April 3, 2015

19 Ka BP old mtDNA H from Cantabria

Jean Lohizun points me to this new study by the EHU-UPV paleogeneticist team, which reviews the ancient DNA evidence from the Cantabrian strip (or "fringe" as they call it) and, most importantly announces the oldest confirmed mtDNA H to date: belonging to an individual from El Mirón cave (Ramales, Cantabria, bordering the Basque Country), which is assigned to earliest Magdalenian culture and dated to 19,000 BP.

Update (Apr 24): the genetic findings of El Mirón were first published (in Spanish) in: M. Hervella et al., El ADN mitocondrial de los cazadores-recolectores de la región cantábrica: nueva evidencia de la cueva de El Mirón, Revista Española de Antropología Física - Vol. 35 (2014). I could not find an online reference but I have a copy of the article thanks again to Jean.

Concepción de la Rúa et al., Ancient DNA in the Cantabrian fringe populations: A mtDNA study from Prehistory to Late Antiquity. Quaternary International, 2015. Pay per viewLINK [doi:10.1016/j.quaint.2015.01.035]


The present mtDNA study on human remains of fourteen archaeological sites from Cantabria, Basque Country and Navarra provided a diachronic overview from Paleolithic–Mesolithic to Late Antiquity period of some communities settled in the Cantabrian fringe. Ancient DNA studies in European human remains indicated a genetic discontinuity between the hunter–gatherers and later populations. However, some of the mtDNA lineages found in the Cantabrian fringe in Paleolithic–Mesolithic times persist in present-day populations.

The mtDNA variability observed in hunter–gatherers and farmers in Europe denoted a complex pattern for the Neolithic transition, occurring along several different routes into and across Europe. The mtDNA lineages found in the Cantabrian fringe indicated that the dispersion of Neolithic farmers had a different genetic impact in this area with respect to Central and Mediterranean regions of Europe. The differences in mtDNA variability were also apparent after the Neolithic, as shown by the genetic distance between the Chalcolithic populations from the Cantabrian fringe and the Bell Beaker Culture (BBC) populations of Central Europe. 

It must be mentioned that they seem to have forgotten the thesis of Marie Lacan[fr], which reported mtDNA H in Linatzeta cave (Basque Country, Epipaleolithic) and Franchthi cave (Greece, Meso-Neolithic transition), among other more recent aDNA sequences. See here for my English language synthesis.

Otherwise they list all the sequences considered in their paper in table 1:

Annotations by Maju: red: El Mirón (new sequence), orange: other Paleolithic or Epipaleolithic sequences

After including Linatzeta (Lacan 2011), we get the following frequencies in the Eastern Cantabrian sub-region (Basque Country + Cantabria) for pre-Neolithic times:
  • H: 4/6=2/3=67%
    • H-CRS (H1 surely): 33%
    • H6: 16%
    • H*: 16%
  • U5: 2/6=1/3=33%
    • U5*: 16%
    • U5b1: 16%
Notice anyhow that if we choose to draw a line between Cantabria and the Basque Country, then we get a sharp contrast: 
  • Cantabria: 100% H
  • Basque Country: 67% U5 + 33% H* (or even an illusory 100% U5 if we use only the table above, ignoring Lacan's data)
Does this apparent sharp contrast make any sense? Well, one possible interpretation comes from carefully taking into account the data we have on Iberian Solutrean and Magdalenian, which indicates that:
  1. South Iberian (from Valencia to Portugal) Solutrean is heavily influenced by the Gravettian substrate (otherwise "pure Solutrean" is restricted to two caves), configuring a unique facies sometimes called Gravetto-Solutrean.
  2. South Iberian Gravetto-Solutrean, probably in its way to Portugal, strongly affected the Upper Paleolithic of Northwest Africa, being a decisive force in the Iberomaurusian or Oranian genesis. Backflows can't be discarded because of the innovation of tanged and winged arrow points, which may have been inspired by North African Aterian technology.
  3. The Portuguese branch of this Gravetto-Solutrean was the actual source (via Salamanca) of Asturian Solutrean, unlike what happened in Cantabria and the Basque Country, directly influenced by Aquitaine. 
  4. In the subsequent Magdalenian there might have been an expansion eastward of the Asturian population, because the facies divide moves to the east (so we have a Cantabro-Astur facies and a Basque facies).
In addition to that, it may be worth considering the issue of North African genetic influence in the Western Third of the Iberian Peninsula, which incidentally and irregularly includes Cantabria but not the Basque Country. Also Chandler et al. 2005 reported high frequencies of mtDNA H (and low of U) in Epipaleolithic Portugal.

