The Maasai: rich ancestry, lactase persistance and low cholesterol

Maasai warriors jumping (cc by javic)

There is a new paper at the Public Library of Science on the genetics of the Maasai with emphasis in diet-related aspects:

Kshitij Wagh et al., Lactase Persistence and Lipid Pathway Selection in the Maasai. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0044751]

Abstract

The Maasai are a pastoral people in Kenya and Tanzania, whose traditional diet of milk, blood and meat is rich in lactose, fat and cholesterol. In spite of this, they have low levels of blood cholesterol, and seldom suffer from gallstones or cardiac diseases. Field studies in the 1970s suggested that the Maasai have a genetic adaptation for cholesterol homeostasis. Analysis of HapMap 3 data using Fixation Index (Fst) and two metrics of haplotype diversity: the integrated Haplotype Score (iHS) and the Cross Population Extended Haplotype Homozygosity (XP-EHH), identified genomic regions and single nucleotide polymorphisms (SNPs) as strong candidates for recent selection for lactase persistence and cholesterol regulation in 143–156 founder individuals from the Maasai population in Kinyawa, Kenya (MKK). The non-synonmous SNP with the highest genome-wide Fst was the TC polymorphism at rs2241883 in Fatty Acid Binding Protein 1(FABP1), known to reduce low density lipoprotein and tri-glyceride levels in Europeans. The strongest signal identified by all three metrics was a 1.7 Mb region on Chr2q21. This region contains the genes LCT (Lactase) and MCM6 (Minichromosome Maintenance Complex Component) involved in lactase persistence, and the gene Rab3GAP1 (Rab3 GTPase-activating Protein Catalytic Subunit), which contains polymorphisms associated with total cholesterol levels in a genome-wide association study of >100,000 individuals of European ancestry. Sanger sequencing of DNA from six MKK samples showed that the GC-14010 polymorphism in the MCM6 gene, known to be associated with lactase persistence in Africans, is segregating in MKK at high frequency (~58%). The Cytochrome P450 Family 3 Subfamily A (CYP3A) cluster of genes, involved in cholesterol metabolism, was identified by Fst and iHS as candidate loci under selection. Overall, our study identified several specific genomic regions under selection in the Maasai which contain polymorphisms in genes associated with lactase persistence and cholesterol regulation.

The study actually has two elements of interest for my point of view, on one side it is the dietary aspects of Maasai genetics underlined in the title and the abstract but then there is a more generic element of understanding the relevant population genetics with the help of STRUCTURE,  reflected in fig. 1 but better addressed in the supplemental materials (Appendix S1).

The Maasai as product of 6 ancestral populations

K=6 is what STRUCTURE indicates as clear best fit (lowest log probability of fit) in a no-admixture model and all the six reconstructed ancestral populations are all present in them (unlike what happens for example with the CEU sample of European ancestry):

From Appendix S1 - click to expand
CEU: European-Americans (USA), ASW: African-Americans (USA)
LWK: Luhya (Kenya), MKK: Maasai (Kenya), YRI: Yoruba (Nigeria)

We can see that the influence of West Eurasian genetics (teal) appears to be almost nil in Africa, although the Maasai (MKK) have some (c. 2%), probably infiltrated via Ethiopia, Somalia or Sudan.

West African genetics (pink) are slightly more influential in the Maasai but only c. 10%.

Instead the Maasai display four different East African specific "ancestral populations" of which two are larger and the other two smaller in the sampled populations:

• The yellow component is almost exclusive of the Maasai (69%), with some very minor penetration in other populations.
• The green component is more outstanding among the Luhya (32%), reaching barely 5% among the Maasai.
• The brown component is again almost exclusive of the Maasai (12%), with some individuals apparently displaying it as very dominant.
• Finally, the purple one is almost exclusive of the Maasai but at much lower frequecies (3%). However it is also dominant in a few individuals.

The fact that the Maasai show obviously marked individual variance at levels not apparent in other populations, and that this variance includes some smaller "mystery" components, seems to mean that they are in ongoing or very recent admixture with other populations (maybe other Maasai clans of distinctive origin, maybe other pre-Bantu East African peoples). It indicates that there is still a lot to research in the Population genetics of East Africa, what requires of extensive new sampling among the many diverse small ethnicities of the Upper Nile and nearby regions.

Yes to milk, no to cholesterol

The other, more central aspect of this study is the localization of specific genomic regions or even alleles that guarantee that this pastoralist people can largely live off the milk produced by their cows and, quite interestingly, not to have circulatory problems because of the associated excess cholesterol.

The authors detected the following regions as very clearly under selection (several approaches being convergent in their detection):

Fig. 5

The first of these regions, in chromosome 2, seems particularly long and selected for both lactase persistence (the ability to digest lactose as adult) and low cholesterol, according to this paper. 

The region in chromosome 7 regulates the enzyme Cytochrome P450, related to oxidation processes in metabolism of lipids, steroids, drugs and toxins, probably also regulating cholesterol.

See also in this blog:

• Claim that cholesterol related gene was positively selected in Africa but not elsewhere
• Positive selection for arthritis and short-size alleles in Eurasia?
• Khoesan genetics helping to understand the evolutionary history of Humankind as a whole
• Khoesan autosomal genetics
• North African autosomal genetics (also considering the Maasai). 
• Chad basin mtDNA
• Sudanese autosomal genetics
• African diversity and the possible origins of Humankind
• Eastern Pygmies are not mtDNA L1

I also recommedn Ethio Helix blog, generally quite informative in all things African and genetic.

