France's autosomal genetics highlight Gascon-Basque distinctive cluster

A rather decent analysis of French autosomal genetics has been privately pre-published recently (thanks to Jean Secques for calling my attention to it and to the lead author for making it available online). 

Aude Saint Pierre et al. The fine-scale genetic structure of the French population. Submitted to the American Journal of Human Genetics in 2015. Freely accessible → ref. LINK, direct PDF link.

A highlight of the study is that the samples all belong to people born in the 1930s and locations refer to their place of birth, so the results should be reflecting the historical demographics of the French Republic in the early 20th century. 

There are no supplemental materials available at this point, so it's only possible to get a glimpse of the general results and we can't go too much into fine detail. These general results are anyhow interesting. Let's see:

Figure 6: Prediction of geographic location of individuals from the test set (n=3,733) using multiple linear regression model. A) Expectation: The seven geographical regions of France according to the geographical coordinates of individuals in the test sample; B) Prediction of geographical coordinates according to the multiple linear regression model.

This figure alone synthesizes the findings: most French citizens cluster in a single unit, which geographically would correspond to NE France (GE region), only SW French (Gascons and Basques mostly) deviate very clearly and roughly fit their own geography towards the Bay of Biscay (or Bay of Gascony, as the French call it). Some samples from the SE (MED and RA regions) also follow this trend. A few outlier samples from the East (GE, RA) look rather Rhenish German, although the lack of controls from outside the Hexagon does not allow me to confirm this appearance. 

You may have noticed that I ignored the IDF samples but that is because it is the Paris region (Île-de-France), which was already back in the 1930s too cosmopolitan to be informative. That is of course reflected in all the results with "orange" dots being nearly of all affinities. 

Follow the principal component analyses, whose more salient information is again the peculiarity of Southwesterners, i.e. Gascons, Basques, and nearby populations.

Figure 2: The scatter plot of the first three PCs from PCA performed on the SNP
genotype data of the 4,433 individuals from the 3 Cities study. Individuals are coloured
according to the region where they were born. (Note: the legend corresponds to both PCAs)

Other than the "Gascon" specificity, which takes over PC1, I'd say that PC2 shows an "anti-Mediterranean" tendency and that PC3 instead shows a "pro-Mediterranean" tendency. This I gather from the relative position of the "red" MED cluster. They both weight the same.

Interestingly there is a prominence of the GO region (Mid-West between the Seine and the Garonne) which may indicate some sort of "Armorican" or "Briton-like" specificity. In appearance it could melt both the "pro-" and "anti-Mediterranean" tendencies but without being able to discern the particular dots (ID and location), I cannot swear for that. 

Much more clear is the "anti-Mediterranean" tendency of Gascons, Basques and allies when they are strongly detached from the main French cluster and instead they show a "pro-Mediterranean" tendency, overlapping at the extreme with the MED cluster, the closer they are to mainstream French. This happens in both PC2 and PC3. 

Little more to say, honestly. Maybe that the small Eastern group of outliers prominent in "anti-Mediterranean" tendency in PC2 probably corresponds pretty well with the outliers of the first graph, which looked German-like. So I guess that the positive side of PC2 probably corresponds with a Northern European tendency.

Interested on what you have to say on this one very particularly, reader.

European cows: overall Neolithic genesis and its sophisticated management in the Scandinavian frontier

Quantity over quality series.

These are two different papers but both deal with European bovine cattle in the Neolithic, hence the bundle.

Amelie Schleu et al. The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genetics 2015. Open access → LINK [doi:10.1186/s12863-015-0203-2]

Abstract

Background

Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication.

Results

Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE.