I guess that other interpretations are possible such a more subtle cline or patchy distribution but I would not discard this hypothesis, which in essence proposes that Solutrean and Magdalenian were in general dominated by U5 but this did not affect (at least not very intensely) most of Iberia, nor surely other regions like Italy or Eastern Europe, where we see haplogroups that are not U5 (Sunghir's and Karelian H, Italian mysterious HV, etc.)

This implies that the main redistribution of mtDNA H in Europe, that part organized around H1 (which also includes H3 and various H*) actually happened mostly in the Neolithic from areas like Portugal. However we know nearly nothing about the Atlantic pre-Neolithic DNA North of the Bidasoa River (some of which could also be H, particularly R*-CRS reported in Britain) so multiple sources are possible. The huge blank of data corresponding to the Western French State and also Atlantic Islands, etc. is crying for a comprehensive sampling, and not just for mtDNA. 

Neolithic Basque mtDNA is unlike what is found in Continental Europe

The authors pay limited attention to the issues relative to Paleolithic and dedicate most of the paper to analyze the Basque ancient mtDNA in contrast to other comparable data from elsewhere in Europe. This is synthesized in fig. 2:

Fig. 2. Multidimensional Scaling analysis (MDS), based on a Fst genetic matrix calculated from the frequency distribution of the mtDNA haplogroups of different populations [Neolithics (green), Chalcolithics (purple), Late Antiquity (red), present-day Near East and northern Caucasus (orange) and Europeans (black)]. Abbreviations for present-day populations in Europe: Eastern Mediterranean (MdE), Central Mediterranean (MdC), Western Mediterranean (MdW), Northeast Europe (NE), NortheCentral Europe (NC), Northwest Europe (NW), Southeast Europe (SE) and Alps (ALP). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.).

Notice that all the ancient mtDNA from the so-called "Cantabrian Fringe" in this graph is from the Basque Country (Navarre included), often outside of the Cantabrian strip and rather from the Upper Ebro basin. Notice also that the all the Chalcolithic data belongs to military contexts from the Ebro Valley and are probably therefore not representative of the overall Basque region, although they may represent well the Upper Ebro in that period (more influenced apparently by Mediterranean inputs of Cardial affinity).

Also I already discussed all this (and more) quite in depth in my dedicated entry of 2013

The authors argue that Germany's Bell Beaker samples (BBC) are not quite similar to the Basque ancient and modern pools, what is true if you are nit-picky enough, but they share the same common tendency in PC1 towards modernity. In contrast all other Neolithic samples are clearly non-modern European and must have been largely suffered by replacement in the Chalcolithic or later periods.

PS- I forgot to mention that apparently Paabo and co. had already sequenced this very same specimen in 2013, yet they have not published anything for unknown reasons, some think that ideological ones. It's of course possible that they do have good reasons but two years is a long time to await publication really, we the people, who pay their salaries and budget with our extreme economic pains, expect reliability from our well-paid researchers.

March 11, 2015

Everything you wanted to know about Balcan and Carpathian Neolithic

Prolific researcher Esther Bamfy recently uploaded to her academia.edu page this most interesting publication, which, even if it is not "recent", has a load of information on the Neolithic of the Balcans, which is crucial to understand that of Europe in general.

Various authors. A SHORT WALK THROUGH THE BALKANS:THE FIRST FARMERS OF THE CARPATHIAN BASIN AND ADJACENT REGIONS. Proceedings of the Conference held at the Institute of Archaeology UCL on June 20th - 22nd, 2005. Freely available at academia.edu → LINK.

The collection is pretty much exhaustive but the paper that most caught my attention was the one by J.K. Koszlowski, titled "Western Anatolia, the Aegean Basin and the Balcans in the Neolithisation of Europe", which underlines that, contrary to pop culture ideas, often making headway into flawed genetic or linguistic studies, the first European Neolithic of Greece (Thessaly and Argolid) can't be related to Western Anatolia, where there was no such Neolithic yet but probably arrived, maybe via Cyprus, by sea.

This is coincident with what I wrote months ago at PPNB ancient mtDNA and its legacy.

But all 18 papers are very much worth reading anyhow, take a look. 

SW Iberia shattered by tsunamis every 700 years

The Lisbon earthquake of 1755 is only the latest example of a long chain of destructive tsunamis affecting SW Iberia and NW Africa, which seem now to be recurrent with a approximate regularity of ~700 years for 8 Mw events and ~3500 years for larger 8.7 Mw ones. Those are the conclusions of a geological study in the coast of Cádiz Province (Andalusia) focused on describing one that left a clear mark in the coastal sediment some 4200 years ago.

