August 13, 2014

Chalcolithic mtDNA from Atapuerca still in the Neolithic range

Bell Beaker Blogger points me to this latest study on ancient mtDNA from the Center-North Iberian Peninsula, including 20 samples from a Chalcolithic site (without Bell Beaker apparently) that clearly shows continuity with mainline Neolithic (Cardium but also similar to Central European Linear Pottery Culture, both sharing the same Thessalian ultimate origins).

Daniel Gómez Sánchez, Iñigo Olalde et al., Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations. PLoS ONE 2014. Open accessLINK [doi:10.1371/journal.pone.0105105]



The results show intense similitude with Catalan Neolithic and Languedoc's Chalcolithic but also with Central European Neolithic. They contrast instead with Portuguese and Basque Neolithic, as well as with Central European Bell Beaker, all them much higher in haplogroup H and, in the Basque case, also in U (being the most modern-like of all ancient mtDNA pools known before the Bronze Age in Europe).

Annotated version of fig. 2
Figure 2. Mitochondrial DNA haplogroup frequency for 21 ancient European samples.

Notice please that the above column for Central European Bell Beaker (BBC) includes the more than dubiously attributed Kromsdorft site, which has a totally different genetic signature. In my previous analysis of European ancient DNA evolution, I treated them separately and I still think that it is much more correct to do it that way.

Notice also that one sample from Mirador was sequenced for autosomal DNA by Evangelia Dasakali, producing an Italian-like sequence, roughly in line with other early European farmers, excepted the Atlantic ones. See here.

So what we see is a "wedge" of Mediterranean or Neolithic ancestry probably penetrating along the Ebro river up to Atapuerca and contrasting with Atlantic Iberian (Basque and Portuguese) ancestry, more modern-like or even "hyper-modern" (by contrast with mainline farmers) in the case of Portugal. This same contrast exists with Central European Bell Beaker sites and also (in the autosomal DNA aspect) with Megalithic farmers from Southern Sweden. 

None of those "modernizing" tendencies can be found instead among Eastern European Neolithic peoples nor among early Indoeuropeans of Central Europe such as those of the Unetice culture. So the overall conclusion can only be that there was in the Chalcolithic (and to some extent Neolithic) a duality of ancestries between the Mainline or Mediterranean (but also Danubian) Neolithic and a more "modern" Atlantic Neolithic, which is related to the Megalithic and Bell Beaker cultural phenomena (and in North-Central Europe also to Funnelbeaker). 

There are still a lot of dark spots in our understanding of how this "modernization" or "Westernization" of the genetic pool happened but, in general terms, it seems to imply a sizable (albeit somewhat irregular) demographic flow from Atlantic Europe into the areas previously occupied by Mainline Neolithic populations of partial West Asian affinity. This is apparent in both mtDNA as in autosomal DNA. 

These sequences from El Mirador (Atapuerca) only underline this phenomenon and the fact that in the Chalcolithic, some 4500 years ago, this process of "modernization" of the European genetic pool was still incomplete.

July 30, 2014

Bell Beaker of Estremadura (Portugal)

This is a very interesting read for everyone interested in the Chalcolithic Era and particularly in the Bell Beaker phenomenon in one of its most crucial areas: the Lisbon Peninsula of Portugal:

João Luís Cardoso. Absolute chronology of the Beaker phenomenon North of the Tagus estuary: demographic and social implications. Trabajos de Prehistoria 2014. Open accessLINK [doi: 10.3989/tp.2014.12124]


The complexity of the Beaker phenomenon in the Tagus estuary does not fit well with the model of three successive groups (International, Palmela and Incised Groups). The above seems to result from the nature of the settlements rather than from its chronology, as all three groups are present during the second half of the 3rd millennium BC. Therefore while artefacts of the International Group predominate in the fortified sites, the Incised Group appears almost exclusively in open sites. The Palmela Group seems of minor importance, at least in the north region of the Tagus River estuary. The remarkable antiquity of Beaker pottery found in the FM hut at Leceia (which dates from the 2nd quarter of the 3rd millennium BC, re-confirmed by AMS dating) has parallels both in the North and South of Portugal, as well as in Spain. Thus we conclude that in the Lower Estremadura (one of the most important regions in Europe for the discussion of the origin and diffusion of Beaker “phenomenon”), the Beaker social formation with its own distinct cultural characteristics, coexisted with local Chalcolithic cultures, although never merged with them.

