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Category Archives: European origins

Neolithic peoples from Britain and Ireland ate a lot of dairies and nearly no fish

I just discussed again the genetic sweep that apparently has happened in Europe after the Neolithic strongly favoring the selection of alleles that allow the digestion of lactose (the sugar present in milk and often in other dairies) by adults. However our knowledge of ancient European genetics is probably not sufficient (nor that of lactose tolerance genetics) and in any case the question remains, where did those lactase persistence (LP) alleles come from if all ancient Neolithic remains test negative?
An interesting possibility is opened by another recent study, not at all genetic in nature but rather bio-archaeological:
Lucy J. E. Cramp et al., Immediate replacement of fishing with dairying by the earliest farmers of the northeast Atlantic archipelagos. Proceedings of the Royal Society B 2014. Open accessLINK [doi:10.1098/rspb.2013.2372]

Abstract


The appearance of farming, from its inception in the Near East around 12 000 years ago, finally reached the northwestern extremes of Europe by the fourth millennium BC or shortly thereafter. Various models have been invoked to explain the Neolithization of northern Europe; however, resolving these different scenarios has proved problematic due to poor faunal preservation and the lack of specificity achievable for commonly applied proxies. Here, we present new multi-proxy evidence, which qualitatively and quantitatively maps subsistence change in the northeast Atlantic archipelagos from the Late Mesolithic into the Neolithic and beyond. A model involving significant retention of hunter–gatherer–fisher influences was tested against one of the dominant adoptions of farming using a novel suite of lipid biomarkers, including dihydroxy fatty acids, ω-(o-alkylphenyl)alkanoic acids and stable carbon isotope signatures of individual fatty acids preserved in cooking vessels. These new findings, together with archaeozoological and human skeletal collagen bulk stable carbon isotope proxies, unequivocally confirm rejection of marine resources by early farmers coinciding with the adoption of intensive dairy farming. This pattern of Neolithization contrasts markedly to that occurring contemporaneously in the Baltic, suggesting that geographically distinct ecological and cultural influences dictated the evolution of subsistence practices at this critical phase of European prehistory.

Not only fish consumption was pretty much abandoned in Britain and Ireland with the arrival of Neolithic (only recovered under Viking influence many millennia later) but the most striking fact is that it was replaced by milk as main source of proteins. 
This fact, considering that farmers studied in Central Europe and Iberia have systematically tested negative for lactase persistence, really opens an avenue for the possible origins of this nutritional adaptation because it is most unlikely that they were such notable dairy consumers without the corresponding digestive ability (even cheese may be harmful to lactose intolerant people unless it is aged, while yogurt was almost certainly not known yet in Europe). 
While the evidence comes from the Atlantic Islands, it is worth to notice that their chronologically late Neolithic has its origins in the much older agricultural cultures of NW France, another blank spot in the ancient DNA map of Europe. Nowadays NW France is high but not particularly high in this phenotype but SW France and Basques have among the highest LP scores (both phenotype and rs4988235(T) genotype) in Europe, together with the Atlantic Islands and Scandinavia. 
Then again it is worth recalling that one of the first areas where the rs4988235(T) allele is found is in the southern areas of the Basque Country, with clear signs of two different populations (one lactose tolerant and the other lactose intolerant) being still in the first stages of contact and mostly unmixed.
This leads us to the issue of Atlantic Megalithism (tightly associated to Atlantic Neolithic) and its still unsolved, but likely important, role in the conformation of the modern populations of Europe. 
Whatever the case the first farmers of the islands were heavy dairy consumers, although in Britain (but not in Ireland and Man) they eventually derived into heavy meat eaters later on:

Figure 1.

Prevalence of marine and dairy fats in prehistoric pottery determined from lipid residues. (af) Scatter plots show δ13C values determined from C16:0 and C18:0 fatty acids preserved in pottery from northern Britain (red circles), the Outer Hebrides (yellow circles) and the Northern
Isles of Scotland (blue circles), dating to (a) Early Neolithic, (b) Mid/Secondary expansion Neolithic, (c) Late Neolithic, (d) Bronze Age, (e) Iron Age and (f) Viking/Norse. Star symbol indicates where aquatic biomarkers were also detected. Ellipses show 1 s.d. confidence ellipses
from modern reference terrestrial species from the UK [19] and aquatic species from North Atlantic waters [13]. (gi) Maps show the frequency of dairy fats in residues from Neolithic pottery from (g) Early Neolithic, (h) the Middle Neolithic/Secondary expansion and (i) Late Neolithic. Additional data from isotopic analysis of residues from Neolithic southern Britain (n = 152) and Scotland (n = 104) are included [19,20].

The data of this study also suggests that the so much hyped high-meat “Paleolithic diet” is more of a Late Neolithic (Chalcolithic) thing, with the real hunter-gatherers of Europe being more into fish in fact.

Correction: I wrongly reported the main European lactase persistence SNP as rs13910*T, when it is in fact rs4988235(T) (already corrected in the text above) This was caused by the nomenclature used in the Sverrisdóttir paper, where it refers to it as -13910*T, which must be some other sort of naming convention. Thanks to Can for noticing.

 

New lactase persistence study rejects "calcium absorption" hypothesis

The “calcium absorption” hypothesis has been proposed as hypothetical mechanism to explain the apparent genetic sweep of lactose persistence alleles in Europe. According to this hypothesis, the possible role of milk in improved calcium absorption would counter the poor vitamin D synthesis in Northern Europe, preventing rickets.
However this hypothesis seems very weak, as I explained recently, notably because bone formation is only one of the various roles of vitamin D and it is probably much more crucial in correct brain development in childhood. Also there is another clear adaptation that actually solves the problem very well: whiter skin able to much more efficiently produce vitamin D in our bodies surfaces by mere exposition to sunlight, a trait that seems to have been increasingly favored after the Neolithic drop in fish consumption (the only actual nutritional source of vitamin D at relevant doses).
This new paper confirms my skepticism.
Oddný Ósk Sverrisdóttir et al., Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. MBE 2014. Pay per viewLINK  
[doi:10.1093/molbev/msu049]

Abstract


Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose – the main carbohydrate in milk – and its production is down-regulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans LP is strongly associated with, and probably caused by, a single C to T mutation 13,910bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remains poorly understood. In this study we examine one of the most widely cited hypotheses for selection on LP – that fresh milk consumption supplements the poor vitamin D and calcium status of northern Europe’s early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB-light levels. None of the 8 samples successfully typed in the study had the derived T-allele. In addition, we reanalyse published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of lactase persistence in Europe.