Yet another dolmen found and dug at Orereta (Basque Country)

A dolmen was found in the area of Txoritokieta (Orereta, a.k.a. Rentería, Gipuzkoa) and excavated by the Arazandi Society of Sciences. Other four megalithic burials are known in the same area. 

It is a simple dolmen (without entrance gallery), with the gate oriented to the SE and built with slabs reinforced by a circular perimeter of stones. The structure also includes a slab acting as floor and was covered by a tumulus of earth and stones.

Sources[es]: S.C. Aranzadi, Pileta.

See also: searcher of megaliths and prehistorical monuments in Gipuzkoa[es/eu].

La Bastida de Totana (Spain) may have been largest city in Bronze Age mainland Europe

Location of La Bastida in the context of El Argar culture (source)

Arguable I guess because it will be susceptible to further research for example in the Castro do Zambujal  (Torres Vedras, Portugal) or in the El Argar culture area itself but that is what the current archaeological team has claimed through a press release (h/t Pileta).

According to the researchers, La Bastida[es] de Totana (Murcia) was back in the day the largest city in all mainland Europe, next only to some Minoan cities of Crete. 

On first read it may sound to exaggeration but, after all, they have pushed forward the age of foundation of La Bastida and hence of El Argar culture to c. 2,200 BCE, some three or four centuries before El Argar proper... what means an older age than the founding of the Mycenaean cities (Mycenae, Athens, Thebes...), which are not older than c. 1600 BCE. 

The civilizations of Los Millares and the already mentioned Zambujal (culture of Vila Nova de Sao Pedro), both in Iberia, are still older (c. 2600 BCE) but now La Bastida de Totana stands between these Chalcolithic civilizations and the Bronze Age ones, whose paradigm is El Argar, of which La Bastida may have been seed.

Hill of La Bastida (Totana, Murcia) - source: La Bastida[es].

Excavated ruins

Honoring its name (etymologically related to "bastion") La Bastida was a heavily fortified city spanning four hectares on top of an strategical hill. Its 2-3 meter thick stone walls are the oldest known of its kind in all Europe, although they have precedents in West Asia:

The fortification consisted of a wall measuring two to three metres thick, built with large stones and lime mortar and supported by thick pyramid-based towers located at short distances of some four metres. The original height of the defensive wall was approximately 6 or 7 metres. Until now six towers have been discovered along a length of 70 metres, although the full perimeter of the fortification measured up to 300 metres. The entrance to the enclosure was a passageway constructed with strong walls and large doors at the end, held shut with thick wooden beams. 

One of the most relevant architectural elements discovered is the ogival arched postern gate, or secondary door, located near the main entrance. The arch is in very good conditions and is the first one to be found in Prehistoric Europe. Precedents can be found in the second city of Troy (Turkey) and in the urban world of the Middle East (Palestine, Israel and Jordan), influenced by the civilisations of Mesopotamia and Egypt. This indicates that people from the East participated in the construction of the fortification. These people would have reached La Bastida after the crisis which devastated their region 4,300 years ago. It was not until some 400 to 800 years later that civilisations like the Hittites and Mycenaeans, or city-states such as Ugarit, incorporated these innovative methods into their military architecture.

Recreation of La Bastida city (source)

Pythos burial, style surely imported from Greece

Contextualizing

For what I have read on the matter, I understand that El Argar culture, often imagined as a centralized state, would have been divided into three regions or smaller realms, of which the area of Totana and Lorca (roughly modern Murcia region) would be the northern one. 

From the pushing backwards of the age of La Bastida I deduce that the this region may well have been the origin of El Argar civilization itself, which surely absorbed Los Millares manu militari later on, maybe leading to the founding of El Argar city as new capital between the two realms, much like Memphis was founded in Egypt after the unification of the Upper and Lower kingdoms. 

I am here speculating a bit of course - feel free to correct me if you know better. 

Besides of El Argar cultural area, the influence of this state may have extended through much of Southern and Eastern Iberia, possibly into all the areas colored in this map:

Possible wider area of influence of El Argar civilization, earliest Bronze (source)

Of course the areas in blank were not empty but had other cultures, in some cases also outstanding civilizations, like VNSP in the following map:

Middle Bronze in Iberia (anti-copyright by me - same one as Sugaar)

In the La Bastida dedicated site you can find much more information in Spanish language, as well as photos, about this fascinating site, which was maybe the navel of much of Europe four thousand years ago. Another complementary source for this entry has been the dedicated page of Murcia regional government. Thanks to both.

Neolithic 'calendar' found in Vietnam

The artifact, marked with ordered dots and strips that may well represent the lunar cycle, was found in Nguom Hau Cave (Na Hang District, Tuyên Quang province, Northern Vietnam). 

A similar artifact was discovered in 1985 not far away: Na Cooc Cave (Thái Nguyên province). 

The calendar has been estimated to be from c. 4000 years ago. 

The stone tool was found in a tomb marked with 14 large stones laid at a length of 1.6m. Bones were found under the stones but no skull was found, with Chung guessing that the skull may have decayed due to the humidity in the cave.

A number of other stone tools were buried with the corpse.

The dig also produced much other information from the Iron Age (3.0-3.5 Ka BP), Late Neolithic (4.0-4.3 Ka BP) and a deeper and very thick Early Neolithic layer consisting of many polished stone axes and other tools.