Fig. 2. Leceia. Plan of the fortified settlement, with the
location of the two Bell Beaker huts identified outside the walls.
One of the important findings of this study is that the Incised Bell Beaker style is strictly contemporary of the International style and not a later development. The difference is that, while the International (or Maritime) high quality pottery style dominated the fortified settlements, their rural hinterland used the more modest Incised style pottery or, in some cases, no Bell Beaker pottery at all. 

The author questions the traditional tripartite division between Early, Full and Late Chalcolithic (with Bell Beaker only present in the late stage) and claims a simpler division between Early and Full/Late Chalcolithic based not only on Bell Beaker presence but also of the more widespread local pottery styles (channeled and acacia-leaf decoration). 

He also argues that, somehow, there was a "cultural" (or is it "class"?) division between the fortified cities and their rural hinterland, division that would reappear later in the Bronze Age. This division is largely defined by certain pottery styles and particularly quality. A possible interpretation I do is that this reflects a division between a cosmopolitan urban "elite" and a rural society that was not immersed in this cosmopolitanism of the fortified towns. The author finds no sign of conflict between the two areas.
On a more global approximation to the socio-cultural reality during the 2nd half of the 3rd millennium BC in Lower Estremadura, we may consider that if Beaker society was segmented with two clearly differentiated components, it may have corresponded nevertheless to a cultural entity as a whole with its own characteristics, at least in the region under appreciation.

The absolute chronology for the earliest bell beakers in Estremadura is 2700-2600 BCE, prior to the transition between the two Chalcolithic phases (c. 2600-2700 BCE in Leceia).

I find the following particularly interesting:
The comparison of chronometric and archaeological results described above suggests that the first Beaker productions in the region of Lower Estremadura (between about 2700 and 2600 BC) coexisted, with lower interaction, with Chalcolithic populations that lived in some fortified sites, as shown by the chronology of the FM hut at Leceia. This is the same period in which fluted pottery typical of the Early Chalcolithic of Estremadura was still used inside this fortified settlement. But in other cases this coexistence was followed by interaction with the inhabitants of those already-existing fortified sites (as found in the fortified Chalcolithic settlement of Zambujal).

This interaction persisted throughout the whole Full Chalcolithic (represented by the characteristic “acacia-leaf” ceramic pattern) until the end of the 3rd millennium BC, as can be seen in almost all the fortified settlements of Lower Estremadura.

Does this support the formation of Bell Beaker as some sort of "sect" or distinctive "ethnic group", which only in a second phase became inserted in the wider local society? One possible interpretation might be that Bell Beaker users could have arrived from elsewhere as some sort of colonists, maybe a colony of specialist traders or metallurgists or even a religious community, but, if so, where from?, because Iberia seems to have the oldest Bell Beaker dates?

Estremadura is today one of the most likely candidates for the formation of the Bell Beaker phenomenon but this paper also mentions similarly older dates in other parts of Portugal, and the same seems true for other parts of Iberia and SE France. Whatever its exact origin, it seems likely that the vibrant and often ill-understood Chalcolithic civilization of Estremadura was surely a trampoline from which the important cultural phenomenon reached other areas of Atlantic (and maybe even inland) Europe.

July 2, 2014

Altitude-adaption in Tibetans is "Denisovan-like"

It seems that archaic humans left a small but critical legacy among us:

Emilia Huerta Sánchez et al., Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 2014. Pay per viewLINK [doi:10.1038/nature13408] 

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau1, 2, 3. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans4, 5, 6, 7, 8, 9, 10, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments.