The study finds most likely that, most likely, there is population continuity between Neolithic farmers and modern local peoples in Northern Iberia and SE France. Technically they could only not reject this population continuity for all population parameters, but, considering that the same tests strongly reject it for Central Europe and Scandinavia, the most parsimonious conclusion is that some important population continuity does exist in SW Europe since Neolithic. In the words of the researchers:

It thus seems likely that population turnover since or shortly after the Neolithic transition has been less severe in southwestern Europe than in central or northern Europe.

However these ancient populations were lactose intolerant (rs4988235(C)) while modern ones in Northern Iberia are massively able to digest lactose (rs4988235(T)). This supports the theory of adaptive sweep for this allele. 
They suspect that the real reason behind the lactose persistence sweep is caused by basic nutritional reasons (calories and proteins) because milk may have been less subject to fluctuations in crops (traditionally cattle ate grass and not cereals, as happens in modern industrial production, while goats have even more varied natural food sources). In such circumstances episodic famines would have strongly favored lactose tolerant phenotypes, more so if lactose intolerant people would have drank milk or ate high-lactose dairies in desperation, causing them potentially deadly diarrhea.
This is not the same but fits well with my class structure hypothesis, outlined recently. The main reason why I favor this hypothesis is that this generalizing pattern should have affected farmers since very early in the Neolithic, even when they were still living in Asia or Greece, so it is very strange that the genetic sweep only appears since or after the Chalcolithic period, when a hierarchical class society is formed everywhere.

Correction: I wrongly reported the main European lactase persistence SNP as rs13910*T, when it is in fact rs4988235(T)
(already corrected in the text above) This was caused by the
nomenclature used in the Sverrisdóttir paper, where it refers to it as
-13910*T, which must be some other sort of naming convention. Thanks to Can for noticing.

See also:

 

Neolithic and Chalcolithic demographics of Western and Northern Europe

Somehow I missed this important study on the Neolithic and Chalcolithic demographics of Europe, as inferred from the archaeological record (h/t Davidski):
Stephen Shennan et al., Regional population collapse followed initial agriculture booms in mid-Holocene Europe. Nature Communications 2013. Open accessLINK [doi:doi:10.1038/ncomms3486]

Abstract

Following its initial arrival in SE Europe 8,500 years ago agriculture spread throughout the continent, changing food production and consumption patterns and increasing population densities. Here we show that, in contrast to the steady population growth usually assumed, the introduction of agriculture into Europe was followed by a boom-and-bust pattern in the density of regional populations. We demonstrate that summed calibrated radiocarbon date distributions and simulation can be used to test the significance of these demographic booms and busts in the context of uncertainty in the radiocarbon date calibration curve and archaeological sampling. We report these results for Central and Northwest Europe between 8,000 and 4,000 cal. BP and investigate the relationship between these patterns and climate. However, we find no evidence to support a relationship. Our results thus suggest that the demographic patterns may have arisen from endogenous causes, although this remains speculative.

The most interesting aspect is maybe that the (apparent) demographic changes are detailed for many regions of Europe, but first let’s see the general outlook for the whole area surveyed (Western and Northern Europe, Iberia excluded):

Figure 2: SCDPD-inferred population density change 10,000–4,000 cal. BP using all radiocarbon dates in the western Europe database.
Colored arrows and their annotations are mine.

I decided that it was important to mark the main cultural episodes for reference.
1st Neolithic refers to Impressed-Cardium and Linear Band Pottery cultures, which arrived almost simultaneously to Germany and France (of the surveyed areas), although the Rhône-Languedoc Neolithic is a few centuries earlier than the arrow, which has been standardized to 7500 BP.
Atlantic Neolithic refers to the quite belated arrival of Neolithic to Britain, Ireland and Northern Europe (standardized at 6000 BP). This process was quickly followed and tightly associated with the widespread cultural phenomenon of Dolmenic Megalithism. It is most interesting that the main deviation from the pattern of regular growth concentrates in this period and is clearly positive.
Corded Ware culture (Indoeuropean consolidation in Central and Northern Europe) affected only to Germany and Denmark-Scania within the surveyed regions. It was followed by a more widespread subcultural phenomenon known as Bell Beaker, which almost invariably cases manifests within pre-existent locally rooted cultures. Neither seems to be correlated with demographic expansions in the general overview.
Now let’s take a look at the regional graphs:

Figure 3: SCDPD-inferred population density change 8,000–4,000 cal. BP for each sub-region.
Colored arrows, excepted the blue ones (which mark the local first Neolithic), are mine and mark general pan-European initial chronologies (not local!) for Megalithism, Corded Ware and Bell Beaker in those regions where they had some clear influence.

Here we can appreciate that:
Atlantic Neolithic and its associated Megalithic phenomenon are clearly related to notable demographic expansions in Ireland, Scotland, South England, Denmark and Scania. Megalithic influence may also be associated with some more irregular growth in South and Central Germany but rather not in France nor West Germany. A contemporary weak and irregular growth in North Germany (Brandenburg, Mecklemburg and Schlewig-Holstein) may be correlated with Funnelbeaker (with roots in Denmark) and the first Kurgan development of Baalberge and successor cultures (with roots in Eastern Europe), which would eventually evolve into Corded Ware.
Corded Ware only seems related to clear demographic growth in Jutland (and less resolutely in Scania). Bell Beaker is only linked with clear demographic growth in Ireland (and much more weakly in South England and Central Germany), while elsewhere it is rather associated with decline.
For the exact extension of the various regions as defined for this study, see fig. 1 (map).
As provisional conclusion, it seems obvious to my eyes that the most important demographic growth processes were the various Neolithic cultures but that the Atlantic Neolithic (and associated Megalithism) was particularly dynamic. In contrast Indoeuropean-associated cultural phenomena had a much weaker impact, with some localized exceptions, and are generally associated with local demographic decline instead, at least judging from the archaeological record.
See also:
 

Italian haploid genetics (second round)

More than a year ago I commented (as much as I could) on the study of Italian haploid genetics by Francesca Brisighelli et al. Sadly the study was published with several major errors in the figures, making it impossible to get anything straight. 
I know directly from the lead author that the team has been trying since then to get the paper corrected but this correction was once and again delayed by apparent inefficiency of PLoS ONE’s management, much to their frustration. Finally this week the correction has been published and the figures corrected.
So let’s give this study another chance:
Francesca Brisighelli et al., Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage. PLoS ONE 2012 (formally corrected in February 2014). Open accessLINK [doi:10.1371/journal.pone.0050794]
 
Notice please that you have to read the formal correction in order to access the new figures, the wrong ones are still in the paper as such. 
The corrected figures are central to the study:

Figure 1 (corrected). Map showing the location of the samples analyzed in the present study and those collected from the literature (see Table 1).
Pie
charts on the left display the distribution of mtDNA haplogroup
frequencies, and those on the right the Y-chromosome haplogroup
frequencies.

