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Monthly Archives: February 2011

Lack of vitamin D also causes allergies among children

In another example of the critical role that vitamin D plays in human development, it has been demonstrated now that children with low levels of this key nutrient develop allergies.
Vitamin D is relatively difficult to obtain from food (mostly fish) but we make it in our skin when irradiated by sunlight. Skin color variation is directly related to this necessity.
In the past lack of vitamin D in children (or their mothers) has been linked to rickets, incorrect brain development, autoimmune diseases and other immunity related problems. Allergies also fall within the problematic of inappropriate immunity and can well be considered autoimmune diseases, even if often mild and with very specific triggers.
Source: Science Daily.
See also:
 
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Posted by on February 26, 2011 in health, human evolution, pigmentation, vitamin D

 

Archaeonews Feb 25

The latest compilation of the sometimes quite interesting archaeological news from around the world by the people at Stone Pages is in my mailbox today. I cannot really pick one or two this time, so I’ll offer you half a dozen instead:

Paleolithic:

Neolithic:
  • 9 meters underwater at the Isle of Wigh… there is a whole Neolithic settlement with incredibly preserved wood artifacts – video at BBC
  • Recognize Somaliland to preserve its Neolithic treasures (right), or why UNESCO will not protect the impressive Neolithic cave art of this very real African state – article at CNN
  • Sauna and pork feast remains at Marden Henge, England. I’d say this pretty much demolishes the idea that saunas have any sort of Celtic or Indoeuropean specific cultural link – article at This is Wiltshire 

Metal Ages:

See also: Stone Pages.

 
 

Craniometrics confirms that Eastern and NE European Neolithic was made by aborigins, not immigrants

On the contrary the same skull-measuring method suggests that there was at least partial replacement in the Balcans and Central Europe, where other archaeological and archaeogenetic evidence also supports such population replacement.
No information is provided for the Cardium Pottery area from Bosnia to Portugal but, considering the archaeological and genetic evidence I’d bet a lot that there was only localized population replacement as well, specially as one moves westwards. Also no information is provided for Atlantic Europe but again I daresay that there is a strong case for demographic continuity here as well. 

The results show that while the initial transition to agriculture in central Europe was the result of migrating farmers from the Near-East and Anatolia, agricultural practices were adopted by indigenous hunter-gatherer populations in outlying regions of Europe. Therefore, instead of employing two competing and mutually exclusive models of biological versus cultural diffusion, a mosaic model of both biological and cultural diffusion is a more appropriate model for this demographic change across Europe as a whole.
Totally agree with this last part. I always found totally annoying that results from Germany and Poland would have to be extrapolated to the whole of Europe when the cultural dynamics were so different in the various regions and periods. This underlines a basic lack of multidisciplinary education on the part of researchers, specially some quite pretentious geneticists.
The paper is authored by Irish researchers Ron Pinhasi and Noreen von Cramon-Taubadel and will be published soon at PNAS.
Open issues:
Where did the colonists originate? It is easy, I understand to detect changes in local population composition, but novely does not necessarily imply direct arrival from the Fertile Crescent. Actually a more nearby origin is likely instead even if there is a chain reaction of sorts. 
What happened to them after that? One thing we have learned from ancient DNA research is that there was demic replacement in Central Europe most probably with Neolithic but also that there must have been another population shift some time after it. We do not see anything like modern mtDNA pools in the area before the Urnfield Culture (late Bronze Age). What does this mean? Did proto-Celts or whoever genocided not just the Neolithic farmers but also the early Indoeuropeans who had vanquished them first? Why do these people show a type of genetic pool apparently once common in SW Europe (high mtDNA H particularly)? 
Complex stuff that I do not dare to answer, specially because the evidence is not yet comprehensive enough.

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Update (Feb 24):
The paper is already up and freely available (thanks to Natsuya for the tip):
Interestingly the Natufian Mesolithic and the Central European Epipaleolithic (“Mesolithic”) samples are totally off the chart, however all other European Epipaleolithic samples, from West and East are within the box of mainstream Westerness by all measures.
However this main group of cranial homogeneity has two clear subsets: one of Anatolian and apparent Neolithic affinities and another that includes all other European Epipaleolithic samples, as well as East European Neolithic ones. Pretty much settling the issue of the origin of Eastern European Neolithic cultures: local development based on occasional contacts, something that was already quite obvious based on archaeology as well (continuity of extended burials with ochre, rustic pottery unrelated to that of West Asian or Central European cultures, high importance of hunt until late dates).
Sadly no data is provided for any West European Neolithic, not even Mediterranean Neolithic with the rather unrepresentative exception of a Chalcolithic Sardinian sample. In this aspect this paper is no help at all.
Following the rather consistent affinities, some observations can be made:

Pan-European Epipaleolithic archetype

Fig. 3, click to expand
Among hunter-gatherers (and Eastern European Neolithics), other than the outliers from Swabia, the main standard is one including SW Europeans (Portugal, West France), a Serbian sample from Vlasac and one of the two Dniepr-Don samples (the one from the Don basin). So we can well talk of a very much homogeneous pan-European type for which the oversampled East Europeans are rather an exception, outliers, yet closer than all Anatolio-Balcano-Danubian-Danish Neolithic peoples.
Two demic flows from highland West Asia are apparent
Based on the rather consistent groupings of Neolithic peoples in the Central European strip, I think that it can well be argued that
  1. Most danubians (LBK) appear to be directly related to Thessalian Neolithic (Nea Nikomedia) and this one to South Anatolian neolithic (Çatalhöyuk).
  2. Eastern Linear Pottery (AVK, Tisza basin) peoples seem to relate best to SE Balcan Neolithic peoples (probably well represented by the Gumelnita Chalcolithic site) and Pre-Pottery Neolithic B of the Upper Euphrates.
  3. Some peripheral groups seem rather distinct and may suggest admixture with natives.
  4. The Körös group is consistently similar to Danish Neolithic peoples of TRBK (Funnelbeaker culture) and this set falls quite apart from the other Neolithic populations in the ME tree, while it falls outside the mains Euro-Anatolian set in the NJ tree. This would be probably best explained if this Hungary-Denmark affinity pre-dates Neolithic. However the only local Paleolithic sample (Vlasac in Serbia) clusters elsewhere, so maybe it means a mixed population after all. In any case I do not think anyone can argue that Körös-TRBK is a purely immigrant population on light of this data.

I tried to visually represent these notions over the map in fig. 1:

My visual interpretation of the affinities revealed in the paper

The solid join-the-dots blue and green lines represent most homogeneous Neolithic subclusters of apparent West Asian origin. The nearby dotted areas suggest hybrid populations at the “margins” of this Neolitic demic expansion (yet in some cases such as Körös or Lengyel, they are rather in the middle of all, not truly peripheral). 
The dashed purple line of course represents the area of aboriginal Neolithic of Eastern Europe, while the dotted purple line around Denmark suggests a highly native but admixed population in that area. I failed to represent the Denmark-Körös connection however.
I also failed to represent the grouping of Lengyel, Michelsberger, LBK West, Blicze Zlote and Chalcolthic Sardinia, whose meaning I fail to comprehend (except that they are probably all admixed Anatolian-European Aboriginal peoples).
 

Laotian genetics (mtDNA)

Laos is a state of Indochina Peninsula (also mainland SE Asia) hosting a huge ethnic diversity. As many as 49 ethnic groups are acknowledged nowadays, often divided into lowland (Lao and others, mostly of Kradai languages), midland (Mon-Khmer and others of mostly Austroasiatic languages) and highland peoples (Hmong and others of Hmong-Mien and Tibeto-Burman languages).
As far as I know the genetics of this part of the World had not been explored in until now:
Fig. 3 – PCA

I’ll excerpt some of the paper’s most interesting insights here:

Major haplogroups and macrohaplogroup structure:

The most prevalent haplogroups were B5a (12%), F1a1a (7.5%), C7 and M7b1 (6% each).
Macrohaplogroup N (including haplogroups A, B, F, N and R) comprised 57% of the samples in 37 haplogroups. 26% of the samples were assigned to haplogroup B, almost equally to B4 and B5. 26 out of the 27 haplogroup B5 samples were found to be haplogroup B5a. 22% of the samples belonged to haplogroup F, of which 79% belonged to F1a and its subhaplogroups.
Macrohaplogroup M (including haplogroups C, D, G and M) comprised 43% in 27 haplogroups. 32% of the samples belonged to haplogroup M, distributed among ten subhaplogroups. 25% of the M samples, however, remained M*. No maternal west Eurasian or African admixture was detected.
The recently described haplogroup M71 was diverse in the Laos sample.

Characteristics of Laotians and some control populations:

The Laos sample showed mtDNA diversity characteristic of Southeast Asian populations. The composition of haplogroups was in agreement with other populations from this region [3- 7,12,17,23-25,35], with haplogroups B4a, B5a, M7b1, F1a and R9 being the most frequent southern aboriginal lineages.
Little Northern contribution was detected. The presence of haplogroups described as Northern (East) Asian [4,6,7,25,36], i.e. A, Z, Y, C, M8a, M9, G2, D and N9, was low in the Laos dataset.
Obviously, the Han population samples did not cluster in the correspondence analysis. Although assigned to the same nationality, they are distant from each other genetically.
It was also meaningful to separate the Hmong and Mien population samples [5], that are usually combined based on linguistics, as they differ genetically (see Figure 4).

Fast post-OoA migration confirmed:

… the novel basal M haplogroups found in high diversity in the Laos sample and surrounding populations support the fast migration and in situ differentiation model (see Figure 3).

In spite of language Laotians are closest to Austroasiatics than Daics:

An interesting picture was revealed (see Additional Files 6, 7 and 8, Figure 4): the ethnic population with the highest similarity to the Laos sample in terms of shared haplotypes, MPD, pairwise FST values and localization in the MDS plot were the Austro-Asiatic [3]. This was unexpected…

… unexpected probably because the assumptions of the authors about the recent demographic history of the region (full of mass migrations towards the mountaintops – what?!) just do not seem to make much sense.

