An estimate of black admixture in white Americans

An ICHG/ASHG 2011 abstract (below) reports some results from a study of the 23andMe database. I see various potential issues with the research as described in the abstract; but while the numbers are not definitive, these estimates are likely to be by far the most accurate to date. What's clear is the overwhelmingly huge majority of white Americans have zero black ancestry. All previous sensible analyses of genetic data agree, and any other result would be difficult to reconcile with American history -- however disappointing that might be to "Multiracial Voice"-types and race denialists.

In 2002, Mark Shriver claimed 30% of white Americans have on average about 2% African ancestry, the average for the population as a whole coming out to about 0.7%. Shortly thereafter, in a different interview, Shriver lowered his estimate, purporting "about 10 percent of [the European-American population] have some African ancestry". Subsequently, another principal of DNAprint revised the estimate still further downward: "Five percent of European Americans exhibit some detectable level of African ancestry". That too was an overestimate. 23andMe, examining the genomes of vastly larger numbers of people using thousands of times as many SNPs, estimates "about 2%" of "European Americans" have any detectable autosomal black ancestry. And three quarters of that 2% have only "about 0.5%" African ancestry (i.e., less than Shriver in 2002 claimed the average American carried).

Exceptions to the "One Drop Rule"? DNA evidence of African ancestry in European Americans. J. L. Mountain1, J. M. Macpherson1, C. B. Do1, B. T. Naughton1, R. A. Kittles2, N. Eriksson1 1) 23andMe, Inc, Mountain View, CA; 2) Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL.

Genetic studies have revealed that most African Americans trace the majority (75-80%, on average) of their ancestry to western Africa. Most of the remaining ancestry traces to Europe, and paternal lines trace to Europe more often than maternal lines. This genetic pattern is consistent with the "One Drop Rule,” a social history wherein children born with at least one ancestor of African descent were considered Black in the United States. The question of how many European Americans have DNA evidence of African ancestry has been studied far less. We examined genetic ancestry for over 77,000 customers of 23andMe who had consented to participate in research. Most live in the United States. A subset of about 60,000 shows genetic evidence of fewer than one in 16 great-great-grandparents tracing ancestry to a continental region other than Europe. They are likely to consider themselves to be entirely of European descent. We conducted two analyses to understand what fraction of this group has genetic evidence of some ancestry tracing recently to Africa. We first identified individuals whose autosomal DNA indicates that they are predominantly of European ancestry, but who carry either a mitochondrial (mt) DNA or Y chromosome haplogroup that is highly likely to have originated in sub-Saharan Africa. Of the 60,000 individuals with 95% or greater European ancestry, close to 1% carry an mtDNA haplogroup indicating African ancestry. Of approximately 33,000 males, about one in 300 trace their paternal line to Africa. We then identified the subset of these European Americans who have estimates of between 0.5% and 5.0% of ancestry tracing to Africa. This subset constitutes about 2% of this set of individuals likely to be aware only of their European ancestry. The majority (75%) of that group has a very small estimated fraction of African ancestry (about 0.5%), likely to reflect African ancestry over seven generations (about 200 years) ago. We estimate that, overall, at least 2-3% of individuals with predominantly European ancestry have genetic patterns suggesting relatively deep ancestry tracing to Africa. This fraction is far lower than the genetic estimates of European ancestry of African Americans, consistent with the social history of the United States, but reveals that a small percentage of “mixed race” individuals were integrating into the European American community (passing for White) over 200 years ago, during the era of slavery in the United States.

Reply to Rienzi on DNAprint, part 2

Rienzi takes issue with "unfavorable comparison" of DNAprint's efforts to higher-resolution exploration of genetic structure.

The issue is not up for debate.

As DNAprint themselves acknowledge, "increasing the number of AIMs is expected to increase the precision of the individual ancestry estimates". Whether we are dealing with personal genetic testing or academic studies using admixture mapping, more markers unquestionably are better (at least well into the hundreds of thousands--not hundreds--of SNPs). Compare the results Rosenberg et al. obtained in 2002 using 377 autosomal STRs and those of Stanford's more recent 650,000 SNP analysis. Intra-European structure is indistinct in the earlier analysis; at higher resolution, the same population samples are cleanly separable.

Rienzi conflates the general principal above with a debate on the merits of specific testing companies. Beyond pointing out that DNAprint has no utility for white Americans or Europeans (even if we are to trust DNAprint's own data, the "admixture" of the typical white American is well below the error thresholds DNAprint acknowledge are built into their tests, which if anything underestimate error), I have little interest in such a debate. And it wouldn't matter if there were no other options for testing--useless shit is useless shit. Still, I'll bite.

To get this out of the way: I have never endorsed a testing company, nor do I advocate personal genetic testing, though it's fine when used by knowledgeable people with reasonable goals (e.g. supporting a paternal-line genealogy through Y-STR testing). Question for Rienzi: why do you keep pushing DNAprint products? I see much emotional reactivity and little practical advice in your DNAprint advocacy. Lay out some scenarios outlining exactly what actions you propose people take based on ABD results.

I'm already on record as stating ML individual admixture estimates without accompanying information on confidence intervals are all but useless. So, given that ABD is also useless, deCODEme and DNAprint are presently battling for last place in the admixture analysis arena. That said, under a reasonable set of assumptions deCODEme's analysis is likely already superior:

• More markers available.
  
• The quality of data from the Illumina BeadChips is comparable to or better than that coming off DNAprint's SNP typing platform.
  