So now we know that the Northern mtDNA pie was duplicated in the original graph and that Central Italians are outstanding in R0(xH,V), which reaches 14% (probably most HV*), while they have some other peculiarities relative to their neighbors from North and South: some less U and no detected V. 
Other variations are more clinal: H decreases from North to South while J and T do the opposite.

Figure 3 (corrected). Phylogeny of Y-chromosome SNPs and haplogroup frequencies in different Italian populations.

In the Y-DNA side, the most obvious transition is between the high frequencies of R1b1a2-M269 (R1b3 in the paper) in the North versus much lower frequencies in the South. But also:
  • J2 is notorious in the Central region (and also the South) but rare in the North.
  • G frequencies in the South are double than those of Center and North.
  • The same happens with lesser intensity regarding E1b1b1-M35 (E3b in the study).
  • In contrast haplogroup I is most common in the North. However the Sardinian and sub-Pyrenean clade I2a1a-M26 (I1b2 in the paper), which is also the one documented in Chalcolithic Languedoc, is rare in all regions.

The study also deals with several isolated populations:

Figure 4. Haplogroup frequencies of Ladins, Grecani
Salentini and Lucera compared to the rest of the Italian populations
analyzed in the present study.

All them show large frequencies of mtDNA H relative to their regions. The Grecani Salentini do have some extra Y-DNA E1b1b1 (E3b) and J2, what may indeed underline their partial Greek origins. The Ladini show unusually high frequencies of R1b*(xR1b1a2) and K*(xR1a,R1b,L,T,N3), while the Lucerans are outstanding in their percentage of G.
I want to end this entry with a much needed scolding to the staff of PLoS ONE for their totally unacceptable original sloppiness and delay in the correction. And my personal thanks and appreciation to Francesca Brisighelli for her indefatigable persistence and enthusiasm for her work, which is no doubt of great interest.
 

Medieval Germans, Hungarians and the spread of lactose tolerance

A new ancient DNA study found that 800 years ago in Dalheim (Western Germany) lactase persistence was already similar to modern day frequencies (h/t to Chad):
Annina Krüttli et al., Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe. PLoS ONE 2014. Open accessLINK 
[doi: 10.1371/journal.pone.0086251]

Abstract


Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.

Table 2. Results of genetic sex and LP allele genotyping.

So lactase persistence was already highly prevalent in West-Central Germany 800 years ago, much as it is today.
Very interesting also is their mention of a previous study in Medieval Hungarians (Nagy 2011, PPV):

A study of medieval Hungary found moderate levels of LP in local
commoners (33%) ca. AD 900–1100, but extrapolating from these results is
complicated by the region’s history of conquest by lactase
non-persistent Asian invaders.

While these frequencies are clearly much higher than Neolithic ones (zero), they were still much lower than present day (c. 60%). 
They also mention the oldest know lactase persistence alleles in Europe, which correspond to Chalcolithic findings in Götland and the Basque Country, albeit still at low frequencies and, in the Basque case, showing strong linkage disequilibrium pointing to an initial admixture episode between two different populations: one lactose-tolerant and the other intolerant. See this previous entry for more details.
As I see it, these two data points help us to better understand the still very wide window when lactose tolerance spread among Europeans, which begins in the Chalcolithic and, at least in the case of Germany, seems closed by the Middle Ages. Although in the Hungarian case remained still half-way in that period. 
It is quite possible that instead of a single selective swap affecting this trait, the process took place in several bouts, each one with their own geography and timeline. 
Still, the reasons behind this apparent positive selection for milk-digesting genes, remain ill-explained at academic level. Recently I tried to articulate a consistent theory on it, based on the fact that the Metal Ages, when this sweep happened almost certainly, were characterized by the accumulation of agricultural resources, wealth and power in few hands, producing a class-structured society in which the vast majority were poor and lived precarious lives, in which the general availability of, particularly, goat milk may have been an important nutritional relief (calories and proteins). See: Is the ability to digest milk in Europeans caused by ancient social inequality?
 

La Braña 1 carried the very rare Y-DNA haplogroup C (possibly C6-V20)

La Braña 1 without makeup
(Check for the updates below, please).

The late Epipaleolithic forager from NW Iberia (previously discussed here) had the patrilineal haplogroup C6, found so far only very rarely among modern Europeans (Scozzari 2012). This, I must say, I know by the moment only from secondary sources (Eurogenes, Dienekes and a personal communication) because I have not been able yet to put my hands on the relevant paper and this key detail is not mentioned in the abstract.

Iñigo Olalde et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 2014. Pay per viewLINK [doi:10.1038/nature12960]

freely available supplementary materials.


Abstract

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe1, 2, 3. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

Relevance for the overall understanding of macro-haplogroup C
Until the discovery of this C6 lineage, there were some strong reasons to suspect that Y-DNA C may have coalesced already in SE Asia or, at least, very close to it, with its subclades forming by pairs a three pointed star with geographical center in that area: C1 and C3 in NE Asia (and America), C2 and C4 in Wallacea and Australasia and C5 and some rather homogeneous C* in India.
The discovery of this C6 lineage and its confirmation as a Paleolithic one in Europe (i.e. not a “recent” arrival from somewhere else) add phylogenetic weight to the Western geography of haplogroup C, one of two main subdivisions of the main non-African Y-DNA lineage CF. However we cannot yet reach to conclusions about the “exact” origins of C because the macro-lineage still awaits improvement of its phylogenetic structure at the basal levels.
In plain language: it is quite likely that C2 and C4 form a monophyletic clade and I would not be surprised at all if C1 and C3 do the same. But then it is also possible that C5 and the Indian C* and/or the European C6 also form their own distinct branches. It is even possible that some of these lineages are related across subcontinental regions, as was recently found within MNOPS (aka K(xLT)). So we need first to know how they relate with each other a the top phylogenetic level before we can rush to any conclusion. In any case the discovery of C6 adds some preliminary weight to the hypothesis of C coalescing when still in South Asia.



Pigmentation genetics

There have been some rush to conclusions on the pigmentation of this and another Western European hunter-gatherer based only on genetics. I think that some of the conclusions are most likely incorrect, at least to some extent, because they are based on a SNP which only weights ~15% on skin coloration.

