the earlier migrants who were evolving in situ and human diversity evolved after that, or whether the earlier migrants subsequently evolved into modern humans in several places all at once with some geneflow from Africa indicating that the biological differences between geographic areas evolved earlier.

      Delete
  3. Is "Out-of-Africa" is not dead nor severely wounded, it juste doesn't tell us the whole story of our recent evolutionary history.

    There were an "Out-of-Africa" event and this event is responsible for a very important part of our genome, in fact the most important part. But there were also some admixtures with other human populations who were present in Eurasia for a long time. I think the contribution of these old eurasian population is about 4% to 10% of modern eurasian populations. That's important but that doesn't mean that "Out-of-Africa" was not a major event for the birth and spread of our species.

    For more informations see the following references:

    A Draft Sequence of the Neandertal Genome

    Genetic history of an archaic hominin group from Denisova Cave in Siberia

    Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

    Archaic human ancestry in East Asia

    Best regards

    Hans

    ReplyDelete
  4. The report means that Out Of Africa is only 95% of the story. Which doesn't make it a distraction, and doesn't mean that we can just assume that the Multiregional Hypothesis is validated.

    (And as for the "teaching-only universities", how will those differ from 4-year liberal arts colleges (as they are called in the U.S.)? The best of those have biology or anthropology teachers who do a remarkably good job of keeping up. But that's not true for all of them.)

    ReplyDelete
  5. It seems to me that the genetic analysis doesn't contradict an "Out of Africa" hypothesis, since the Neanderthals and presumably also the Denisovans resulted from an earlier and more primitive human migration also out of Africa, at least as I understand it. This new evidence just revises the idea of Homo Sapiens replacing these earlier but closely-related species with a, to my mind more likely, notion that there was some interbreeding that went on before the modern species prevailed.
    The "Is 'Out-of-Africa' Dead ..." headline seems a bit more provocative than it need be since the roots or our species appear to lie in that continent one way or another.
    I'm not an evolutionary biologist though--just someone who always has been fascinated by the science that helps to reveal our origins--hence one reason I follow your blog. Is there really that much controversy within the field over this most recent evidence or is it rapidly becoming the prevailing view?

    ReplyDelete
  6. Thanks, Professor. I'm definitely sharing this.

    ReplyDelete
  7. Just goes to show you there are few absolutes in biology. There was introgression between human species, but the major story remains OoA. Perhaps we just need to amend the story to "mostly out of Africa"? If you ask me (didn't you?) your headline is an example of science journalism sensationalism.

    ReplyDelete
  8. So when you say "dead or severely wounded," are you speaking only about the most recent migration? In other words, what are your thoughts if any regarding whether the homo ancestral lineages of Neanderthals and Denisovans had African origins, or whether they were truly indigenous to other regions?

    ReplyDelete
  9. Hah! I know you are thrilled that the Times article played up the adaptationist perspective on why we have this material in our genome:

    The value of the interbreeding shows up in the immune system, Dr. Parham’s analysis suggests. The Neanderthals and Denisovans had lived in Europe and Asia for many thousands of years before modern humans showed up and had developed ways to fight the diseases there, he said in an interview.

    When modern humans mated with them, they got an injection of helpful genetic immune material, so useful that it remains in the genome today. This suggests that modern humans needed the archaic DNA to survive.

    ReplyDelete
  10. I always find people's reactions to this question so interesting!

    Most people never understood clearly that the Out of Africa hypothesis was specifically about a dispersal and replacement of humans outside Africa within the last 100,000 years. No anthropologists have claimed that humans originated anywhere other than Africa. At issue is whether modern humans originated as a new species with replacement of previous humans outside Africa, like the Neandertals. We now know that some Africans did disperse within the last 150,000 years, making up a large majority but not all of the ancestry of people outside Africa today.

