Is American genetic diversity enough?


In the nearly 20 years since the draft of the human genome was complete,* we’ve moved on to bigger and better things. In particular, researchers are looking to diversify their panels of human genetic diversity, because of differences between groups matter. You can’t just substitute them for each other genetically.

There have been efforts to diversify the population panels recently, but that prompts the question whether American population coverage is sufficient. My first thought is that the genetic diversity in the USA is probably getting us 90% of the way there. Consider Spencer’s comment about Queens, it’s the most ethnically diverse large conurbation in the country.

There are some gaps though. In Who We Are David Reich points out the distinctiveness of Indian population genetics. The subcontinent has lots of large census populations which have drifted upward deleterious alleles due to long-term endogamy. And, many of these populations don’t have a strong representation in the Diaspora.

In contrast, much of the rest of the world is panmictic enough that an American panel can pick up most of the variation. American Chinese are skewed toward Guandong and Fujian, but a substantial number of people from other parts of China have arrived in the last generation. Regional structure is not so strong that you’ll miss out on too much, aside from very rare variants which are more extended pedigree scale rather than population scale.

There are small populations such as Hadza, Khoikhoi, and Pygmies in Africa which are probably going to be missed by American population panels, but the total census size of these groups is pretty low (for comparison, there are 1 million Pulayar Dalits in the state of Kerala alone). Much of the rest of Africa is West African variation well represented in African Americans, and Bantu and Nilotic variation probably captured my immigrant communities.

I’d propose supplementing American genetic diversity with sampling Cape Coloureds in South Africa.

* No discussions about how the genome isn’t totally complete. I know that.

6 thoughts on “Is American genetic diversity enough?

  1. Yes, my first thought was that there must be Khoisan ancestry in Cape Coloured people from South Africa — of whom there must be a good number in the NYC area?

  2. Cape Coloured people from South Africa
    or white people from South Africa, like an acquaintance of mine whose grandparent has been reclassified from Coloured to White back in the years when it was easier. It ended up a closely guarded family secret, of course, only rediscovered in a DNA genealogy test, but they soon found Coloured 2nd cousins the older generation always knew about.
    But what is this”enough” thing, Razib? Is it enough to detect a few megabases of ancestral segments? Or a whole genome? Or a few hundreds as needed for minor allele survey? Or thousands needed for GWAS?

  3. You’re also not going to find many people of Papuan or Australian aboriginal descent living in New York either.

  4. @MM – When in doubt, read. “Even Oceania covered by Pacific Islanders.”

  5. No, I saw that, and I agree with Razib that studying Americans can get us 90% of the way there, but I wouldn’t rely on very admixed groups to extrapolate too much about their ancestral components. Polynesians (many of whom are admixed with Europeans and even Chinese these days) can only tell you so much about Papuans, and even less about Australians. Better to just take a field trip and sample real Australo-Melanesians IMO.

  6. Some Islanders are high % Papuan. Vanuatu people are >90% Papuan, the rest Austronesian, and have already participated in studies including, from memory, one by Reich and Skoglund.

    “Just take a field trip…” – yeah, good luck with that. Sampling Papuans and Australians is not easy – Eske Willerslev went to some obviously extreme lengths in very remote locations and did heroically well to persuade the number of groups that he did in PNG and Australia to participate, but evidently was unable to persuade speakers of non-Pama Nyungan languages to participate; he didn’t say so, but it is a very obvious lacuna that he would have wanted to fill if he could.

    https://www.nature.com/articles/nature18299

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