Judging on the figures (freely accessible, it seems), La Braña 1 carried two pigmentation alleles of gene SLC45A2 now rare among Europeans (but common elsewhere, i.e. the ancestral variant):

  • rs16891982, which affects hair color (7x chances of black hair among Europeans)
  • rs1426654, which affects skin pigmentation to some degree (correlated with skin color in Indians, irrelevant among modern Europeans because of fixation, weights only ~15% in Cape Verdeans’ skin coloration). 

Notice that while you can find online reconstructions that give La Braña 1 a very dark coloration, this is not necessarily the case at all but rather an oversimplistic  interpretation based only on one allele, allele that is not just dominant in West Asians and Europeans but also, for example, among Gujaratis, who are quite dark for European standards.

    It seems correct anyhow that this allele was only brought to Europe with Neolithic farmers (Stuttgart had it) but its alleged effect on pigmentation seems very much exaggerated.

    Fig. 4 from Beleza 2013 highlights that no single gene is decisive in skin pigmentation.

    It is probable anyhow that La Braña 1 had black hair.
    It is much more plausible that he had blue eyes because these are much more directly regulated by simple genetics.
    Continuity of immunity genetics
    La Braña 1 also had three immunity related alleles (derived variants) that have been retained at least to some extent by modern Europeans:
    • rs2745098 (PTX4)
    • rs11755393 (UHRF1BP1, related to lupus)
    • rs10421769 (GPATCH1)
    Comparison with global populations
    Fig. 5 (ED) offers various comparisons of La Braña 1 and Mal’ta 1 (from Siberia) with modern humans from around the World:

    Extended Data Figure 5: Pairwise outgroup f3 statistics.
    a, Sardinian versus Karitiana. b, Sardinian versus Han.
    c, La Braña 1 versus Mal’ta. d, Sardinian versus Mal’ta.
    e, La Braña 1 versus Karitiana. The solid line represents y = x.
    We can see in them that, La Braña 1 clusters well with modern Europeans, while Mal’ta instead strongly tends towards other Asians, often clustering with Pakistanis (“Central/South Asia” metapopulation).
    Maybe the most interesting graph is c, where we can see how the various populations deviate from the y=x line in the direction of La Braña (Europeans, West Asians) or Mal’ta (Native Americans particularly).
    Comparison with Neolithic samples and modern Europeans

    Extended Data Figure 4: Allele-sharing analysis.
    Each panel shows the allele-sharing of a particular Neolithic sample from refs 1 and 3 with La Braña 1 sample. The sample IDs are presented in the upper left of each panel (Ajv52, Ajv70, Ire8, Gok4 and Ötzi). In the upper right of each panel, the Pearson’s correlation coefficient is given with the associated P value.

    In all cases Swedes (SE), followed by Polish (PL), etc. share the greatest amount of alleles with La Braña 1, although I’m not sure if the differences are really that relevant (is really 69.3% significantly different from 68.7%?)
    In the vertical scale we can observe how the various populations tend more or less strongly towards various Neolithic samples (again with the same doubts about the significance of the differences). In the first row they are compared with Götland’s Pitted Ware individuals (of plausible Eastern European origins: strong cultural connections with Dniepr-Don Neolithic). Here Central Europeans show the greatest affinity with Ajv52 and Ajv70 (Basques Bulgarians also score high). There are some differences in the case of individual Ire8, whose closest modern relatives seem to be the Dutch. Swedes only score high re. Ajv52 but low to the others, while Finns score neutral-to-low relative to all them.
    The lower row compares with to mainstream Neolithic samples: Gok4 was a Megalithic farmer from SW Sweden and Ötzi was a Chalcolithic shepherd from Southern Tirol. The Swedish farmer is best approached by the Dutch, followed by various West-Central Europeans, while Basques Bulgarians, Finns and Swedes score low here. In the case of Ötzi nobody scores particularly high (some tendency in Switzerland and nearby areas), while Finns score clearly low.
    And that’s all I can say without direct access to the study. Enjoy.

    Update: I already got the paper (thanks again to the donor), I’ll see to update as need be once I have time to read it. Minor urgent edits above in red (and slashed out text).

    Update (Jan 29): The supplementary data is freely available (LINK) but I could not find it earlier. Almost all the information is in it, including a long list, much longer than mentioned above, of the SNPs found in La Braña 1, compared to various modern population frequencies. I don’t have time right now to dwell on it but I guess from a first read that I will have to amend some comments made on the issue of pigmentation above.

    Regarding the Y-DNA haplogroup, it is important to notice that its adscription withing haplogroup C seems very clear but its assignation to C6-V20 is more dubious because of the low quality of the genome. Only the V20 marker could be assigned, so the authors themselves are in doubt and wonder if it could alternatively be C* or C5, both with a South Asian affinity.

    In this sense I think it is worth noticing that the reference Y-DNA site ISOGG has recently revised the phylogeny of macro-haplogroup C and that they have already renamed C6-V20 as C1a2, making it a relative of the minor Japanese lineage earlier known as C1 (now renamed to C1a1), similarly South Asian C5-M356 has been renamed to C1b. So C1 is now perceived as a lineage that spans all Eurasia with an arguable South Asian centrality.

    Another (Papuan?) lineage once known as “C6″ has long vanished from the phylogeny because of lack of plural samples, I understand.

     

    Is the ability to digest milk in Europeans caused by ancient social inequality?

