Scandinavian hunter-gatherers had double west-east origins

SHG origins' mystery solved? What about possible Norwegian "EHG-like" genetic influences into Atlantic Europe?

Torsten Günther, Helena Malmström, Emma Svensson, Ayça Omrak et al. Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation. bioRXiv 2017 (pre-pub). DOI:10.1101/164400

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

Fig. 1:

Mesolithic samples and their genetic affinities – (A) Map of the Mesolithic European samples used in this study. The pie charts show the model-based [16,17] estimates of genetic ancestry for each SHG individual. The map also displays the ice sheet covering Scandinavia 10,000 BP (most credible (solid line) and maximum extend (dashed line) following [10]). Newly sequenced sites are shown in bold and italics, SF11 is excluded from this map due to its low coverage (0.1x). Additional European EHG and WHG individuals used in this study derive from sites outside this map (...)

Intriguingly, Swedish Epipaleolithic peoples (SHG) have the light skin variant in the gene SLC45A2, variant that is now uniformly spread through all Europe and accounts for 15% of the skin color variance in a key Cape Verde study and that was so far attributed solely (or almost solely) to Neolithic farmers (among which it was fixated and who had indeed a very large genetic impact in the European subcontinent). They also have the blue eyes allele, as Western Hunter-Gatherers did. However, if we are to follow, Günther's explanations in this video, the variance of looks in Epipaleolithic Scandinavia was greater than in present day. 

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PS- Legend says that when my namesake Fray Luis de León returned to his classroom after five years imprisoned by the Inquisition, he began his class with these words: "As we were saying yesterday..."

Expect less lengthy articles because I really want to use this blog as open notebook, and not spend so much time following news and dissecting them thoroughly, so my style may become a bit more telegraphic. 

I also don't know for how long I will be able to continue blogging, as my personal economic situation is bad and worsening and you never know when police may come and arrest you for saying "fuck the king" or whatever other quite reasonable opinion. We live very troubled times and I'm personally quite bad at winning.

Also my apologies in advance if I fail to quickly approve comments. I usually check my email once per day or so but sometimes I just forget. Please, be patient if that happens: I only censor fascism, racism, sexism and homophobia (and those individuals who have managed to really get on my nerves, and they know who they are). Sadly I have to keep pre-moderating all comments, else the lonely troll will get away with his abuses.

Gobero (Green Sahara key site) documentary

This site of Gobero (Niger) was news in the archaeology and anthropology circles a few years ago and today I stumbled on this quite nice video documentary on it that I believe will be of interest for many readers:

Amesbury has Epipaleolithic roots

Old map of Avesbury and the nearby hillfort

Recent field work at the town of Amesbury, specifically in Blink Meadow, has resulted in it being proclaimed in the media as "the oldest town in Britain". What it really means is that the site was occupied and had ritual significance before the Neolithic, since c. 8820 BP.

A possible reason for the magnetism of this location is that a nearby spring has the "magical" effect of turning some types of flint to a bright pink or fuchsia color. This is caused by certain algae but it must have appeared miraculous to ancient peoples. 

The district now proclaimed oldest continuously inhabited town in Britain has a large complex of ritual sites dating to the Chalcolithic period ("Neolithic" in British archaeo-slang).

It also includes a large Iron Age hillfort of unusual shape, inadequately named as "Vespasian's Camp". This fort which continued in use in the Roman period is suspected by many to be the real Camelot.

Pink colored flint pieces from Amesbury

Sources and more details: The Archaeology News Network, Express.

Lochsbour's IBD in modern Europeans is greatest among Danish but most direct among French

This is a most interesting issue I forgot to discuss when previously addressing the massively interesting Lazaridis et al. study on European ancestry based on ancient autosomal DNA (see here and here). 

Identity by descent (IBD) data shows interesting differences between populations in Supplemental Information's article 18. While Stuttgart's (early farmer) ancestry is more or less the same by both measures (Sardinians first, followed by Slovakians and some other Balcanic and Central European populations), there are important differences in the ancestry of Lochsbour (Epipaleolithic hunter-gatherer from Luxembourg). While the Danes score highest in overall IBD block number (rough relatedness to Lochsbour) it is the French who score highest in IBD length (indicating a more direct relatedness, even if in smaller amounts). 