Benjamin Koster & Klaus Reicherter. Sedimentological and geophysical properties of a ca. 4000 year old tsunami deposit in southern Spain. Sedimentology 2015. Pay per view → LINK [doi:10.1016/j.sedgeo.2014.09.006]

Paper freely available at Researchgate anyhow.


The coastlines around the Gulf of Cádiz were affected by numerous tsunami events damaging infrastructure and causing countless human losses. A tsunami deposit at Barbate–Zahara de los Atunes, Spain, is located at various heights above mean sea level and shows several characteristics indicative of high-energy event deposition. This study uses sedimentology, foraminifera assemblage, magnetic susceptibility, X-ray fluorescence analysis, ground penetrating radar (GPR) to support an interpretation of high-energy deposition and determine the deposit's transport mechanisms and sediment source. Radiocarbon and optically stimulated luminescence dating of the tsunami deposit reveals ages of ~ 4000 BP and does not support the AD 1755 Lisbon event as suggested in former publications.

I fin this particularly interesting because the city that was for some 1500 years the main one of Atlantic Europe, central in both Megalithism and Bell Beaker, the so-called Castro do Zambujal (Torres Vedras, Portugal), was abandoned c. 1100 BCE after the canal of 10 km. that linked it to the ocean was silted, maybe by one of these devastating tsunamis.

This event, as well as many other details (length of the canal, geographical location beyond The Pillars, Mycenean Greek influence in presumably rival El Argar civilization, number of princely tombs, extension of Megalithism to "Lybia and Tyrsenia"...) fit strangely too well with the narration of Plato about Atlantis, which would then have happened just some 900 years (and not 9000) before his life. With less detail, the Mycenaean presence in Iberia would also correspond well with two of the mythical works of Herakles (Hercules): the conflict with Geryones and the stealing of the Hesperian apples by cheating Atlas. The early Greeks, whose influence in El Argar B is very apparent in the adoption of pithos (jar) burial, would have gone there largely in search of tin, the strategical mineral of the Bronze Age, which was only found in abundance in NW Iberia (and Cornwall but that source was exploited only later, it seems). 

February 13, 2015

Kurgan ancient DNA suggests major impact in North-Central Europe

After many rumors and pointless discussions based on them, finally the Haak et al. study on ancient Kurgan DNA is available only (pre-pub format):

W. Haak et al., Massive migration from the steppe is a source for Indo-European languages in Europe. bioRxiv 2015 (freely available pre-pub) → LINK [doi: http://dx.doi.org/10.1101/013433]

The study expands on previous work by Lazaridis 2014 by including a much larger array of ancient DNA from Germany and Hungary, as well as some key ancient DNA from Russia and also some complementary samples from Northern Iberia.

Autosomal DNA

Even if the authors admit it is difficult to properly quantify, there are clear tendencies that are outlined in fig. 2:

Figure 2: Population transformations in Europe. (a) PCA analysis, (b) ADMIXTURE
analysis. The full ADMIXTURE analysis including present-day humans is shown in
Extended Data Fig. 1.
Annotations in red by me.

The main inferred processes of demographic formation of the modern European genetic pool are outlined:
  1. A baseline of Epipaleolithic hunter-gatherers that pulls in the PC 1 towards the left (geographically would be the Atlantic). I call this layer Paleo-European (PE).
  2. A first replacement by Neolithic farmers of Thessalian origin (already discussed in depth in Lazaridis 2014), who were similar to modern Sardinians. I call this layer Neo-European (NE).
  3. A reflux of Paleo-European genetics that alters the Neo-European layer somewhat. This can be associated to Atlantic Neolithic flows (i.e. Megalithism, Funnelbeaker, etc.) We can call this stage Neo-European-2 (NE2).
  4. A second replacement wave by Steppe tribals, certainly bringing the Indoeuropean languages (IE).

Modern European populations align well along a IE-NE2 axis, whose midpoint seems to fall on North France, depending of course on which references you choose. I drew that axis as dotted red line. It is not substantively different from the Dimension 2 axis, although it is slightly slanted because the IE invaders obviously carried more PE than the NE layer. This new PE is not WHG (Magdalenian) but EHG (Eastern Epi-Gravettian) however - and hence its tendency towards Paleo-Siberian genetics (Ma1 or "ANE").

So Dimension 1 quite apparently contrasts the Paleo-European vs the West Asian components. What does Dimension 2 express? A quite apparent element is the Paleo-Siberian tendency. Alternatively it can also be considered to express the distinction between Lowland and Highland West Asians. Finally it can also be expressed as IE vs NE. All three are surely just variants of the same continental vs peripheral opposition, which is weaker than the PE vs West Asia one.

