The non-European ancestry of Afrikaners

A few years ago I got some South African genotypes. Some of the individuals were clearly African. A few mapped perfectly upon Northern Europeans. But many of the samples consistently were European but shifted toward non-European populations.

Based on history of the assimilation of slaves into the European population of Cape Colony in the 18th century, my assumption is that these individuals are Afrikaners.

Recently I realized that Brenna Henn had released some more Khoisan samples, so I decided to look at this question of admixture again. The two Khoisan populations are the Nama and the Khomani. I removed those with lots of Bantu and European admixture and combined them together into one population.

Running unsupervised Admixture shows how distinct the South African whites are.

The average Utah white in this sample (this population is a mix of British, German, and Scandinavian in ancestry) is 99% European modal cluster, and 1% South Asian. The average for the white South Africans in this data set is 94% European modal cluster. The residual is 1% East Asian (Dai modal), 1% Khosian, 1% non-Khoisan African, and 2% South Asian.

I ran Treemix a bunch of times, and every single plot came out like this when I ran it for three migrations:


The gene flow from the Utah whites to the Gujuratis is simply an artifact of the fact that the Gujurati sample is mixed caste, and some of the Brahmin or Lohannas have more “Ancestral North Indian.” The gene flow from the Europeans to the Khoisan is probably real, or, might be due to pastoralist admixture via East Africans. The last migration arrow goes from the African populations to the South African whites, with a shift toward the Khoisan.

I also ran a three population test where A is the outgroup, and B and C are a clade. A significantly negative f3-statistic indicates admixture in population A. The negative values are listed below:

A B C f3 f3-error Z-score
Gujrati Dai UtahWhite -0.00121718 0.000140141 -8.68539
South_Africa EsanNigeria UtahWhite -0.00127718 0.000147982 -8.63059
South_Africa Khoisan_SA UtahWhite -0.0012928 0.000151416 -8.53802
Gujrati South_Africa Dai -0.000778791 0.000155656 -5.00329
South_Africa Dai UtahWhite -0.000541974 0.000133262 -4.06699
South_Africa UtahWhite Gujrati -0.000103581 8.46193e-05 -1.22408

This aligns well with the Admixture results. Afrikaners have both African ancestries, and, Asian ancestry.

In James Michener’s The Covenant one of the plot lines alludes to mixed ancestry in one of the Afrikaner families. The results above suggest that mixed ancestry is very common, and perhaps ubiquitous, in this population. True, there are some Afrikaners such as Hendrik Verwoerd who migrated to South Africa from the Netherlands in the past century or so, but these are uncommon to my knowledge.

Books you look at but don’t buy

A little while ago I was curious about the books people looked at through my links which they nevertheless did not buy. More precisely I was looking at a 90 day interval. The top book people clicked but did not buy was Introduction to Quantitative Genetics. I know this is an expensive book, but if you can afford it you should buy and it read it. The reasoning is that quantitative genetics is no longer an abstruse topic, as I’m seeing economists conflate correlation of traits between relatives and narrow sense heritability. People have opinions on this topic. Loads.

If you talk about regression to the mean, but barely understand how it works, perhaps you should read Introduction to Quantitative Genetics.

Here the remaining of the top 15 (in order from most clicked to least):

The Journey of Man: A Genetic Odyssey
The Harlot by the Side of the Road: Forbidden Tales of the Bible
Defenders of the Truth: The Sociobiology Debate. This is a good book. I’ve read it three times.
The History and Geography of Human Genes
George R. R. Martin’s A Game of Thrones 5-Book Boxed Set
Principles of Population Genetics. Really readers? This is why more of you are not HWE aware….
Adaptation and Natural Selection
The Nurture Assumption
1491: New Revelations of the Americas Before Columbus
In Gods We Trust
Sewall Wright and Evolutionary Biology

Also, I can go back to 2014. Looking over 90 days from 2014, 2015 and 2016, here are the top 15:

2014 2015 2016
Principles of Population Genetics Freedom at Midnight The Great Ordeal
In Gods We Trust Power and Plenty Sex Segregation in Sports
The Bible with Sources Revealed Why Sex Matters The Dialectical Imagination
Why Sex Matters The Origins of Theoretical Population Genetics The History and Geography of Human Genes
The Transparent Society The Mating Mind Python for Data Analysis
The First Man in Rome Mutants Plagues and Peoples
The Barbarian Conversion In Gods We Trust Grooming, Gossip, and the Evolution of Language
Nature’s God 1491: New Revelations of the Americas Before Columbus 1491: New Revelations of the Americas Before Columbus
Introduction to Quantitative Genetics A History of the Byzantine State and Society Why Sex Matters
The Rise of Western Christendom Principles of Population Genetics Taboo
The Great Arab Conquests The Journey of Man: A Genetic Odyssey Design Patterns
Religion Explained A Concise Economic History of the World A Beautiful Math 
The Nurture Assumption The Man Who Would Be King and Other Stories The Great Human Diasporas
1491: New Revelations of the Americas Before Columbus The Genetics of Human Populations The Seven Daughters of Eve
The Invisible Gorilla A Beautiful Math   Calculus Made Easy

Why Sex Matters has always been a book that gets a lot of clicks. I think it is the title. But it’s rather old now, and on an old fashioned topic: sex differences. Totally milquetoast in the 2000s, but probably very problematic today….

