August 27, 2012

Out-of-Iberia (Arenas et al. 2012)

A new paper argues that the SE-NW gradient of genetic variation in modern Europeans is consistent with a large Paleolithic contribution of the European gene pool if modern Europeans are principally descended from people who spent the last Ice Age in the Iberian refugium.

In my opinion, the question cannot be solved on the basis of modern populations alone: clines do not carry dates, and can be formed by accretion of different events operating under the constraints of a given geography. Ancient DNA has already begun to inform our view of the past:  we now have data from Mesolithic Iberians, the presumable denizens of a pre-farming refugium, and they do not appear closely related to modern Iberians. Moreover, Europe as a whole shows discontinuity between Neolithic and Mesolithic populations, and even between Neolithic and modern ones.

If humans expanded from Iberia in postglacial times, and modern Europeans are largely descended from them, then it is strange that the gene pool of Mesolithic Europeans  is so restricted: why didn't the Out-of-Iberians create a modern European-like mtDNA and Y chromosome gene pool in the thousands of years intervening between deglaciation and the available DNA samples?

Arguably, the ancient DNA record of Europe (except in the case of mtDNA) is still in its infancy and there may be more surprises to come. But, the way things look like right now, Paleolithic genetic continuity does not seem warranted. As more ancient samples accumulate from different regions and different periods, we will see how clines of variation in modern populations were formed. But, if history of the field is any guide, we're probably in for a few strange surprises.

Mol Biol Evol (2012) doi: 10.1093/molbev/mss203

Influence of admixture and Paleolithic range contractions on current European diversity gradients

Miguel Arenas et al.

Cavalli-Sforza and colleagues (1963) initiated the representation of genetic relationships among human populations with principal component analysis (PCA).Their study revealed the presence of a southeast–northwest (SE-NW) gradient of genetic variation in current European populations, which was interpreted as the result of the demic diffusion of early Neolithic farmers during their expansion from the Near East. However, this interpretation has been questioned, as PCA gradients can occur even when there is no expansion, and because the first PC axis is often orthogonal to the expansion axis. Here, we revisit PCA patterns obtained under realistic scenarios of the settlement of Europe, focusing on the effects of various levels of admixture between Paleolithic and Neolithic populations, and of range contractions during the Last Glacial Maximum (LGM). Using extensive simulations, we find that the first PC (PC1) gradients are orthogonal to the expansion axis, but only when the expansion is recent (Neolithic). More ancient (Paleolithic) expansions alter the orientation of the PC1 gradient due to a spatial homogenization of genetic diversity over time, and to the exact location of LGM refugia from which re-expansions proceeded. Overall we find that PC1 gradients consistently follow a SE-NW orientation if there is a large Paleolithic contribution to the current European gene pool, and if the main refuge area during the last ice age was in the Iberian Peninsula. Our study suggests that a SE-NW PC1 gradient is compatible with little genetic impact of Neolithic populations on the current European gene pool, and that range contractions have affected observed genetic patterns.



apostateimpressions said...

Has anyone compared the meso European samples with modern Siberian?

Do we know for sure that the meso European population wasnt Siberian-like rather than Caucasian-like?

East Asian-like sdmixture in modern northern Europeans? The north European component is like the Gedrosia component (which is like the Caucasus component with some East Asian) and the Atlantic Med (which is like Caucasus with some North Euro (which has East Asian)) with some additional East Asian component? Is there really anything there apart from Caucasus and something East Asian-like? (The Mongolian phenotype is possibly later?)

princenuadha said...

Just a technicality.

"A new paper argues that the SE-NW gradient of genetic variation in modern Europeans is consistent with a large Paleolithic contribution of the European gene pool if modern Europeans are principally descended from people who spent the last Ice Age in the Iberian refugium."

This is actually just a statement of fact. If Europeans principally descended from the iberian refugium (a subset of paleolithics), then Europeans by necessity have a large paleolithic contribution.

I think it should be said like "the SE NW cline in Europe is consistent with a large genetic contribution from the iberian refugium."

Amanda S said...