Together with other findings, the evidence mounts for inhabitation from at least 8000 years ago in this area. 

Source: Viêt Nam News (via Pileta).

Portugal: 'austerity' may close Côa Park

Côa engravings (CC by Henrique Matos)

Côa Valley is not just a fantastic natural park in the NE of Portugal but also one of the key areas of European Prehistory, hosting the famous mural engravings the Upper Paleolithic.

The Portuguese government decided on Tuesday (Sep. 25) to suspend its existence and is considering its complete dismantling, as part of the austerity efforts imposed by the IMF and the EU. 

The cost of the park is 1.4 million euros yearly.

No cuts are known to affect the Armed Forces for example, even if Portugal has not known enemies anymore and could do with just some patrol ships. 

Source: RTP Noticias[por] (via Pileta).

September 26 - closed because of general strike

For what they were... we are adheres to the general strike against social expending cuts, which simply put: kill people and destroy societies. This strike has been called separately in the Basque Country, Greece and Galicia - as far as I know.

I may comment further if there are important news in my other blog, For what we are... they will be, but expect no activity whatsoever in this blog until Thursday. 

Sorry for whatever inconvenience.

Closed!
September 26 - General Strike
For labor and social rights
Let's face the cuts, the reform and the impositions!

Chalcolithic Iberian script?

La Zarcita vessel

This is not really news but something that has been around since the 1950s but that, because of the attitude of (excessive?) scientific prudence of the researchers has never been known except to a few specialists. 

A few years ago however, Dr. Ana María Vázquez Hoys, re-discovered the inscribed artifacts in the Museum of Huelva, proposing that maybe there was a Chalcolithic script in Southern Iberia some in the 4th or 3rd millenium BCE, some two millennia before it is commonly accepted that writing arrived to Iberia, via the Phoenicians (but with scripts that have at best a very oblique connection with the Phoenician abjad).

Personally, I just learned about them today, thanks to an archaeology series in state TV, that is almost always worth watching in spite of the horrible schedule (early in the morning).

Of course the inscribed artifacts are isolated anomalous findings, much as is the case with the even older Vinča symbols from the Neolithic Balcans, but they are well documented and the inscriptions, whatever they are or mean, are very real.

One of the inscribed artifacts is a round ceramic piece with a canalization along its diameter it, arguably resembling a vagina and initially described as "arrow polisher" but that could well have some sort of ritual purpose. This object originated in San Bartolomé de la Casa (Huelva province).

San Bartolomé inscribed "vulva"

Tracing of the signs above by Vázquez Hoys

The other object is a legged tray or vessel, also made of local clay with pyrite granules, only shows a few characters. It has the same Megalithic period chronology and was found in La Zarcita (Huelva prov.) It probably had ritual use as well.

Outline of La Zarcita vessel, showing the inscriptions (by Vázquez Hoys)

Main online source: UNED page on the matter by Dr. Vázquez Hoys[es].

Khoesan genetics helping to understand the evolutionary history of Humankind as a whole

A reader sent me a copy of this letter or short paper on South African autosomal genetics:

Carina M. Schlebusch, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science 2012. Pay per view ··> LINK [doi:10.1126/science.1227721]

[Note-update (Oct 2): the supplemental material is free and very very extensive: a must read for genetic data-miners and all those interested in getting deeper and more extensive info, even if just on the ethno-historical background of the populations considered in the study, something that most people, including myself, only know rather shallowly].


The paper has several points of interest but is specially useful, complemented by previous studies like Pickrell 2012, to better understand the aboriginal and modern genetics of Southern Africa, which is analyzed, for example as principal component (and other) analysis relative to geography.

Fig. 1. (click to expand)

(A) Sampling locations.
(B) Principal components analysis (PCA) of African individuals showing PC1 and PC2 rotated to fit geography.
(C) PCA for Khoe-San populations (∼ 2.3M SNPs).
(D) Pairwise FST for sub-Saharan populations (excluding Hadza, see fig. S24 for comparison)
(E) Prediction of the genetic components from geographic, linguistic and subsistence covariates. The predictive error relative to geography is given for each combination of covariates (values < 1 show improved predictive capacity compared to geography).

Also an Admixture analysis with an estimate divergence tree that is off in chronology by about 100% or even more. When will geneticists learn to calibrate their "molecular clock" speculations on archaeology? When?!

Here you have it, annotated by me (in red):

Fig. 2.(click to expand)
(A) Rooted population topology from a concordance test approach (14). Nodes with bootstrap support < 50% are collapsed (dashed lines), all other nodes have bootstrap support > 85%.
[Annotations in red by Maju]
(B) Clustering of 403 sub-Saharan African individuals (∼ 270k SNPs), assuming 2 to 11 clusters.
(C) Clustering of 118 southern African individuals (∼ 2.3M SNPs), assuming 2 to 8 clusters. Compare with fig. S16 that include recently admixed individuals.

