Which population is most genetically distant from Africans? Amerindians

By Razib Khan | August 19, 2010 9:37 am

abofig331bYesterday I stated that it was wrong to think of any non-African population as more genetically distant from Africans. Well, I was wrong. Sort of. This is obviously a case where I had a model in mind, and went looking for visuals which reinforced the story I was going to tell. As noted in the comments of the previous page I should have double-checked Fst values. Fst basically measures the difference in gene frequencies between populations. Or more specifically, the proportion of the genetic variation which can be partitioned across two groups. It is the famous value, 0.15, which tells you that 15% of the variation in genes is between races, and 85% within races.

It was actually not too easy to find Fst tables looking around in papers yesterday, but one reason is that more recently people have been abandoning matrix displays in tabular form for visual representations. It turns out there was just such a representation in my post on Australian Aboriginal genetics. The tree is scaled, so you can see the length of 0.01. The distance between termini indicates Fst magnitude. As you can see there are tight geographical clusters. Additionally, as noted in the previous post on Aboriginal genetics this particular representation in tree form is a touch misleading insofar as several of the populations are admixed. But, for the purposes of yesterday’s post you see quite clearly that the distance between African’s and Amerindians is the greatest in magnitude. Then East Eurasians/Oceanians, and finally West Eurasians.


So what does this mean? And why is this so? I think I won’t revise my model of the out of Africa migration. I don’t think there was serious secondary migration out of Africa after the initial one (at least until recently). And yet somehow the indigenous populations of the New World are more genetically distinct. This is because of genetic drift. Specifically, a set of serial founder events, where the genetic variation was reduced and ancestral allele frequencies changed rapidly. When a population goes through a bottleneck, and then becomes isolated, it “goes its own way,” as there isn’t gene flow to requilibrate the frequencies. The push east, to Australasia and to the New World, was accompanied by founder events due to fissioning off of small groups from the main ancestral population. From what we can tell there was relatively little gene flow after the initial settlement of the New World and Oceania (actually, there may have been several waves into the New World to be fair, but it looks like there wasn’t enough Eurasian gene flow to dampen the reduction in heterozygosity caused by bottlenecks).

There are some cases in Europe and European descended populations of something similar happening. Iceland for example has been relatively isolated since its initial founding by people of Norwegian and Celtic origin. Combined with a small long term effective population size through several bottlenecks, what you see in Iceland are deviations from the ancestral gene frequencies due to the wild swings of random genetic drift. So Icelanders have the same common ancestors as other Europeans if you move far back enough in generations, but evolutionary parameters have reshaped their genetic character as a people to a greater extent than the other descendants of the common ancestors who remained in Europe.

The main reason I would suggest I was “sort of” wrong is that I don’t want people to misconstrue the higher Fst values of Amerindians with the idea that their African ancestors were different from the African ancestors of Eurasians or Oceanians. 50 to 100 thousand years ago presumably the common ancestors of all non-Africans were the same set of recent migrants. It just so happens that some of the subsequent descendants of the modern humans went on something of a wilder evolutionary ride than the others.

Note: I put a little thought about what I should call the native inhabitants of the New World. Outside of the United States in the other New World nations I know that “Native American” isn’t necessarily popular, but terms like “indigenous” and “Aboriginal” might confuse Americans. “American Indian” sounded like something from a Census form, and as a brown person I wasn’t going to use the word “Indian.” So I settled on Amerindian.

CATEGORIZED UNDER: Genetics, Genomics, Human Evolution
  • http://infoproc.blogspot.com steve hsu

    Thought I would copy this comment on your earlier post here in case anyone wants to see a table of Fst values.

    ****

    Here is an Fst table for you:
    http://www.nature.com/ejhg/journal/v16/n12/fig_tab/ejhg2008210t1.html#figure-title

    It only has YRI (Nigerians) as the African sample, though. You can see that the lowest Fst relative to YRI are Romania and Spain at .14-ish, whereas the largest values are for China and Japan at just over .19. No Native American or Polynesian numbers given. In case you are curious the Fst between east Asia and western Europe is about .1 whereas, e.g., China and Japan are only separated by .007 and France-Germany by .0008. So the genetic “distance” (defined as Fst) across Eurasia isn’t that much smaller than the distance from southern Europe to Africa.