    I’ve got involved these days in a discussion at Dienekes’ Anthropology Blog on the causes of lactase persistance (LP), i.e. the ability to digest milk as adults, in Europe. 
    The discussion orbits around a recent pay-per-view study by O.O. Sverrisdóttir, which claims, with some soundness for what I can discern, that LP in Europeans must have gone through positive selection. 
    Actually the study, as most of its kind, deals only with one LP marker, the well known SNP rs4988235, whose T variant allows adults (in dominant fashion) to digest milk, an ability often lost after weaning. 
    As I discussed back in 2010, there must be other such SNPs because actual LP phenotype only partly corresponds with the known LP alleles. But for whatever is worth, this is the (2010) “known allele” LP map:
    In Europe at least, it essentially corresponds with the T variant of rs49235, which concentrates in Scandinavia, Atlantic Islands and the Basque/SW French area. 
    At first I boarded the discussion with perplexity, because, even if the positive selection argument seems sound, it seems hard to find a reason for it: milk is not such a “great” source of food, excepting the issue of calcium and a high content of protein and fat, and the occasional claims that it is related to vitamin D deficiency seem extremely feeble because this vitamin is present at extremely low frequencies in natural milk, being rickets (where milk’s extra calcium could play some role) only a “less important” side effect of vitamin D deficiency, because its main harmful effect is to impair early brain development, a most serious problem for which calcium seems quite meaningless. So why would the ability to digest milk would have become such a matter of life or death to be actively selected for generation after generation until near-fixation?
    A key piece of information is that not a single sequenced Neolithic farmer has ever been found to carry the relevant LP allele (being all CC) and only since Chalcolithic we begin to find some TT and CT individuals. These are found in Sweden and in the southern areas of the Basque Country (see here for a lengthier discussion):
    • In Götland (Pitted Ware culture) only 1/20 alleles was T (i.e. 1/10
      persons had the CT combo, all the rest being CC and therefore likely
      lactose intolerants). 
    • In Longar (Navarre, dated to c. 4500 BP)
      1/7 individuals was TT, while the other six were CC (intolerant). There
      were no CT cases.
    • In San Juan Ante Porta Latinam (SJAPL, Araba, dated to c. 5000 BP), 4/19 were TT, 2/19 were CT, while the remaining 13 were CC.
    In the Basque cases we can appreciate that there must have already been two different populations regarding this SNP, because the CT cases are rare, implying that the two groups were only beginning to mix. It is worth mentioning that the Basque sites are odd in several aspects: on one side they seem to be military cemeteries (mostly males, arrow injuries and arrow points) and, on the other, they are rather exceptional in the Basque historical sequence of mtDNA pools (a lot more K and some other lineages than usual, less H and U).
    But a key finding in this study is that a Neolithic sequence from Atapuerca (near Burgos city, historical Basque SW border) was again CC for the relevant SNP (and therefore likely lactose intolerant). So it is very possible that proto-Basques did not have the T allele in notable frequencies either (although I keep some reservations for lack of larger samples).
    Whatever the case, if the T allele was selected positively as it seems, there must be a powerful reason for it. Was it cows, as some have claimed a bit too vehemently? I doubt it. 
    Why? Because for all we know from the Middle Ages, a period very similar in many aspects to the Metal Ages, it were goats and not cows the main providers of milk. This makes total sense because the hardy goats are rather inexpensive to rear, while cows are more costly and were often reserved for traction jobs. In most cases, cow produce, be it milk or meat, was an expensive luxury apt only for the upper echelons of a society that was becoming more and more hierarchical and unequal since precisely the Chalcolithic period. 
    Some oral accounts I have heard tell that not so long ago “acorn bread and goat milk” were often staple for the poor. In other areas maybe it was not acorn bread but, say, oat meal (or whatever else), but almost certainly the milk came almost invariably from goat udders, which very efficiently transform leaves and almost any vegetable, even thorny ones, into milk (and meat) for our consumption.
    It is crucial to understand that only if milk was a key survival staple, LP would have become fixated. Otherwise people would have preferred alternative foods and survived in similar shape, so positive selection would never have happened at this locus (non-LP individuals would have survived easily, selection would never have happened or would have been mild enough to retain much greater diversity). 
    It is also crucial to understand that, for all we know, this positive selection only happened since the Chalcolithic, i.e. when social stratification, inequality and private aristocratic property became common. Obviously the upper classes (or castes) had no problems accessing high quality foods, including meat, but the masses probably had growing problems in this aspect as the land and cattle became more and more concentrated in few hands. 
    Even where a wide class of free peasants existed, as was probably the case in much of Atlantic Europe, these were surely often not well-off enough to afford dairy cows. Instead goats would have been available for almost everybody, even the poorest of farmers. And very likely they were the only steady supply of proteins and fat, mostly via milk.
    Plausibly this need of extra nutrients of animal origin was more intense in the Atlantic areas of Europe because cereals do not perform so well in the prevalent humid conditions. Also before the medieval development of the heavy plough, the deep Atlantic soils were not at all as productive as they are now (and that’s why NW Europe only got its economic prominence in the last millennium, being before a peripheral area to the much more productive Mediterranean climate). 
    But climatic and agricultural issues aside, I strongly suspect that the main driver of LP positive selection, were goats, because these and their dairy produce were almost certainly available for almost everyone and, in the Metal Ages, the vast majority of people were farmers, often rather poor peasants who had to rely on their goats for survival, very especially in the bad times.
    I really do not see any other explanation that fits the data.

    PS- This social inequality & goats argument makes sense assuming that the positive selection theory is correct. However before I fully embrace it, I would need a half-decent sample of aDNA sequences from the Atlantic areas of Europe, notably Britain & Ireland, the Basque Country & SW France and mainland Scandinavia, where the T allele peaks. I say because what we find in some Chalcolithic sites, notably in the Basque Country, rather strongly suggests that there was already a TT population somewhere and we have not yet found it. So maybe some of the premises of the positive selection theory are not as sound as I said above – but we do not know yet.

     

    Andalusian mtDNA highlights W-E differences

    The issue of W-E genetic differences in Iberia has been discussed before in this blog by guest author Argiedude on the grounds of Y-DNA, showing that roughly the Western third of Iberia is distinct from the rest, most notably because of its higher presence of North African lineage E1b-M81. However the differences also appear in the mtDNA, even if they may be a bit more subtle because they cross with a N-S gradient of sorts.
    A new study focused on the matrilineages of two characteristic Andalusian provinces, Granada in the East and Huelva in the West, underscores that this difference is very real.
    Candela L. Hernández et al., Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region. BMC Genetics 2014. Open accessLINK [doi:10.1186/1471-2156-15-11]

    Abstract (provisional)


    Background


    The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region.


    Results


    The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population.


    Conclusions


    The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia. 

    Naturally the most noteworthy data is the frequency of mtDNA haplogroups in the two sampled populations:

    A map comparing this data with some other areas of Iberia (mostly the West) is also provided:

    Figure 3 – mtDNA haplogroup profiles registered in some populations of the Iberian Peninsula. The two Andalusian subpopulations studied here are marked with a red arrow. Codes are as in Additional file 3.
    What makes Onubenses (the inhabitants of Huelva, ancient Onuba, West Andalusia) peculiar in relation to their Granadino neighbors is their lower frequency of H (notably H*, H3 and H5), along with their higher frequencies of K1, U3a and several North African related haplogroups (U6, L1b and L2). The peculiarities of Granadinos (notably the high H5 frequency) are not so notable in comparison.
    Some of these Onubense peculiarities are reproduced in other parts of West Iberia, notably the low frequencies of H (but not at all in the NW corner), the presence of U6 (notably in North Portugal and also, not shown here, among the Maragatos of the León-Galicia border area) and to some extent the elevated frequency of K and some L(xM,N) lineages (varied localized frequencies).
    Much of this seems best explained by ancient flows from NW Africa (flows which may be Neolithic, Paleolithic or from the Metal Ages but hardly related to Phoenician or Muslim colonization, which had no W-E gradient whatsoever) but I have some qualms about the quick identification by the authors of the origins of Onubense high K1 in that area. At the very least it must be noticed that, unlike the other African markers, K1 is much more common towards the Eastern parts of NW Africa and is also found at similarly high frequencies in many parts of Europe, such as France and Central Europe.
    K1 was first spotted in Iberian ancient DNA in the early Neolithic (Los Cascajos, Navarre), and was an important Neolithic lineage through Europe. While I can’t discard the North African suggested origin, I think that other possibilities are at least as likely.
    On U6, the presence of the very rare U6c, one of two basal lineages of U6, only found previously in 5 Moroccans, 10 Canarians and in one Italian, reinforces the idea of U6 expanding from West to East (against what most conclusions suggest on the most unclear grounds) with a most likely Moroccan origin. In turn this raises the question on how pre-U6 arrived to Morocco, especially as the Aurignacoid Dabban industries now seem to never have gone further West than Cyrenaica, opening the possibility of this lineage having arrived to NW Africa via Europe, where we know that U in general was common in the Upper Paleolithic, and which clearly influenced North Africa at the Oranian (aka Iberomaurusian) cultural genesis (LGM) via Morocco (Taforalt and other sites).
    On the L(xM,N) lineages, it is worth mentioning that Cerezo 2012 claimed that some of them may be pre-Neolithic in Europe, especially L1b1a variants, which are widespread at low frequencies through Europe with an Iberian centrality.
    The overall picture is maybe best visualized by the Hierarchical Cluster Analysis:

    Figure 5 – Hierarchical Cluster Analysis (HCA) of 53 populations based on their mtDNAdiversity. The haplogroups used here are marked with arrows (vectors). Populations are indicated with numbers as in Additional file 3.
    Cluster 1 is particularly noticeable for its high frequency of mtDNA H, being composed by mostly Iberian samples (along with South Germans and some Sicilians). Granada, as well as nearby Córdoba, sit here (even if with a tendency towards the more mainstream European Cluster 2). Huelva is not too remarkable when compared with other European samples in the mtDNA HCA, although it does show some deviation towards NW Africa, clustering closest to Canarians.
    In spite of the good frequency of North African samples, it must be noted that the horizontal axis, in essence contrasting Europe vs. West Asia, has a weight of almost 50%, while the vertical axis, contrasting these two vs. North Africans (and the Sámi) only weights 13% (axis are almost never of the same relevance in PCA-like graphs, even if they are presented as such).
    In synthesis: NW Africa had some minor but significant genetic influence in the West Iberian third, long before the Muslim period, and this mtDNA study ratifies these distinctions in the particular case of Andalusia, adding some rich detail of data.
    Also, as the authors underline in their discussion, the issue of European genetic influence in North Africa still requires some serious investigation.
     
     

    Ancient European DNA and some debatable conclusions

    There is a rather interesting paper still in preparation available online and causing some debate.
    Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. BioArxiv 2013 (preprint). Freely accessibleLINK [doi:10.1101/001552]

    Abstract

    Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

    Haploid DNA
    The Lochsbour skull.
    The prominent browridge
    is very unusual for
    Paleolithic Europeans.
    The new European hunter-gatherer samples carried all Y-DNA I and mtDNA U5a and U2e.
    More specifically, the hunter-gatherer mtDNA lineages are:
    • Lochsbour (Luxembourg): U5b1a
    • Motala (Sweden):
      • Motala 1 & 3: U5b1a
      • Motala 2 & 12: U2e1
      • Motala 4 & 6: U5a2d
      • Motala 9: U5a2
    Additionally the Stuttgart Linear Pottery farmer (female) carried the mtDNA lineage T2c1d1.
    The Y-DNA lineages are:
    • Lochsbour: I2a1b*(xI2a1b1, I2a1b2, I2a1b3)
    • Motala 2: I*(xI1, I2a2,I2a1b3)
    • Motala 3: I2*(xI2a1a, I2a2, I2b)
    • Motala 6: uncertain (L55+ would make it Q1a2a but L232- forces it out of Q1)
    • Motala 9: I*(xI1)
    • Motala 12: I2a1b*(xI2a1b1, I2a1b3)
    These are with certainty the oldest Y-DNA sequences of Europe so far and the fact that all them fall within haplogroup I(xI1) supports the notion of this lineage being once common in the subcontinent, at least in some areas. Today I2 is most common in Sardinia, the NW Balcans (Croatia, Bosnia, Montenegro), North Germany and areas around Moldavia.
    I2a1b (which may well be all them) is currently found (often in large frequencies) in the Balcans and Eastern Europe with some presence also in the eastern areas of Central Europe. It’s relative I2a1a is most common in Sardinia with some presence in SW Europe, especially around the Pyrenees. I2a1 (probably I2a1a but not tested for the relevant SNPs) was also found, together with G2a, in a Chalcolithic population of the Treilles group (Languedoc) and seems to be somehow associated to Cardium Pottery Neolithic.
    If you want my opinion, I’d think that I2a before Neolithic was dominant, like mtDNA U5 (and satellites U4 and U2e), in much of Central and Eastern Europe but probably not in SW Europe, where mtDNA U5 seems not so much hyper-dominant either, being instead quite secondary to haplogroup H (at least in Western Iberia). But we’ll have to wait until geneticists manage to sequence Y-DNA in several SW European Paleolithic remains to be sure.

