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Monthly Archives: December 2010

Before I forget again: I found the reference for L2 among the Sakai (Semang) – M51a1 probably in fact

This is something that has shown up in some discussions and I had totally forgotten where I had found this reference of one Negrito from the Malay Peninsula with an L2 lineage. It is from Tanaka 2004 (table 2).
It might be a misclassification but in any case there it is. If correct, it could be a remnant from the less lucky lineages which also took part in the Eurasian colonization, along M and N but were drifted out.
Just for the record.

Update: misclassification almost certain: checking the sequence, which is a mere HVS-I one, always confsing, I realize that it lacks a key mutation defining L2  at 16390 and the other HVS-I site at the root of L2 is identical to the one of L3 (site 16311 towards CRS in both cases). Then checking within L3, I soon found that M51a1, a South Asian haplogroup, I believe, is at least as likely to correspond to the sequence described:

“Also striking is the presence in Sakai of an unequivocal representative (16223–16274–16278–16294–16309) of the sub-Saharan African L2a haplogroup (Torroni et al. 2001)”…

I did not check further because I realize now it is surely a case of misidentification because of excessive reliance on HVS-I, which is not enough in most cases to describe a haplogroup with safety. 

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Posted by on December 30, 2010 in East Asia, mtDNA, out of Africa

 

Conservative brains are full of fear

Fans of the classical (but probably incorrect) blank slate hypothesis of the human brain won’t like this: new research (not yet published at a peer review journal, will be in the near future) has found that conservative people have a larger amygdala, a primitive almond-shaped part of the brain responsible for fear and anxiety.
It is unclear if this physical/neurological trait is caused by the ideology, which is clearly based on fear of any change and attachment to some learned values, or if, inversely, it is the biological trait which causes conservative ideology. Different research, earlier this year found that people with more liberal ideology tend to share a variant of the DRD4 gene, which may be a cause of openness to novel ideas (which in turn may increase adaptability, as hyper-specialists invariably go extinct in the long term).
Source: Salon
Also, in regard to the role played by the amygdala in fear, you may be interested in this story (another scientific research) about a woman whose amygdalas were destroyed by a disease and who feels no fear whatsoever (what also has its downsides: fear is a natural emotion or instinct that plays a clear role in survival).
Additionally, Razib mentions today that conservatives (in the USA) tend to be fatter than average. Maybe they have to compensate for their quasi-permanent state of panic by giving themselves continuous treats?

Update (Jan 13): Amygdala stores “Pavlovian fear conditioning”  according to the latest PLoS ONE paper on the matter by H.G. Bergstrom and colleagues.

 
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Posted by on December 30, 2010 in biology, human genetics, mind, psychology

 

Aurochs mtDNA in Italian cattle

Aurochs fighting wolves by H. Harder
The same as Neanderthals did not completely go extinct but live in us (albeit in very small apportion), another magnificent creature from old also survived extinction by means of hybridization.
Mitochondrial DNA haplogroups known to be from ancient aurochs, whose last known representative died in 1627, have been discovered in Italian cattle, amounting to as much as 1.5% of the sampled individuals.
The lineages belong to three haplogroups: P, Q and R. P and Q had already been sequenced in pre-Neolithic European bovines (aurochs) but so far no P had been detected among modern cattle (in this case only one individual). A novel haplogroup, R, was also sequenced in several animals and, because of its even more archaic phylogeny, it is also believed to be an aurochs and not a domestic lineage.

Fig. 2 full Q, P and R sequences, including one from a British aurochs (18)

 

2010 review

Some anthropology, genetic, prehistory and similar outstanding blog instances from 2010 at For what we are…. and its predecessor, Leherensuge (until September). 

January:

In the month of Janus, bifaced god of gates, I did not focus in anything (two faces are too many faces, Janus)

February:

In the month of purification I took some time to refine my view of the Eurasian dispersals:
 

March:

In the month of Mars, god of war, I was pretty much focused on Africa, though also had something to say about East Asia (nothing to do with war that I know however, sorry Mars)
Reviewing African mtDNA by parts: L0, L1, L2 and L5, L3’4’6
Are we overlooking the signature of the Out of Africa migration? (ancient L(xM,N) clades in North Africa and Arabia)

Genetics of the Mlabri (in their East Asian context)

Draft analysis of the HUGO consortium paper

Also a warning on how insignificant can be statistical significance.

