August 15, 2012

The genetic history of Europeans (Pinhasi et al. 2012)

This is a nice paper with extensive references on the topic of European origins. Two of its co-authors, Joachim Burger, and Ron Pinhasi are leading a couple of exciting new ancient DNA projects that will probably flood us with interesting new data in the years to come.

From the paper:
Human evolutionary history includes all the complex demographic, natural selection, and stochastic processes that have shaped our species. Despite the limitations of genetic and archaeological data to inform on all the details of human evolution, they constitute an irreplaceable source of information to appraise the key episodes that are likely to have had major impacts on patterns of genetic, morphological, and cultural variation. When considering AMH in Europe, three such critical periods are apparent: (i) the expansion of AMH out of Africa and their colonization of Europe approximately 45 000 years ago (45 ka), (ii) the last glacial maximum (LGM) and the formation of uninhabitable areas in Europe between 27 and 16 ka, and (iii) the arrival of Neolithic culture in southeast Europe and its spread throughout the rest of the continent between 9 and 5 ka. Here we review genetic evidence describing these major demographic episodes in the context of archaeological and chronological data. 
I have postulated that there was at least one important post-5ka event affecting Europe. But, in order to understand how events played out before 5ka and the present, we must first understand the background of what was taking place in Europe before 5ka.

On the earliest settlement of Europe:
Until recently, the earliest date for the first appearance of AMH in Europe had been set to around 42 to 43 ka solely based on their proposed association with Aurignacian artifacts (Table 1) [5,6]. New direct radiocarbon dates of fossils support this view and indicate that AMH appeared in Europe by 44.2– 41.5 calibrated (cal.) ka BP at Kent’s Cavern in southern England [6] and by 45–43 cal. ka BP in Grotta del Cavallo, Italy [7], whereas Neanderthals did not survive in most of Europe and the Caucasus after 39 cal. ka BP [8,9].
These dates are so close to the MP/UP transition in the Levant (49-46 cal ky BP), with the Aurignacian appearing shortly thereafter in both Central Europe and Italy. It would appear that modern humans swiftly colonized Europe after they made the crucial UP leap. Of course, in my opinion, this population was ultimately descended from inhabitants of Arabia, escaping post-70ka climatic deterioration and pre-100ka with the archaeologically attested Nubian Complex. But, in any case, it is probably the last crucial step, when humans went into warp drive post-50ka that led to the first modern human colonization of Europe and ultimately the extinction (or absorption?) of the Neandertals.

But, the early colonizers were in for a rough patch of climate that last for several millennia, making whole parts of Europe uninhabitable, and allowing few ones to survive in the south of the continent:
After the disappearance of the Neanderthals and particularly during the LGM, the northern parts of Europe were covered by ice sheets, leaving humans to survive in poorly resourced environments [10,11]. Parts of northern Europe were either completely abandoned [12] or sparsely populated [13]. The archaeological record of this period catalogs a complex series of interrelated material cultures that vary in their geographic ranges and temporal durations (Table 1). Spatial patterns of material culture change have been interpreted as indicating colonization of regions up to 52 degrees N latitude during the Gravettian, followed by partial or complete retreat of most northern populations by 24 ka, and recolonization of these regions by 20–16 ka, with some continuity of occupation in more southern latitudes [14]. However, the extent to which material cultures correspond to distinct human populations, and to which their distribu- tion changes through time correspond to demographic pro- cesses, remains unclear. 
The following table presents a very useful summary of archaeological developments in west Eurasia:

So far, we have substantial autosomal data of modern humans only from the Mesolithic onwards (Iberia), but also mtDNA from much older specimens of the Gravettian in Italy and Russia.

Apparently, other people are looking to extract ancient genomic DNA from older remains as well:
A group led by evolutionary geneticist Johannes Krause of the University of Tubingen, Germany, is trying to remove and reassemble nuclear DNA from the bones of roughly 20,000-year-old people in Europe. If successful, that effort will provide the first look at whether Stone Age humans carried more Neandertal genes than people today do. “It’s a completely open question whether more interbreeding occurred in the past than what we’ve found so far,” Krause says.
But, let's see where things stand now.