Additionally the authors think that they have located a number of key genes that appear to have been selected for among some Khoesan groups and/or diversified around the time of the first human split c. 100 200 millennia ago, such as:

• MYPN (myopalladin) - associated with muscle growth and function
• ACTN3 - associated with “fast twitching” muscles and elite athletic performance
• MHC - major histocompatibility comple
• PRSS16 and POM121L2 - thought to protect against infectious diseases
• ERCC4 regulators - related to pigmentation
• ROR2 - involved in regulating bone and cartilage development

Also the following regions appear to have suffered intense selective pressures among early Homo sapiens in general, always according to the authors:

• SPTLC1 - involved in hereditary sensory neuropathy
• SULF2 - that regulates cartilage development
• RUNX2 - related to morphological differences with other Homo species, notably Neanderthals (frontal bossing, clavical morphology, bell-shaped rib cage, and regulating the closure of the fontanel which is crucial for brain expansion)
• SDCCAG8 - involved in microcephaly
• LRAT - associated with Alzheimer's disease 

 

Thus, three of the top five regions contain genes involved in skeletal development, and syndromes associated with mutations in these genes display similar morphological features.

While also:

Including SULF2, three of the top five candidate regions are thus associated with neuronal function.

All this falls within expectations, I'd say, but nevertheless most interesting to know in such detail and precision.

Epipaleolithic and Neolithic burials found in Morocco

Just a short heads up notice because nothing seems to have been formally published or even radiometrically dated yet but Press News Africa reports (h/t Pileta) that two human burials have been found some 300 km East of Rabat, in the village of El Ksir (near Aïn Tajoudate, El Hajeb province). 

As I say, the two skeletons are yet to be dated with C14 but from the stratigraphic context it is estimated that they are from 6-8 Ka. ago one and from 8-14 Ka ago the other. Both are male and seemingly buried in flexed position inside oval tombs with the most recent one having a scraper as only grave good, while the other had a limestone slab on top of the tomb.

La Braña connection?

It would be extremely interesting if DNA is extracted and analyzed from them, of course. But specially what I have in mind right now is the possible relationship between their burial style and that of La Braña (León, NW Iberia), which, as I mentioned back in the day, is not typical from local Paleolithic, rising more questions than answers.

As you may know, Western Iberia and very specially some mountain areas of León, show unusually high levels of North African genetics (always minor but clearly significant for Europe). And, as you may remember, the La Braña composite appeared to show a consistent 10% of African admxiture (either East African, or Khoisan or just generic African, all which can be hypothetically consistent with untested North African admixture).

If I'm correct on this, it would imply that the North African minor affinity that characterizes Western Iberia and specially the mountain areas of León would be as old as the Epipaleolithic, maybe even older, supporting my old hypothesis of genetic exchange across Gibraltar Strait occurring mostly in the period of the Oranian (Iberomaurusian) genesis and the cultural backflow associated to the introduction of winged and tanged points into the Southern Iberian Gravetto-Sloutrean, which seems to be behind the Solutrean of Asturias as well. 

Just a possibility at the moment but a thread that I deem interesting to follow in the archaeo-genetic labyrinth. 

Claim that cholesterol related gene was positively selected in Africa but not elsewhere

This is one of those genetic studies whose claims are so strongly counter-intuitive that I do not know what part to believe the less. However the raw data is clearly there and that is interesting to know in any case, even if we are to systematically doubt all the claims built around that core:

Rasika A. Mathias et al., Adaptive Evolution of the FADS Gene Cluster within Africa. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0044926]

Abstract

Long chain polyunsaturated fatty acids (LC-PUFAs) are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA) from plant-based medium chain (MC) PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS) gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ~85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60–80 kya.

Whether it is true that those fatty acids are so desperately needed for bigger brains or not really so much, allow me to remain healthily skeptic to begin with (any report on elephants for example, whose diet is purely vegetarian but do have big complex brains?)

I will also remain skeptic of the fact, which is implied by the study, of a primitive vegetarian or almost vegetarian diet of Homo sapiens in Africa: I do not think that such an a priori claim can stand at all. The same logic that applies in Africa should apply in Eurasia-plus but the fact is that Eurasians retain the ancestral allele and related genetic bloc without obvious damage to the brains.

There should be another explanation therefore: for example a founder effect at the Eurasian initial "out-of-Africa" bottleneck after a process of near fixation at previous, or maybe even adaptive introgression from Neanderthals in this aspect.

Finally the authors use absolutely wrong age estimates, all founded in that nonsense as is the molecular clock. According to the authors:

Studies suggest that anatomically modern humans arose in Africa approximately 150 thousand years ago (kya), expanded throughout Africa ~60–80 kya, and to most parts of Europe and Asia ~40 kya[1]–[6].

A paper that insists in such an obvious error should never pass the peer-review process, in my not-so-humble opinion.

Even if we ignore the absurdity of this molecular-clock-o-logic pseudoscientific insistence, and accept that we have to double or more than double the age estimates to be back into the common sense zone, or better, just ignore them altogether, we still have the problem of why would the allele and the whole genetic block around it be almost fixated in Africa but not at all in that African-derived subset that is Eurasia and the smaller continents.

Figure 3. Geographic distribution of derived allele frequencies in a 100 kb region surrounding rs174537 in the 52 populations represented in the Human Genome Diversity Panel Data. Panel A represents physical position of the SNPs relative to genes in the region, Panel B is SNP name (derived allele), Panel C is frequency of derived allele (in orange) in the populations clustered based on geography, Panel D is an indication of the allele associated with increased LC-PUFA metabolism in published association studies, and Panel E is the detailed overview of rs174537 showing is near fixation within Africa.

SNPedia reports slightly less dramatic levels of fixation in Africa for rs174537 itself but nothing that is too important.

So we do have a clear case of an allele that has been selected for in Africa but, crucially, not elsewhere. 