The difference between the French and Danish is quite significant, I believe, and seems to suggest that Lochsbour's relatives had a direct impact on modern French genetics, while the impact of Lochsbour as such on other populations should be considered more indirect (i.e. via other hunter-gatherer populations). 

This implies that there was some important diversity among the hunter-gatherer groups that influenced modern European genetics and that Lochsbour must be considered a mere generic proxy. Possibly if Motala or La Braña would have been used as reference instead, we would get some important differences in the results, as would be the case if Balcanic or Eastern European hunter-gatherers would be thrown into the equation, no doubt. 

You may have noticed that there are some notable samples unmarked in the graphs, that's because they are colonial populations such as Zimbabwean or North American Whites, whose exact ancestry is not easy to track. The green and red texts are my illustrative additions.

While not marked, I find also notable and rather perplexing that Lebanon shows up as the fourth non-colonial population more related to Lochsbour by IBD length, after Scotland but before Ukraine, the Netherlands and Sweden.

In any case you can parse the data for the 10 more notable samples of each measure in the supplemental material, chapter 18.

Referenced study:

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. BioArxiv 2013 (preprint). Freely accessible → LINK [doi:10.1101/001552]

Revised Lazaridis study on ancient ancestry of Europeans

The already famous Lazaridis et al. study on the contribution of various ancient populations to modern European genetics has gone through a revision which does not alter the fundamental conclusions reached in the past but does add some interesting nuances, new graphs and some new data.

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. BioArxiv 2013 (preprint). Freely accessible → LINK (last version) [doi:10.1101/001552]

Most up to date supplementary info → LINK

For background see this previous entry.

Scandinavian hunter-gatherers deviate towards Siberia

Among the new data (or maybe data I skipped in the first read?) is the fact that the ancient Epipaleolithic individuals from Motala (Sweden) deviate towards Mal'ta-1 (Siberia), something that neither Lochsbour (representing Western hunter-gatherers) nor Stuttgart (representing early farmers) do.

This implies that there were already some differences in the Epipaleolithic era among European hunter-gatherers, with those of Magdalenian background lacking the Siberian (ANE) component, which is found however in Scandinavian ones (of Ahrensburgian background?) This may help explaining the extra ANE affinity in Northwest Europe, which is otherwise hard to understand. 

It also suggests that Eastern European hunter-gatherers were already in the Epipaleolithic more akin to Siberian ones than those from the West and South of the subcontinent, as well as those from West Asia (otherwise Stuttgart, which has partial West Asian ancestry would show increased affinity). Of course this can only be confirmed by direct analysis of Eastern European Paleolithic remains but seems quite likely in any case.

Principal component analyses (lots of them!)

Ancient samples projected on the global PCA:

Fig S1-10: projection of ancient samples onto global PCA dimensions 1 & 2

In this global PCA, EEFs overlap well with the reduced modern European sample (Basques and Sardinians only) and the West Asian one (Georgian, Palestinian Bedouins). However projected hunter-gatherers from Europe and Siberia show a clear "other Asian" deviation. Why? For the very same reason that South Asians and Melanesians do, even if they are clearly distinct populations: because the frame gives them no other choice: they are not quite like modern Europeans and they do not have any African tendency either, so the other populations that are somewhat akin to them are other Asians and there they go. 

That's why PCAs must always be taken with a preventive dose of salt: they are very nice visualization tools but they depend too much on the sampling strategy and its intrisical bidimensional limitations. 

Modern West Eurasians projected to a PCA of three ancient samples:

Fig. S10-3 Projection of West Eurasian populations onto the first two principal components
inferred using Loschbour, Stuttgart, and MA1 (full version).

Quite curious: all West Eurasians cluster tightly in comparison to their ancient "ancestors". It is likely that dimension 2 should be scaled down because the second component is always smaller than the first one (often around half). However I could not find a clear datum to proceed so I retained the original equal scale even if it can be a bit misleading. 