    Joe Felsenstein's reaction is very common among geneticists, I've heard it from several other people as well. It is true that more than 90% of our genetic variation comes from Africa within the last 150,000 years. But the Out of Africa hypothesis became prominent because it attempted to explain certain genetic observations: Humans have low heterozygosity; Africans have greater heterozygosity than other populations; the roots of most gene trees are African; the time to most recent common ancestor of some genes (e.g., mtDNA) are less than 200,000 years ago. Over the last 20 years, we have learned that all of these observations are consistent with a very different scenario in which ancient non-Africans like the Neandertals also contributed to our ancestry. This is a real scientific change, and in my opinion saying that the story is "95% Out of Africa" really minimizes how our knowledge about human genetics has advanced.

    ReplyDelete
    Replies
    1. At another level, doesn't this just open up the debate (again) as to whether it is Homo sapiens neanderthalensis instead of Homo neanderthalensis, and likewise Homo sapiens denisova versus a distinct species?

      -The Other Jim

      Delete
  11. As I learned it decades ago, the multiregional hypothesis said that Homo ergaster migrated out of Africa, producing H. erectus in Asia, then everybody sat tight and evolved into the various H. sapiens races in place. It was always hard to figure out how all those diverse populations could become modern H. sapiens without major interbreeding. Recent discoveries just seem to more nail the coffin more firmly shut on that idea.

    Because of that context, to me these discoveries don't deny the "out of Africa" hypothesis so much as add complexity to it. There must have been at least three major radiations: H. ergaster/erectus out of Africa, Neanderthal/Denisovian presumably out of Africa, and modern H. sapiens out of Africa. The modern H. sapiens expansion wasn't as neat as its earlier proponents suggested, but if 90+% of the modern human genome comes from that expansion from Africa, I'd say the "out of Africa" hypothesis won.

    ReplyDelete
    Replies
    1. The one Barbara described is the version I was taught in an Anthropology undergrad course in ~1995. Not the interpretation John Hawks supplied...

      -The Other Jim

      Delete
    2. This is not a good description of the multiregional hypothesis by the late 80s, which suggested hybridization between local populations and waves of populations migrating out of africa. The evidence was the maintenance of regional traits (I'm not sure why temporally-convergent evolution was ruled out). If this is what you were taught then your professors were painfully out of date. But I'd hate to blame the professor. My students have all sorts of misconceptions of what I say.

      Delete
    3. I'm 8000km away from home, or I would see if I still have the course notes and text book.

      - The Other Jim

      Delete
  12. My question is: why are Neanderthals and Denisovans called different species, when modern homo sapiens were clearly able to interbreed with them?

    ReplyDelete
    Replies
    1. Because absolute inability to interbreed is not the criterion for different species status. The term "species" is an abstraction that simplifies the complicated interactions in nature. If there's one hybrid between populations A and B in a million years, does that mean they're one species? How about one per year? How about a hundred per year? There really is no sharp dividing line. In practice, if two populations live in the same area and still retain distinct genetic and phenotypic characteristics, we tend to call them different species even if there's a fair amount of interbreeding going on.

      Delete
    2. the tens of thousands of populations of stickleback inhabiting lakes up and down the west coast of north america maintain local differences but are not recognized as different species. It would be absurd to name them all. And giving the different ecotypes specific status wouldn't really reflect relatedness.

      Delete
    3. That's why I specified "in the same area", i.e. in sympatry. The isolating mechanism under the BSC can't be purely geographic (though that would be fine under the phylogenetic species concept). At any rate, you seem to be using the "human convenience species concept", in which recognizing differences is a bad idea if it would require too many names. Now, if limnetic and benthic populations in a single lake maintain their separate characters, and are largely reproductively isolated from each other, they should under the BSC be considered separate species. If limnetic populations from different lakes are not reproductively isolated from each other, they are one species under the BSC. Same with benthic populations. If that creates a problem with relationships, well that's just a case in which our simplified abstraction doesn't represent reality all that well.