My highly skeptical questions are: 

1. How can this have happened in Africa prior to the migration out of Africa, as the authors claim, but not affect that African subset that was the migrant "out of Africa" population, whose formation necessarily happened after the African expansion and close to the overall origin(s) of that African expansion?
2. If the fixated allele is so important for brain function how is it that many Eurasians-plus, who lack the allele are not plainly dumb? How did they survive along time?
3. Do the authors have any archaeological evidence that vegetarian sources of food, notably oils, were so extremely important in African Middle Paleolithic (Middle Stone Age)? I do not think so, not at all.
4. How do the authors explain the lack of selection for this allele in South Asia, a region where total or almost total vegetarianism (dairies excepted) has been very common for many millennia.
5. How do the authors explain the lack of selection out of Africa or even what would seem to be a tendency for the opposite selection trend in parts of East Asia and Native America?

Actually the only well known adaptive role of this SNP is that it protects against cholesterol but not the allele that appears to have been selected in Africa but the "blue bloc" that survived out if it (and may have been selected for in some regions, speculatively). TT homozygotes, and only them, have lower LDL-C and total cholesterol.These are only truly common among SE Asians and Native Americans (or Mestizos).

So what do we make of this? In truth no idea: the authors hypothesis is there but I fail to find merit in most of it. It may be just a matter of refinement of the original hypothesis however - your take.

Younger Dryas meteorite impact theory consolidated

The revealing micro-spherules

After sometimes heated debates, it seems that the theory of a meteorite impacting on Earth, probably above Canada, at the beginnings of the Younger Dryas and probably related to megafauna extinctions seems to be gaining more and more weight.

Malcom A. LeCompte et al. Independent evaluation of conflicting microspherule results from different investigations of the Younger Dryas impact hypothesis. PNAS 2012. Pay per view (for 6 months/depending on world region) ··> LINK [doi]

Abstract

Firestone et al. sampled sedimentary sequences at many sites across North America, Europe, and Asia [Firestone RB, et al. (2007) Proc Natl Acad Sci USA 106:16016–16021]. In sediments dated to the Younger Dryas onset or Boundary (YDB) approximately 12,900 calendar years ago, Firestone et al. reported discovery of markers, including nanodiamonds, aciniform soot, high-temperature melt-glass, and magnetic microspherules attributed to cosmic impacts/airbursts. The microspherules were explained as either cosmic material ablation or terrestrial ejecta from a hypothesized North American impact that initiated the abrupt Younger Dryas cooling, contributed to megafaunal extinctions, and triggered human cultural shifts and population declines. A number of independent groups have confirmed the presence of YDB spherules, but two have not. One of them [Surovell TA, et al. (2009) Proc Natl Acad Sci USA 104:18155–18158] collected and analyzed samples from seven YDB sites, purportedly using the same protocol as Firestone et al., but did not find a single spherule in YDB sediments at two previously reported sites. To examine this discrepancy, we conducted an independent blind investigation of two sites common to both studies, and a third site investigated only by Surovell et al. We found abundant YDB microspherules at all three widely separated sites consistent with the results of Firestone et al. and conclude that the analytical protocol employed by Surovell et al. deviated significantly from that of Firestone et al. Morphological and geochemical analyses of YDB spherules suggest they are not cosmic, volcanic, authigenic, or anthropogenic in origin. Instead, they appear to have formed from abrupt melting and quenching of terrestrial materials.

Most interesting in this research is that it was done directly at an archaeological layer of the Clovis clulture, what makes the chronology very solid.

Also the authors claim that some of the negative reports did not follow the protocol to detect the spherules and that is why they missed them, stirring controversy.

Partial source: Science Daily.

See also for background (this blog and its predecessor in reverse chronological order):

• More evidence in support of the Younger Dryas impact theory (2012)
• Clovis impact theory: scam? (2011)
• Clovis impact theory rejected (2010)
• Clovis impact theory finds new support (2010)
• More evidence for Clovis age meteorite impact (2009)

Wax' dental filling in Neolithic Slovenia

Figure 1.
The Lonche jaw.
Scale bar, 10 mm.

While dentists and their oversized bills are a modern development, ancient peoples also had to face the painful and sometimes deadly problems derived of damaged teeth. In some cases they found what seem to be acceptable home-made solutions:

Federico Bernardini et al. Beeswax as Dental Filling on a Neolithic Human Tooth. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0044904]

The authors mention previous findings in Pakistan (regularly modified cavities) as the actual known oldest record of non-extractive dentistry, dating to 7500-9500 years ago (Coppa et al. 2006) but this one seems to be the oldest record of effective preserved filling. 

The finding corresponds to an individual known as Lonche 1, found in the cave of Lonche in 1937 when the area was Italian territory (now it belongs to Slovenia) and preserved in the Natural History Museum of Trieste with a not of limited informative value about the context of the finding: Upper Pleistocene fauna, believed originally to be one of the oldest human findings in the region. 