Google still wants to be Apple (sort of)

Google Is Buying HTC’s Smartphone Expertise for $1.1 Billion. This, after Google has already bought and sold Motorola. Remember when Microsoft bought part of Nokia?

The problem is that Apple and Samsung are starting to create a duopoly. And though most phones run Android, iPhones are much more profitable. There’s a reason many companies develop for iOS but not Android. A friend at Google years ago bemoaned how much more profitable iPhone owners were compared to those bought Android phones.

With all that being said the Apple launch and comments on this blog have convinced me I’m not going iPhone. I don’t know if I’ll go for an HTC, Motorola or Samsung. But for me a phone is functional, not an accessory. Perhaps that explains some of the psychological reasons that iPhone owners spend so much more money on apps….

Tales of the Arabian week

This summer I had the pleasure of spending a week in July visiting a Gulf nation which was not Saudi Arabia. It was so hot and humid that my glasses would fog over in the 110-degree weather (Fahrenheit). The reason I went was for a possible business opportunity. As someone who is an atheist from a Muslim background, I am not keen on visiting a Muslim majority country (sorry to be Islamophobic, but Muslim majority countries scare me, so I’m literally phobic). But an opportunity is an opportunity, and off I went.

In hindsight, I should have been less fearful. Though there are cases of Western passport holders from Muslim backgrounds getting in trouble, in general, they seem to have given me the same latitude as other non-natives. Getting drunk at Nobu and eating too much delicious food is nothing I can complain about. Staying at the Four Seasons meant that every morning I could order and compose a breakfast which was a nice international melange of flavors.

The only amusing mishap I can report is that one evening I went to get dinner at the hotel restaurant with the friend who I was on the trip with. He’s a white American. He also is a teetotaler. I ordered a glass of red wine and when the server came back (the same who I had ordered from) he placed the alcohol next to my friend. He was quite embarrassed when he realized what he’d done.

In terms of religion, the region is very conservative. But that conservatism primarily applies to natives. Since the natives mixed so little with the majority expat population diversity and pluralism did not seem to be very difficult to maintain. Diversity and pluralism did not impact the natives, and expats tended to live in their own communities. On the flight back an American kid who had spent two years in the Gulf did complain that outside of their compound there was a problem with local officials capriciously enforcing rules such as that which banned sleeveless shirts. Apparently, local kids of good background got more slack on these norms, probably because they were well connected.

It was definitely a caste society. The native population is by and large leisured. Asians did most of the productive work. Every driver we had was a Filipino. The wait staff was a mix; South Asian, Eastern European, East Asian, Southeast Asian, African. We visited several facilities where all the security seemed to East African. Many higher level service professionals were from other parts of the Middle East. There were a fair number of Muslim Southeast Asians in professional roles. Everyone knew their place. The staff at the hotel were exceedingly obsequious.

There was no pretense at democracy or liberty. Rule of law was on the whims of the local aristocracy. Expats were basically a servile caste. I only interacted with professionals or the hotel staff, not the working class. But even they were aware that their residence permits could be revoked at any time. There were stories of people who were jailed for getting on the wrong side of an aristocrat. If they neared power, they had to know who to cultivate.

I always say that Robert Kaplan’s 2000 book The Coming Anarchy should have been titled “The Coming Oligarchy.” My experience in the Gulf definitely showed me an illustration of that sort of society. There was some degree of comfort and affluence, but it was juxtaposed against a regression away from modernity as we’d understand it, with its legal egalitarianism.

It left me with the only solution to inequality that I can see in the near future: make sure you are nearer to the top.

A plethora of secondary worlds

A short write-up, Why build new worlds, which surveys the origins and of secondary creations such as Middle Earth.

One aspect of these attempts at world-building is the most detailed ones invariably borrow and reconfigure aspects of our own universe. This is obvious in The Song of Ice and Fire, and explicit in The Lord of the Rings, in which Tolkien was striving to create a mythology for the Anglo-Saxon peoples. Guy Gavriel Kay takes this tendency of drawing from our world to an extreme in works such as Sailing to Sarantium, which has numerous characters who are clearly modeled upon figures from our world’s history. Similarly, Kate Elliott’s Crown of Stars series is pretty obviously set in 10th century Germany. And she says so in the afterword of the first book if I recall correctly.

