Monthly Archives: April 2011

O2b and other Y-DNA from Korea and surroundings

In another discussion, Terry brought up this recent paper on O2b and Korean patrilineages (with important references to the rest of East Asia) that I believe is worth mentioning:
Much of the paper is tainted by insistence on lineage age speculations (TMRCA) which help nothing, are unscientific and induce confusion. However I do find interesting that they seem to find (figure 3) that SE Asian instances of O2b (O2b* and O2b1) are derived and not ancestral in relation to NE Asian ones. Hence the occasional O2b found in SE Asia (Indonesia, Vietnam, Thailand, etc.) looks like having originated in Korea or nearby. 
On the other hand the haplotype neighbor-joining structures for O3 and C still look like rooted in the South. In relation to NE Asian C (C1 and C3) I find most curious that a single Korean haplotype would seem to hold together C1 and C3, maybe indicating a joint origin within C for these two NE Asian haplogroups.
Overall I get the impression of a South to North colonization in East Asia, which pretty much set the fundamentals of modern population genetics in the whole region. This process was surely followed at a later time by some North to South backflow, which does not need to be “Neolithic” (beginning in South China at least as early as in the North) nor “Han” (in many cases the relevant haplogroups are definitively not found among North Han but Koreans, Japanese, etc.), it may well be, at least partly, related to the extension of blade industries since c. 20 Ka ago, phenomenon that might have got a southwards pointing vector. 
In any case, an important reference for data miners. 

Posted by on April 30, 2011 in East Asia, population genetics, Y-DNA


74th anniversary of the destruction of Gernika

Gernika Oak (source)

Gernika is the only town I know in the Basque Country that lacks of an old quarter. Everything, excepting some peripheral buildings, is new, built in the last seventy or so years.

Gernika and not Guernica, mind you, because Gernika is the Basque spelling and also the Spanish spelling Guernica is misleading in English, making people mispronounce Gwarnikah, when it is actually Garnikah – pronunciation is exactly the same in both languages: Basque and Spanish, only spelling changes. 
74 years ago the town of Gernika, the historical capital of Biscay, was totally destroyed by the systematic bombardment by the Nazi Condor Legion, sent to support the fascists in spite of the supposed international embargo to both fighting sides. This fact underlines that United Kingdom (more or less reluctantly seconded by France) supported the Fascist side in the Spanish Civil War, by means of impeding the legitimate government from getting international support (only some lesser, costly and highly conditional Soviet support arrived besides the enthusiastic but ill equipped international brigades), while the Fascists got all the support they wanted and more from Italy and Nazi Germany.

Before the destruction (source)
In fact they were Italian brigades the ones that marched over most of Biscay after German airplanes bombed not just Gernika but also Durango and other localities. In fact it was largely an Italian and German full fledged invasion with the complacency of Great Britain, who forced France to accept this arrangement (and later used it as cannon fodder against Germany in WWII anyhow). 
Bundesarchiv Bild 183-H25224, Guernica, Ruinen74 years ago, in April 26 1937, at 15:37, sirens scared the town. It was monday, market day. For the first time in history a town was totally razed by an air bombardment. Years later, as other cities like Dresden or Hiroshima were also totally razed in the course of WWII, Gernika would seem by comparison pecata minuta, but in it its day it truly impressed the global collective psyche. It was not so much the few thousand dead (not many compared with the million who died in the whole war) but the fact that a civilian town had been so barbarically razed, looking to cause terror rather than military goals. 
In addition the town, as historical capital of Biscay, held and still holds an oak tree that was symbol of Basque freedoms, under which the Parliament of Biscay had been gathering since memory exists, since at least the 11th century (eventually a building was built by the tree). and where the monarchs of Castile (later Spain) took oath of respecting the Basque self-rule. Then of course the painting by Picasso also helped to emphasize the horror and confusion that such a war crime caused all around.


A few days later the Italian columns took the whole district, marching on an ill defended Bilbao, from where I now write these lines, and from there westwards to Cantabria and eventually Asturias too. Eventually they would take the whole state, ending the Republic and suppressing the long-lived self-rule of Biscay and Gipuzkoa. The scars of this war and the fascist dictatorship that ensued for decades, effectively destroying two generations, still persist. 

Because, Gandhi dixit, violence engenders violence.

The “Guernica” to Gernika (in Gernika)

Bamboo knives? Darts?