However radiocarbon analysis performed directly on the bone provides an age of 6655-6400 cal. BP, corresponding to the Neolithic (Cardium Pottery, post-Vlaška phase). The authors provide us with a succinct description of the cultural context that I truly appreciate:

The area, at the northern shore of the Adriatic Sea, is rich in archaeological cave sites and rock shelters, many of which were occupied during recent prehistory and mainly used for stabling animals. In fact, the Neolithic economy of the karstic area was mainly based on sheep breeding [8]. The neolithization process spread through northern Istria and Trieste Karst in the middle of the 6^th millennium BC, coming from the south along the eastern Adriatic coast, and is referred to as the so-called Vlaška Culture. This culture shows connections with the Danilo Culture of central Dalmatia and the first Neolithic sites of the Friuli plain and lasts up to the beginning of the 5^th millennium BC. The post-Vlaška assemblages (5^th millennium BC) are not yet well understood and a clear chrono-cultural sequence is not available. It seems that there was no substantial change with respect to previous pottery shapes, some of which disappeared [9], [10]. However, a few and new typological elements suggest cultural affinities with Dalmatia (Hvar Culture) and northern Italy (Square Mouthed Pottery Culture).

Alert: Foissac cave threatened by pig farm expansion

The expansion of an existent pig farm from 1000 to 8000 heads per annum threatens to contaminate the cave, inhabited in the Chalcolithic and Paleolithic, with pig manure.

Foissac (Aveyron department, Languedoc) is particularly wealthy in burial, pottery and other Chalcolithic remains, which are preserved in situ because of exceptional conservation conditions (it was dug up by F. Rouzaud, M.-A. Garcia and H. Duday between 1978 and 1988). 

More recently (2006) a branch of the same cave was found to have Paleolithic rock art, which would be at risk by this farm. 

There is an ongoing public inquest (ending on September 27) which has been given no publicity. However you may want to write to the authorities at the following address:

Monsieur Le Commissaire Enquêteur
Mairie de Causse et Diège, Loupiac
12 700 CAUSSE ET DIEGE.

There is also an online petition that you may sign.

More information (in French language in principle) at:

Sébastien du Fayet de la Tour : sebastien.dufayet@voila.fr
mobile phone : 06 11 75 97 02
Grotte de Foissac : 05 65 64 60 52

Source: Hominidés.com.

See also the official site of the Foissac Cave.

Beautiful polished axe from Arunachal Pradesh

From the Archaeology Network:

A prehistoric tool of Neolithic period has been found in Taksing under Upper Subansiri district, bordering China.

The Neolithic axe-head found at Taksing [Credit: Arunachal Front]

Tade Ebo, Taksing  CCR evangelist and one Talin Rigia handed over the axe-shaped Neolithic tool to research director Dr. Tage Tada on September 12, which is now on display in the Itafort Archaeological Museum here.

The tool is of rectangular in shaped and made out of diorite black stone. Both the surfaces are fully grounded and finely polished but a few sears are seen in the lateral margin of the tool. The cutting edge very sharp, convex and bifacially beveled. The shape, size and workmanship of the tool indicate that it was used as axe by the people in the Neolithic age, most probably for the purpose of agriculture and farming.

Tada informed that this was the first finding from the remote Indo-China (Tibet) border. “The possession of the tool will provide opportunity to the students of archaeology of the state for its further investigation and add definite information on the prehistoric period of the area”, he added.

The Director further said that in Arunachal Pradesh, local people believe such prehistoric tools possess certain sprits. Some believe that such object comes from sky while other believes that such tools are used by the malevolent sprit. “In Taksing the local Nah and Tagin people believe that this has fallen from sky used by malevolent sprits, thus they are very scared of touching the artifact.”

Source: Arunachal Front [September 16, 2012]

______________________________________________

Geographical and anthropological note: Arunachal Pradesh is effectively administrated by India as state but also claimed by China (via its annexation of Tibet). For what I care it belongs to its own peoples, a diverse array of mostly Tibeto-Burman ethnicities. From an anthropological viewpoint the whole region so-called NE India (between Bangla Desh and Burma is transitional between South Asia and SE Asia.

Overwhelming evidence of the use of decorative feathers by Neanderthals

Neanderthal with feathers (Gibraltar Museum)

This research should delight all those interested in the so-called "modern human behavior" or "symbolic behavior", and specially those who emphasize that Neanderthals were at similar levels as is our species, H. sapiens, in this aspect.

Clive Finlayson et al., Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0045927]

Abstract

The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham's, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.

In brief: Neanderthals did use feathers from raptor and corvid avians and used them with almost all certainty for decorative, ritual or other cultural purposes.

Figure 2. Distribution of archaeological and paleontological sites with 50% or more of the suite of 18 raptor-corvid species identified in the text.

See also articles at: Pileta[es/en], BBC.

300,000 year old wooden spears found in Germany

Warning: while the findings are correctly reported for what they are, they seem to be very old news, not from 2008-12 but from 1994-98 (h/t to Eurologist). It's possible that the opening of a new museum next year triggered the press release, which is in any case unacceptably misleading.

However as the data is valid and the findings interesting in their own right, I won't delete this entry.

One of the Schöningen spears

Eight wooden spears and remains of many large mammals have been found in an abandoned mine in Schöningen (Lower Saxony, Germany). The area was underwater before the mine explotation began what explains (because of low oxygen) the exceptional preservation of the weapons, though to have been made by Homo heidelbergensis, such as the contemporaneous specimen from Steinheim, the direct ancestor of Neanderthals.

The bones of large mammals -- elephants, rhinoceroses, horses and lions -- as well as the remains of amphibians, reptiles, shells and even beetles have been preserved in the brown coal. Pines, firs, and black alder trees are preserved complete with pine cones, as have the leaves, pollen and seeds of surrounding flora.

Another findings from the last several years of research in this site are a water buffalo, a well preserved aurochs, as well as other artifacts, bones and wood - all them apparently from more recent periods.