While not exactly, Lochsbour and Stuttgart explain the bulk of European (and West Eurasian!) ancestry, at least in comparison to the quite outlying Mal'ta-1 sample, representing ancient Siberians. 

Detail (zoom in) of this PCA:

Fig. S10-4 (I annotated the three ancestral tendencies with arrows for easy of view)

As expected Eastern/SE populations deviate more towards Stuttgart, Western/NW do towards Lochsbour and in general Northern populations deviate slightly towards Mal'ta, also in West Asia (i.e. Iranians, Turks).

Modern European PCA with ancient samples projected on it:

Figure S10.5: Projection of ancient samples onto the “European” PCA (annotations in gray are mine)

Something the authors notice is that their PCA does not approximate a map of Europe, as happens in some cases. They dedicate some time to evaluate this discrepancy, comparing with the PCA of Novembre et al. 2008. The differences are caused because the latter used many more NW and Central European samples and instead had way too little Eastern European ones. 

This highlights that sampling strategy is of utmost importance when analyzing autosomal DNA, not just in PCAs because oversampled populations would tend to cope the axes (or components). This should be obvious but is way too often ignored, what may result in spectacular magic hat tricks but hampers serious science. 

This is one of the reasons why I do not trust too much autosomal DNA analysis: lack of the fundamental rigor. This is of course not a defect in this particular study but it happens often in many others, scholarly and amateur alike. 

The authors believe that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW⁸, something that is consistent with their ancient admixture findings elsewhere in the study. 

FineStructure PCA output

A key point in this study is that only Sardinians and Basques can be modeled as simple EEF-WHG admixture, all the rest of Europeans needing of the MA1 component to be explained. This is much easier to visualize in the following graph.

We also processed the ChromoPainter/ChromoCombine output with fineSTRUCTURE1 using 250,000 burnin and 2,500,000 runtime MCMC iterations. Fig. S19.2 shows a Principal Components Analysis by fineSTRUCTURE which strongly resembles that of Fig. 1B.

Fig. S19-2 (annotated in gray by me)

Here we can see that only Sardinians (and quite insistently Canarians), Basques and some populations related to these (North Iberians, South French) are actually close to the Stuttgart-Lochsbour axis. All the rest need a third ancestry for explanation, which is approximated by MA1 (not plotted but whose tendency I annotated).

Notice that in this case the two ancient samples are not projected, as in the previous graphs but actually computed as part of the wider West Eurasian population.

This does not deny that other NE European populations have greater affinity to Lochsbour (fig S19-3) but it seems clear that this affinity must be mediated by another branch of ancient European hunter-gatherers, one that existed in Eastern Europe, rather than in the West, and that it had more ancient Siberian (MA1) affinity. It is also likely that this Eastern European aboriginal population was the one which brought the extra MA1 affinity to the rest of Europe, most likely in the context of Indoeuropean (Kurgan) migrations. Along with it they probably also brought extra WHG-like admixture (but actually from an Eastern European source).

The extra MA1 tendency is also present in West Asia. This may have two alternative or complementary explanations:

1. There have been also significant Siberian-like intrusions in West Asia after the Neolithic.
2. This extra ancient Siberian affinity is in fact (largely?) pre-Neolithic but the founder population of West Asian roots which triggered the European Neolithic in Thessaly was particularly removed from this admixture and more akin to Palestinians or peninsular Arabs than to other West Asians.

Sicilians, Maltese and Ashkenazi Jews are different

These three are the only European populations which have a poor fit with the triple admixture model (EFF+WHG+ANE), suggesting that they have fourth party inputs, most likely extra admixture from West Asia. 

This is apparent in the previous graph too (among several).

