The brambly bush of humanity

By Razib Khan | September 18, 2012 11:53 pm

Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.

But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:

At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work of ancient admixture in Africa (e.g. Hammer et al. 2011, Lachance et al. 2012). We will likely discover a bunch of cryptic somewhat distinct ancient populations, that we’ve previously [rightly] grouped into a relatively small number of labels based on their morphology and timing in the fossil record. We are not going to have names for many of these groups, but with large amounts of genomic data [ancient and modern] we are going to find all sorts of population structure. The question then becomes not an issue of naming these populations, but understanding the divergence and population genetic relationship among them.

This is a bold contention, and I suspect some physical anthropologists will take issue with it. But it’s a testable prediction. We’ll know if it’s panned out in 2020. I may still be blogging between now and then, and so I will now self-importantly label this “Coop’s Conjecture.” Is there anyone who wants to wager some money on Coop’s Conjecture? Any side of the bet you think is a sure thing?

  • http://www.genomesunzipped.org J Pickrell

    I’d wager he’s right. In a few years, we will be doing really cool popgen on populations that we never knew existed, and for which no remains exist today.

  • http://johnhawks.net/weblog John Hawks

    I’m also one who thinks we are discovering populations we genuinely didn’t know about. But this can be taken to an extreme. The world was not full of dozens of distinct human species. Yet so far we are examining them with very simplistic population genetic models that assume the ancient populations began in total isolation. When we begin considering population dynamics in a more realistic way, we are going to reduce the perception that they were unique and increase our knowledge of how they varied over space.

    I think with this perspective in mind, Coop’s criticism — that there was a cryptic population *like* Neandertals that mixed with humans — becomes much more simple. Some geographic variants of Neandertals mixed more with dispersing Africans than others, and some Neandertals had previously exchanged more genes with contemporary Africans than others.

    We used to consider fossils in a simplistic way, every new one representing a previously unknown species. This remains credible as long as they are very few in number.

  • http://dispatchesfromturtleisland.blogspot.com ohwilleke

    I’d wager that Coop is wrong. While the potential to discover new fossil remains is impossible to assess, especially in an era when a handful of teeth can provide a nearly complete DNA profile, the inferences that can be drawn from analysis of whole genome population genetics (which predicted Neanderthal and Denisovan admixture before direct comparison was possible) is very comprehensive and these data seem to show a very modest level of archaic admixture in a pretty minor subset of Africans with probably not more than two or three archaic species in Africa (in addition to Neanderthal admixture and Denisovan admixture).

    I think that we could very well discover traces of multiple rounds of admixture with some regional variation (initial Out of Africa, West Eurasian, East Eurasian, Upper Paleolithic European) with the same species, but the population genetic based measure don’t leave a lot of room for new discoveries.

    Sure, maybe we have 0.1% of something we haven’t predicted. We could also discover some other kind of archaic admixture in a branch of the modern human tree that has long since gone extinct but can be analyzed directly via ancient DNA. But, the upper limits on those percentages in modern populations is pretty small, the West Eurasian hominin fossil record is reasonably complete, and any new species of East Eurasian hominin in the period from 1.8 mya to about 0.5 kya pretty much has to be derived from Homo Erectus (e.g. probably H. Florensis).

    Indeed, I am more inclined to think that very detailed analysis of specific archaic SNPs in large populations will allow us to reconstruct in detail the DNA of the archaic homins who actually admixed and will shift the paradigm towards one with smaller numbers of admixture events at times of very small founding populations. For example, I wouldn’t be at all surprised if by 2020, we are able to show definitively that the total number of Denisovan individuals who admixed with modern humans in all of the genetic history of modern humans who have descendants living today can be counted on your fingers and then amplified due to the expansion of a very small founding population for Melanesia and Australia.

  • Chad

    My bet is on Cooper.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #4, how about coopman?

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #2, i think there is implicitly a lot of typological thinking that will melt away. no idea how to render this well in english though.

  • Sandgroper

    @5 LMAO

    I was going to vote with Joe until I saw John’s answer.

    What I would really like to be able to do is plot the population dynamics somehow in multiple dimensions of space and time. The one thing I do feel confident about betting on is that such a plot would look ever so complicated.

  • http://gcbias.org Graham

    On some level there is no way I can be wrong about this [so save the name for one of my more bat s#%t crazy ideas]. I’m not claiming that there are unnamed fossil species out there, for a start I find such debates pretty dry. I’m simply saying that population structure is a popgen certainty. Given enough markers we can detect incredibly subtle population structure, so archaic populations will have population structure. It is doubtful that the sequenced Neandertals belong to the exact same “population(s)” as that which admixed with Eurasians. What matters then is how close the sequenced Neandertals are to the population(s) archaic population that contributed the material to modern humans [e.g. as measured by Fst], and how these populations are related to one another.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    [e.g. as measured by Fst]

    bingo, something to dispute in terms to expectations. unfortunately, not too many ppl have intuitions about Fsts.

  • Chad

    hahaha, my bad…thats a typo, my bet is on Coop

  • ackbark

    Razib, don’t know if anyone’s mentioned this, but your rss feed isn’t working. For me, anyway.

  • Sandgroper

    @8 – OK, I’ll put money on that (not risking much – John Hawkes referred to evidence of population structure in Neanderthals quite a while ago). I don’t know much, but I reckon I know batshit when I see it, and that ain’t it.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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