I must mention that fig. S5.2 offers a slightly different view:

Figure S5.2: PCA analysis with ancient individuals projected onto the variation of the
present-day ones.

Notable is that the NE-IE axis (not drawn) appears more slanted, with most modern populations showing greater excess of PE tendency and less "obviously" resolved by the late Chalcolithic populations (LNE/EBA in the authors terminology). 

As I said above, it seems very difficult to objectively measure the exact fractions of admixture (the tendencies are clear but the quantification not so much) and something that is becoming more and more painfully obvious is that Atlantic European ancient genomes are needed to explain the changes that happened prior to the arrival of Kurgans. Particularly it'd be most interesting to get ancient samples from: Portugal (Neolithic, Megalithic and Bronze Age), Basque Country and Gascony (Neolithic and Megalithic at the very least, preferably from the coastal regions), Brittany and West France (Neolithic, Megalithic 1 and Artenacian), Belgium (non-LBK Neolithic), Britain (several regions preferably, as the British Neolithic seems to have strong regional differences), West Germany (Michelsberg culture). This array or at least a sensible part of it could shed light on key processes taking place before and after the Kurgan migration. Bell Beaker samples from outside Central Europe would also be very interesting. 

I would also be interesting to see a PCA without West Asians, whose presence quite apparently does not add much to the analysis. It is known that when the PCA is European-only (or mostly), Basques and Sardinians display clearly different polarities (typically Sardinians vs Russians in PC1 and Basques vs Caucasians in PC2). It would be very interesting to observe how these ancient samples behave in a Europe-only PCA.


A lot of the upheaval was around the fact of the finding of some R1b in Samara Valley. This is very interesting indeed but it is not the kind R1b that can be considered ancestral to modern European mainline R1b-M412. It is mostly of a different haplogroup whose modern distribution is unknown to me: R1b-Z2103.

*Update: some people have commented that R1b-Z2103 is found in West Asia and some Volga peoples.

Schematically (following YSOGG), R1b-M343 and its sole relevant subclade R1b1-M415 are structured as follows:
  • R1b1a (L320)
    • R1b1a2a1 (L51/M412)
      • R1b1a2a1a (P311) 
        • R1b1a2a1a1 (U106) → NW Europe
        • R1b1a2a1a2 (P312/S116) → SW Europe with scatter elsewhere in the continent, including Ireland, Britain, Italy... Found in Kromsdorf (late Chalcolithic)
    • R1b1a2a2 (CTS1078/Z2103) → found in Samara culture
  • R1b1b (M335) → minor, West Asia
  • R1b1c (V88) → Mediterranean and Africa, particularly important in Sardinia and Central-East Africa.
Note: for further information on European R1b see HERE and HERE.
Otherwise all the spotted R1b in this study is R1b1*: in Samara culture and in Neolithic Aragon (NE Iberia), both of which are hard to relate to anything of modern relevance.  

Corded Ware is associated to R1a only at this time. So at least in Europe it makes good sense to associate Kurgan expansion with R1a expansion. 

Mitochondrial DNA

There is plenty of mtDNA data but most is recycled from previous studies so not really novel. An interesting detail is that there is no or nearly no mtDNA H within the Kurgan (IE) samples, strongly suggesting that their migration was largely male-biased, at least initially. As happens with Y-DNA R1b, Kurgan immigrants cannot be associated to any increase of mtDNA H, whose origins must therefore be sought in some other origin (namely: Atlantic Neolithic).

Note: my apologies for being so extremely passive in my blogging activity. I don't really know how to explain other than feeling OLD AND TIRED and needing LOTS of "me time". It's time for others to pick up the torch, I guess.

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]


Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

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.
This study: El Mirador (MIR). Published prehistoric cultures [21]: Hunter-gatherer central (HGC), Linear Pottery culture (LBK), Rössen culture (RSC), Schöningen group (SCG), Baalberge culture (BAC), Salzmünde culture (SMC), Bernburg culture (BEC), Corded Ware culture (CWC), Bell Beaker culture (BBC), Unetice culture (UC), Funnel Beaker culture (FBC), Pitted Ware culture (PWC), Hunter-Gatherer south (HGS), (Epi) Cardial (CAR), Neolithic Portugal (NPO), Neolithic Basque Country and Navarre (NBQ), Treilles culture (TRE), Hunter-gatherer east (HGE), Bronze Age Siberia (BAS), Bronze Age Kazakhstan (BAK).

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.