June 04, 2013

IBD sharing between Iberians and North Africans (Botigué et al. 2013)

An interesting new paper documents an excess of IBD sharing between Iberians (excluding Basques) and North African (and particular NW African) populations.

It would have been nice if the authors had used techniques such as rolloff and ALDER or those of Jin et al. (2012) to say something about the time/nature of the admixture event detected via IBD sharing; insteady, they use variance in admixture proportions, which gives a probably much noisier estimate, with the basic idea being that in the first few generations post-admixture there are individuals with much varying admixture proportions, but these tend to be homogenized over time.

The occurrence of North African-specific admixture in SW Europe has long been suspected on the basis of Y-chromosome/mtDNA work (e.g., the presence of E-M81 which is probably the best North African marker in existence). It also makes sense, because of the limited occurrence of Sub-Saharan markers in Iberia: such elements did not, presumably, fly over North Africa, but landed in Iberia via people who were themselves admixed.

A couple notes of caution:

(i) the use of ADMIXTURE as a means of estimating admixture proportions is dangerous in this case, because of the hybridity of "North Africans" themselves, which according to published estimates experienced Sub-Saharan African admixture in the last few thousand years. In my own experiments it is clear that "North Africans" are a mixture of three basic components related to Europe, Sub-Saharan Africa, and the Near East. Nonetheless, in my own experiments I do also get an excess of the component I've labeled "Northwest African" in Iberia that is not shared by Basques or French.

(ii) as I've emphasized before, IBD sharing between populations does not indicate the direction of gene flow. One would have to look at the ancestry of the shared segments to determine their origin. To give a simple example, an IBD segment shared by a Spaniard and a Mexican could be European, African, or Native American, and -thanks to historical knowledge- we can be fairly sure that the number of such segments is also in the given order.

Given that Iberia is the neighbor of NW Africa one would not be surprised if there was gene flow in both directions, and while North Africa gene flow into Iberia is one possible explanation, some of the gene flow may have gone the other way, e.g., with contacts during the Pax Romana, fleeing Iberian Muslim in the post-reconquista period, Barbary pirates attacking Christian ships and the like. In any case, it would be interesting to catalogue IBD shared segments between Iberia and NW Africa in terms of their geographical origin.

(iii) the sources and timing of admixture could potentially be determined by ancient DNA work. The three most recent time periods are related to the slave trade (both European of Africans and vice versa), the Islamic period, and the Roman Empire. Presumably, with the sampling of enough individuals, that type of admixture ought to manifest in populations living before/after each of these three events.

In any case, this is an interesting paper which is also accompanied by publicly accessible data.

PNAS doi: 10.1073/pnas.1306223110

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

Laura R. Botigué et al.

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

Link

9 comments:

andrew said...

"It also makes sense, because of the limited occurrence of Sub-Saharan markers in Iberia: such elements did not, presumably, fly over North Africa, but landed in Iberia via people who were themselves admixed."

The more plausible alternative, of course, would not be flight but maritime travel. There are archaeologically attested Iberian contacts with the Canary Islands and Britain, which call for similar levels of maritime skill, quite far back in pre-history and sporadic population exchange with sub-Saharan African by peoples with such a long maritime tradition at any time in the prehistoric era or in unattested events in the early historic era (don't forget that Spain financed the tour of Columbus to the Americas and many other early maritime explorers) could easily lead to cryptic sub-Saharan ancestry in modern Iberian populations that would be indistinguishable from much earlier exchanges after fifteen or more generations in which introduced sub-Saharan African alleles could reach fixation.

Onur said...

Pity they did not analyze any northern West Asian population other than Cypriots, any population from the Caucasus, and any population from the Pontic steppe region. This deficiency affects their conclusions and their IBD sharing maps in a negative way.

Mark D said...

"Given that Iberia is the neighbor of NW Africa one would not be surprised if there was gene flow in both directions, and while North Africa gene flow into Iberia is one possible explanation, some of the gene flow may have gone the other way"

I would take this as a given. The historic references of conquests, migrations and back-migrations are too numerous to mention. I think Gibraltar has seen more movement of people than the Hellespont.

truth said...

No Sardinians and S.italians samples, useless study.

terryt said...

"The more plausible alternative, of course, would not be flight but maritime travel".

Of course. We can assume that the first immigrants into the Mediterranean islands were capable of reaching both Europe and North Africa. That alone would lead to considerable mixing of populations around the Mediterranean, including both the northern and southern coastline.

Dr Rob said...

A good paper looking at all marker systems was recently done by Currat et al

Dr Rob said...

http://www.biomedcentral.com/1471-2148/10/237

Sgt. Gil said...

European gene flow to North Africa: The last of the Vandals {with an element of the Alans} disappeared among the Berbers after defeat by the Byzantines in 534 AD

Mark D said...

"European gene flow to North Africa: The last of the Vandals {with an element of the Alans} disappeared among the Berbers after defeat by the Byzantines in 534 AD"

Yet there are some very interesting hot spots of R1b in tribal Algeria (non-French). Possibly these were vestiges of Neolithic migrants on their way west? More study is needed in North Africa with much greater sampling.