I have a question about the Iberian refugium which I'm hoping that someone can answer. My understanding is that archaeological finds show that the northern-most ice age Europeans in Western Europe lived in Southern France and Southern Germany.

As temperatures rose and more land opened up for animals and vegetation, I would think that it would be most likely that this north of the Pyrenees hunter population would be the one that expanded northwards rather than a migration of people from south of the Pyrenees which is implied in the Out-of-Iberia scenario. Is there any evidence that humans were ever exclusively dwelling south of the Pyrenees during the late ice age period?

Anonymous said...

Watch out Amanda. This is a pro-neolithic replacement blogsite. :)

The Frence Basque north of the Pyrenees show evidence of being a relict population, as do the Basque from the south of the Pyrenees. I dont think we can be more specific than Iberia-ish. Iberia on the plains has received a lot more population influences than isolated regions like the Pyrenees.

There are patterns of R1b subclades that look a lot like expansion out of Iberia. But North Africa is still a possible source. Plus there may have been something happening around Doggerland as well.

The exact timing of this however is subject to smoking hot debate. Some say paleolithic, others Bronze age.

"Out-of-Iberians create a modern European-like mtDNA and Y chromosome gene pool"

I think it is widely perceived that H subclades and R1b subclades are the signatures of "Out of Iberia". Although Y haplogroups seem to be remarkably unstable, so perhaps they should be abandoned for these kinds of studies.

Fanty said...

@Amanda S:

This is a map of settlements found after the last ice age:

I dont know if this is complete.
It has a "0" placement in Northern Spain and Southern France labelt "Place of Origin" but with no dating.

It virtually claims, the oldest post-ice age finds with dating, so far are from Southwest Germany and Southeast France.

Southwestgermany, after new calibration: 15870 years before present.

As far as I recall it, thats also the region where the Iberian variant of R1b has the highest microsatelite diversity. (all other Westeuropean R1b clades also have their highest diversity in southern Germany.


This map here rates that region as "Tundra", during the maximum of the glacier expansion:

eurologist said...

Yes, usually the refugium is called Franco-Cantabrian and not Iberian. But I agree that there should have been stratification: the last people entering would have been on the northernmost (or northeastern) edge, and would have dominated expansion during warming.

I once came upon a description of a possible Southern German LGM camp site - but that was before recalibrated dating. I agree that there is little evidence of occupation in SW Germany during LGM, but a small population in the upper Rhine valley is still a possibility based on climatic arguments. Some of the earliest post-LGM sites are in Switzerland and SW Germany.

Fanty, I believe the coloring on the second map you linked to must be wrong. The dark "olive" probably should be the light-brown "Mediterranean Vegetation" (otherwise missing) instead of leaf and mixed forest, based on the fact that those regions were extremely dry (even for current Mediterranean circumstances).

The map is still useful, since among other things it shows how easy it was for populations from the eastern plains (including NE of the Caspian) to migrate into Europe along the edge of the ice sheet after LGM (think Hamburger and Ahrensburger cultures). I am a firm believer in one or two eastern refugia, and the possibility that Siberian autosomal and mtDNA in Europe may date this far back.

Jack Rusher said...

Do you have the data for Oetzi and the Neolithic Swedes in SNP format somewhere handy? I'd love to have a look at it.

pconroy said...

Remember that the Saami and Berbers are linked by an mtDNA clade that is only an estimated 9,000 years old.

I postulated years ago that the Saami might have been part of a Mesolithic population that lived near the snow line - when it was in mid-France and just followed their reindeer herds each Spring and Fall, until thousands of years later, they were in Northern Scandinavia. Meanwhile another part of this population migrated South to become Berbers.

More here:

Amanda S said...

Thanks, everyone. The Franco Cantabrian refugium concept makes much better sense.

Tiger Mike said...

Annie Mouse said..
"The Frence Basque north of the Pyrenees show evidence of being a relict population, as do the Basque from the south of the Pyrenees"

What evidence are you citing? How old do you mean when you say relic?

From what I'm seeing that diversity for R1b is fairly low among the Basques. What data are you looking at?