 
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Posted by on February 19, 2011 in Laos, mtDNA, out of Africa, population genetics, SE Asia

 

Jericho’s tower had astronomical relevance

Astronomy was clearly important in the lives of the ancients, it seems. It was at least the case in early Neolithic Jericho, whose seemingly classless society built a stonewall dominated by which was probably the tallest building back then: a tower at least 8.25 m tall (left).

Interestingly it has been discovered now that the tower is aligned with the summer solstice in a way that, when the Sun sets that evening, the shadows of the nearby hill envelop first the tower and then the whole town.


Roy Liran and Ray Barkai, Casting a shadow on Neolithic Jericho. Antiquity, 2011. Freely accesible. 

 
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Posted by on February 18, 2011 in astronomy, Neolithic, Palestine, West Asia

 

Brazilians are much more homogeneous than ‘racial’ categories suggest

This is a very revealing paper on Brazilian genetic makeup and the shallowness of racial classification in general:
Abstract
Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a “total ancestry” estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries – a phenomenon described and intended as the “whitening of Brazil” – is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

Real ancestry of various regional populations divided by racial self-description (fig. 2):

It is I think quite interesting to realize that racial categories are often meaningless in representing the real ancestry of individuals collectives. This is specially true for the brown (pardo) and black (preto)  categories but, in the north specially, it is also very true for the category white (branco). In this sense, the Brazilian census would probably do well dropping racial categories altogether, as they are obviously without meaning. 
Overall Brazilians seem mostly of European ancestry (60-80%), with some lesser regional variability, as is very apparent in figure 3:

Native American ancestry is rather homogeneous by regions, making up 7-10% of the ancestry except in the North (Amazon) region, where it’s double (19%). African ancestry is somewhat more important and also regionally variable: 10% to 29% (this last in the Northeast).
Notice anyhow that the samples were collected in six specific cities and that specially the vast Amazon region is probably under-represented (as the only sample comes from Belem, a large city of the coast). I’d dare say that the vast Brazilian interior (all samples are from the coast) must be stronger in Native American ancestry, even if we do not consider the surviving aboriginal populations, but only the creoles.
 

Hainan islanders’ matrilineal relations

Location of Hainan (red)

The Li or Hlai are a Kradai-speaking people from Hainan, today a province of P.R. China and the only one which is fully insular (besides the claimed but not controlled Taiwan). However in the Pleistocene Hainan used to be a peninsula and therefore an affinity with mainland peoples was to be expected. 

Effectively there is such affinity, notably with the people of Guangxi Zhuang, who are still largely also speakers of Kradai (or Tai-Kadai) languages (Zhuang specially). This and other findings are detailed in this new paper:
Key excerpts from the paper:

We found that Hainan islanders showed close relationship with the populations in mainland southern China, especially from Guangxi. Haplotype sharing analyses suggested that the recent gene flow from the mainland might play important roles in shaping the maternal pool of Hainan islanders. More importantly, haplogroups M12, M7e, and M7c1* might represent the genetic relics of the ancient population that populated this region; and 14 representative complete mtDNA genomes were further sequenced.

The predominant haplogroups in southern China and Southeast Asia: haplogroups B, F, and M7 together account for ~ 69%, 71%, and 63% of the maternal gene pools of the populations Li-BT, Li-LD, and Li-QZ, respectively (Table 1). The prevailing haplogroups in northern China, such as haplogroups A, D4, G, and Z, were rare or even absent in the three Li populations.

The genetic difference between Hainan islanders and populations from the mainland was statistically significant (p < 0.001, Analysis of molecular variance, AMOVA), whereas the difference between the Li populations (Li-BT, Li-LD, Li-QZ, Li-TZ, and Jiamao) and non-Li populations (Cun, Danga, and Lingao) was not (p = 0.147±0.010, AMOVA).

In general, the mtDNA haplogroup profiles of Hainan islanders are similar to the profiles of the populations from mainland southern China. (…) Especially, most Hainan islanders were clustered with some populations from Guangxi (Figure 3). This pattern was also reflected by the genome-wide data: the Jiamao population in Hainan Island was clustered with the Zhuang population (i.e. the dominant minority ethnic group in Guangxi) (…)

Additionally there are some interesting data mines in the additional files and the figures. Sadly at the moment of me reading the provisional manuscript, most of these figures suffered from critical crop errors and cannot therefore be used (fixed, see below) to illustrate the results of the study.

Update (Feb 17): the illustration errors have been fixed (sometimes writing an email is worth it) and now they can be used to better understand the genetics of the area. For example:

From fig. 6: frequency of mtDNA M12

PC analysis, Hlai (Li) people are to the bottom left

 
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Posted by on February 16, 2011 in China, East Asia, mtDNA, population genetics, SE Asia