About a week ago I put up a post put on an analysis of a paper which reported on the ancestral make up of 50 Cubans (as well as assorted other Hispanic/Latino groups). One aspect of the paper which was somewhat notable is that 1 out of 3 Cubans were 90 percent or more European in ancestry. The notability of this is that is that 5 out of 6 Cuban Americans identify as white. That is, of European ancestry. The main caveat here is that these Cubans were sampled from New York City, and to a lesser extent the Midwest. The fact of non-European admixture in putatively white European individuals from Latin America is not surprising. Our prior expectation should be that the admixture is non-trivial, though not preponderant. For example, the majority of the white population of Argentina has Amerindian ancestry (or, more precisely ~15 percent of the aggregate ancestry of Argentineans is Amerindian). At least notionally Cuba is a much more racially mixed culture than Argentina, so non-white admixture in even white Cubans is not surprising.

Based on the above paper (and the data which you can find on other Latin American whites), as well as the genotyping of two Cuban American acquaintances, I asserted that on the order of ~10 percent of the ancestry of the average white Cuban was going to be African. Naturally this prompted some objections. Some of the individuals were not too polite. I think the primary issue that I have to be honest about this is this: I don’t really care too much about the topic on a visceral level. Now, I’m interested in it. And the specific cases illuminate a greater whole, which comments upon various demographic and population genetic dynamics. But I don’t have a strong investment in the specific instance of the particular ancestral quanta of Cubans, or any other group really.

Second, there was some objection to punctilious attention to scientific methodology, such as representativeness and sample size. This is a serious objection in the abstract, but the reality is that a generation of genomics has been performed with lineages as unrepresentative as “Utah whites.” Science and knowledge seeking is frankly operationally an ad hoc and sloppy process, without great attention to the book of proper scientific methodology. When we don’t have much information, any extra information is often useful, so long as we keep in mind the error that this introduces into the process.

All that being said, one commenter brought to my attention an interesting paper. It reports 6 percent African ancestry in a very large population of white Havana Cubans. The main downside is that they used only 60 SNPs, as opposed to the 60,000 SNPs in the above study. Of course those 60 SNPs would be “ancestrally informative,” but at 6 percent vs. 10 percent (my prior estimate), I’m not sure that I should totally trust the precision and update my values. But I think that nevertheless this study converges upon the same qualitative result: white Cubans, like white Latin Americans in generally, seem to usually exhibit non-trivial amounts of non-European ancestry.

But in the interests of moving the discussion forward, the commenter who brought the above paper to my attention supplied two 23andMe genotypes of Cuban Americans: herself and her husband. I will now refer to her as “Cuba 1” and her husband as “Cuba 2.” I created a pooled data set of the following populations:

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A comment below prompted me to recheck the browser stats on the web. People are now starting to give Google crap for not having really hit the jackpot on anything since Gmail, especially after the flubs with Google Wave and Buzz, and the mixed reviews at best for Google+. But it looks like Chrome may actually reach a plural majority this year. Back in the day (i.e., 1990s) control of the majority browser share was actually a big deal. My earlier hunch that eventually Chrome will start eating into IE’s user base more than Firefox’s seems to be panning out.

He’s a similar chart from the w3schools website (because it’s a tech oriented site IE automatically suffers a penalty, but the overall trends are similar):

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A man of astonishing multitudes?

Daniel MacArthur points me to one of the funniest historical genetic popular write-ups I’ve seen in years. Study reveals ‘extraordinary’ DNA of people in Scotland:

Researchers believe that Scotland’s location could be a factor in the “astonishing and unique” origins of people from the country.

In a statement, Dr Wilson and Mr Moffat said: “Perhaps geography, Scotland’s place at the farthest north-western end of the European peninsula, is the reason for great diversity.

“For many thousands of years, migrants could move no further west. Scotland was the end of many journeys.”

I am aware that modern Scotland does emerge from a rather patchwork ethno-cultural background. That is, it is the fusion of Gaels (the Scots), Picts, the Norse, the Strathclyde Britons, and of course the German speaking Anglo-Saxon populations migrating up from Northumbria. But the “astonishing and unique” genetic heritage of the Scots seems as plausible as the culinary delights of haggis. From what I recall genetic diversity drops off as you go north and west in Europe because the effective population drops (less gene flow with surrounding populations because there are fewer surrounding populations). Rather than gene flow in, like the British Isles as a whole it seems that there is likely to be a whole lot of Scot in the rest of the world due to the migrations of its Diaspora.