    You might find some of the figures at the link below of interest.

    http://infoproc.blogspot.com/search?q=fst

  • bioIgnoramus

    “Amerindian” is fine by me.

    ““Native American” isn’t necessarily popular” – that could be both because it’s lousy English, and because historically it was used in its correct sense in English to mean someone born in the Americas, and therefore introduces confusion to anyone trying to read some history.

    “”Aboriginal” might confuse Americans”: or anyone else who’s got used to its application to the Abos of Australia.

    ““indigenous” … might confuse Americans”: there you’ve got me – why on earth would that be?

    Mind you, for something that’s both unambiguous and terse, I favour “Injun”. If, however, I were persuaded that Indigenous Americans genuinely disliked it, I’d think again.

  • http://infoproc.blogspot.com steve hsu

    Shouldn’t massive genetic diversity in Africa imply huge Fst distances between the different branches of the tree in the blue Africa cluster on your figure? I’ve never looked closely at Fst between different African sub-populations, but according to your figure they aren’t very different from inter-European or inter-Asian values. Among the groups in your Africa cluster are, e.g., YRI (Yoruban) and SAN (San bushmen), so that tree covers quite a range of populations, yet the Fst distances are not so large.

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

    steve, yeah, that was my thought too. i gotta reread tishkoff’s big african paper. i scanned it and the supplements for Fst tables, and there wasn’t any. but there were other mentions/representations. OTOH, aren’t they kind of huge compared to what you see in europe and east asia?

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

    re: african Fst. if it’s a proportion of between/(within+between), then pairwise comparisons might not show that much greater african Fst in relation to increased variation because both might be increasing at the same time.

  • Matt

    “When a population goes through a bottleneck, and then becomes isolated, it “goes its own way,” as there isn’t gene flow to requilibrate the frequencies.”

    Apologies if I’m stating the obvious (and something you’ve already implied) but my understanding is that would only apply to selectively important genes though and that gene flow short of total replacement would never be able to recalibrate selectively neutral genes to the same frequency. With a bottlenecked or founder effect population still looking like a subset on its neutral genes, even when, theoretically, everything selection has seen has moved to the same frequencies, assuming the same environment and fitness of all genes.

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

    matt, you’re right. i was just using an island + infinite population model. reconnection would equilibrate in that case with migration.

  • http://infoproc.blogspot.com steve hsu

    “re: african Fst. if it’s a proportion of between/(within+between), then pairwise comparisons might not show that much greater african Fst in relation to increased variation because both might be increasing at the same time.”

    It’s possible that within-group variation is masking much larger between-group variation in Africa, at least as far as Fst. Can’t figure out the answer without looking more directly at the underlying quantities. But how much variation can there be among, e.g., the San hunter gatherers?

  • Johan Viklund

    Is the original question about kinship or similarity? These two concepts are very different. I interpreted it as beeing about kinship, in which case your previous post is correct (distance is uninteresting, common history rules), but if it’s about similarity, then this one is correct. I guess I get confused since my default is phylogenetic thinking.

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

    But how much variation can there be among, e.g., the San hunter gatherers?

    the bushman paper indicated lots i thought. in fact, cuz they used SNP-chips geared toward detecting euro variants prolly an underestimate.

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

    john, i don’t know. also, i don’t think lay people make the distinction.

  • Insightful

    Razib, Dienekes responded to your post on his website: http://dienekes.blogspot.com/2010/08/which-population-is-most-genetically.html

    Yoruba are closer to (in order): to Caucasoids, East Asians, Amerindians, in that order. Distant from all, but not equidistant.