Tree modeling for the origins of the ancestral populations

From fig. S16-2 (allowing for five admixture edges)

From fig. 16-4 (full-genome coverage, allowing for 5 admixture edges and using Dai instead of Onge)

The basic topology of the tree is consistent (excepted the partial change of the location of Karitiana Native Americans, which depends on the greater affinity of the East Asian sample used and is essentially neutralized by the admixture edge with Onge or Ma1 respectively). The main admixture events are:

1. The Karitiana (and Amerindians by extension) are clearly a mix of East Asians plus Ancient Siberians of Western affinity (MA1), which is represented differently in both trees.
2. Early European Farmers (Stuttgart, Iceman) have clear "Basal Eurasian" admixture (which can be interpreted as North or East African input and/or a residual ancient Arabian element, probably both)
3. La Braña also has "Basal Eurasian" admixture (surely from NW Africa, what implies that the North African component in Western Iberia is pre-Neolithic)
4. Motala has Ancient Siberian (MA1-like) admixture
5. Mal'ta 1 probably has some East Asian admixture
6. Ötzi the Iceman might have some Western Hunter-Gatherer admixture (~3%)

Of the three Western branches, MA1 is the more distant one. That implies that West Asia and Europe were also exchanging genetics in the Upper Paleolithic, while Siberia remained more isolated in comparison. That stands even when East Asian admixture into MA1 is accounted for. 

A Lochsbour's cousin in West Asia

The authors compare and analyze many models of possible admixture leading to the known ancient and modern populations. They seem to favor this one in the end:

Figure S14.20: A model for Near Eastern populations with Ancient North Eurasian admixture.
Stuttgart is a mixture of Near_East and a sister group of Loschbour (UHG: Unknown Hunter-
Gatherers); A Test population (shown here) is a mixture of Near_East and a sister group of MA1.

This scheme suggests that ancient West Asian ("Near East") populations were closer to ancient Europeans (Lochsbour) than to ancient Siberians (MA1). It also suggests an unknown relative population of Lochsbour (UHG) as partial ancestor of early European farmers (Stuttgart). This population is speculated to have lived in the Balcans. 

An issue here is that most modern West Asians and all Caucasian peoples actually have too much MA1 affinity to be a good fit for the (ancient) Near East proto-population concept. About 12-13% among West Asians (Cypriot, Druze) and as much as 29% among Caucasians. They are actually more like "Test" than like "Near East".

The authors conclude that they don't really know if this extra MA1-like ancestry is old or recent. If old, it would imply either two different populations of West Asians or, as they say, the expansion of a West Asian population with extra "Basal Eurasian" ancestry. 

This brings us to a key question: what is actually "Basal Eurasian"?

What is "Basal Eurasian"?

Notice that "Basal Eurasian" is defined as phylogenetically intermediate between the Mbuti and Eurasian-plus populations. Quite misleadingly the node is described as "Non-Africans" but that does not need to be true at all. It is just downstream of one of the most ancient African sub-branches, that of Pygmies, so it can still represent African populations which are or were closer to the out-of-Africa branch. 

There is no formal ascertainment whatsoever of what is "Basal Eurasian", no comparison with other African populations and no even formal consideration of the (very likely) possibility of various isolate ancient populations existing in NW Africa or Arabia. This is clearly a flaw. 

A key piece of information here is that La Braña (ancient NW Iberian hunter-gatherer) consistently shows "Basal Eurasian" admixture. This admixture is much more likely to have arrived from North Africa than anywhere else. NW African genetic markers are still apparent in Western Iberia in fact and there is strong archaeological support for Iberia-NW Africa interaction in Solutrean/Oranian times. 

We can only consider in fact this "Basal Eurasian" idea as a mere indicator of African-like affinity, even if it's not Mbuti but something else. This something else can be in fact several things:

• NW African Aterian residual in the case of La Braña
• Arabian OoA residual influence in the case of EEF
• Direct NE African admixture in the proto-EEF West Asian population, strongly indicated by the NE African E1b-M78 (notably its subclade E1b-V13) in ancient Neolithic and modern European Y-DNA.

I am particularly inclined to suspect an almost direct migration from Palestine to Thessaly at the origins of European Neolithic. After all both non-European lineages found in early European farmers (E1b-V13 and G) are common in that area. But of course an Anatolian intermediate station cannot be excluded.

In any case I'd suggest to change the terms "Basal Eurasian" and "non-Africans" by something more neutral, maybe "Ultra-Mediterranean" and "Proto-Eurasian" respectively, where both concepts are allowed to be African, at least partly so.