    Autosomal DNA and derived speculations
    Most of the study (incl. the must-read supplemental materials) deals however with the autosomal DNA of these and other hunter-gatherers, as well as of some Neolithic farmers from Central Europe and Italy (Ötzi) and their comparison with modern Europeans. 
    To begin with, they generated a PCA plot of West Eurasians (with way too many pointless Bedouins and Jews, it must be said) and projected the ancient Europeans, as well as a whole bunch of Circum-Pacific peoples on it:
    The result is a bit weird because, as you can see, the East Asians, Native Americans and Melanesians appear to fall way too close to the peoples of the Caucasus and Anatolia. This seems to be a distorting effect of the “projection” method, which forces the projected samples to align relative to a set of already defined parameters, in this case the West Eurasian (modern) PCA. 
    So the projection basically formulates the question: if East Asians, etc. must be forcibly to be defined in West Eurasian (WEA) terms, what would they be? And then answers it as follows: Caucasian/Anatolian/Iranian peoples more or less (whatever the hidden reasons, which are not too clear).
    Similarly, it is possible (but uncertain) that the ancient European and Siberian sequences show some of this kind of distortion. However I have found experimentally that the PCA’s dimension 1 (but not the dimension 2, which corresponds largely to the Asian-specific distinctions) still correlates quite well with the results of other formal tests that the authors develop in the study and is therefore a valuable tool for visualization.
    But this later. By the moment the PCA is asking and answering three or four questions by projecting ancient European and Siberian samples in the West Eurasian plot:
    • If ancient Siberians are forced to be defined in modern WEA terms, what would they be? Answer: roughly Mordvins (Afontova Gora 2) or intermediate between these and North Caucasus peoples (Mal’ta 1).
    • If ancient Scandinavian hunter-gatherers are forced in modern WEA terms, what would they be? Answer: extreme but closest (Skoglund) to Northern European peoples like Icelanders or Lithuanians.
    • If ancient Western European hunter-gatherers are forced in modern WEA terms, what would they be? Answer: extreme too but closest (La Braña 2) to SW European peoples like Basques and Southern French.
    • If ancient Neolithic/Chalcolithic farmers from around the Alps and Sweden are forced in modern WEA terms, what would they be? Answer: Canarians (next close: Sardinians, then Spaniards).
    Whatever the case, there seems to be quite a bit of autosomal diversity among ancient Western hunter-gatherers, at the very least when compared with modern peoples. This makes some good sense because Europe was a big place already in Paleolithic times and must have harbored some notable diversity. Diversity that we may well find to grasp if we only sample people from the same areas once and again.
    On the other hand, they seem to cluster in the same extreme periphery of the European cluster, opposed to the position of West Asians, and therefore suggesting that there has been some West Asian genetic flow into Europe since then (something we all assume, of course). 
    Using Lochsbour as proxy for the WHG (Western hunter-gatherer) component, Mal’ta 1 as proxy for the ANE (ancient north Eurasian) one and Stuttgart as proxy for the EEF (early European farmer) one, they produce the following graph (to which I added an important note in gray):
    The note in gray is mine: highlighting the contradictory position where the other Western hunter-gatherers may fall in because of assuming Lochsbour as valid proxy, when it is clearly very extreme. This was not tested in the study so it is inferred from the PC1, which seems to best approach the results of their formal tests in the WHG vs EEF axis, as well as those of the WHG vs Near East comparisons.
    I tried to figure out how these formal tests are reflected, if at all in the PCA, mostly because the PCA is a much easier tool for comprehension, being so visual. Eventually I found that the dimension 1 (horizontal axis) is very close to the genetic distances measured by the formal tests (excepted those for the ANE component, obviously), allowing a visualization of some of the possible problems caused by their use of Lochsbour as only reference, without any control. Let’s see it:

    The same PCA as above with a few annotations in magenta and green
    While not exactly, the slashed vertical magenta line (median in the dimension 1 between Lochsbour and Stuttgart) approximates quite well the WHG vs EEF values measured in the formal tests. Similarly, the slashed green axis (median in PC1 between Lochsbour and an good looking Bedouin) approximates to a great extent the less precise results of the formal tests the authors applied to guesstimate the West Asian and WHG ancestry of EEFs, which ranged between 60% and almost 100% West Asian (my line is much closer to the 60% value, which seems more reasonable). 
    When I tried to find an alternative median WHG/West Asian line, using Braña 2 and the first non-Euro-drifted Turk I could spot (Anatolia is much more likely to be the direct source of West Asian ancestry in Europe than Bedouins), I got exactly the same result, so no need to plot any second option (two wrongs sometimes do make one right, it seems). But when I did the same with La Braña 2 and Stuttgart I got a genuine good-looking alternative median line, which is the slash-and-dot magenta axis.
    This alternative line is probably a much more reasonable 50% WHG-EEF approximation in fact and goes right through Spain, what makes good sense for all I know.
    Of course the ideal solution would be that someone performed good formal tests, similar to those done in the study, with Braña 2 and/or Skoglund, which should be more similar to the actual WHG ancestry of modern Europeans than the extremely divergent Lochsbour sequence. An obvious problem is that La Braña produced only very poor sequences but, well, use Skoglund instead or sample some Franco-Cantabrian or Iberian other Paleolithic remains.
    Whatever the solution, I think that we do have a problem with the use of Lochsbour as only WHG proxy and that it demands some counter-testing. 
    What about the ANE component? I do not dare to give any alternative opinion because I lack tools to counter-analyze it. What seems clear is that its influence on modern Europeans seems almost uniformly weak and that it can be ignored for the biggest part. As happens with the WHG, it’s quite possible that the ANE would be enhanced if the sequence from Afontova Gora is used instead of that of Mal’ta but I can’t foresee how much. 
    Finally some speculative food-for-thought. Again using the visual tool of the PCA, I spotted some curiosities:

    Speculative annotations on the PCA

    Most notably it is apparent that the two WHG populations (Western and Scandinavian) are aligned in natural axes, which seem to act as clusters. Extending both (dotted lines) they converge at a point closest to some French, notably the only “French” that tends towards “Southern France” and Basques. So I wonder: is it possible that these two WHG cluster-lines represent derived ancient branches from an original population of SW France. We know that since the LGM, the area of Dordogne (Perigord) was like the megapolis of Paleolithic Europe, with population densities that must have been several times those of other areas. We know that this region was at the origin of both Solutrean and Magdalenian cultures and probably still played an important role in the Epipaleolithic period. 
    So I do wonder: is that “knot” a mere artifact of a mediocre representation or is it something much more real? Only with due research in the Franco-Cantabrian region we will find out. 
     

    Basque and other European origins according to ancient mtDNA

    This is a (partly shortened) version of an article I wrote recently in Spanish language for Ama Ata.
    For reasons of the variegated methodology used by the various researchers this comparison across time and space has to be simplified. Still it is a valuable insight on the demographic changes produced in the Neolithic and later on in three European regions: Germany, Portugal and the Basque Country. 
    Germany
    As you surely know already, the results of archaeogenetic sequencing in Central Europe have produced quite perplexing results: not just the Neolithic wave seems to have caused major changes but also this one was victim of similarly radical later changes in the demography. Visually:

    The first period when we see an mtDNA pool similar to the modern one is already in the Late Bronze Age. However we lack data for all the early and middle Bronze Age and the data of the late Chalcolithic already points to the components of this modern pool being present, albeit in a very fragmented form. If anything there was still excess of L(xR), i.e. N(xR). 
    This late Chalcolithic and Bronze Age knot of Central European demographic history is still to be solved. But something we can already say for sure: the Neolithic wave was of dramatic consequences in this region but itself was wiped out by later, still ill understood, secondary waves.
    Portugal
    This area is not so well documented, however the data we do have still provide a very interesting sequence of the demographic history of SW or West Iberia. Visually again:

    One of the problems here is, quite evidently, that sequencing only the HVS-I region is not at all enough to identify some very important haplogroups, particularly H. We can reasonably think however that most or even all of the R* sequences are actually H.
    We see some but not-so-radical changes with the arrival of Neolithic: some apparent decrease of U (halved) and L(xR), a +33% growth of H and first detection of HV0 (probably V). However these changes seem to have been partly countered by Chalcolithic, plausibly by means of blending between first farmers and more purely aboriginal populations. Overall I am very much tempted to think that the arrival of Neolithic to (South and Central) Portugal only caused mild demic changes. 
    This fact, together with the extremely high frequencies of haplogroup H and the key role played by SW Iberia in the formation of Dolmenic Megalithism, as well as their pivotal role in Bell Beaker, including the existence of a major civilization (Zambujal, VNSP), the first one ever in Atlantic Europe, makes this area highly suspect as a possible origin for the spread of mtDNA H in Western Europe to the frequencies that we find today (c. 40-50%).
    However we have only very limited archaeogenetic data from other Atlantic Megalithic regions and in general from Megalithic burials and it is at least possible that Armorica (Brittany, West France) or Denmark and the nearby Low Germany regions played important roles in this spread, which we see so dramatically exemplified in the German Bell Beaker sample. 
    When the finger points to the Moon, the fool looks at the finger. Portugal could be the Moon but it may just be the finger, so I will remain cautious at this stage of research. Whatever the case it does seem to me that Megalithism is a likely source of that excess H (Bell Beaker being just the finger here, almost for sure).
    I must add that there seem to be some important demic changes since Chalcolithic in Portugal. Tentatively I will attribute them to the intrusive SW Iberian “horizons” (proto-Tartessian?) and/or the Luso-Celtic invasions of the Iron Age. 
    Basque Country
    My main aim in all this compilation was, as in a sense in all my diving into prehistoric research for so many years now, to find an answer to the mystery of the origin of Basques and Basque language. 
    In the last few years we have been blessed with some important and revealing archaeogenetic research in this area, and therefore I could build also an informative graph for the Basque Country:

    Very synthetically, I think that we can see here, much as in Portugal, some not too radical changes with the Neolithic arrival, and then relative stability until present day. This is coherent with the Basque Country not having suffered effective Indoeuropean invasions, unlike Portugal.
    However I strongly feel the need to look at the fine detail in the Basque Neolithic transition, because it has some interesting question marks:

    Seen as that, it would seem like the Neolithic-induced demic change was more important in Navarre and less in the Western Basque Country. However the two Ebro basin sequences (both Fuente Hoz and Los Cascajos) are very high in U* and low in U5, which is so far the only U subclade sequenced in the Paleolithic of the Basque-Cantabrian area. At this point I do not really know how to interpret this fact nor even what kind of U sublineage is that one.
    What I do know is that, on one side, the Biscay-Gipuzkoan area seems to have been initially unaffected by Neolithic demic waves and that the Paternabidea sequence is very very similar to modern day Basque average (and even more in its own sub-region).
    It is very possible that the Basque periphery, notably the Ebro banks, suffered more intense demic changes than the core Basque areas of the piedmont. However, when compared with other European regions (very especially Central Europe) the Basque genetic pool seems quite stable since Neolithic times. 
    Is Basque language Neolithic?
    Even if genetics and language need not to be tightly related, of course, the question of the origin of Basque language and the proposed Vasconic language family, believed to have been spoken in much of Europe at some point in Prehistory, are indeed related to the genetic origin of the Basque people. 
    There are four main models for the origin of Basque and Vasconic:
    1. Magdalenian (Paleolithic) origin in the Franco-Cantabrian region some 17-15,000 years ago (incl. possible sub-waves like Tardenoisian/geometric Epipaleolithic).
    2. Neolithic origin.
    3. Megalithic origin.
    4. More or less recent (Iron Age?) arrival, defended by mostly by the fanatics of Indoeuropean continuity. 
    We can safely discard #4 only based on archaeology but the genetic aspect seems to add even more weight to this dismissal, after all it is Indoeuropean speaking peoples the ones which show obvious signs of demic change, sometimes very dramatic, not Basques.
    Personally, and with due caution, I would also cast doubt on #1, partly because the Vasconic substrate area seems to include strongly many parts of Italy like Sardinia, in principle unaffected by the Magdalenian expansion, and I would also include at least to some extent parts of the Balcans (for example the Ibar river in Kosovo). 
    So I am rather inclined for model #2, i.e. that Vasconic was the language family spoken by European Neolithic peoples with roots in Thessaly (pre-Sesklo→Mediterranean Neolithic, proto-Sesklo→Balcano-Danubian Neolithic). I cannot of course exclude a possible re-expansion of some of those languages within the Atlantic Megalithic phenomenon, which I would deem responsible of the expansion of much of mtDNA H up to modern frequencies, however I doubt this one is the source because it is difficult to explain the presence of Vasconic in many pockets in which Megalithism was at best very secondary or did not exist at all (for example most of the Ancient Iberian area, Sardinia, the Balcans, etc.)
    So my tentative proposal is that there was a root Vasconic spoken some 9000 years ago in Thessaly (Northern Greece), which split (as per archaeology) in two branches:
    • Southern or Western Vasconic (Impressed-Cardium Pottery and related cultures, including the Megalithic urheimat in Portugal). 
    • Northern or Eastern Vasconic (Red-White Painted Ware in the Balcans and later Linear Pottery in Central Europe).
    Basque, ancient Sardinian, Iberian and the hypothetical lingua franca associated to Megalithism would belong to Southern Vasconic. Danubian Neolithic peoples would have spoken Northern Vasconic instead but, as we can see, they were eventually all but wiped out by secondary arrivals from West and East. Even the very Balcanic core areas of Thessaly, Macedonia and Serbia also suffered an invasion early on by peoples with Beige-Black pottery (Vinca-Dimini) surely related to Tell Halaf. So the main survivor to the Metal Ages was Southern (Western) Vasconic, which was then wiped out (excepted Basque) by the Indoeuropean invasions of Celtic and Italic peoples. 
    We can still see fossils however. One of my favorite examples is the Latin particle bi- (as in bilateral, bilingual, etc.), which seems derived from Vasconic bi (two, at least in modern Basque) and unrelated to PIE *dwos. Also the English words kill and ill, which seem related to Basque verb hil(-du) (pronounced /hill/ or /ill/ and meaning to die or to kill, depending on how you conjugate it). Again both English terms do not have any apparent PIE origins, although they may derive from proto-Germanic. These are just examples, of course, there seems to be much more to be researched.
    Appendix: detail of the data and bibliography: LINK.
     
     
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