Conclusions

The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

Jurt J. Gron et al., Cattle Management for Dairying in Scandinavia’s Earliest Neolithic. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0131267]

Abstract

New evidence for cattle husbandry practices during the earliest period of the southern Scandinavian Neolithic indicates multiple birth seasons and dairying from its start. Sequential sampling of tooth enamel carbonate carbon and oxygen isotope ratio analyses and strontium isotopic provenancing indicate more than one season of birth in locally reared cattle at the earliest Neolithic Funnel Beaker (EN I TRB, 3950-3500 cal. B.C.) site of Almhov in Scania, Sweden. The main purpose for which cattle are manipulated to give birth in more than one season is to prolong lactation for the production of milk and dairy-based products. As this is a difficult, intensive, and time-consuming strategy, these data demonstrate complex farming practices by early Neolithic farmers. This result offers strong support for immigration-based explanations of agricultural origins in southern Scandinavia on the grounds that such a specialised skill set cannot represent the piecemeal incorporation of agricultural techniques into an existing hunter-gatherer-fisher economy.

Sudan and South Sudan autosomal genetics

Quantity over quality series.

Begoña Dobon et al., The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Nature - Scientific Reports 2015. Open access → LINK [doi:10.1038/srep09996]

Abstract

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

Figure 3: ADMIXTURE results for the 14 populations.

Ancient mtDNA from Romania

Quantity over quality series.

Montserrat Hervella et al. Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0128810]

Abstract

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.

Table 2. Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.

Please notice that, contrary to what the abstract says, I do not consider that Boian-Maritza and derived cultures belong to any second wave from Anatolia but rather to the wider Danubian (LBK-derived) Central European macro-culture. There was indeed a second wave from Anatolia (Halaf-related, it seems) but it mostly affected Greece, Macedonia and Serbia (Vinca, Dimini and related cultures). It briefly affected Bulgaria and Wallachia as well but this Danubian Boian-Maritza wave from the North neutralized its influence. 

Gumelnita (Karanovo-Gumelnita) culture is particularly remarkable as civilization center of ancient Europe before the Kurgan (Indoeuropean) invasions. They were strongly involved in the earliest development of bronze metallurgy known to date (oddly enough considered "late Neolithic" in this study).

Rather than thinking that these cultures (Boian →→ Gumelnita) had a major effect on European genetics, I'd say that they reflect greater degree of "Europeanization", if anything. Anyhow the key marker here is (as usual) mtDNA H but in no case (except one Late Bronze individual) is H1, so we are rather talking of other less influential sublineages.

Pondering the Middle Paleolithic of South Africa

Quantity over quality series.

Sylvain Soriano et al. The Still Bay and Howiesons Poort at Sibudu and Blombos: Understanding Middle Stone Age Technologies. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0131127]

Abstract

The classification of archaeological assemblages in the Middle Stone Age of South Africa in terms of diversity and temporal continuity has significant implications with respect to recent cultural evolutionary models which propose either gradual accumulation or discontinuous, episodic processes for the emergence and diffusion of cultural traits. We present the results of a systematic technological and typological analysis of the Still Bay assemblages from Sibudu and Blombos. A similar approach is used in the analysis of the Howiesons Poort (HP) assemblages from Sibudu seen in comparison with broadly contemporaneous assemblages from Rose Cottage and Klasies River Cave 1A. Using our own and published data from other sites we report on the diversity between stone artifact assemblages and discuss to what extent they can be grouped into homogeneous lithic sets. The gradual evolution of debitage techniques within the Howiesons Poort sequence with a progressive abandonment of the HP technological style argues against the saltational model for its disappearance while the technological differences between the Sibudu and Blombos Still Bay artifacts considerably weaken an interpretation of similarities between the assemblages and their grouping into the same cultural unit. Limited sampling of a fragmented record may explain why simple models of cultural evolution do not seem to apply to a complex reality.

Ket genetics: strong "ANE" and a paleo-Eskimo link

Quantity over quality series.

Pavel Flegontov et al. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. BioRxiv 2015 (pre-pub). Freely accessible → LINK [doi: http://dx.doi.org/10.1101/024554]

Abstract

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, determined mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that the Kets belong to the cluster of Siberian populations related to Paleo-Eskimos. Unlike other members of this cluster (Nganasans, Ulchi, Yukaghirs, and Evens), Kets and closely related Selkups have a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.