Figure 3: A haplotype network based on the number of pairwise differences between the 40 most common haplotypes.
The haplotypes were defined from all the SNPs present in the combined 1000 Genomes and Tibetan samples: 515 SNPs in total within the 32.7-kb EPAS1 region. The Denisovan haplotypes were added to the set of the common haplotypes. The R software package pegas23 was used to generate the figure, using pairwise differences as distances. Each pie chart represents one unique haplotype, labelled with Roman numerals, and the radius of the pie chart is proportional to the log2(number of chromosomes with that haplotype) plus a minimum size so that it is easier to see the Denisovan haplotype. The sections in the pie provide the breakdown of the haplotype representation amongst populations. The width of the edges is proportional to the number of pairwise differences between the joined haplotypes; the thinnest edge represents a difference of one mutation. The legend shows all the possible haplotypes among these populations. The numbers (1, 9, 35 and 40) next to an edge (the line connecting two haplotypes) in the bottom right are the number of pairwise differences between the corresponding haplotypes. We added an edge afterwards between the Tibetan haplotype XXXIII and its closest non-Denisovan haplotype (XXI) to indicate its divergence from the other modern human groups. Extended Data Fig. 5a contains all the pairwise differences between the haplotypes presented in this figure. ASW, African Americans from the south western United States; CEU, Utah residents with northern and western European ancestry; GBR, British; FIN, Finnish; JPT, Japanese; LWK, Luhya; CHS, southern Han Chinese; CHB, Han Chinese from Beijing; MXL, Mexican; PUR, Puerto Rican; CLM, Colombian; TSI, Toscani; YRI, Yoruban. Where there is only one line within a pie chart, this indicates that only one population contains the haplotype.

See also this entry on Neanderthal introgression being subject to positive and negative selection.

Sino-Basque is not for real

Unmistakable evidence: beret-wearing Chinese!
(humorously borrowed from Zubia-Qiao blog,
which is about real Basque-China relations)
Linguistic speculation haunts us and today I stumbled on this paper, which has an interesting introduction but ends up claiming the extremely unlikely Sino-Caucasian family (including Basque and what-not):

Murray Gell-Mann, Ilia Peiros & George Starostin, Distant Language Relationships: The Current Perspective. Available at academia.eduLINK

I admit I have been skeptic of the Sino-Caucasian hypothesis since I tried once to learn some Chinese and was surprised of how little this language actually resembles Basque. Probably a random African or Australian language is not more different than Chinese is to Basque, or so I thought without having performed until now any formal test of the hypothesis.

There are a lot of reasons: the general skepticism of most linguists but also the lack of any apparent archaeological or meaningful genetic relationship since maybe 60 Ka ago (or, if Sino-Tibetan is related to Amerind and other Native American languages, since c. 45 Ka ago at the latest).

But the hypothesis continues to have some currency and today I finally decided to test it following the Swadesh-100 method suggested in the paper. The result:

Sino-Tibetan/Basque/English Swadesh-100 comparison (open office ODT format, similar to Excel - if anyone has a problem, please ask and I will upload an Excel version of it). 

Conclusion: Basque is not more related to Sino-Tibetan (either Mandarin or Burmese) than English is. If anything, the opposite is true, although the low level of plausible cognates for both languages (5-7%) seems merely stochastic noise, or maybe in some case wanderworts. Of course, the exact number of similar words (possible cognates) depends on one's permisivity but the pattern is so similar for the three possible pairings that, if there is any relationship at all, it must include English and therefore Indoeuropean.

Check it yourself, of course.

June 29, 2014

Pan-Homo split: 11-17 million years ago



cc Matthew Hoelscher





This is probably the more synthetic paragraph from the study:

13 million years of the hominid line








Sahelanthropus (from


June 21, 2014

Claim of 13 Ma Pan-Homo split






Atapuerca skulls show "intermediate" features

H. heidelbergensis from Atapuerca
Cranium 5 "Miguelón"
(CC by José Manuel Benito)






Atlas of Inuit trails

An anthropological and geographical resource that may be of interest:


From the Introduction:



Partial image of the atlas

June 15, 2014

Mexico's Native American diversity

Interesting study on Mexico's Native American diversity:



Fig. 1-D



K=9 (fig. 2-B-part)









  • K=12: Tarahumara
  • K=14: Nahua-Purepecha-Totonac
  • K=15: Tepehuan
  • K=16: Purepecha + Jalisco-Nahua
  • K=18: Triqui
  • K=20 Totonac

Mestizo ancestries



A more regionalized approach to Iberian ancestry could also be interesting.



June 14, 2014

Ancient inter-continental admixture in the Horn of Africa











The authors conclude with the following remarks (emphasis mine):
