Beyond trees and European trees

By Razib Khan | March 7, 2012 6:59 pm

Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there’s a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow and admixture. In the guts of the paper though Pickrell et al. use their framework to identify some novel patterns. For example, that Cambodians may be descended in small part from some basal Eurasian lineage (~15 percent), perhaps their equivalent of “Ancient South Indians”? Using ADMIXTURE and such it has long been evident that there’s something funny there. My own working assumption was that the relatives of “Ancient South Indians” could be found in Southeast Asia, though these results (preliminary as they are) might imply something even more interesting. Second, there is a tidbit which might lend support to the fans of the Solutrean model, or can be interpreted in that way (I suspect that it does not, but it could be spun in such a fashion).

Next, a provocative post with the title Northwest Eurasians + Southwest Eurasians + Mesolithic survivors = modern Europeans:

For a long time, it was generally accepted that Europeans were direct descendants of Palaeolithic settlers of the continent, with some Middle Eastern ancestry in the Mediterranean regions, courtesy of Neolithic farmers. However, in the last few years, largely thanks to ancient DNA results, it dawned on most people that such a scenario was unrealistic. It now seems that Europe was populated after the Ice Age in a big way, by multiple waves of migrants from almost all directions, but especially from the southeast.

Getting to grips with the finer details of the peopling of Europe is going to be a difficult and painstaking process, and will require ancient DNA technology that probably isn’t even available at the moment. However, the mystery about the basic origins and genetic structure of Europeans was solved for me this week, after I completed a series of ADMIXTURE runs focusing on West Eurasia (see K=10, K=11, K=12, K=13 and K=14). The map below, produced by one of my project members, surmises very nicely the most pertinent information from those runs (thanks FR7!). It shows the relative spread of three key genetic clusters, from the K=13, in a wide range of populations from Europe, North Africa, and West, Central and South Asia. The yellow is best described as Mediterranean or Southwest Eurasian, while the cyan and magenta, which are sister clades, and can be viewed as one cluster for the time being, as Northwest Eurasian.

How plausible is this? I would rank it more plausible now than the idea of continuity from Pleistocene populations, and more plausible than a two-population admixture model (i.e., Pleistocene man + Neolithic man). But the reality is that I wouldn’t be surprised if it isn’t more complicated than the outline above. I am starting to think, as suggested in the post, that using modern populations in a given area as a “reference” for ancient populations in that region area may be misleading us. For example, modern Anatolians or Levantines are often used as pegs for ancient Near Easterners who migrated to Europe. Though not totally bunk, I think this tends to underestimate the demographic heft of migrations of farmers, because we’re probably not sampling from the exact group of farmers. This would not matter if there was singularly one locus of the origination of agriculture from which all subsequent agriculturalists derive, but it may not be so pat. There may have been a few peoples in the Fertile Crescent who took to farming at about the same time. I suspect that one branch pushed out into the Western Mediterranean, and on toward Atlantic Europe, before being mostly replaced in the Middle East.

In any case, goods times. There are hints that some geneticists are currently examining a lot of ancient DNA, so I think the answers will be forthcoming.

MORE ABOUT: Human Genetics
  • Dwight E. Howell

    I don’t think the fertile crescent actually maps well with the very first farmers or the groups that expanded outward into Europe.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    who the hell cares what you think? elaborate why you think that in detail in concrete substantive terms. otherwise don’t opine, i don’t care.

  • http://forwhattheywereweare.blogspot.com/ Maju

    Why would farmers be replaced? I find strikingly difficult to replace people who are attached to their land plot and who have large population densities.

    Also what Howell (#1) says makes some sense: the Greek (or more properly “Thessalian”) Neolithic is very old, having one of the oldest dates for pottery in the Western parts of Eurasia (China or Japan are clearly older in this matter, although surely their pottery is pre-Neolithic. pre-agrarian). It’s likely that Anatolian farmers had some influence in the development of Greek (and maybe also Thracian) Neolithic but the exact process is mostly unknown, largely because we know little of West Anatolian Neolithic.

    In any case, when you compare for example Çatalhöyuk with Sesklo… there’s almost no similitude other than mere farming: they are very different cultures in nearly everything. An arguably closer comparison has been made with Hacilar but, really, when you compare pottery styles (Hac1, Hac2, Sesk1, Sesk2) the comparison seems very weak (and Hacilar has home structures like Çatalhöyuk, not like Sesklo). So we are still needing a good archaeological explanation for the genesis of the first European Neolithic in Thessaly c. 7000 BCE, barely a millennium after the first PPNB, which is the first consolidated Neolithic of all in West Eurasia (but still without pottery).

    So for all practical purposes we should begin in Greece or in general in the Balcans (Thrace may be a second origin, while the Cardium Neolithic of the Adriatic Balcans has very limited precursors in Thessaly). Claiming an Anatolian origin right now seems difficult to support on light of the archeology we know. Of course there must have been some cultural flow but it’s not clear at all if that implied migrants, how many and how they interacted with the Epipaleolithic natives.

    It’s also not clear which is the origin of Epipaleolithic Anatolians by the way. It’s a poorly known period again and some elements like rock art appear to have Western European or at least Dalmatian roots, although an Egyptian connection (Qurta) may now be claimed as well.

    For me the only clear origin of European Neolithic(s) is in the Balcans (although Eastern European Neolithic has an independent genesis) and the connections with West Asia remain blurry, even if they should exist somehow.