Ancient mtDNA sequences recovered from three Upper Paleolithic and 14 Mesolithic and Neolithic hunter-gatherers all belong to the mtDNA haplogroup U [48], currently found at frequencies between 1 and 7% in most modern European populations, but at up to 20% in Baltic populations and around 40% in Saami. Interestingly, almost all pre-Neolithic hunter-gatherers from Central and Northeastern Europe sequenced to date, and the majority of European post-Neolithic hunter-gatherers, carry U-type mtDNA [48,49] (Figure 1a,c). There are three exceptions: two Italian individuals with N* and pre-HV types [50], and one from Sweden [46]; the latter dating to the late Neolithic and possibly being the result of an admix- ture event with incoming farmers. In all other hunter- gatherer samples, the now common mtDNA lineages H, T, K, and J are absent, suggesting that these mtDNA lineages were introduced during the Neolithic period. 

The mtDNA evidence is indeed the strongest argument for large-scale population replacement during the Neolithic, a scenario which has found support by the sequencing of Neolithic hunter-gatherers from Gotland Sweden and Mesolithic ones from Iberia.

The authors note that while early farming groups largely lacked mtDNA haplogroup U, the later ones possessed it to some extent:

Maps showing Europe in times slices and depicting the locations from which ancient mitochondrial DNA (mtDNA) sequences were retrieved. Squares represent hunter-gatherer individuals and circles represent farming individuals. Lineages belonging to the U-clade are shown in red. Other lineages are shown in yellow. (a) Paleolithic and Mesolithic hunter-gatherers 13 500–8300 BP (plotted on a map of Europe during the last glacial maximum ca 22 000 BP). All Pleistocene hunter-gatherers analyzed to date carry mitochondrial lineages that belong to one of the U-clades: U2, U4, or U5. (b) Early farmers 7600–6500 BP. The map illustrates the approximate arrival times and duration of the earliest Neolithic cultures (in years BP). Very few of the early farmers belong to one of the U-clade mtDNA haplotypes, indicating discontinuity between Paleolithic/Mesolithic hunter-gatherers and early farmers [48,64]. (c) Later hunter-gatherers 6500–4500 BP. Whereas early hunter-gatherers carry exclusively mitochondrial U-lineages, later hunter-gatherers show additional lineages that are also present in early farming groups (b), pointing to a possible admixture between the groups or a change in lifestyle of former farmers back to hunting-gathering in Northern Europe. (d) Later farmers 6500–4500 BP. Compared to the period of the first appearance of farmers, late farmers have a significantly higher frequency of U-lineages. This can be explained by increasing rates of admixture between farmer and hunter gatherer groups during this period and by the adoption of a farming lifestyle by hunter-gatherers. The maps are adapted from [69] and show datapoints from [46,48,51, 54–56,61,62,64,70,71]. Abbreviation: BP, before present. 

And, of course, we have the ubiquitous Y-haplogroup G2a as the lineage par excellence of the first European farmers:

In contrast to mtDNA, ancient Y-chromosome data has until recently been less informative, but a single Y-chro-mosome haplotype (G2a) in 20 of 22 male individuals from the Late Neolithic cave site at Treilles [62] led to the hypothesis that a small male founding population arrived in Southern France, probably by a maritime route from the eastern Mediterranean, in the early Neolithic. The same haplotype was also found in five of six individuals from the Avellaner Cave [61] and in one out of three Central Euro-pean LBK individuals [63]. If authentic, the presence of the Y-chromosome haplogroup G2a in 26 of 31 Neolithic individuals from Germany, France, and Spain is both surprising and intriguing, but this requires further examination. 
The only high coverage genome sequence of a prehistoric European individual is that of the Tyrolean Iceman, Oetzi, a 5300 year-old individual from South Tyrol, which was recently reported at 7-fold coverage [45]. Comparison with 1300 contemporary Europeans indicated closest genetic affinities with southern Europeans, particularly inhabi-tants of the Tyrrhenian Islands. Intriguingly, this is also the region where the Y-chromosome haplotype of the Ice-man is found at highest frequency, and this haplotype belongs to the same G2a haplogroup described above.
And of course:
Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires.
The recovery of the European past has only just begun.

Trends in Genetics doi:10.1016/j.tig.2012.06.006

The genetic history of Europeans

Ron Pinhasi, Mark G. Thomas, Michael Hofreiter, Mathias Currat, Joachim Burger

The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.



Maju said...

