Africa in 12 ADMIXTURE chunks

Gene Expression
By Razib Khan
Apr 7, 2011 12:21 AMNov 20, 2019 1:59 AM

Newsletter

Sign up for our email newsletter for the latest science news
 

Some have asked what the point is in poking around African population structure when Tishkoff et al. and Henn et al. have done such a good job in terms of coverage. First, it is nice to run your own analyses so you can slice & dice to your preference, and not rely on the constrained menu provided by others. There's value in home cooking; you can flavor to your taste. Second, you never know what data people might leave on your doorstep. I've received the genotypes of three Somalis. Nothing too surprising, a touch more Cushitic than the Ethiopians in Behar et al., but interesting nonetheless. Also, you can see how ADMIXTURE tends to come to weird conclusions in certain circumstances. Below is a K = 12 run ~50,000 SNPs. I've included in a few Behar et al. and HGDP populations to the Henn et al. set, as well as pruned a lot of the African groups which seem redundant in terms of information. I've added a few geographically informative labels as well. Observe below that there is a Fulani cluster. I think this is pretty much an artifact. At K = 7 the Fulani have a majority component which is modal in West Africa & Bantu speakers, and a minority component which is identical to the one modal in Mozabite Berbers from Algeria. The Mozabites reside in the far northern Sahara, and their modal component drops off as one goes east toward western Asia and the eastern Mediterranean. I suspect that what is showing up in ADMIXTURE is the ancient hybridization of the Fulani, and perhaps their demographic expansion from this core group. We have some glimmers of the prehistory of the Fulani, and no expectation for them to be such a distinctive cluster, so I naturally jump to these inferences. But it does make me reconsider the nature of the "Sandawe," "Mbuti" or "San" clusters in ADMIXTURE. These populations are culturally distinctive in deep ways from their neighbors, so a reflexive inference one might make is that they're "pure" ancient substrate groups which have been overlain and marginalized by their Bantu neighbors. But their prehistory is far murkier than the Fulani because of their geographical isolation, so there is far less to go on. These "ancient" isolated groups themselves may have gone through the same sort of distinctive recent ethnogenesis processes which we presume occurred with the Fulani (also, in the plot below the Biaka are pure; but in most of the bar plots they have a minor element which they share with their neighbors, probably due to greater admixture and interaction between western Pygmies and their Bantu neighbors than among the easter ones).

OK, now let's prune some of the "pure" and extraneous populations. Additionally, I'll remove some of the K's. So the proportions are going to be recalculated with a new base. So, keep in mind that the South African Bantus show elevated West African in part because the Khoisan proportion was removed, inflating the percentages for all the other elements.

Now let's look at the pairwise Fst values between inferred populations. Remember, this

0 free articles left
Want More? Get unlimited access for as low as $1.99/month

Already a subscriber?

Register or Log In

0 free articlesSubscribe
Discover Magazine Logo
Want more?

Keep reading for as low as $1.99!

Subscribe

Already a subscriber?

Register or Log In

Stay Curious

Sign up for our weekly newsletter and unlock one more article for free.

 

View our Privacy Policy


Want more?
Keep reading for as low as $1.99!


Log In or Register

Already a subscriber?
Find my Subscription

More From Discover
Stay Curious
Join
Our List

Sign up for our weekly science updates.

 
Subscribe
To The Magazine

Save up to 40% off the cover price when you subscribe to Discover magazine.

Copyright © 2025 LabX Media Group