• One assumes deCODE uses a similar or the same (relatively simple and old) algorithm used by DNAprint.
  
• Though unfortunate, I don't see the absence of an Amerindian parental population as that huge an issue at the moment--DNAprint seems to have trouble distinguishing IA and EA admixture anyway.

Unless deCODE screwed up their math or chose to analyze only a tiny fraction of the available SNPs when calculating admixture, their estimates are already more precise than those of DNAprint.

More significantly, there's nothing to stop the deCODEme customer from doing his own admixture analyses. He can:
(1) Download his own genotype data.
(2) Download reference data. In addition to HapMap samples, we now have access to the 650,000 SNP data sets for the HGDP samples. More data sets will likely become available in the future.
(3) Run analyses with freely available software (e.g. STRUCTURE, frappe, ADMIXMAP).

It's true that such analyses on large data sets are computationally intensive. I don't consider this a valid excuse for companies, but, regardless, it should not deter the individual. Moreover, processing costs continue to fall and a new approach claims better results with fewer computational resources:

LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote. Our empirical results show that LAMP is significantly more accurate and more efficient than existing methods for inferrring locus-specific ancestries, enabling it to handle large-scale datasets. We further show that LAMP can be used to estimate the individual admixture of each individual. Our experimental evaluation indicates that this extension yields a considerably more accurate estimate of individual admixture than state-of-the-art methods such as STRUCTURE or EIGENSTRAT, which are frequently used for the correction of population stratification in association studies.
[. . .]
We tested LAMP extensively on various datasets of admixed populations generated from the HapMap resource. Our simulations show that LAMP is significantly more accurate than state-of-the-art methods such as SABER and STRUCTURE. In addition, LAMP is highly efficient, with a running time that is about 200 times faster than SABER and about 104 times faster than STRUCTURE. The efficiency of LAMP allows us to estimate ancestries across the genome in several hours on a single computer.
[. . .]
A number of recent studies have produced panels of AIMs in admixed populations;33, 34, 35, 36 AIMs are SNPs that have differing frequencies in the ancestral populations. It is possible that the AIMs might be used to improve the accuracy of individual admixture prediction done by STRUCTURE or other methods, including LAMP. However, the AIMs have disadvantages because there is a risk of over fitting, and the studied population might be somewhat different than the population for which the AIMs were found. As we show here, in an era where the genotyping technology is getting cheaper, it is useful to use the entire set of genotyped SNPs in the analysis of population stratification.

The Watson analysis speaks poorly for deCODE's ethics, but due to the data quality confound says little about the accuracy of their admixture estimates. (Watson's genome was sequenced by 454 at 6 times coverage. Which lengths of DNA got sequenced was up to chance, which means some segments weren't sequenced at all, and others were sequenced an inadequate number of times. This is not an issue with the BeadChip platform.)

Reply to Rienzi on DNAprint

Rienzi draws the attention of unnamed "phenotypists" (*) to the following passage from the latest DNAprint publication (text quoted by Rienzi in bold):

There are relatively few genomic regions that differ substantially among populations. Yet, based on continental origin and ethnogeographic affiliation, some phenotypes (e.g., skin color, height, facial features, and hair textures) exhibit substantial variation as a function, seemingly, of genetic ancestry. Given the substantial interindividual variability in admixture proportions within most historically intermixed populations, the relationship between overt phenotypes and genetic ancestry (or social constructs) is tenuous. For example, dark skin color imparted by eumelanin expression would not be a good indicator of West African ancestry, since many other populations such as Australian, Melanesian, and South Asians also express higher levels of eumelanin and exhibit darker skin color. In other cases, cryptic population structure contributed by recent ancestral admixture can be common for many populations, yet not always appreciable and certainly not quantifiable through self-assessment or visual cues. Hence, the practice of binning persons into single population groups can be inaccurate, and can confound genetic associations contributing to both type I and II errors.

Naturally, if Mark Shriver wrote it, it must be true. However, I'm unclear why the heavily-couched and citation-free assertion warrants my attention. The claim concerns "historically intermixed populations"--e.g. Aframs and mestizos--rather than white Americans.

The population structure of white Americans has been investigated at resolutions much higher any ever used by DNAprint. What (not so) cryptic population structure did researchers uncover? You should already know this:

European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. . . . components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure.
[Discerning the ancestry of European Americans in genetic association studies..]

Likewise for Europeans:

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations.
[Analysis and application of European genetic substructure using 300 K SNP information.]

Put it to sleep. White Americans are not "historically intermixed" with nonwhites to any significant degree, however much you might wish it to be so. Nor is there any evidence "ancient admixture" is an important source of genetic structure in Europe (at least within the major population blocs). The relevant distinction is not between those who have a Nigerian or Mongol in the woodpile and those who don't, but between those of Northern or Central European origin and those of Southern European origin. You know which you are. Your 100% IE certificate can't change that.

More later.

(*) I am the "phenotypists" (sic) in question. I recognize the existence of no such category. It is practically a tautology to note that the definitive answers to questions of genetic relatedness are to be found in the genome. But not quite yet and not by Rienzi's favorite company. ABD tests 176 SNPs. Out of about 10 million. (Then there's the other 2.99 billion base pairs.) For now, I'll trust my eyes, thanks. This man is not 21% East Asian, and telling him he is does not advance European interests--no, it led a white man to start speculating about descents from Attila.