      Delete
  13. At another level, doesn't this just open up the debate (again) as to whether it is Homo sapiens neanderthalensis instead of Homo neanderthalensis, and likewise Homo sapiens denisova versus a distinct species?

    It ends the debate, if you (as I do) use the Biological Species Concept.

    ReplyDelete
    Replies
    1. Only if your version of the BSC requires absolutely no introgression. Dunno about primatologists, but certainly ornithologists are willing to allow a few genes to wander about here and there. Otherwise there would be, for example, only one species of duck rather than 150 or so. Evolution being what it is, isolation is a matter of degree, and the boundary between "one species" and "two species" can be fuzzy.

      Delete
    2. Sorry for the delay.

      So, we are now agreed that there were three ancient subspecies of Homo sapiens who have all contributed to modern human genomes. Given the confusion brought up between your description of the Multi-Regional Hypothesis, and the one that Barbara (Feb 12, 2012 07:45 PM) and I were taught, shouldn't we be making sure these news items are clear on these points? The impression being given is a between-species cross, and many of us had this "incorrect" version of the MRH taught to us.

      This is exciting stuff, but our excitement seems to be allowing us to really muddy the waters of what the non-experts understand is going on.

      -The Other Jim

      Delete
    3. BSC still has to draw an arbitrary line somewhere - a line that does not exist in real life. So, whatever BSC is (and my feeling is that different people understand it differently), it still leaves room for the obviously futile debates.

      Delete
    4. So, we are now agreed that there were three ancient subspecies of Homo sapiens who have all contributed to modern human genomes.

      We are not. They are either three subspecies or three species. Either is possible. The question, under the BSC, is whether there was relatively free interbreeding when the opportunity presented itself (subspecies) or whether there was a substantial barrier to interbreeding that was sometimes crossed (species). As these are points on a continuum, there may be no completely satisfying answer. As DK says, the line is arbitrary even if the endpoints are not.

      Delete
  14. If 'modern' humans are a result of african, neanderthal, and denisovan lineages mixing, then perhaps there's many other lineages out there too that were added to the mix. If Europe (for an admitedly wide definition of europe) could host both the neanderthals and denisovans, then it seems possibly that there were other 'contributing' populations out there.

    And if that's the case then we're not 'out of africa'. There'd just be some genes that flowed population by population out of africa, and some genes that flowed out of the edge of the ice sheets, and some that flowed out of the steppes, that all merged over time into modern humans.

    And as far as N and D being different species despite being able to intebreed with anatomically modern humans, well, then they violate the biological species concept, which is just one of many.

    Even if this is the case, it still looks like humans are a really well mixed population (and, iow, people in say Cornwall aren't especially different from people in Canton).

    ReplyDelete
    Replies
    1. Quantity counts. According to about 20% of your genes, you're more closely related to a gorilla than to a chimpanzee. So is there in fact no true phylogenetic tree of primates? Similarly, if most people are more than 95% African, does it make sense to say there are just different genes from various places?

      None of this violates the BSC unless you take an extreme version that requires 100% genetic isolation and 0% interbreeding. Nobody I know of, at least anyone who works with real organisms, does this, because it results in silly classifications like (to repeat my favorite example) all ducks being a single species because they occasionally hybridize, even across genera.

      Delete
  15. So instead of "out of Africa" it's "out of Africa then mate with others who left africa much earlier"?

    ReplyDelete
  16. If Neanderthals and Denisovans died out 30,000 years ago, that would be about 1000 generations. The odds that one of their genes would be found in a modern human would be astronomically small.

    If Homo sapiens and Neanderthals/Denisovans shared common genes, say from a common ancestor, how would one discern that a particular gene came from Neanderthals/Denisovans and not from Homo sapiens?

    ReplyDelete
  17. Does the biological species concept "states"/implies that there's only real biological species when the possibility of gene flow via interbreeding is "100%" ruled out?