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Here’s a quick follow-up on the study which purported to illustrate the shortcomings in genomic risks prediction, and received major media coverage:

Neil Risch, PhD, a leading expert in statistical genetics and the director of the UCSF Institute for Human Genetics, agrees with one major conclusion presented by the study authors, the Times reporter, and other experts quoted in media coverage: genomic studies are more valuable for their potential to lead to a better understanding of diseases globally than for their predictive power for any individual patient.

This position has been “in the air” for a few years. But I think we ought to reiterate something: genomics intersects with structural and molecular biology, as well as statistics. In other words, genomes are concrete things in the world, and their biophysical nature naturally has great relevance for understanding the etiology of diseases, even if they are of limited use in a purely statistical sense. The field even has something for those who are suspicious of hereditarian arguments in general: epiogenomics.

23andMe has done some great things, and I highly recommend its service to friends. But I’m really glad that CeCe Moore is being consulted by them in regards to improving their ancestry feature set. Below are the “ancestry paintings” for myself & my daughter.

According to 23andMe I’m 40% Asian, and she is 8% Asian. Obviously something is off here. The situation easily resolved itself when I tuned my parameters and increased my sampled populations in Interpretome. But it just goes to show you the limits of this sort of thing without fine-grained control of the details of the analysis.

 

I am not particularly mystical or sentimental about genetics. I favor openness. But I just started getting my daughter’s results back from 23andMe, and some of her coefficients of relatedness to her grandparents deviated sharply from 0.25. As I have blogged about this possibility I was obviously aware of the abstract probability here; but it is a different thing altogether to be faced with reality. How exactly does one go about explaining that one of your parents is ~50% closer genetically to their grandchild than the other? I don’t think it matters really in a concrete sense for them, but divulging this information makes me somewhat uncomfortable. Many, many, others are going to be confronted with these issues. We don’t have social norms yet. This isn’t cut & dried like paternity. Thoughts?

Is 4-Year-Old as Smart as Einstein? Not Quite, Scientists Say:

One of the latest members of the high-IQ club Mensa is a mere 4 years old, with an IQ of 159 — but psychologists warn against pulling out the Albert Einstein comparisons just yet.

…

“All you’re doing with IQ testing is testing within a certain age group,” Lawlis told LiveScience, explaining, “You’re saying the 4-year-old is smarter than 99.5 or 99.8 of [her] age group, but that doesn’t mean you can compare to another age group.”

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Prompted by miko’s skepticism about the utility of WORDSUM (a vocab test) across subcultures, I went and looked for SAT data. My assumption was that math sections are more “culture-fair” (though from what I gather ETS tries hard in various ways to be culture-fair in general). The data was not hard to find:

You can also check the ACT results.

Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis:

Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that “statistical maps” based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide formal tests of these qualitative observations, we describe a Procrustes analysis approach for quantitatively assessing the similarity of population-genetic and geographic maps. We confirm in two scenarios, one using single-nucleotide polymorphism (SNP) data from Europe and one using SNP data worldwide, that a measurably high level of concordance exists between statistical maps of population-genetic variation and geographic maps of sampling locations….

There is concordance. But look at the figure below. On the left are populations where they were sampled, and the right shows the populations displayed in a manner to reflect genetic distances.

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Well, almost no one:

“The unspoken central reason for the societal taboo and the penal ban on incest is the possibility of hereditary defects — a factor that Strasbourg only hinted at. But the intention behind the eugenic argument is one that is indefensible, and not just in Germany with its terrible Nazi past: The increased risk of hereditary defects does not justify a legal ban. Otherwise you would have to legally ban other risk groups, like women over 40 or people with genetic diseases, from having children. Does anyone truly want to prevent predictable disabilities using penal measures and thus deny disabled children the right to life in 2012? That’s absurd. And yet such fears of genetic damage are precisely what shape the punishibility of sexual intercourse between siblings.”

There are a set of arguments against near relation incest which strike me as generally ad hoc. And there’s social science to back that up. Incest is reflexively disgusting to most people (depending on how it is categorized). But disgust alone is not a sufficient grounds for banning a practice in educated circles today, so people create rationales after the fact. David Hume would not be surprised.

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