    However there was a second wave in the Balcans (and only there) c. 5000 BCE, the black and beige painted ware complex (Vinca and Dimini cultures specially, ex1, ex2), which is accompanied by destruction of some villages (fire) and has almost for sure an Anatolian origin (may be rooted in PPNB and is often compared with Can Hassan in Turkey).

    So if you want to imagine that the ancestors of early European farmers (whom we know now are largely not the ancestors of modern Europeans anyhow) were replaced in their homeland, you have to extend that homeland to much of the Balcans. One might then imagine a relation with E1b-V13 for Vinca-Dimini but… now we know that this E1b-V13 key lineage was already among Cardium Pottery people as far west as Catalonia.

    So no, really not: the pieces of the puzzle do not fit with a second mass replacement scenario in the Balcans.

  • Eurologist

    Since the authors limited the number of admixture events studied, West Asia to Europe would need its own, dedicated analysis. It is interesting, though, that inclusion of Oceanians changes things around – in particular, that a population bearing Caucasians and Russians becomes progenitor to SW Asians and Europeans. In the end, there are likely too many admixture events to create a single useful tree for that region – although it would be interesting to see if the dominant tree from such a calculation reflects more of an ancient vs. neolithic pattern. Within Europe, the work so far seems to show dominance of a northern/central European migration path vs. a Mediterranean one – but is that ancient, neolithic, or IE – or a combination of all?

    In addition to the ancient element in Cambodians, which was somewhat expected, I find it interesting that the calculations seem to show a Siberian origin of almost all East Asians – i.e., perhaps more of a continental vs. coastal migration in that region. We knew this from the studies of ancient Siberian and Beringian sites (migration starting some place in central Siberia, and moving east) – but how did they get there, in the first place? Of course, as in the case of Europe, this seems to require a dedicated analysis to better distinguish recent migrations and admixture due to rice farming.

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

    Thanks for the kind words about the paper.

    “My own working assumption was that the relatives of “Ancient South Indians” could be found in Southeast Asia,”

    That’s my working model as well, for what it’s worth.

    “Second, there is a tidbit which might lend support to the fans of the Solutrean model, or can be interpreted in that way ”

    I’d honestly never even heard of the Solutrean model before you wrote a bit about it here. I find it more plausible that Siberian populations 15kya were admixed with a Northern European-like population. Other people have looked in much more detail (any detail at all really) at populations in this part of the world, so you’ll see a “real” analysis at some point soon.

  • http://dienekes.blogspot.com Dienekes

    The simplest explanation is that many “Native Americans” are recently admixed with Europeans.

    http://dienekes.blogspot.com/2011/09/latent-admixture-causes-spurious-serial.html

  • Charles Nydorf

    Good times, indeed!

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    I find it more plausible that Siberian populations 15kya were admixed with a Northern European-like population. Other people have looked in much more detail (any detail at all really) at populations in this part of the world, so you’ll see a “real” analysis at some point soon.

    yeah. that’s what i think too. or more precisely there was ‘circumpolar’ gene flow.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Also what Howell (#1) says makes some sense

    well, after you explained your opinion it does. i had no idea what he was talking about and why. if he was gordon childe unadorned opinions would suffice, but otherwise, no.

  • pconroy

    @Razib, @Dr Pickrell,
    I’m 90% sure that both of your suggestions are wrong.

    @Dienekes,
    I’m 90% sure you are correct.

    The reason is that both my father and mother are related to a supposedly 100% Mayan, called Carlos Solis. My father shares 2 segments with him and my mother 1 segment. When I corresponded with his daughter Yolanda Tamer, about 1.5 years ago, she said that surprisingly his Y-DNA was I1 – which has the highest frequency in Sweden today, with lesser amounts in Scandinavia, Holland the the Isles and Germany.

    She said that Dr Doug McDonald indicated that her father’s European admixture was “strongly Irish or Orcadian”. As she has made her father’s results public on HIR Search, you can take a look for yourself:
    http://hiropractic.snpology.com

    So you can see my parents Michael Conroy and Margaret Conroy share segments, but also relatives like Michael Rice. All these people share ancestry from the South East of Ireland. Since I’m assuming that her father does not have admixture in the last 150-200 years – or else he’d probably know about it – then I suspect that the admixture event happened in the 1500-1700 time span.
    So the clue as to who this mystery Irish person was, would be:
    1. Someone probably from the South East of Ireland
    2. Someone probably carrying a Norman or Viking name – based on Y-DNA
    3. Most likely male

    One name immediately comes to mind that fits the bill, he was an Irishman, born in 1611 from Wexford, of Norman origin, a spy, a linguist, a polymath, a soldier, drafter of the FIRST Proclamation of Independence in the Americas, and a NOTORIOUS WOMANIZER, who lived for years among the Maya. He was none other than William Lamport (AKA Guillén de Lampart, AKA Guillén de Lombardo):
    http://en.wikipedia.org/wiki/William_Lamport

    http://www.historyireland.com/volumes/volume9/issue3/features/?id=250

    William lived among a group of Irishmen, who had dealings in Mexico, see here:
    http://www.irlandeses.org/0903_005to020.pdf

    Equally, this informs us of the existence of close
    networks of communication between people of
    Gaelic origin in American territory. From this
    case it is clear that Diego Nugencio, Juan
    Lombardo, Diego de la Concepción, Miguel de
    Santa María, Thomas Gage, Tomás de León and
    Guillermo Lombardo himself, as Fabio
    Troncarelli suspected, exchanged impressions
    with those of their nation.

  • pconroy

    Comment in moderation

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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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