Source: Science Daily.

Dolmen destroyed in Galicia in search of non-existent "treasury"

Archaeologists revise the destroyed site

An excavator machine destroys a 6000 years old mámoa (dolmen tumulus, usually with a dolmen inside) in the parish of Pinzás (Tomiño, Galicia). It is speculated that the vandals were searching for mythical treasury. In the past many dolmens were broken in and vandalized for similar reasons but this is the first case ever known, I think, to have been done with modern machinery for such a reason.

If anyone wonders, there's no treasury in them. At least no treasury other than archaeological knowledge and the pride of a deeply rooted history.

Source[es]: Faro de Vigo (via Pileta).

Candidate genes for facial morphology

Figure 4
candidate SNPs
click to expand

So far, in people of European ancestry from Germany, Netherlands, North America and Australia:

Fan Liu et al., A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans. PLoS Genetics 2012. Open access ··> LINK [doi:10.1371/journal.pgen.1002932]

Abstract

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes—PRDM16, PAX3, TP63, C5orf50, and COL17A1—in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facial features. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facial morphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications.

Bronze Age settlement under the streets of Ankara

While it is well known that Ankara was once the Easternmost Celtic capital (Ancyra, capital of Galatia) not much is known of the previous period, specially not before the Iron Age, when it became an important Phrygian town founded by the mythical King Midas.

While some layers of the Bronze Age (Hittite influence) were dug in the mid 20th century, no such research has taken place since 1960. The new research at Çayyolu mound has found a diverse array of objects from this era (between 5000 and 3000 years ago) like pottery, hair ties, animal figurines and beads, that will in due time serve to better understand the proto-history of the area. 

The researchers hope to reach to Chalcolithic layers, never before researched in the Turkish capital. 

Source: Hürriyet Daily News (h/t Pileta).

The "Little Ice Age" of the Bronze Age

It has been known now that, roughly coincident with much of the Western and Central European Bronze Age, a strong cold spell similar to the Little Ice Age, which marked much of Modern Age.

I. Schimmelpfennig et al., Holocene glacier culminations in the Western Alps and their hemispheric relevance. Geology 2012. Pay per view ··> LINK [doi:10.1130/G33169.1]

Abstract

The natural variability of Holocene climate defines the baseline to assess ongoing climate change. Greenland ice-core records indicate warming superimposed by abrupt climate oscillations in the early Holocene, followed by a general cooling trend throughout the middle and late Holocene that culminated during the Little Ice Age (LIA). Tropical precipitation changes correlate with these patterns throughout the Holocene. Here we use mountain glaciers in the European Alps to reconstruct the regional Holocene climate evolution and to test for a link between mid-latitude, North Atlantic, and tropical climate. Our precise 10Be chronology from Tsidjiore Nouve Glacier, western Swiss Alps, indicates a glacier culmination during the earliest Holocene ∼11.4 k.y. ago, likely related to the Preboreal Oscillation. Based on our data, no Holocene glacier advance of similar amplitude occurred until ∼3.8 k.y. ago, when the glacier reached LIA limits. The 10Be ages between 500 and 170 yr correspond to the LIA, while the youngest 10Be ages overlap with the historically recorded post-LIA glacier positions. Integrating our data with existing records, we propose a hemispheric climate link between the Alps, North Atlantic temperature, and tropical precipitation patterns for the Holocene, supporting the concept of a pervasive climate driver. These findings from northern mid-latitudes are consistent with the hypothesis formulated for the tropics that the Earth's thermal equator, responding to North Atlantic temperature changes, might have migrated southward throughout the Holocene, reaching the southern turning point toward the end of the LIA.

The river Thames froze often in the 17th and 18th centuries (A. Hondius)

 
The dates mentioned, between c. 1800 and 1200 BCE are coincident with the bulk of the Bronze Age in Europe (except for the Balcans and West Asia, where is the late phase of the Bronze Age). Ironically it was a rather prosperous and interactive period that ended up in many civilizational collapses from Iberia to Anatolia soon after the temperatures went up again (beginnings of the Iron Age). 

By this I am not implying that the temperature cycle and the prehistory/proto-history cycle are related in any obvious way but can't help notice that "our" Little Ice Age was also a period of expansion and prosperity (at least for some) and that we may now be heading to civilizational collapse as well as temperatures raise. Just a coincidence maybe...

More details at PysOrg (h/t Pileta[es]).

Italian and Sardinian autosomal genetics

A new paper investigates the genetic structure of Italy:

Cornelia di Gaetano et al., An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0043759]

The results confirm that Sardians are a very distinct population and show that Italians essentially seem to cluster with mainland Europeans (NW Europeans in principle but Iberian or Balcanic comparisons are missing), West Asians and Sardinians in this order.

There is some N-S gradient in the Peninsula and Sicily but it's mostly determined by an increasing West Asian affinity in the South. Central Italians stand between North and South but clearly closer to the North but many individuals from NW Italy (Liguria and Piedmont, as well as some Sardinians) actually cluster with Southern Italians as well as with "mixed" Sardinians (those Sardinians who stand between the main insular cluster and the peninsular one).

