January 13, 2012

Back to (North) Africa (Henn et al. 2012)

A great new paper has just appeared, presenting new data, new conclusions about African prehistory, and new methodologies. I'll have to read it before I comment on it, but since it's open access you can read it for yourselves.


The new data are publicly available here, with information about samples here.
The new PCADMIX software is also available.

PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397 

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations 

Brenna Henn et al.

 North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.



Azerty said...

what about the Haplogroup results "Y dna and mtDNA ?

I think the only Biggest problem there was the SSA.

Onur Dincer said...

The Tunisian Berber population seems to have been extremely isolated during the recent centuries. This makes it unreliable as a Berber population. Any inferences regarding Berbers and North Africans in general based on this Tunisian Berber population should be regarded with caution. The ADMIXTURE component modal in the Tunisian Berber population must be nothing but an artificial result of the extreme recent isolation of that community. This is apparent from the fact that at K=2 the Tunisian Berber individuals are indistinguishable from non- or almost non-recent-Negroid-admixed North African individuals irrespective of language while they are all distinguished from Europeans and non- or almost non-recent-Negroid-admixed Qataris.

EuroAlpine said...

One more paper that shows us that in most places there is no easy one way tree-like gene flow. And even the ways of aDNA, Y and mt are pretty different. Genome-wide SNP genotyping array data (730,000 sites) and ADMIXTURE versus PCADMIX sounds interesting. I guess the sample data is not publicated? Hope more of this type of papers will follow on interesting population isolates in Europe and surrounding regions.

Onur Dincer said...

I think what essentially genetically distinguishes the Tunisian Berber population from North Africans in general is that the ancestors of the Tunisian Berber population became isolated during the Islamic era and as a result was not genetically affected by the Trans-Saharan slave trade, which is largely an Islamic era phaenomenon.

pconroy said...

What's up with the Tunisians? Are the samples closely related or is this a genuine cluster? If so is this some kind of Phoenician mix going on, that shakes out at higher K?

Are the Bulala in any way related to the Garamantes?

Old map based on Ptolemy's, showing the Garamantes just north of the river Ger, which is probably the Niger:

Charles said...

We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya).

These dates seem to fit in pretty well with the transaharan slave trade among other historical phenomena.

idurar said...

Nothing new here.

The estimation of West African influence is line with what we already know: most individuals of the very heterogenous southern Moroccan group are mixed (and some even mainly SSA!). Only 6 of them are typical north Africans.
Generally, at K=2, we can easily spot the outliers in all North African groups.

The Tunisians are related to each other (we already know that too) so it's not useful at all, just like Mozabites.

Anyway, hope the data will be available for the Dodecad Project.

jes-r said...

The genomes from this study are available here:


I hope Dienekes does his own analysis on this data-set soon.

Dienekes said...

I hope Dienekes does his own analysis on this data-set soon.

Due to the use of an Affymetrix chip, there are only ~30k SNPs in common between this data and the other data in my project/commercial data. If I ever update the 'africa9' calculator, I will probably take a look at this data, as that calculator is also based on a smaller number of markers.

EuroAlpine said...

"Affymetrix ... only ~30k SNPs in common"
Very bad/sad. Hope future chips will be overlapping SNPs much better.

Azerty said...

hey guys have you noticed , pierre zalloua "the biased expert who has claimed that phoenicians were J2 Y DNA, lool " and many other lebanese are there while some DATA are not available"THE most Important one"?

terryt said...

"Genomic Ancestry of North Africans Supports Back-to-Africa Migrations"

What was that about Y-chromosome haplogroup E again?

Razib Khan said...

62 K in common with HGDP alone. OK for ADMIXTURE. definitely OK for PCA.

Alice C. Linsley said...

Dr. Pierre Zalloua's connection of Lebanese to older Mediterranian substata common to Tyre is credible. The Horim (Jewish ancestors) were related to the Tyrian royalty.