Update (Apr 23): see also here for some curious aspects of Lochsbour's IBD ancestry.

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 view → LINK [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 Europe^{1, 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.

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 accessible → LINK [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. 

Madagascar inhabited long before Austronesian arrival

These findings revolutionize the understanding of the prehistory of the island, until now believed to have remained uninhabited until the arrival of peoples of Austronesian stock some 1500 years ago (with some scattered evidence of earlier inhabitation but nothing too conclusive). New archaeological data pushes back the first colonization period to some 4000 years ago, a time when Malayo-Polynesian culture was still restricted to, roughly, the Philippine archipelago.

Robert E. Deward et al., Stone tools and foraging in northern Madagascar challenge Holocene extinction models. PNAS 2013. Pay per view (6-month embargo) → LINK [doi:10.1073/pnas.1306100110]

Abstract

Past research on Madagascar indicates that village communities were established about AD 500 by people of both Indonesian and East African heritage. Evidence of earlier visits is scattered and contentious. Recent archaeological excavations in northern Madagascar provide evidence of occupational sites with microlithic stone technologies related to foraging for forest and coastal resources. A forager occupation of one site dates to earlier than 2000 B.C., doubling the length of Madagascar’s known occupational history, and thus the time during which people exploited Madagascar’s environments. We detail stratigraphy, chronology, and artifacts from two rock shelters. Ambohiposa near Iharana (Vohémar) on the northeast coast, yielded a stratified assemblage with small flakes, microblades, and retouched crescentic and trapezoidal tools, probably projectile elements, made on cherts and obsidian, some brought more that 200 km. 14C dates are contemporary with the earliest villages. No food remains are preserved. Lakaton’i Anja near Antsiranana in the north yielded several stratified assemblages. The latest assemblage is well dated to A.D. 1050–1350, by 14C and optically stimulated luminescence dating and pottery imported from the Near East and China. Below is a series of stratified assemblages similar to Ambohiposa. 14C and optically stimulated luminescence dates indicate occupation from at least 2000 B.C. Faunal remains indicate a foraging pattern. Our evidence shows that foragers with a microlithic technology were active in Madagascar long before the arrival of farmers and herders and before many Late Holocene faunal extinctions. The differing effects of historically distinct economies must be identified and understood to reconstruct Holocene histories of human environmental impact.

Notice that this colonization is also older than the Bantu expansion and therefore these settlers must have been pre-Bantu peoples of East African roots.

Source: Al-Hakawati

The sites are located in the North tip of the island, what is consistent with arrival through Comoros, the most natural route between East Africa and Madagascar, which  requires the sailing of some 190 miles (~350 Km) of open sea.

Otherwise the narrowest extent of the Mozambique Channel, between Angoche and Tambohorano, is of some 460 Km. The small island or Juan de Nova (uninhabited except for a military garrison) lies to the south of this other potential sailing route.

The toolkit found in the key site of Lakaton'i Anja includes many microliths, as well as some larger tools, made of chert and obsidian. This last must have been brought from far away, as there are no sources of the volcanic glass in Northern Madagascar.

An important point is that these new dates show that human inhabitation did not kill the Malagasy megafauna right away but that instead humans and giant animals shared the environment without immediate catastrophic consequences, which would only happen in the last two millennia.

Partial source: Rhett A. Buttler, Madagascar occupied by humans 2,500 years earlier than previously thought, Wild Madagascar (via Pileta).

Was the grove snail Epipaleolithic livestock in Western Europe?

Cepaea nemoralis
(CC by Papa Lima Whiskey 2)

The problem of disjunct distribution of Western European species or, in this case, subclades of a single species is nothing new and has been startling biologists for almost two centuries already, with particular interest of Irish-Iberian, Breton-Iberian or just general Irish-continental disjunct relationships of various species (the so called Lusitanian distribution). Among them is the iconic strawberry tree (madroño in Spanish, found in Ireland but not Great Britain) but also a number of small land animals: the Kerry slug (found in NW Iberia and SW Ireland only), the Quimper snail (found in NW Iberia and Western Brittany) or the Pyrenean glass snail (found in the Pyrenees and Ireland).