    “Drift” gets invoked so often, so it is worthy to consider if it is responsible for the greater distance of Amerindians to Africans. “Drift” can indeed shift allele frequencies in a small population, and increase Fst. However, there are dozens of small and isolated populations throughout Eurasia, yet none of them are more distant from Africans than Amerindians are. If “drift” is responsible, then we would expect some isolated Eurasians to repeat the pattern of greater distance that Amerindians present. Good luck finding any study where any Eurasian population is more distant to Africans than (unadmixed) Amerindians are.

    There is no need to invoke “drift” to explain Amerindian-African distance, as there is a simpler explanation: Amerindians, unlike Eurasians, are more distant from Africans, not because of “drift” shifting their allele frequencies, but because they lacked the opportunity for substantial gene flow with Africans.

    It is worthy to revisit the Fst table: Amerindians are 1/5 further from Africans than East Asians are because they spent about 1/5 of the time since “Out of Africa” isolated from Africans. East Asians had about 60 thousand years worth of opportunities for gene flow with Africans (however limited), while the corresponding time for Amerindians is about 45-50 thousand years.

    There is actual evidence for post-Out of Africa gene flow between Africa and Eurasia, but not between Africa and the Americas. It comes from the YAP marker of the human Y-chromosome. This defines the DE-YAP clade of the Y-chromosome phylogeny. This clade is absent in the Americas, but it is present in Africa, West and East Eurasia. Africa and West Eurasia share the E subclade, and East Eurasia possesses the D subclade.

    What YAP tells us is that Out-of-Africa was not a one-time event: there has been subsequent gene flow linking Africa and Eurasia, and YAP is the smoking gun for this gene flow (*) There is no way around it: post-OOA men bearing YAP Y-chromosomes spread across a range spanning drom Nigeria and South Africa to the isles of Japan, but not into the Americas. These were not necessarily the only conduits for post-OOA gene flow, but they prove the existence of such gene flow.

    Moreover, the greater proximity of Caucasoids to Africans can also be explained by the joint possession (by Africans and Caucasoids) of the E subclade of YAP (at the exclusion of East Asians and Negritos, who possess the D subclade).

    In conclusion: the population that is most distant from Africans are Amerindians. They are more distant not because of drift but because of an earlier (10-15kya) cessation of any important gene flow between them and the rest of the species: about 1/5 less gene flow => about 1/5 more distance (relative to East Asians). Finally, this cessation of gene flow does not only make sense archaeologically, but is also evidenced genetically by the prevalence of the YAP marker, which records African-Eurasian contacts (and a nested subset of African-Caucasoid contacts) at the exclusion of Amerindians.

    (*) The direction of this gene flow is contested as both Eurasian and African origin of YAP have been proposed. That’s not important however, as YAP links Africa and Eurasia at the exclusion of the Americas either way.

  • http://lablemminglounge.blogspot.com Lab Lemming

    Re: #2:
    Abo=nigger in terms of appropriateness in polite society, so please find a different term.

  • Marnie

    “From what we can tell there was relatively little gene flow after the initial settlement of the New World and Oceania (actually, there may have been several waves into the New World to be fair, but it looks like there wasn’t enough Eurasian gene flow to dampen the reduction in heterozygosity caused by bottlenecks).”

    There may be a way to test Dienekes’ hypothesis that Amerindian populations are the most genetically distant from Yorubans based on the time they have been isolated from Eurasians and Africans.

    Edward Vadja, working primarily from linguistic data, suggests that there are three separate migrations into the Americas: Amerindian, Na Dene and Eskimo-Aleut, with Ameridians being the first migrators and Eskimo-Aleut being the last. The Fst distance between these groups and the Yoruba should be highest for Amerindians and lower for the Eskimo-Aleut.

    There probably is not a time continuum of genetic crossover between Eurasians and Africans, but it would be interesting to see how these Fst numbers correlate with hypothesized dates for Eurasian-African genetic crossovers, if they are known.

    One note of caution: Dienekes’ Fst numbers for Amerindians are taken from a paper on Koreans, with the Amerindians used only as a reference point. The Amerindian sample is comprised only of 16 people.

