RSS

Category Archives: Neolithic

SW African Bantu matrilineages

Prolific researcher Chiara Barbieri has put online another interesting study on African genetics, this time about the Bantu populations of Southwestern and Central-Southern Africa (i.e. Namibia, Angola, Botswana and Zambia).
Chiara Barbieri et al., Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa. bioRXiv 2014. Freely accessible (pre-pub) → LINK

ABSTRACT

Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift and differential female admixture with local pre-Bantu populations.

Figure 1: Map showing the rough geographical location of populations, 
colored by linguistic affiliation. Abbreviations of population labels are 
as specified in Table 1.

In spite of the Bantu-centric approach of the study, which also has its merits, my greatest interest is rather in the less typically Bantu lineages, which speak of admixture with several pre-Bantu populations.
In this sense I find the following highlights:

Fig. S2 (annotated in green by Maju): CA plots based on haplogroup frequencies. Left: all the dataset, right: excluding outliers.

L3d and L3f founder effect:
The Himba and Herero, as well as the non-Bantu pastoralists Damara make one distinctive cluster defined by the high frequencies of haplogroup L3d, as well as L3f (not present among the Damara but found among the Kuvale). As discussed in the paper, the Himba and Herero may be related to the Kuvale of SW Angola but they have notable differential levels (or directionality) of aboriginal admixture. 
As both L3d and L3f are present in West and East Africa alike, it is interesting to track the specific subhaplogroups implicated in this founder effect, something done in fig. 4. 
The main L3d sublineage is L3d3a1, whose haplotype network shows a largely Khoisan centrality (not Damara) although this node is shared also by some unspecified “other Bantu”. The Southern Africa specificity of L3d3a was already noticed in the past (see here). So it is very possible that we are before an aboriginal Southern African lineage, maybe arrived with the first Khoisan Neolithic (or whatever other ancient flow) rather than a Bantu-specific founder effect. 
The main L3f subhaplogroup is L3f1b4a, which seems more specifically Bantu, with a major branch concentrated among the Himba, Herero and Kuvale. This lineage is not found among the Damara in spite of the other strong affinity of this Khoisan population towards the Himba and Herero. L3f1b is found in Southern Africa, Kenya and Oman (per Bihar 2008), so we are probably before a distinctive East African element, not too likely to be genuinely Bantu but possibly just assimilated into Bantu ethnic identity. 
Even if both lineages converge in the Himba and Herero, they are almost certainly different inputs, one of Damara (herder Khoisan) origin and the other of Bantuized East African origin maybe.
L1b founder effect:
L1b is essentially a West African lineage concentrated in the Sahel area from Chad westwards (although L1b1a2 is from the Nile basin). A particularly high frequency population are the Fulani pastoralists, original from the Westernmost African plateaus, who ruled many kingdoms in West Africa between the collapse of the colonial rule by Morocco and the consolidation of the European conquest of the continent.
As this study does not dwell in sublineages, we cannot understand the most likely specific origins of it among several Southern African populations, specifically the pooled NE Zambians (13%) and the Fwe and Shanjo of SW Zambia (24-27%).
In any case it is a notorious founder effect, almost absent in other Bantus of the area (0-10%).
Typical L0d Khoisan admixture:
This element is concentrated in Botswana (~25%) and with highest frequencies in the SW Kgalagadi (53%). It is also important among the Kuvale of SW Angola (21%). Other Bantu populations in this dataset have frequencies under 10%, some even zero. The Damara have 13%.
We know from previous studies that it is also found at high frequencies among the Xosha of South Africa (L0d3).
While L3h appears marked in the graph, the lineage is in fact absent in all populations except at very low frequency among the Kuvale (2%), so it does not seem actually of any relevance. 
Less typical L0k around SW Zambia:
While L0k is generally considered an aboriginal Southern African lineage it has a much more northernly distribution than the more common and surely older L0d. Its area of greatest commonality seems to be SW Zambia (see here and here).
This study confirms this distribution:

Supplementary Figure S3[A]: Haplogroup frequencies of important haplogroups in the populations studied here. A: Haplogroups L0d and L0k.(…)

The size of the circles is proportional to the sample size.

High frequencies of L1c (Pygmy admixture marker) among Southern African Bantus:
An interesting element is the commonality of L1c, typical of Western Pygmies and some other populations from Gabon (possibly representative of the wider West-Central Africa jungle region, not too well studied otherwise), among almost all Bantu populations in this dataset. 
The exceptions are the Herero, Himba, Kgalagadi and Tswana (0%), as well as the NE Zambians (4%). All the rest have frequencies between 12% and 30%. Even the non-Bantu Damaras have 11% of it.
In my understanding this almost certainly implies a notable level of admixture with Western Pygmies of the Bantus from especially Angola and West Zambia. A phenomenon that may be widespread in Central-West Africa. 
It is notable however that at least many of the populations with the highest likely Khoisan admixture (in its various forms, discussed in the previous sections) have the lesser frequencies of L1c (Pygmy admixture). So to a great extent these two aboriginal influences in Bantu mtDNA seem mutually exclusive and were probably produced after settlement rather than “on the march”. 
This in turn arises some interesting questions about the ethnic geography of Africa before the Bantu expansion. 

Update: I just noticed that Ethiohelix has parsed the haplogroups’ frequency into a very helpful chartLINK.

See also:
Advertisements
 

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:
 

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. 
 