April:

In the month of… maybe Venus (nobody seems to know for sure), goddess of love and passion… I kept looking at genetics and their relevance in prehistory. The heat came from the volcanoes, I guess.
Why European R1b1b2a1 cannot be Neolithic (as some people insist on claiming against even their own data)

Was Toba really so bad?

Second look at the HUGO paper

May:

In the month of Maju I did not rest. Well, actually it is the month of Maia goddess of fertility, but Maju may be related to the maypole celebrations traditional in many parts of Europe, not in vain the Basque God Maju or Sugaar and his consort and most Goddess Mari recreate the World every Friday night by means of sex, of which is said that the fertilizing storms are born. Even if the corresponding ritual orgies are not anymore performed, thanks to Christian persecutions, I guess that there is still enough sex through the World to keep the wheel running. 

But remember that Basque legend also says that the World will come to its end when crossroads are everywhere. Look around you and despair, ye mortal.
Was I fertile this month of fertility? I’m not sure but we did learn in that date that Neanderthals and our kin were inter-fertile indeed. And this is the likely most important single news of the year, at least in the fields of genetics and prehistory.
Neanderthal gene flow found in modern humans, which I (or others) explored in greater depth here, here, here, here and here
Sardinian Neolithic art in danger (Berlusconi cheapskate!)

Artificial bacteria created in vitro

June:

In the month of Juno, jealous Olympian wife, torturer of Io and destroyer of mighty Troy, I was really overwhelmed by the massacre of peace activists on the Mavi Marmara by Zionist commandos. But there was some other materials flowing later in the month as well. 
Oddly enough,  some were precisely about Jewish genetics:
Jews are Phoenicians, Palestinians are Jews, based on Behar 2010, came to confirm my suspicions about modern Western Jews having originated not in Palestine but in the Hellenistic Diaspora. This is a suspicion I had since long before and that was reignited earlier that month by another paper by Atzmon, discussed in a single article, where I also dealt with Basque genetics.
Another key finding is a foot bone from Philippines, dated to c. 67 Ka ago, which may be that of a modern human (or maybe not).

I also revisited the historical battle of Noain, where Basques and our Gascon allies were defeated by the huge Castilian army.
Discovery of C1d in South America questions the two waves model of American colonization

July:

In the month of Julius Caesar, conqueror of Gaul and then of Rome itself, and great propagandist of himself…
… we discovered that the ancestors of Gauls practiced prime quality surgery already in the Neolithic.

Infamous archaeologist Julio Nuñez destroyed a whole section of the Vasco-Roman site of Iruña-Veleia with reckless use of a mechanical excavator (more here, here, here, here and here)

Breastfeeding confirmed to increase IQ… a lot.

New paper on human autosomal genetics at global level, also another one on Korean genetics specifically.

We found that a huge meteorite hit Egypt just some 5000 years ago.

I also decided to split Leherensuge in two.

August:

In the month of Octavius Augustus, whose rule falls around the non-existent year zero of the euphemistically called common era (CE)…
We learned something more about ancient Danish mtDNA, specially that haplogroup I has decreased notably since the Viking era.
On the other hand, our doubts became greater about one of the first mode 4 (or Upper Paleolithic) techno-cultures of Europe: the Chatelperronian, as the Neanderthal adscription of this culture was challenged by two popes of archaeology.
We got also a rare peek to ancient French mtDNA from the Megalithic period.
The eternal debate about the origins of archery got some evidence supporting its development at least 60,000 years ago

And the Clovis Impact theory was rejected… but wait, because it was claimed again true a few weeks later.

September:

In the seventh month… oops the ninth, what were Romans thinking when they chose this name? They could count in spite of those horrible Roman numerals, believe me, just that they began the year in March… until they decided to do otherwise.
We got confirmation that the chimpanzee-bonobo split must be moved back to 1.3 million years, what in turn affects the Pan-Homo divergence age, which is of (at least) 8 million years (and not those absurd figures you may read around of 5-7 million years). This has important implications when considering the molecular clock (or as someone said: molecular compass), implications that are often ignored, producing absurd misunderstandings. 