There are also cases of subclades within an otherwise widespread species which show a similar pattern. In 2003, Masheretti et al. demonstrated that the Irish variant of the pygmy shrew had its greatest affinity with populations of Andorra, in the Eastern Pyrenees, from which they are descended.

This study illustrates a similar case but affecting the snail species Cepaea nemoralis (grove snail or brown lipped snail), whose Irish lineages are mostly derived from Iberian ones and in most cases from the Eastern Pyrenean haplogroup C.

Adele J. Grindon & Angus Davison, Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans. PLoS Genetics 2013. Open access → LINK [doi:10.1371/journal.pone.0065792]

Abstract

The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared “Lusitanian” history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.

The evidence gathered by this study is most readily visible in fig. 2:

While it is not the focus of this study, we see here two other cases of probable disjunct distribution:

• Hg D is found in Iberia, Ireland, small pockets in Britain and SW France but also in North and Central Europe.
• Hg F shows also disjunct presence in Cornwall, far away from the main cluster around the Bay of Biscay.

The authors of this and previous studies have suggested that this distribution may have to do with intentional transport (as livestock) in the process of the colonization of the Atlantic Islands in the Epipaleolithic. In support of this claim, there is enough fossil evidence of the snail in the island:

Fossil material indicates that this species has been continuously present in Ireland for at least 8000 years (Newlands Cross, Co. Dublin: 7600+/−500 BP Cartronmacmanus, Co. Mayo: 8207+/−165) [7], [8].

In other cases, such as the inedible Kerry slug, we may suspect unintentional transport and therefore we would be justified to imagine a later time frame for their arrival to Ireland, possibly in the Chalcolithic-Megalithic period, but the evidence for C. nemoralis is highly suggestive of intentional transport in the Epipaleolithic. We can therefore say that the humble grove snail was one of the first domestic animals of Europe, possibly second after the dog.

Korean petroglyphs at risk by reservoir

A group of very beautiful South Korean petroglyphs that seem to represent whale hunting and are dated some 6000 years ago are being damaged by a water reservoir that provides water for the city of Ulsan. 

The Bangudae petroglyphs, discovered in 1971, are submerged under water seasonally, raising great controversy in the East Asian country. It seems that even President Park is greatly concerned about them, something not too usual in a politician, while the Cultural Heritage Administration is demanding measures to protect the ancient rock art, namely to keep water levels low enough. 

However water utilities claim that it is impossible to meet such demands while providing water to the seventh largest South Korean city. The Ulsan city government is proposing to build a wall around the petroglyphs in order to protect them while keeping the water levels, this however would cause environmental damage to the area, disqualifying the site for UNESCO World Heritage protection schemes.

Source: cinabrio.over-blog[en/es] (incl. several pictures and press articles).

Ancient Jomon mtDNA from Japan

Udege family

There is some debate about the connection between the Jomon period (Japan's ceramic but pre-agricultural period, extending between c. 16,000 to 2300 years ago) and the Ainu, as well as Ryukyuans and other peoples, including mainstream Japanese. A new study provides some extra bits of information to fuel the debate:

Hideaki Kanzawa-Kiriyama et al., Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. Anthropological Science 2013 (advance publication). Open access → LINK [doi:10.1537/ase.121113]

The researchers sequenced ancient mtDNA from Jomon remains from a shell mound of Sanganji (Fukushima), which produced two M7a2, one N9b2 and one (incomplete) N9b* sequences.

Referring to previous similar studies as well, they produced the following tables:

From this data it would appear that the ancient Jomon people would be most closely related to modern Udegey (or Udege) from the Amur region of Eastern Siberia (with the possible exception of the Kanto Jomon, who may be closest to Ryukyuans instead).

The Sanganji sample is included pooled into Tohoku Jomon

The Ainu, it must be said, are next in line after the Udege, and I wonder if recent admixture may be distorting their relation. Another issue is that in such an extensive period of almost all the Holocene and even some millennia into the Pleistocene, there may have been flows and variability also within the Jomons (the Sanganji shell mound is dated to c. 4000-2500 BP, for example).