But one aspect of this borrowing from our own world is that like Tolkien there is a focus on Northern European source material. Since most of the buying public are probably white for English speaking fantasy that’s a reasonable choice. But sometimes you get an author who mines a whole different part of the world, and the result can be very fascinating. Martha Wells’ Wheels of the Infinite has issues with plotting and character development, but it’s imagining of a fantastical Angkor-like civilization is beautifully rendered.

If there is one area which I thought would be excellent source material for a secondary world, it’s the highlands of Ethiopia. I’d love to read fantasy which draws upon this land’s history, in a part because most people (including me) would not have as clear of a sense of who was based on someone real and the correspondence of events to those in our world’s history.


Stanislav Petrov and our common humanity

The first time I watched Gorky Park in the 1980s I remember how strange it was to see citizens of the Soviet Union, or as we called them all then irrespective of ethnicity, “Russians,” with normal human motivations and concerns. In other words, depicted in the fullness of their humanity.

As a child in Reagan’s America what we knew about Russians was that they were citizens of the Soviet Union, and what we knew about the Soviet Union were military parades and the dour mien of their leaders. When Mikhail Gorbachev emerged on the scene it didn’t really humanize the citizens of the Soviet Union. Rather, he was a totem or exemplar of a new spirit in the world, and that perhaps we weren’t all doomed to nuclear annihilation.

As for Russians. Who were they? In the 1990s they were our allies somehow, at least on paper. I think the truth of the matter is that we did take advantage of them as a nation and a people who were experiencing difficulties, insofar as America maneuvered itself into even more advantageous positions while they were down on their luck. Eventually, the images of godless Communists faded in the 1990s…to be replaced by kleptocrats and Russian mafia.

This is not to say I do not believe Communism was evil. I do believe it was evil. But, normal human beings with the same concerns and aspirations as those in the West were part of a system, which on occasion made them the tools of evil in this world. For that, perhaps they must be judged. Some say the same of American citizens. I may disagree in the particulars…but the principle is the same.

I bring this up because recently we found out that Stanislav Petrov died last spring. His story is well known at this point; he made a judgment call and ignored a false alarm that five American ICBMs were headed toward the Soviet Union. He acted humanely in a moment of high drama. As an American we are so often drilled into repeating the mantra we are the “good guys.” Petrov shows us that decency persisted even in the “evil empire.”

Amazon pepper sauce

Something different today when it comes to the condiment of choice. So I’m privileged to work at a company where the boss adds different hot sauces to our Instacart orders for the office. So we get to sample the good with the bad (usually not bad, just not exceptional).

You stumble upon some real gems in that way. The Green Amazon pepper sauce isn’t the hottest that’s graced my palette by a long-shot, though it packs more of a punch than tabasco. But its tart pungency gives you a huge wallop. Think the pepperoncinis you used to get with pizza or in antipasto. But livelier and spicier.

Overall a definite keeper, Green Amazon is literally flavorful, with tang and spiciness, and a bit of savor as well.

Population structure in Neanderthals leads to genetic homogeneity

The above tweet is in response to a article which reports on the finding past month in PNAS, Early history of Neanderthals and Denisovans. It’s open access, you should read it. I don’t think I’ve reviewed it because I haven’t dug through the supplements. To be frank this is a paper where you pretty much have to read the supplements because they’re introducing a somewhat different model here than is the norm.

I talked to Alan Rogers at SMBE about this paper. Broadly, I think there might be something to it, and it’s because of what David says above. It is simply hard to imagine that Neanderthals could be extremely successful with such low genetic diversity as we see, and spread so thin. Now, the Quanta Magazine tries to emphasize that the effective population is not the true census population, but I wish it would have explained it more clearly. Basically, the size that is relevant for breeding is obviously not going to the same as a head count. And, because effective populations are highly sensitive to bottlenecks you can get really small numbers even when the extant population at any given time may be large.

The PNAS paper makes some novel inferences, and I’ll set that to the side until I read the supplements. But I don’t think it’s crazy that population structure within Neanderthals could be leading to lower total genetic diversity.

Release the UK Biobank! (the prediction of height edition)

There’s so much science coming out of the UK Biobank it’s not even funny. It’s like getting the palantír or something.

Anyway, a preprint, submitted for your approval. A vision of things to come? Accurate Genomic Prediction Of Human Height:

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate ~0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction. The variance captured for height is comparable to the estimated SNP heritability from GCTA (GREML) analysis, and seems to be close to its asymptotic value (i.e., as sample size goes to infinity), suggesting that we have captured most of the heritability for the SNPs used. Thus, our results resolve the common SNP portion of the “missing heritability” problem – i.e., the gap between prediction R-squared and SNP heritability. The ~20k activated SNPs in our height predictor reveal the genetic architecture of human height, at least for common SNPs. Our primary dataset is the UK Biobank cohort, comprised of almost 500k individual genotypes with multiple phenotypes. We also use other datasets and SNPs found in earlier GWAS for out-of-sample validation of our results.

A scatter-plot is worth a thousand derivations.

You know what better than 500,000 samples? One billion samples! A nerd can dream….