Ancient East Asian Y-DNA maps

I’m fusing here data from two different and complementary sources:
  • Hui Li et al. Y chromosomes of prehistoric people along the Yangtze River. Human Genetics 2007. → LINK (PDF) [doi:10.1007/s00439-007-0407-2]
  • A 2012 study integrally in Chinese (so integrally that I don’t even know who the authors are → LINK) but whose content was discussed in English (after synthetic translation) at Eurogenes blog. I deals with a variety of ancient Y-DNA from the Northern parts of P.R. China.

Update (Dec 25): much of the Northeastern aDNA is also discussed in an English language study (h/t Kristiina):

Yinqiu Cui et al. Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. BMC 2013. Open access LINK [doi:10.1186/1471-2148-13-216]

    Combining the data from both sources, I produced the following maps:

    Neolithic (before ~4000 BP):

    Metal Ages (after ~4000 BP):

    Discussion
    I find particularly interesting the first map because it outlines what seem to be three distinct ethnic (or at the very least genetic) regions in the Neolithic period:
    • A Central-South region dominated by O3
    • An Eastern area around modern Shanghai dominated by O1
    • A Northern region dominated by N
    Later on, in the Metal Ages, a colonization of the North/NE by these O3 peoples seems apparent, followed, probably at a later time, by a colonization of the West (Taojiazhai).
    We do not have so ancient data for the West but we can still see a diversity of lineages, notably Q (largely Q1, if not all), C (most likely C3, also in the NE) and N (also in the NE). While the arrival of O3 to this area was probably late, the arrival of R1a1a is quite old, however it is still almost certainly related to the first Indoeuropean migrations eastwards, which founded the Afanasevo culture in the area of Altai.
    I find also very interesting the presence, with local dominance often, of N (including an instance of N1c) and Q in the Northern parts of P.R. China, because these lineages are now rather uncommon but are still dominant in Northern Asia, Northeastern Europe and Native America. The fact that they were still so important in the Northern Chinese frontier in the Neolithic and even in the Metal Ages should tell us something about their respective histories and, in the case of N, origins as well.
    It is also notable that no D was detected anywhere. However the regions with greatest D frequencies like Tibet, Yunnan or Japan were not studied.
     
    9 Comments

    Posted by on December 15, 2013 in aDNA, Bronze Age, China, East Asia, Iron Age, Neolithic, Y-DNA

     

    Rhône-Provence Bell Beaker

    Just a brief note on two French language papers from a decade ago that have shown up in my academia.edu alerts.
    The most relevant one because of its wider scope is:
    Olivier Lemercier, Muriel Pellissier & Yaramila Tchérémissinoff, Campaniforme et sépultures, au-delà du standard. La place du Campaniforme dans l évolution des sépultures du sud-est de la France au 3e millénaire avant notre ère. Proceedings of the International Conference held at the Cantonal Archaeology Museum (Sion, Switzerland), 2001. → available (with free registration) at academia.edu.

    Abstract (only part in English)


    Where are the famous Bell Beaker individual burials in the south east of France? What is the nature of the burials wherein we actually find Bell Beaker elements ? And what kind of Bell Beaker is it ? And also : where does the Bell Beakers stand in the evolution of the funeral architectures and rites between the end of the Middle Neolithic and the Early Bronze Age? Answering these questions, thanks to the presence of more than a hundred funeral sites in the area, would change our vision of the Bell Beakers fenomenon itself. These questions are also the occasion to present the diversity and the traditions of the funeral practices by the 3rd millenium BC.

    I took some time to read it in spite of my limited skills at French (but it’s still Romance, so well… any educated Romance speaker can read it with some effort) and the overall conclusions are not too surprising: Bell Beaker is not only a burial thing, Bell Beaker appears in burial contexts of older local tradition, etc. 
    The details and nuances are many more, of course. On one side the authors discern (much as it happens overall within European Bell Beaker) three groupings: 
    • Corded style in Ardèche
    • International style in the left margins of the Rhône
    • A local variant in the later period
    Notice that the authors argue that both the Corded and International styles are roughly contemporary. I can’t judge this but, if real, it may mean a blow against the classical notion of Corded style being older and arriving to SW Europe via the Rhône. 
    Another interesting aspect of the paper is that the authors argue for overall continuity of burial styles, which are varied:
    • individual burials with roots in early Neolithic
    • collective burials of both dolmenic-megalithic and cave typology
    • other rarer types, with a handful of examples each
    Bell Beaker seems mostly related to collective burials, although in the BB period Megalithism seems to recede somewhat in favor of collective burials in caves, a tradition common in other parts of Europe, especially in the South and SW. This really casts all kind of doubts about BB in this region being able to be explained as some sort of migration from Central Europe (or anywhere else) because, unlike in this Indoeuropeanized area, BB individual burials as such are extremely rare; instead we must talk of BB elements inserted in local traditions of collective or “clannish” nature, just as we can see in Iberia and other Western areas where Indoeuropean influences was still non-existent. 
    The other paper is:
    Robin Furestier et al., 1974-2004 le site du Fortin-du-Saut (Châteauneuf-les-Martigues, Bouches-du-Rhône) et le Campaniforme 30 ans aprés. Congrès du Centennaire: Un siècle de construction du discours scientifique en Préhistoireavailable at academia.edu (registration needed as well).
    This is about a particular Bell Beaker site near Marseilles, whose typology seems mostly influenced by the Portuguese VNSP civilizational center. Otherwise there is other non-BB pottery without decoration and what seems locally rooted stone tools and arrow points.
    If you are fluent in French and happen to find out any error in my interpretation, please feel free to correct me in comments, thanks in advance.