As previously mentioned, Clovis Impact theory was vindicated on new evidence. 
A Homer Simpson gene was discovered, seriously. If you think you are dumber than you should, this may be the reason. 

News from the promising research on the Neolithic of Western Turkey began flowing with the finding of a seal near Izmir (left).

October:

I opened this blog and its sibling dedicated to more current affairs, Leherensuge was discontinued

Another West Turkey Neolithic site near Bursa reveals full family execution.
I discussed a series of key papers on the coastal Out-of-Africa migration, revealing the importance of the Persian Gulf “oasis” or the riverine corridors of India. 
Neolithic genocide fans felt sad as most Danubian ancient mtDNA N1a happens to be European
I revisited the Eurasian mtDNA macro-haplogroups and the demographic expansion they describe.
It became known that ancient Europeans of Gravettian culture already milled grains and rhizomes to make flour, which they could surely keep and process better.
I revisited, with the help of Dr. Bocquet-Appel, the population densities of European Upper Paleolithic, which have a strong southwestern concentration, specially after the LGM.
Cyprus Neolithic was revealed to be extremely old. 
I revisited the explosions within human expansion by pondering the mtDNA star-like structures.
Mutation rate was confirmed to be low (slow)… I laughed mischievously on this.

November:

Again we got scientific news (that other scientists insist in ignoring) about the actual age of the Pan-Homo split, which is c. 8 million years ago, not less. This allows Salanthropus Tchadiensis, Toumaï (left), likely to be in our genealogical tree.
New ancient DNA from Elbe Danubians confirms that these Neolithic people are not clearly ancestral to modern Europeans, not even in Central Europe.
I realized that ancient Europeans from Sunghir, Russia, show the earliest unmistakable mtDNA H, c. 25,000 years ago.
I began producing some updated ancient DNA maps for Europe. I promise to complete this task in 2011, this is one of my new year compromises.
This month I also let myself speculate about some linguistic among unrelated (or not clearly related) European and other languages (here and here). A philologist from Iowa came to my help in relation to the widely shared term for bear.

December:

It was modeled how hunter-gatherers probably slowed down farmers’ advance upon the arrival of Neolithic to Europe and other densely populated areas.
We knew of more violent deaths at the Neolithic site of Aktopraklık, near Bursa, Turkey.
A violent injury on a Bronze Age Manchego man (living in the motte-and-bailey of the left) gave me the chance to revisit this most interesting period in the Iberian Peninsula.
In a quite bad week overall, I was for the first time in my almost four year-long history of blogger, suddenly deprived of my Google account altogether. Luckily I could recover it later but all looked pretty bad, automated, impersonal and wrong… so I am considering migrating to WordPress.
A new paper on mtDNA U6 confirms it to be original from North Africa, probably the westernmost parts. 
And finally the other DNA-bomb of the year: besides Neanderthal admixture, Melanesian people also display some input from another group, the so called Denisovans (probably a Neanderthal-Erectus hybrid).
 
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Posted by on December 28, 2010 in blogging

 

Excellent synthesis of the situation of the Iruña-Veleia controversy at Noticias de Alava

Historian Estitxu Briñas (also member of the SOS Iruña-Veleia association)  has today published an article at Noticias de Alava, in which the pitiful and highly embarrassing situation of the Iruña-Veleia scandal is synthesized masterfully.
Those readers with knowledge of Spanish language may want to read the original article: Iruña-Veleia: todavía estamos a tiempo. For the rest, I will try to synthesize here the main points.
Briñas congratulates for the cessation of the former Deputy (provincial minister) of Culture, Lorena López de Lacalle (on unrelated political issues) because she is clearly the main political actor in this shameful abuse. She expresses her hope that this circumstance offers an opportunity to straighten the wrongdoings of the last two years.
The first and main wrong was the Foral Order of November 19th 2008 by which the former archaeological company in charge of the Vasco-Roman urban site, Lurmen, saw its excavation permit removed, the site was closed and the state attorney is asked to proceed against the archaeologists.

