Wednesday, April 19, 2017

Further to the Last: New Light, Not Necessarily On The Converting Sacrament

Lameen and Graydon have been bugging me for years to subject my crackpot hypothesis to DNA testing. It may seem like I've been ignoring them, but, in reality, I've been creating elaborate counterarguments in my head, which I would have talked about already were it not for Windows doing a forever update while I lounged around in pyjamas on my Surface. (It's a day off, first of seven. What can I say? Pizza later.)

In retrospect, my time might have been better spent watching the latest episode of Agents of Shield than spinning my theories in my head. Say what you want about Hydra, but they're damn good DNA testers. 

Test this. (The model isn't credited, except presumably on an expired American Apparel page, but the cropped top is Raglan Jaquard.)
Eric Durand, J. Michael Macpherson, David Reich and Joanna L. Mountain are also good genetic testers. But, first, let's look at something cool.

The last column is because this is about a Skeptical Inquirer article about ancient Canaanites being maybe the ancestors of modern native North Americans. Oh, those wacky Mormons. 

The X2a bands show that there's room for future discoveries. We wouldn't even know that there was an X sub-haplogroup present in aboriginal American populations from the Mound City samples alone. That said, we have a pretty solid overall profile of the mitochondrial DNA picture of pre-contact Eastern Woodland Indian populations, thanks to the Hopewell horizon's enthusiastic bone-gathering. This is important, because genetic genealogists trace regional ancestry through three major inputs: autosomal DNA, present in X chromosomes; Y DNA, which is passed purely through the father's line; and mitochondrial DNA, the most recent and most exciting discovery, and present only in the ovum, and thus passed exclusively matrilinearlly.  Of these, autosomal DNA loses Native American flavour after six generations, while Y DNA mutates so slowly that half of Native Y DNA is shared with common ancestors who spread into northern Asia and Europe two Ice Ages back. So if you are looking for Native ancestors in commercial DNA testing, as many people at my stage of life are, it's pretty much mitochondrial DNA you need to look at, and, subject to new research, if you have a Cherokee great-grandmother, you can only prove it genetically by testing with X2a, D, C, B or A haplogroups.  

That being said, I'm a complete amateur at everything but history of science (humblebrag appeal to authority!), so let's look at the testing.

"We find that many self-reported European Americans, predominantly those living west of the Mississippi River, carry Native American ancestry (Figure 3B). We estimate that European Americans who carry at least 2% Native American ancestry are found most frequently in Louisiana, North Dakota, and other states in the West. Using a less stringent threshold of 1%, our estimates suggest that as many as 8% of individuals from Louisiana and upward of 3% of individuals from some states in the West and Southwest carry Native American ancestry. . ."
For African Americans,

[T]he frequency of European American individuals who carry African ancestry varies strongly by state and region of the US (Figure 3A). We estimate that a substantial fraction, at least 1.4%, of self-reported European Americans in the US carry at least 2% African ancestry. Using a less conservative threshold, approximately 3.5% of European Americans have 1% or more African ancestry (Figure S8). Individuals with African ancestry are found at much higher frequencies in states in the South than in other parts of the US: about 5% of self-reported European Americans living in South Carolina and Louisiana have at least 2% African ancestry. Lowering the threshold to at least 1% African ancestry (potentially arising from one African genealogical ancestor within the last 11 generations), European Americans with African ancestry comprise as much as 12% of European Americans from Louisiana and South Carolina and about 1 in 10 individuals in other parts of the South (Figure S8).
Most individuals who have less than 28% African ancestry identify as European American, rather than as African American (Figures 4 and 5A ). Logistic regression of self-identified European Americans and African Americans reveals that the proportion of African ancestry predicts self-reported ancestry significantly, with a coefficient of 20.1 (95% CI: 18.0–22.2) (Table S6 and Figure S9).
The hotlinks don't go to the images, but they do tell you where to find the figures in the article, so I'm keeping them.
And the ancestral connections are sex-biased:

Fitting a model of European and Native American admixture followed later by African admixture, we find the best fit with initial Native American and European admixture about 12 generations ago and subsequent African gene flow about 4 generations ago.
Non-European ancestry in European Americans follows a sex bias in admixture contributions from males and females, as seen in African Americans and Latinos. The ratio between X chromosome and genome-wide Native American ancestry estimates in European Americans shows greater Native American female and higher European male ancestry contributions (Tables 1 and S4). Though we do not observe evidence of a sex bias in African ancestry contributions in European Americans overall, analysis of only those individuals with at least 1% African ancestry reveals 15% higher African ancestry on the X chromosome relative to genome-wide estimates (p value 0.013). This increase suggests female-African and male-European sex bias in European Americans that follows the same direction as in African Americans and Latinos, with greater male European and female African and Native American contributions.
And, of course
We find very low levels of African and Native American ancestry in Europeans with four grandparents born in Europe. We estimate that only 0.98% of Europeans carry African ancestry and 0.26% of Europeans carry Native American ancestry. These levels are substantially lower than the 3.5% and 2.7% of European Americans who carry African and Native American ancestry, respectively.
Our results provide empirical support that, over recent centuries, many individuals with partial African and Native American ancestry have “passed” into the white community,79, 80 with multiple lines of evidence establishing African and Native American ancestry in self-reported European Americans (see Subjects and Methods). Though the majority of European Americans in our study did not carry Native American or African ancestry, even a small proportion of this large population that carry non-European ancestry translates into millions of European Americans who carry African and Native American ancestry. Our results suggest that the early US history, beginning in the 17th century (around 12 generations ago), might have been a time of many population interactions resulting in admixture.

So there you go. I'm not completely crazy.  


  1. Also of interest:

  2. Given the track record of alleged pre-Clovis finds, I'm more than a little surprised that Nature was willing to publish a site with no (human) bones.

    This is the kind of thing that must really frustrate paleoarchaeologists. "This stone has been modified!" "No, this shape is consistent with erosion!" Then, repeat, in a louder voice.

  3. The estimates of African ancestry are probably very conservative, as they relate only to very recent contributions.

    As one geneticist pointed out, everyone in Europe is descended from Charlemagne (he lived long enough ago, and left enough descendants, for his genes to have diffused very widely). By the same token, we are all descended from Africans imported around the same time into Spain, Sicily and North Africa, from those brought to Portugal in the 1400s, those in Egypt and so on. Any genes they contributed would just constitute the "normal" European background by now.

  4. I just dipped into the wiki article on Most Recent Common Ancestor. It seems that most estimates of the time depth to the last person who is in everyone's family tree (two to four thousand years) is based on mathematical modelling and depends heavily on "first contact" assumptions with the Americas and Australia. I think that's a bit rubbish, since you don't have to go all Kon-Tiki to note inter-hemispherical contact via the Torres Islands and trans-Bering Strait communities.

    So it's nice to have a model based on a virus study instead, that says 3100 years ago. That is, 1100BC.

    That is, the beginning of the Iron Age. Cool!