Let's see:

Figure 1. SNP-Based PC of 1,262 individuals from 10 sub-populations.
The Italian population plotted onto the first two principal components defined by the European HGDP-CEPH populations and CEU HapMap data. Scatter plot of the first two principal components, obtained using R software (prcomp). Analysis based on 125,799 autosomal SNPs. Individuals included belong to Northern Italy (N-IT): black dots, Central Italy (C-IT): red dots, Southern Italy (S-IT): green dots, Sardinian (SAR): blue dots... 
[the original legend does not explain well the other populations (too many blatant errors in the text) but it's obvious that the group to the top-right corner are other Europeans (French, CEU), while the group to the center-left are West Asians (Druze, Palestinian, Bedouins) and Mozabites. Larger images can be downloaded from the paper].

In this first characterization we see a primary duality between Europe and West Asia (the Paleo-Neolithic dichotomy probably) and a secondary one between Sardinia and mainland Europe.

Figure 2. SNP-Based PC of 1,014 individuals from the Italian dataset.
A. A Scatter Plot of the Italian population of the first two principal components obtained via R software (prcomp). Individuals included belong to Northern Italy : black dots, Central Italy : red dots, Southern Italy : green dots, Sardinian: blue dots.
B. Italian population without the Sardinian-projected scatter plot of the first two principal components obtained via the R software (prcomp)
[larger images can be downloaded from the paper]

Here we see (A) a main dichotomy between Sardinia and Peninsular Italy (with Sicily) and a secondary N-S gradient. However in (B) it becomes more obvious that to some extent there are two distinct clusters: Southern and Central-North Italy with certain clear separation.

However, and this is quite interesting some North Italians strongly cluster with Southern Italians. Razib mentions this fact as signature of internal Italian migrations but individual migrations would not look that way because the genetic distinction would have diluted in the meantime, appearing at most as intermediate. What we see instead is preserved genetic identity, not too diluted or not diluted at all, with Southern Italy in many Northern Italians.

Who are these Northern Italians, I wondered then. The answer is in the supplements:

Hidden population structure within the Italian dataset. Scatter plot of the first two eigenvectors based on 125,799 autosomal SNPs and 1,012 individuals. Colors represent the four different macro-areas; green- Southern Italy (Apulia, Calabria/Sicily, Campania, Basilicata), red- Central Italy (Tuscany, Lazio, Emilia Romagna and Abruzzo/Marche), black- Northern Italy (Piedmont,Liguria, Aosta Valley and Lombardy), blue- Sardinia (these samples were labeled for the linguistic area). Subjects are symbol- labeled by municipality. Information on municipality was not used for calculations.

[click to expand]

In this image we can appreciate how all Northern Italians clustering with Southern Italians are from two specific regions: Liguria and Piedmont (Piemonte), the Northwestern regions of Italy, bordering France. What do these two regions have in common? All I can think is that, in ancient times they were mostly inhabited by the Ligures, a pre-Indoeuropean people plausibly descendant from the first Neolithic colonization (Cardium Pottery, via the Chassey-Cortaillod-La Lagozza cultural complex). 

Roman region of Liguria (Regio IX)

We are also provided with a bayesian cluster analysis, for which K=4 seems the most valid result (K=3 and K=5 also give low cross-validation values but do not seem more informative):

Figure 3. Clustering of the European, Northern African and Middle Eastern individuals by the Structure software.
Model-based ancestry analysis based on a subset of HGDP-CEPH and HapMap CEU data using the merged data of 126K autosomal SNPs. Ancestry for each individual was inferred using ADMIXTURE [50] at K = 4. Abbreviations as in Figure 1.

This confirms four clusters: Main European (green), Sardinian (red), West Asian (blue) and North African (purple). 

I tend to consider the West Asian component as the main Neolithic input in Europe, although, of course other DNA sections may well have traveled around in that period or later on. 

I also find notable that Sardinian affinity exists among Italians, French and North Africans (surely via Iberia) but almost not among North American Euro-descendants (CEU) of NW European origin and West Asians, who instead do sport some notable Mainline European affinity. 

It's also interesting that CEU are among the most North African related of all European populations.

Some prehistoric and proto-historic speculation

IF, and only IF, the affinity of Ötzi with Sardinians can be considered representative of how most Italy was in the Chalcolithic (and not a random fluke specific of that man or his mountain community), then, we should consider two further waves into Italy: (1) of West Asian affinity (maybe from the Agean since the Bronze Age or even before) and (2) of mainland European affinity (Indoeuropeans: Italics, Celts).

IF this is correct then the Ligures would not be so much descendant genetically from La Lagozza-Chassey, as I said above but from the "Aegean" wave. This would also be consistent with some individual Tuscans clustering with Southern Italians as well (historical Etruscans are one of the culminations of these Aegean waves together with the Greek colonies). 

But sincerely, I am not aware of any such Aegean flow arriving to the proto-historical Liguria, are you?

So I must consider that there is another possibility: that the Sardinian element represents only one of several Neolithic (or maybe even Paleolithic but nothing clear here) elements in Italy, maybe associated to Y-DNA I2a (strong in Croatia, Bosnia, etc.), while the other, the one most akin to West Asia, would be related to Y-DNA E1b-V13 (strong in Greece and Albania) and maybe other patrilineages from the Eastern Mediterranean like J2b, etc. Both E1b-V13 and I2a are know from ancient DNA from the Neolithic of the Western Mediterranean, so they did indeed take part in these migrations.

Then the "Greek" or "Aegean" (or "Albanian" if you wish) component was reinforced by Bronze Age flows while the "Dalmatian" one was diluted instead by the successive Indoeuropean (Kurgan) waves.

I'll leave it this way until more evidence comes forward.