It would be too long to describe the many irregularities in which the Provincial Government incurred in such fateful day, suffice to say that the decision was adopted when only one of the ten reports of the Commission had been handed in and that the final conclusions, included in little more than half a sheet, were written by a provincial public servant; these needed to be redacted before the meeting because they were given to Eliseo Gil [the chief archaeologist] at the exit and the signatory public servant was present in that meeting.

The fact that the judge in charge has been demanding for some time that scientific analysis of the exceptional findings are performed is clear indication that the alleged falsification is not proven at all.
She proposes that the Provincial Government sends the artifacts (mostly inscribed shards, in Basque and Vulgar Latin, along some drawings) to some European laboratory specialized in archaeometry.
She also says that the ten Commission’s reports do not at any moment prove the alleged falsehood of the graffiti. (Actually most are only linguistic speculation with zero probatory value). In contrast, there are 16 reports, performed by prestigious scientists, that support that the artifacts are most likely genuine, including one by prestigious Bermudan archaeologist Edward C. Harris. These reports add up to 1800 pages have all been created altruistically without pocketing a single cent, while those of the Commission are of barely 400 pages and each one had a cost of €1800 to the taxpayer.
A further issue, denounced also by me, is the method of excavation of Julio Núñez, the new director of Iruña-Veleia and a member of the Commission (the only archaeologist in a mostly linguistic array of “experts”). As you may know Núñez mechanically excavated in few days a whole section of the site down to 1.5 meters, dumping all the archaeological layers without any consideration into rubbish piles, which cannot anymore produce an stratigraphy of any sort and even damaging some of the structures (see video below).
Also, Briñas informs us that SOS Iruña-Veleia has contacted a reputed European laboratory which would perform the analysis, with guarantee of conclusive results and no damage to the pieces, on ten key items for the price of €12,000, cost that SOS Iruña-Veleia offers to pay. This analysis could well be complementary to the one by scientific police, ordered by the judge but delayed by the Provincial Government, which has ignored the order. 
Finally, the historian retakes the question asked by the former Deputy López de Lacalle: how would the reputation of the University of the Basque Country end if a new commission of experts is called and new analysis are performed? Precisely that is the crux of the matter: how the Basque academy has been able to bring such a shame on themselves, not clarifying the doubts but performing a mere, corrupt, paperwork routine to make sure that the findings would be declared false without any evidence.
Further information in English:
In other languages:
 

Explaining ‘Denisovan’ and also ‘Neanderthal’ admixture: the simplest scenario

I have recently discussed the Denisovan admixture in Melanesians discovered by the Neanderthal Genome Project and I discussed back in its day the Neanderthal admixture in all non-Africans (see here and here).
While the Neanderthal admixture episode may be easy to explain and was thus explained by Green et al. as happening early in the migration out of Africa, probably before arrival to South Asia. The Denisovan admixture in islands far away from Altai is not so easy to understand and has not been satisfactorily explained by anybody I know so far.