Whatever the case, it seems clear that N9b was an important matrilineage among ancient Jomon peoples, while M7a (now most common among Ryukyuans) was present but less common, with the Sanganji sample being rather exceptional in this.

Spring near Stonehenge occupied since Epipaleolithic

(CC by Jeffrey Pfau)

The spiritual relevance of Amesbury may well stem from a much older time than Neolithic or Chalcolithic. Recent research at a spring not far from Stonehenge has got radiocarbon dates of c. 7500 years ago, some three millennia before the building of the world-famous monument, and up to 4,700 BP, when the megalith was already in use.

The low budget research project led by David Jacques of Open University, who had spotted the site, known as Vespasian's Camp, just a mile north of Stonehenge, in air photos a decade ago. The site had never been researched before.

The findings imply some sort of continuity between the Epipaleolithic and Late Neolithic (i.e. Chalcolithic), although the details have yet to be systematized. 

Source: BBC News (includes video).

Fu 2013: new ancient mtDNA sequences and "molecular clock" madness

It took me quite a while to get time to look at this study in some depth and when I finally did I must say I was rather disappointed. In any case the popular demand makes necessary to discuss it.

Qiaomei Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes. Current Biology 2013. Pay per view → LINK [doi:10.1016/j.cub.2013.02.044]

The study has two aspects: one, of great interest, which is the sequencing of a number of ancient remains, the other a complex and quite poorly explained and rendered speculation on how these sequences could be used to produce a refined molecular clock. 

Ancient mtDNA sequences

Most of the sequences used by Fu et al. in their molecular clock speculations are new and that part is very interesting:

I have highlighted in lime green the new sequences, otherwise also noted by the marker b. It is of note that the "Crô-Magnon 1" sequence produced a C14 age of just a few centuries, being therefore removed from the collection. Other Crô-Magnon 1 remains produced no useful data. 

The authors also decided to discard as possibly contaminated the UP sequence  from Pagicci Str. 4b. I have highlighted in red why they decided to do so: because the C→T misincorporation rate, characteristic of ancient remains, is too low, what makes contamination at least a serious probability. 

So we have as new data for the Upper Paleolithic landscape in Europe that the people of Dolni Vestonice carried lineages U* (found also in Swabian Magdalenian) and U8, in the line of haplogroups K, U8a (Basque) and U8b (Eastern Mediterranean). Also some late UP and Epipaleolithic sequences from Oberkassel (Low Rhineland, Germany), Loschbour (Luxemburg) and Continenza (Abruzzo, Italy) are U5b variants, consistent with other findings from various parts of Europe. In Paglicci (Apulia, Italy), another sequence yielded U2'3'4'7'8'9, surely an extinct variant of the ancestor of U8 and U2 (among other lineages). No radiocarbon date is available for any of the Italian remains.

In East Asia, Boschan, with B4c1a, provides one of the first Epipaleolithic sequences for the region. 

Molecular clock madness

The authors seem to intend, or so declare, to refine the molecular clock estimates by means of using these sequences as intermediate calibration references. Here I get the first big question: with all the literature on ancient DNA, why only these sequences? No idea.

Then the contradictions arise. I believe that I have synthesized the most obvious ones in the following marginal annotations (in red) to their molecular clock estimates:

Furthermore, the authors claim in the text that U5 is the oldest branch to diverge from U, however their TRMCA figure is of only 34.4 Ka BP (coding region), while Kostenki 14 has an age of 38 Ka BP and already carried U2, what really makes this claim extremely unlikely: U2 and its ancestor U2'3'4'7'8'9 should be considered the oldest U sublineage. 

I do not understand either why they force age estimates for many lineages for which they have no working aDNA references and instead desist of estimating the age of lineages for which they have several calibration points, like U2'3'4'7'8'9 or B4'5 (aka B). 

In brief: the claims of this paper on molecular-clock-o-logy are ill-explained, confusing, incoherent... a total mess. The raw data on ancient mtDNA is however good looking and of doubtless interest.