Tarim Basin mtDNA

Quantity over quality series.

Chuxian Li et al. Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China. BMC Genetics 2015. Open access → LINK. [doi:10.1186/s12863-015-0237-5]

Abstract

Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

Note: R* is not "Western" but undefined and quite possibly Eastern.

Quantity, quality and mood.

As you surely have noticed, I'm not anymore writing even a fraction of what I used to. Largely this owes to my own mood but also to the time that requires doing things properly (a good article takes between half to two 8-hrs workdays, not counting the time invested in general information). As result I have accumulated a huge list of "to do" bookmarks, many of which I will never address at all. 

In fact you can follow some of the stuff I read and never get to comment in this bilingual prehistory Google group. 

However I do want to at least briefly comment some of the latest stuff, taking advantage of my impulsiveness. So I will make a series of short entries, priming quantity over quality, so readers can get at least some basic info. This will be today and I don't promise anything for tomorrow.

Honestly, some days I feel that my productivity has become so low that I could well close shop. Other days I feel like trying to get the blog back on its feet but admittedly these are the rarer ones.

Weed evolution in the context of earliest proto-farming in Palestine

Ohalo II, at (often under) the Sea of Galilee, is probably the oldest site of sedentary proto-farming, dating to before the Last Glacial Maximum, experiment that may have been interrupted afterwards. A new study finds the first signals of not just many edible plants that would eventually become crops but also the signature of evolution of weeds already towards the forms we are familiar with nowadays.

A. Snir et al., The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0131422]

Abstract

Weeds are currently present in a wide range of ecosystems worldwide. Although the beginning of their evolution is largely unknown, researchers assumed that they developed in tandem with cultivation since the appearance of agricultural habitats some 12,000 years ago. These rapidly-evolving plants invaded the human disturbed areas and thrived in the new habitat. Here we present unprecedented new findings of the presence of “proto-weeds” and small-scale trial cultivation in Ohalo II, a 23,000-year-old hunter-gatherers' sedentary camp on the shore of the Sea of Galilee, Israel. We examined the plant remains retrieved from the site (ca. 150,000 specimens), placing particular emphasis on the search for evidence of plant cultivation by Ohalo II people and the presence of weed species. The archaeobotanically-rich plant assemblage demonstrates extensive human gathering of over 140 plant species and food preparation by grinding wild wheat and barley. Among these, we identified 13 well-known current weeds mixed with numerous seeds of wild emmer, barley, and oat. This collection provides the earliest evidence of a human-disturbed environment—at least 11 millennia before the onset of agriculture—that provided the conditions for the development of "proto-weeds", a prerequisite for weed evolution. Finally, we suggest that their presence indicates the earliest, small-scale attempt to cultivate wild cereals seen in the archaeological record.

Large monolith found underwater near Pantellaria (Sicily)

A large human-made monolith has been discovered underwater in the Pantellaria shoal, submerged since the end of the Ice Age.

E. Lodolo & Z. Ben-Avraham. A submerged monolith in the Sicilian Channel (central Mediterranean Sea): Evidence for Mesolithic human activity. Journal of Archaeological Science, 2015. Freely accessible → LINK [doi:10.1016/j.jasrep.2015.07.003]

Other source: Pileta de Prehistoria. 

While it is hard to argue that the monolith is not man-made, as it has three holes of the same size in non-random positions, I would take with a pinch of salt the claim that the would-be standing stone or menhir has been there since the 10th millennium BCE, when the shoal was flooded by seawater. 

Instead I would consider the following scenarios as plausible:

1. The land could have been at higher absolute altitude in the past and sunk because of local techtonics. It is, we must not forget, a very active geological area.
2. The monolith could have just sunk when being transported on a ship of some sort between islands. The ship, made of wood and ropes would leave no obvious trace.

So I'd rather imagine the stone to have been produced in the Chalcolithic Megalithic context that has some relevance in the area, very especially the fascinating case of Maltese Megalithism, which spans between 3600 and 700 BCE.