What were the Denisovans?
Denisova cave
First of all we have not a very clear idea of what kind of hominin were the Denisovans. Well, actually we know that their tooth clusters with Indonesian H. erectus, H. habilis and australopithecines (but also with the H. sapiens of Pestera cu Oase, quite divergent from the rest in this aspect).
We also know that the Denisovan mtDNA belongs to a branch older than that of H. ergaster and descendants, because it is almost twice older in its divergence from that of Neanderthal and Sapiens mtDNA (both derived from H. ergaster c. one million years ago by all accounts that make any sense). What diverges in the common tree of Humankind (senso lato) almost twice that time? Asian H. erectus, believed to derive from a population represented by H. georgicus.
Nothing else does. Hence the Denisovan mtDNA, found in two different individuals (a finger and a tooth actually) must be that of Asian H. erectus.
However the Denisovan nuclear DNA is not so distant from Neanderthals. What does it mean? Most probably that they were a hybrid Erectus-Neanderthal population, what fits well with their presence in Altai (at the crossroads of known homelands of both species), their use of Mousterian technology (typical of Neanderthals) and the presence of Neanderthals in similar dates at nearby sites.
So my theory about Denisovan identity is this one: they were a hybrid population of Neanderthals and H. erectus, with maternal lineages of the latter species and technology of the former.
Melanesians in Siberia? No way!
blond Melanesians
Quite obviously Melanesian ancestors were never in Siberia. This is not just a matter of the coastal migration model, that also, but specially a matter of pigmentation. The name Melanesia means Islands of the Blacks in modified Greek and, if the ancestors of these peoples would have been in Siberia for any extended period, they would have lost their tropical pigmentation for sure because otherwise they would not be getting enough vitamin D and their children would be extremely unfit for that reason (retarded, schizophrenic, rickety, etc.) And, as the case of Native Americans clearly illustrates, re-evolving black pigmentation, once it is lost, is no easy matter. In maybe 15,000 years tropical native Americans have only got a tan.
So the ancestors of Melanesians and other very dark tropical Asians have definitively not lived in Siberia at any time. Besides, it is totally non-parsimonious in what regards to modern human mtDNA and Y-DNA spread, the tropical route is much more logical and natural.
So they must have admixed with some relative of Denisovans elsewhere, for example in Sundaland, where some Homo erectus are known to have lived in dates that are perfectly compatible with this scenario. An encounter of the first of our species arriving to that area and Homo erectus soloensis is almost sure to have happened.
So we do have a plausible and even likely scenario for this admixture event in the ancestors of Melanesians, not in Altai but in SE Asia.
Admixture detection by proxy… interesting.
Certainly that we can detect admixture happening in Java by studying distant relatives in Altai is interesting. And it makes sense. If you compare a modern French-Vietnamese with French and Altaians it’s likely that he will appear as a mixture of French and Altaians, even if the proportions may not be exactly correct.
I’ll get to this matter of proportions later on because it is relevant too.
What happens if we get the son of an Punjabi and Vietnamese and compare with French and Altaians? He will surely still show up as admixed. A simplistic conclusion might be that he is descendant from French and Altaians. This conclusion would be wrong, even if the confusion is understandable.
The Narmada hominin and “Neanderthal” admixture
Narmada skull
Thinking about this brought me (with some important help from readers – feedback is crucial) to the mysterious Narmada or Hathnora hominin (see here for an open access reference), the oldest of really big-brained humans and possibly a relative of Neanderthals (but not a true Neanderthal, among other reasons because they did not use Mousterian technology but Acheulean). The skeletal record of South Asia is quite scarce but this big-headed hominin is the last people we know about before African-like Middle Paleolithic technology appears c. 120,000 years ago (see here), probably with the first members of our species.
Yes, you read right: 120,000 years ago (more or less), the idea of a much more recent Out of Africa is almost certainly wrong, even if you will surely read such nonsenses for a while: the molecular clock pseudo-science cannot overrule archaeology.
It is at this moment uncertain whether the Narmada specimen and the probably much larger population it belonged to was a descendant of H. erectus or a descendant from H. heidelbergensis (and hence closely related to Neanderthals). Depending on which of these two options is correct, the scenario presented below will make sense or need to be revised.
I will consider, as suggested here by Michael Petraglia, that the Narmada specimen and related Indian population of the Early Paleolithic (which lasted until c. 100,000 years ago) were descendant of H. heidelbergensis, and hence cousins of Neanderthals. Why? Because they had Acheulean technology, which is associated with at least the late H. ergaster.
If this is correct, when we talk (after Green 2010) of Neanderthal admixture at low levels in non-African modern humans we may well be talking of admixture with anything within the broader Neanderthal family, in other words, with its ancestor H. heidelbergensis (cousin of our most direct ancestor H. rhodesiensis) and their descendants (Neanderthals and others, including probably the Narmada hominin and broader Acheulean-using population of South Asia.
A hypothesis strongly consistent with the coastal (or tropical) migration model
And I finally reach here to my hypothesis, to my explanation of the admixture episodes revealed by the Neanderthal Genome Project this eventful year of 2010. And I will do it with few words:
click to expand
The first admixture refers to the general non-African admixture with “Neanderthals”, which would actually have happened with their Indian cousins instead upon arrival to South Asia. This admixture would have affected all non-Africans, but as the case of the Karitiana (who only show some 0.9% of such admixture, much less than the rest) evidence, maybe not all populations exactly in the same amounts.
The second admixture refers to the specifically Melanesian hybridization with “Denisovans”, which would actually have been with their Indonesian pureblood relatives, H. erectus soloensis.
Makes sense? I think so. Of course, it is not set on stone but it seems a good hypothesis and should at least get some people chewing on this.
Special thanks for some key references to Terry T.  and Manju (but in general to all readers who take part in the discussions at the comments sections: keep the flow of ideas vibrant, please). I suspect that Terry will not like my conclusions because they end up in the coastal migration model that he hates so much. But well…
Appendix 1: the real apportion of Melanesian admixture with archaic hominins may be lower than suggested by Reich 2010.
They suggest (supp. info 8) that Melanesians would have as much as 7.4% of admixture with archaic species: 4.8% Denisovan plus 2.5% Neanderthal. But, if Denisovans are hybrids of H. erectus and H. neanderthalensis (as seems most likely, see above), then the real admixture with H. erectus would be an undetermined percentage but always less than 4.8%. As we know that the Neanderthal (or Heidelbergensis) component is 2.5%, it is most likely that the actual Erectus admixture in Melanesians is of only 2.3% or 2.4%, totaling 4.8%.
Appendix 2: very serious inconsistencies in the age estimates derived from nuclear DNA in Reich 2010.
In supp. info. 6, the authors provide data of genetic divergence between various modern populations, Neanderthals and Denisovans, expressed as fractions of the Homo-Pan divergence. They use the wrong time frame for this event (6.5 Ma) but even then the results make no sense.
Using a much more correct (according to modern best scientific understanding) of 8 million years, I get that the age of the migration Out of Africa would have happened between 650,000 and 500,000 years ago. The first figure is the distance between Yorubas and non-Africans and the latter the one between non-Africans.
This is a total nonsense (120,000 years makes sense, add some tens of thousands more if you wish but half a million years is simply not possible) and there must be a critical error somewhere. However I have not been able yet to discover what exactly is wrong. In any case, word of warning about accepting molecular clock age estimates in general and in particular when using nuclear (autosomal) DNA for this purpose.
 