The paper is obsolete before publication. Several different studies have located haplogroups other than "U" (specifically H) in SW Paleolithic Europeans. Anything that does not consider this fact is simply put wrong.

Cf. Lacan 2011, Hervella 2012. Plus previous reports of presumable H in Epipaleolithic Portugal and UP Morocco.

Also U should not be considered as a single haplogroup for any prehistorical reconstruction purposes restricted to Europe but as several sublineages. We should be talking of U5 (or maybe U5a and U5b), U4, U2, etc. There's no reason to believe that mtDNA U arrived to Europe as a single founder effect and actually the overall super-haplogroup U looks like having originated in West or Central Asia, with only some branches arriving to Europe (others to Africa, etc.)

Dienekes said...

We've covered that topic before. The authors of the current paper are certainly aware of the Hervella et al. paper:

"A comparison of 49 mitochondrial DNA sequences
from Upper Paleolithic, Mesolithic, Neolithic, and Bronze
Age sites in Northern Spain with other European mitochondrial
data from prehistoric periods, using FST distances
and associated multidimensional scaling plots
[60], indicated no statistically significant differences
among hunter-gatherer samples from Iberia, Central Europe,
and Scandinavia, but did show differences between
hunter-gatherers and later Neolithic, Bronze Age, and
modern samples. However, the Neolithic samples from
Spain were distinct from the LBK sample from both Central
Europe and modern European samples, suggesting
heterogeneity among European Neolithic populations."

Dienekes said...

I will also add that the publication of Sánchez-Quinto (2012) further strengthens the case for U-related sublineages dominating pre-farming Europeans.

That paper appeared too late to be in the references of the new one.

Anonymous said...

That is all very interesting. What strikes me first is the complete lack of interest in pre Epipaleolithic and Neolithic haplogroups of hunter/gatherers existing in the Near East/Anatolia/Levant. Everything is centred on Europe and those ancient inhabitants of Europe as if those hunter/gatherers just grew out of the soil without any ancestry from anywhere else. I think the net should be opened wider to include ancient and contemporaneous aDNA results from the Near East/North Africa.

A second observation is the usage of terms Mesolithic, Neolithic, Epipaleolithic, Paleolithic and so on are cultural terms with wide dates. Some of those overlap in time, and do not give a proper estimation of the age of aDNA results. The results so far have come mostly from the interface between the Mesolithic and the Neolithic where both populations hunter/gatherers and farmers occupied the same regions. That is true of those Neolithic results for Sweden, and the results of those ancient Spaniards. It would be better to use actual proven dates for aDNA results instead of using those cultural tags which can be misleading, giving an overestimation of age when the results come from the interface period of contact by hunter/gatherers and farmers. The Swedish farmer woman buried under that dolmen was born in Sweden not Mediterranean Europe or the Near East.10

German Dziebel said...

"These dates are so close to the MP/UP transition in the Levant (49-46 cal ky BP), with the Aurignacian appearing shortly thereafter in both Central Europe and Italy. It would appear that modern humans swiftly colonized Europe after they made the crucial UP leap."

There are no intermediate cultures between West Asia and Western Europe at that time, there are no associated human remains. MP-UP transition happened independently several times in human history. Even Neandertals transitioned to a blade complex independently.


You're making the same mistake as the coastal migration theorists: in the absence of evidence for a migration, let's call it "swift."

Mark D said...

Has there been established through aDNA analysis any link between the Capsian culture of North Africa (10-6 ka BP) and those of Mesolithic or Neolithic Europe? I've been intrigued by the relativley high percentage (~15%) of R1b (and blue eyes) of the Berber Kabyles of Algeria. It would seem logical to me that north-south migration between Europe and North Africa was as prevalent then as it was in the historical periods, being such a short hop across the Gibraltar straits, and could account for much of the Neolithic settlement of Iberia if not of much of Western Europe, rather than overland from the East.

There was an excellent article you covered in January, "Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, et al. (2012) Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397" but it didn't seem to address this issue, unless I missed something.

Maju said...

Are you censoring me?

Dienekes said...

the complete lack of interest in pre Epipaleolithic and Neolithic haplogroups of hunter/gatherers existing in the Near East/Anatolia/Levant.

More difficult to extract DNA from these regions, but the BEAN project will try, at least for Anatolia.