    In addition to looking at Beringia migrations, it would also be interesting to look at the “still in Siberia” suspected groups of origin for the Eskimo-Aleut and Na Dene.

    Please see Dienekes’ blog for references.

  • Marnie

    Sorry, misspelt Edward Vajda’s name in the above post.

  • http://www.kinshipstudies.org German Dziebel

    “I think I won’t revise my model of the out of Africa migration. ”

    But other people do. If you look at “A New Genetic Map of Living Humans
    in Interconnected World Regions” autosomal tree published by DNA Tribes (http://www.dnatribes.com/populations.html) you’ll see that highest Fst values in the Americas can apparently lead to the effective reversal of traditional out-of-Africa phylogenies, with the principal split now being between Amerindians and non-Amerindians and not between Africans and non-Africans.

    I also added a few thoughts on the debate at Dienekes, with a couple of references to the studie that indicated the lack of bottleneck effects in Amerindian populations..

    http://dienekes.blogspot.com/2010/08/which-population-is-most-genetically.html

  • Jason Malloy

    “Shouldn’t massive genetic diversity in Africa imply huge Fst distances between the different branches of the tree in the blue Africa cluster on your figure? “

    See also:

    “The average nucleotide diversity for the 50 segments is only 0.061% ± 0.010% among Asians and 0.064% ± 0.011% among Europeans but almost twice as high (0.115% ± 0.016%) among Africans. The African diversity estimate is even higher than that between Africans and Eurasians (0.096% ± 0.012%)… Thus, Africans differ from one another slightly more than from Eurasians

  • onur

    How are Southern Africa and Madagascar in the same cluster on that DNA Tribes map? Are the genetic effects of the Austronesian migrations so weak in Madagascar?

  • onur

    How are Southern Africa and Madagascar in the same cluster on that DNA Tribes map? Are the genetic effects of the Austronesian migrations so weak in Madagascar?

    Especially in the light of the fact that Madagascar was very probably totally uninhabited until the arrival of the Austronesians from the east.

  • http://www.kinshipstudies.org German Dziebel

    “The average nucleotide diversity for the 50 segments is only 0.061% ± 0.010% among Asians and 0.064% ± 0.011% among Europeans but almost twice as high (0.115% ± 0.016%) among Africans. The African diversity estimate is even higher than that between Africans and Eurasians (0.096% ± 0.012%)… Thus, Africans differ from one another slightly more than from Eurasians“

    But, to quote from Tishkoff, “The Genetic Structure and History of Africans and African Americans,” 2009: “The proportion of genetic variation among all studied African populations was 1.71% (table S3). In comparison, Native American and Oceanic populations showed the greatest proportion of genetic variation among populations (8.36% and 4.59%, respectively)…”

  • Matt

    ““The proportion of genetic variation among all studied African populations was 1.71% (table S3). In comparison, Native American and Oceanic populations showed the greatest proportion of genetic variation among populations (8.36% and 4.59%, respectively)…”

    I’d think if you have a typical amount of absolute variance between populations, but a very low relative degree of absolute variance within population, then the proportion between of between population variation will rise, even though it isn’t particularly extraordinary in absolute terms (even if it’s smaller). Perhaps that explains this (although I’d expect that Africa’s East-West axis facilitated greater population expansions across the whole continent as well).

  • http://www.kinshipstudies.org German Dziebel

    “I’d think if you have a typical amount of absolute variance between populations, but a very low relative degree of absolute variance within population, then the proportion between of between population variation will rise, even though it isn’t particularly extraordinary in absolute terms…”

    You can describe it in these terms. IMO, a great amount of “relative” variation and a small amount of “absolute” variation is more characteristic of Mid-Upper Pleistocene human/hominin populations than what we currently observe in Africa, which must have been more fragmented and isolated from each other than modern human populations. Notably, the amount of linguistic variation is the greatest in America (140 language families) and Oceania (50 or so language families in PNG) and very moderate, if not limited in Africa (20 language families), which maps very nicely on the sharp contrast between high relative variation in America and low relative variation in Africa (as measured by Fst).

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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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