Bar-Yosef splitting bamboo with simple stone tools
There is a long held idea among prehistorians that maybe, only maybe, the peoples of SE Asia used bamboo-made tools instead of stone-made ones, what would explain the relative scarcity of stone tools in this area before the Hoabinhian (or rather its predecessor: the Son Vi culture) and the fact that they are mostly flakes and cobbles, not blades.
The hypothesis was floating around for decades but was never, I understand, tested in any practical way. Now a team lead by O. Bar-Yosef and manned by the expert hands of knapper Metin E. Eren, have attempted to reproduce these alleged bamboo knives.
They found that making with the simplest stone tools them was relatively straightforward (see video) but that, once created, they’d lose their edge quickly. Also the ability of bamboo knives to cut hides was poor even if they are useful to cut meat.
On the other hand, Eren was able to produce which is maybe the most critical bamboo tool needed: a spear or dart. While bamboo knives were surely useless in comparison with simple stone flakes, bamboo darts may have been a critical component of the Paleolithic toolkit: the hunter’s weapon.
Of course, bamboo proved itself ideal for basketry and container creation.
Direct sources:

ArchaeoNews April 23

A quick review to some of the most interesting archaeological news from the Stone Pagesnews bulletin:

Oldest (c. 6000 years ago) European depiction of magic mushrooms (Psylocibe sp.) is in Central Spain (left). An even older one is known from Algeria (c. 9000 years ago). (New Scientist).
A very interesting research article by George Nash et al. on the Llwydiarth Esgob stone can be found at Past Horizons.
Neolithic houses found under modern ones in Saxony (Germany) (Google – Canadian Press).

South Asia
Dolmen burials discovered in Central India. The newly found megalithic sites near Nagpur are among the northernmost ones of this Iron Age cultural and spiritual phenomenon (Times of India).
East Asia

Before the outrigger?
Bamboo knives excellent for meat but awful for hides, and they dull quickly. Practical research by O. Bar Yosef, M.I. Eren and others sheds light on the bamboo knife speculations regarding Eastern Asian Paleolithic (SMU Research Blog). This is so fascinating that I’ll write a separate entry later on.
Rising Seas transformed rice farmers into fishermen at Fuzhou (SE China), what might have triggered the Austronesian expansion (New Scientist)


Oldest cloth from Peru (left) is 12,000 years old (Past Horizons, Eureka Alert)
7000 years old human remains found in Iowa during sanitation works (Fox News)

The Africanness of Europeans (and West Asians)

Sincerely not my ideal of research on population genetics but this new paper still offers some stuff to chew on:
An important bias is the lack of other West Asian or North African references. The paper deals with Europeans, Jews and Palestinians (with emphasis in the comparison with the Yoruba outgroup YRI) and that’s about it (we also find Turks in the supplements). This has interest, of course, but also has huge limitations. 
Specially problematic, considering that the paper tries to study an apparent African component in West Eurasian populations, is the lack of North African references. 
The authors fail to see it but for me it is transparent that what they identify as “African admixture” is nothing but North African admixture, surely related to the expansion of Y-DNA E1b (though not strictly so). The origin of this lineage is surely in NE Africa, around modern Sudan, and arrived to West Asia and Europe surely by two main routes:
  1. Via West Asia and Greece and then with the Neolithic flows.
  2. Via West Iberia and then through the Atlantic (mostly) with Dolmenic Megalithism.
In order to illustrate my point, I shall borrow here an image from a previously discussed paper:

The YRI component vanishes when Iberians and NW Africans are directly compared
The authors also pretend to be able to pinpoint the approximate age of such alleged (and ill understood to them) “admixture” but their dates make no sense whatsoever. At least not for me. So I’ll ignore that part.
We lack of a good source population: HapMap Yorubas YRI can only be a proxy outgroup and the various Palestinian groups can only be an already much admixed proxy. But estimating from several sources (including this PCA, from this earlier entry) I believe that the “YRI admixture” approximates 1/3 of the true admixture with the original Low Sudanese or Upper Egyptian main true source (?) of West Eurasian Africanness.
So all the results should be multiplied by three to estimate the apportion of “Nubian” input. A “Nubian” true original population is anyhow an approximation, because in the Iberian case most of the Africanness is in fact of Moroccan or otherwise NW African origin, with no immediate ties with Sudan (E1b1b1b1-M81). 
If so, I estimate, based on table 2 (and multiplying by three), that there is roughly the following fractions of Nubianness:
  • Palestinians c. 30%
  • Portuguese c. 6% (notice that the actual amount of North African component in West Iberia is more like 9%, so we are underestimating here the real “Moroccanness” by 50% – this is probably because Moroccans are quite less Yoruba-like than Nubians)
  • South Italians c. 5%
  • Spain c. 3% (4.5% is probably more realistic for “Moroccanness”)
  • Sardinians and North Italians c. 0.6%
  • Ashkenazi Jews c. 8%
  • Other Jews c. 12%
Whiter than thou…
And that would be what I’d have to say on this only somewhat interesting paper but I happened to dig into some of the supplementary material and I’d say that fig. S1 has some interest. 
Of course it has some interest for those who enjoy racialist (tending to racist) comparisons. The lack of other outgroups like East or South Asians, allows for a very black and white (literally) reading of this material. That’s why the title of this section, because in most racialist forums there is not going to be a blacker than you argument, certainly not involving European populations.
Interestingly there are very few populations whiter than HapMap’s CEU sample. As you may know this strange sample that pretends to represent Europeanness in so many simplified genetic studies is made up of Caucasoid people from Utah (USA): it’s not even a true European sample. However it seems representative enough for English-plus (most white Utahns claim English or, some, Danish ancestry, according to US census data).
Following fig. S1, most populations are actually blacker than CEU, so to say, i.e. they tend towards YRI at least slightly more than CEU. I could only spot two exceptions: Orcadians and  Basques. So we can well say that CEU are, at least in contrast to Africa, a paradigm of Europeanness (after Orcadians and Basques) – however no judgment can be made in relation to other outgroups (from Asia) based on this paper’s data.
Some significant structure within Europe
An interesting element in this supplemental fig. S1 is the second (vertical) dimension. In most tripartite comparisons between CEU, YRI and another European population, CEU and the other Europeans overlap in the second dimension, which only reflects diversity within Yorubas themselves. I understand that if Yorubas are more internally diverse than these two European populations, the potential structure between NW Europeans (CEU) and the compared third population is not-significant, trivial, irrelevant. 
This is the case for: Swedes, Irish, Germans, German-Swiss, Belgians, Scots, Orcadians, Dutch, French-Swiss, French (two different samples), Polish, Austrians, Hungarians, Czechs, one of the two Russian samples (POPRES), Spaniards, Portuguese, Bosnians, Croatians, Romanians, Greeks, one of the two Italian samples (CEPH-HGDP), Tuscans, Italian-Swiss. This was also the case for Turks (not technically European) but not for any of the other West Asian (Palestinian) samples nor the Ashkenazi Jewish one (which is the most Europanized of all Jewish subgroups). 
Among Europeans, a number of populations show more structure in comparison to CEU (and hence the majority of Europeans) than Yorubas show among themselves, defining a second dimension in intra-European terms. These “outlier” European populations are:
  • Basques
  • Russians CEPH-HGDP (which I believe are from the Far North and have probably a strong Finnic component)
  • Italians POPRES (which are partly from the South – North Italians alone did not contrast much with CEU)
  • Sardinians
In addition all the Palestinian groups (“Palestinian”, “Druze”, “Bedouin”) also show such contrast with CEU, as do Ashkenazi Jews but not Turks.
Follow the four relevant eigenvector graphs:

Comparison with Basques

Comparison with POPRES Italians

Comparison with Sardinians

Comparison with CEPH-HGDP Russians

Posted by on April 23, 2011 in Africa, autosomal DNA, Europe, North Africa, West Asia


Haplogroup O3 downstream structure refined

A new paper has revised some details of the phylogeny of Y-DNA haplogroup O, specially of O3:
Shi Yan et al.,  An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics, 2011. Pay per view. [doi: 10.1038/ejhg.2011.64]
A copy of the paper can be read (for a year) here.
Most importantly, three subclades (O3a1, O3a2 and O3a4 prior to this review) have been joined in a single subclade of O3a that gets the name O3a1, defined by newly described mutations L127, KL1 and KL2.
Former O3a3, the most common lineage in China, is now relabeled O3a2 (per the paper’s proposal) and subclade O3a3b2 (P164) goes up in the hierarchy as O3a2c, absorbing its “uncle” (O3a3c – M134) as a subclade (now O3a2c1) and becoming independent from its former “father” lineage O3a3b (M7), which retains the name.
Another subclade moved up in the phylogenetic hierarchy is former O2a1a (PK4), which is now revealed to be ancestral (and not descendant) to former O2a (M95). 

Figure 1 should help understanding these changes:

click to expand

The three regions (East, North, South) refer to regions of China (rough references: Shanghai, Beijing and Guangzhou respectively, I guess). Most haplogroups are quite evenly distributed but some are only (or almost only) found in the South. These are (by the new nomenclature):  O1a2, O2a*, O2b and O3a2a. Inversely O3a1a is not found in the South (dominant in the East instead). Notice that because of the samples being taken from students at a Shanghai university, East China is oversampled.

A discussion in Chinese can be found also in this Forum of Molecular Anthropology. Thanks to Natsuya for the info.

Posted by on April 22, 2011 in China, East Asia, population genetics, Y-DNA


A one-dimensional universe at the Big Bang?

This is so weird and intriguing that I can’t but make a quick comment on it. Two US scientists, Jonas Mureika and Dejan Stojovic, are proposing a radical rethink of what we understand as the basic physics of our universe: they suggest that, at the Big Bang, the Universe had only one dimension (like a line), acquiring then two dimensions (plane) and then three (space), and probably soon a fourth (if not already). 
This radical rethink seems to have been pushed by the advances (and lack of them) in the fields of Physics and Astrophysics in the last decades, when questions have been piling up and convincing answers have been lacking instead. 
These problems include the fundamental incompatibility between gravito-centric General Relativity and particle-centric Quantum Mechanics, the mystery of the Universe’s accelerating expansion (which seems to demand extra dimensions) and serious issues with the elusive (and maybe non-existent) Higg’s Boson. 
By reflecting this new proposal I do not mean to adhere to it but I do like the principle they begin from: maybe something fundamental is wrong in the way we think Physics, so exploring radically new venues may be the way out of an otherwise unsolvable problem. 
They are thinking out of the box and that is something I really like and that often brings real solutions in all fields. 
The new theory has been published in the Physical Review Letter (pay per view) and is also discussed in its essentials at Science Daily.
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Posted by on April 21, 2011 in astronomy, physics, science