Three Generations of Autosomal Mapping — A Case Study


n opportunity recently arose to collect autosomal admixture mapping data for three generations of one family, a family that has European, subsaharan African, and Asian admixture. The results are educational. They exemplify the heredity of ancestry-informative DNA markers. They show, on the one hand, that the transmission of ancestry-informative markers from one generation to the next is predictable. On the other hand, they also show that each transmission is random, so that predictions must rely on probabilities. Such blending of randomness with predictability is usually hard to explain. The following case history makes it clear. See the sidebar at the end of this article for details of testing and tabulation.

The First Generation

The first-generation grandfather’s genetic admixture is approximately 75 percent European, 13 percent subsaharan African, and 12 percent Asian. The grandmother’s is 90 percent European, 0 percent African, and 10 percent Asian.

To estimate the possible results in the second generation, visualize the two grandparents’ genomes as decks of ten cards each. Seen thus, the grandfather has one African card and one Asian card in his deck of ten. The grandmother has one Asian card. All the other cards are European. Genetically speaking, in this analogy every child’s ten-card genome is created by shuffling the two parental ten-card decks together into a pack of twenty cards, and then dealing out ten of them to form the child’s new genome.

Let us compute how many African cards the offspring of the two grandparents in this real family will get, given that there was only one African card in the merged pack of twenty. He might get none (by not receiving the one African card in the pack). Or he might get that one card. But he cannot get two or more African cards because there was only one African card available in the twenty-card parental pack. Similarly, he might get no Asian cards, or one, or two, but no more than two because there were only two Asian cards available.

The First and Second Generations

The actual second-generation result is shown. The second-generation individual (the father of the third generation) inherited 89 percent European admixture, 10 percent African, and 1 percent Asian. In other words, he inherited the single African card, but neither of the two Asian cards.

The second-generation mother has 51 percent European admixture, 22 percent African, and 27 percent Asian. In the analogy, this comes to two African cards and three Asian cards.

Let us now predict the results in the third generation. The combined pack of twenty cards in this generation contains three African cards (one from the father and two from the mother) and three Asian cards (all three from the mother). So the third generation offspring might inherit zero through three African cards and zero through three Asian cards. Given that six out of the twenty cards are non-European, it is very likely that any third-generation child will receive some non-European cards.

All Three Generations

The actual result for the third generation is as follows. The older child inherited 66 percent European admixture, 21 percent African, and 13 percent Asian. In other words, he inherited two of the three available African cards and one of the three available Asian cards. The younger child inherited 80 percent European admixture, 7 percent African, and 13 percent Asian. In other words, he inherited only one of the three available African cards and only one of the three available Asian cards.

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Two tangential points: First, the “Asian” percentages shown are the sum of “Native American” and “East Asian” percentages.¬†Second,¬†admixture was estimated by ancestry-informative markers, not by whole-genome pattern-matching.

The “Asian” percentages shown are the sum of “Native American” and “East Asian” percentages. This is because it is hard to distinguish Native American from East Asian markers when estimating continent-of-ancestry admixture percentages. People from Mongolia crossed Beringia 20 millennia ago. Their descendants colonized the Americas and are now known as Native Americans. But people from Mongolia also swept over Asia and Eastern Europe nearly a thousand years ago. Their descendants merged with pre-existing populations everywhere from Hungary to China, including Pakistan and India. And so the same markers appear throughout Asia and the Americas, but with lower frequencies in western Europe or Africa. Although Ancestry-by-DNA computes separate numbers for “Native American” and “East Asian” percentages, the fact that the markers are virtually indistinguishable led this study to sum them together.

Admixture was estimated by ancestry-informative markers (AIMs), not by whole-genome pattern-matching. Two competing admixture-estimating methods are in use today. The AIMs method pre-identifies a hundred or so autosomal polymorphisms that are known to correlate strongly with continent of ancestry. For example, the Duffy-null adaptation that confers immunity to Plasmodium vivax in heterozygotes appears in 999 out of every thousand west Africans but in only 1 out of every thousand Europeans. The second method performs pattern-matching of a person’s entire genome against known populations, measuring the numerical similarity to each population. This method does not consider whether any given similarity relates to continent of ancestry. This study used the first method. Specifically, it used admixtures measured by Ancestry-by-DNA.

Frank W. Sweet is the author of Legal History of the Color Line (ISBN 9780939479238), an analysis of the nearly 300 appealed cases that determined Americans’ “racial” identity over the centuries. It is the most thorough study of the legal history of this topic yet published. He was accepted to Ph.D. candidacy in history with a minor in molecular anthropology at the University of Florida in 2003 and has completed all but his dissertation defense. He earned an M.A. in History from American Military University in 2001. He is also the author of several state park historical booklets and published historical essays. He was a member of the editorial board of the magazine Interracial Voice, and is a regular lecturer and panelist at historical and genealogical conferences. To send email, click here.

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