Modeling cultural diversity, local extinctions, etc.

Before I forget, just a quick mention of another potentially interesting paper published at PLoS ONE this week:


L.S. Premo and S.L. Kuhn, Modeling Effects of Local Extinctions on Culture Change and Diversity in the Paleolithic. PLoS ONE 2010. Open access.

Abstract
The persistence of early stone tool technologies has puzzled archaeologists for decades. Cognitively based explanations, which presume either lack of ability to innovate or extreme conformism, do not account for the totality of the empirical patterns. Following recent research, this study explores the effects of demographic factors on rates of culture change and diversification. We investigate whether the appearance of stability in early Paleolithic technologies could result from frequent extinctions of local subpopulations within a persistent metapopulation. A spatially explicit agent-based model was constructed to test the influence of local extinction rate on three general cultural patterns that archaeologists might observe in the material record: total diversity, differentiation among spatially defined groups, and the rate of cumulative change. The model shows that diversity, differentiation, and the rate of cumulative cultural change would be strongly affected by local extinction rates, in some cases mimicking the results of conformist cultural transmission. The results have implications for understanding spatial and temporal patterning in ancient material culture.

This mention is not adhesion. I find the modeling potentially interesting in its essentials but I surely have many discrepancies on issues such as assuming tiny “populations” of some 25 individuals in black and white (life or death) states. Such size is ok with operative hunter-gatherer bands but these are not “sovereign” units but just dynamic and fluctuating economic ones, integrated in larger groups. Probably a better size would be something like 100 or 200 people but again integrated into larger units of several hundreds to several thousands (tribes or nations).

Also we have to consider that people change “clans”, for example when marrying. So cultural, as well genetic flow is persistent at least within the borders of the ethnicity, which are anyhow generally open. So I guess that the modeling needs a lot of refinement but still it is a curious speculation – or exploration if you wish.

Something I do agree is in the authors founding their research on previous works that strongly suggest that population size and specially connectivity is critical in driving and maintaining the rhythm of innovation.