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Monthly Archives: September 2012

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:

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).

 
2 Comments

Posted by on September 27, 2012 in archaeoastronomy, archaeology, East Asia, Neolithic, SE Asia, Vietnam

 

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!
 
6 Comments

Posted by on September 25, 2012 in blogging, general strike

 

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. 
 
5 Comments

Posted by on September 21, 2012 in Africa, Epipaleolithic, Iberia, Morocco, Neolithic, North Africa

 

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.