    As far as I know, or as I "accept" a biological species concept, it would have that, say, humans, gorillas and chimpanzees are different biological species, even though the physiological possibility of interbreeding and gene flow can't be totally ruled out, as far as we know (or as I know). So, extending "this" biological species concept to the issue of modern human origins, it could well be that Homo sapiens and Homo neanderthalensis (+denisovans perhaps) were different biological species, even at the time of hybridization events. That is, supposing that we don't have such an amount of neanderthal inheritance to require that hybridization was essentially physiologically unhampered. But I don't think the current picture looks like this; AFAIK what it seems now is that it's either "out of Africa" with some admixture every now and then, perhaps some selection here and there (more likely, IMHO), OR "out of Africa" being nearly completely integrated and having lots of children with everyone in the way out, but eventually reaching a virtually complete genetic substitution of of "non-African" alleles (IMHO less likely, requiring things like more extraordinary selective advantages for African alleles and phenotypes, and/or at least huge waves of recurring OOA "pure" sapiens migrations eventually dwarfing the frequencies of neanderthal/other archaic alleles -- somewhat less unlikely I guess).



    By the way, is there anything new/interesting regarding the role of our robertsonian translocation in this whole mess? Do we know whether neanderthals also inherited it from a common ancestor or not? I recall seeing some paper or thesis suggesting it was fairly recent and that it could fit nicely with/explain quite a few particularities of the human origins. I don't remember what exactly or if it was as recent as to exclude neanderthals, though, I happen to have my own wild layman/agnostic speculations about it and I can't remember the differences anyomore.

    ReplyDelete
  18. And what about gene flow from neanderthals/Eurasians with neanderthal/archaic admixture back to Africa? It used to be a part of "multiregional origin of modern humans", comprehending Africans.

    But it seems that it's pretty much discarded, except perhaps for North Africans. However I recall one paper hypothesizing that some of the neanderthal admixture had to do with genes related with the immune system. It was before the draft genome, and as far as I recall, they took the pattern of distribution and variation of such alleles as evidence of neanderthal introgression.

    Those alleles are, however, found in some African populations, which was not known at the time or overlooked I guess. Are they ruled out as neanderthal inheritance just because they're present in Africans? Is the same tell-tale pattern found on Africans for such alleles? Are they in the neanderthal draft genome? What implications does it have on another study which similarly (I guess) inferred archaic admixture in Africa (from archaic Africans, not neanderthals)?


    Yet one more question, if that can be really described as such. Is it possible that the neanderthal admixture isn't really neanderthal after all, but in fact heidelbergensis admixture, or something like that? I guess so, it's more or less a different version of the "deep structure" scenario. I have the impression/guess that there is the possibility of very complex scenarios with things like tiny populational "bridges" (a "second hand" admixture, so to speak) for such admixture making it less "direct" than it may sound when we speak of the subject; that is, perhaps those who really mated with neanderthals are waves of sapiens that, regardless of being sapiens, we don't use to think of them as ancestors of modern Eurasians and Oceanians, regarding them as a "dead end" of pioneers (such as Qafzeh and Skhul, for example, not that I'm taking the looks as evidence for neanderthal admixture though, I mention them just as they're thought to be a dead-end of "archaic sapiens", AFAIK).

    Not that I have any problem with my neanderthal alleles, anyway, or with Africans not having them. I just find interesting how many possibilities there may be to explain the same data.


    I guess I should have posted it all in some more specialized list or forum, I got somewhat excited I guess...

    ReplyDelete
  19. out-of-africa is a politically correct myth

    Cro Magnon is found in eartern US and Western Europe, originating in the middle in the Atlantic, not Africa. (haplogroup X, clovis/solutrean)

    look up Guanches of the Canary Islands, and the origin of Cro Magnon RH negative Blood.

    ReplyDelete
  20. RH-negative supremacism is funny.

    ReplyDelete