Whole genome sequencing of ~1000 humans from diverse populations

There’s a new preprint out at bioRxiv that presents the results from sequencing 929 high coverage genomes from 54 diverse human populations. Lots of interesting information regarding genetic variation, demographic patterns over time, and admixture among different groups. Check it out:

Insights into human genetic variation and population history from 929 diverse genomes

Here’s one finding that I thought was pretty interesting:

We next studied the extremes of human genetic variation by identifying variants that are
private to geographic regions (excluding individuals with likely recent admixture from other
regions). We find no such private variants that are fixed in a given continent or major region
(Fig. 3A-C). The highest frequencies are reached by a few tens of variants present at >70%
(and a few thousands at >50%) in each of Africa, the Americas and Oceania. In contrast, the
highest frequency variants private to either Europe, East Asia, the Middle East or Central and
South Asia reach just 10-30%. This likely reflects greater genetic connectivity within Eurasia
owing to culturally driven migrations and admixture in the last 10,000 years, events which did not involve the more isolated populations of the Americas and Oceania (1), allowing
variation accumulating in the latter to remain private. Even comparing Central and South
America, we find variants private to one region but absent from the other reaching >40%
frequency. Within Africa, ~1000 variants private to the rainforest hunter-gatherer groups
Mbuti and Biaka reach >30%, and the highly diverged San of southern Africa harbour
~100,000 private variants at >30% frequency, ~1000 at >60% and even about 20 that are
fixed in our small sample of six individuals.

In other words, they found no fixed differences between major geographic groups of humans, but plenty of variants that are unique to particular populations (particularly in Africa) at medium or high frequency.


Very interesting.

So there is variation unique to particular areas, but nothing guaranteed to be different. So much for polygenesis!

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I haven’t read the paper, but that’s not quite an accurate paraphrase of what you quoted. There are (a few) variants that are fixed or nearly fixed in one large region and virtually absent in another large region (the Duffy null allele and a pigmentation-associated variant in SLC24A5 come to mind), but these are not entirely restricted to one of their defined population groups.


Fair enough. Using only their particular geographic subgroup definitions, no private allele has reached fixation within the region it’s found in, although a few variants in Africa come pretty close.

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