December 30, 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. 

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.

December 29, 2010

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)

December 28, 2010

2010 review

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


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


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


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.


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


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


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


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.


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.


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).


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.


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.


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).

December 27, 2010

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:

December 25, 2010

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.

December 23, 2010

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.


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.

Mitochondrial DNA D and C (new paper)

I'm a bit overwhelmed by information of all kinds and real life issues, so I fear I will have to pass quickly and maybe shallowly over this paper, which anyhow seems an important reference for the understanding of the colonization of NE Asia (and America).

The most important substance is without doubt the clarification of the phylogeny and the graphs showing by color codes the spread of these two lineages. They also propose archaeologically consistent colonization and recolonization scenarios for NE Asia and even NE India, however their reliance on the most uncertain molecular clock methodology is at least arguable.

Haplogroup C

Haplogroup C is derived from CZ, which in turn is derived from M8, which is a basal subclade of macro-haplogroup M. Overall it is removed from the M node by 9 coding region mutations (plus 3 in the control region).

South/Central Siberia, NE Asia, East Asia, India, Europe

C1 probably arose in Beringia (most subclades are Native American, not shown in the graph). 

C4 and its "granddaughter" C4a are claimed to have expanded first prior to the LGM, the other major sublineage, C4b, instead is said to be of more recent spread (Holocene). Take these dates with a tablespoon of salt, because they may well be much older and totally different of these descriptions.

A new basal subclade, C4e, has been described with presence in Altai.

C5 is claimed to have a post-glacial-maximum expansion time-frame.

C7 is said to be the most ancient subclade (but still too recent for my opinion) and has a more southernly distribution (East Asia and NE India), yet the graph clearly shows it is also present in America.

A more complete phylogeny is available in the supplemental material. 

Haplogroup D

Haplogroup D is a basal subclade of macro-haplogroup M, only separated from the ancestral node by two mutations (both in the coding region). It is also a most diversified haplogroup.

South/Central Siberia, NE Asia, East Asia, India, Europe
The authors give an older age of expansion for haplogroup D (35-37 Ka) but still quite a bit short for my understanding, which should make it roughly synchronous to the colonization of West Eurasia since c. 50 Ka ago.

D4, D5 and D6 are also given pre-LGM expansion ages.

There is some refinement of the structure of D4b1a2a, which is now divided into two subclades: D4b1a2a1 and D4b1a2a2, D4b1a2a1 is further subdivided into D4b1a2a1a and D4b1a2a1b.

D4j gets new subclades: D4j4, D4j5, D4j7, D4j8, D4j9 and D4j10, with southernly distribution.

Chronology note

The authors seem puzzled not to have found any molecular clock guesstimate that correspond with the archaeologically defined earliest colonization of North Asia, c. 40 Ka ago (Altai), however this colonization of "Aurignacoid" industries is surely unrelated to these East Asian lineages and most likely related to West Eurasian ones (though unclear which ones).

But more "puzzling" is the following:

Importantly, we have not found in northern Asia any genetic signatures of sufficient antiquity to indicate traces of pre-LGM expansions, that originated from the Upper Paleolithic industries that were present both in the southern Siberia and Siberian Arctic, and that date back to ~30 kya, well before the LGM [1], [34], [36]. Apparently, the Upper Paleolithic population of northern Asia did not leaving a genetic mark on the female lineages of modern Siberians.
This is probably wrong and surely caused by excessive reliance on molecular clock methodologies measuring not from ancestral nodes but from present day sequences, which  (I understand) are generally conservative towards ancestral values because of the effects of drift, which naturally favors the older and most common variants, except maybe in random accidents or very very small populations.

Not to mention the usual and awfully wrong practice of  calibrating human genealogy using a Pan-Homo divergence well under the most likely age of 8 million years (or more).

So add 20-30% to every age guess you see using the molecular clock methodologies, unless some major improvements are being used or there are other reasons to believe the estimate is correct. This is not any method but a safety measure.

Denisova hominins, Neanderthals, Melanesians and so on...

A new "bomb" has been dropped by the Paabo team and their Neanderthal Genome Project. This review is just a very preliminary approach to really heavy material, dealing essentially with the autosomal DNA of the Denisova hominins, now sequenced, but also with their relations with Neanderthals and us.

A tooth found in the same cave carried mtDNA very similar to that of the finger bone. The tooth is morphologically distinct from both H. sapiens and H. neanderthalensis.

David Reich et al., Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010. Pay per view (supplementary material is freely available). 

Denisova closer to Neanderthals?

NJ tree
You are by now probably familiar with the Denisova hominin, a mere finger bone found in a cave from Altai (Mousterian context). While the mitochondrial DNA placed Denisova's lineage almost twice as distant as our divergence from Neanderthals, the autosomal DNA makes Denisovans a closer relative to Neanderthals (left). 

However I'd take this with a pinch of salt because autosomal DNA is subject to admixture and may therefore indicate a hybrid population or even individual. 

For example it could well be the case that Denisovans were a hybrid population of H. erectus and H. neanderthalensis (or a related species such as H. heidelbergensis). Or your best guess.

Also you may notice that in the above tree H. sapiens populations appear unusually divergent. This is not a distortion of this graph only, but it is also sustained when the Chimpanzee outgroup is taken into account, yielding age estimates for the autosomal divergence of our species that are several times older than that achieved by comparison of haploid lineages or justified by the archaeological record. 

So I am quite uncertain on how to read this and if errors are happening that cloud our understanding.

Are Melanesians more admixed with Denisovans? Are Native Americans less admixed with Neanderthals?

The possibility of Melanesians being slightly admixed with Denisovans is probably the most explosive aspect of the paper. Following Supplementary Information 8, the authors find some greater similitude between Melanesians and Denisovans than any other Eurasian population.

A visual explanation is in the following eigenvector graphs:

Notice that the second image is nothing but a high resolution zoom of the central clump in the first one (H. sapiens). Only at such high resolution three micro-clusters can be noticed, apparently reflecting different admixture levels with Neanderthals and Denisovans. 

To further clarify this matter, the authors resort to statistical methods that confirm these clusters and maybe add some information on several individual populations' admixture levels (not anymore just the four Eurasian populations represented above but also others). These calculations show that effectively Melanesians are slightly but significantly closer to Denisovans, while also retaining the general Neanderthal admixture of all non-Africans (or almost all). 

And I say almost all because the Karitianas (a Native American nation of Brazil) are found to have much lower Neanderthal blood than other non-Africans.

The estimates for Neanderthal admixture in Eurasians are overall of c. 3%, with the following variations:
  • Cambodian 4.4%
  • Mongolian 4%
  • Han Chinese 3.2%
  • French and Sardinians 2.6%
  • Melanesians 2.5%
  • Karitianas 0.9%
Additionally Melanesians have c. 4.8% of Denisovan genetic contribution, totaling c. 7.4% of archaic admixture.

Update (Dec 25): it may well be only 4.8% of total archaic admixture if Denisovans were hybrids of Neanderthals and H. erectus (see here - scroll to near bottom).

Note: I have a technical doubt because in table S8.2, French appear quite closer to Neanderthals than Sardinians, who seem less admixed than all other non-Africans but the Karitiana, but in table S8.3 they are given the same values of admixture. At the moment I do not understand why this difference in the values, really.

In the same table S8.2 French, Han and Cambodians (and only them) also appear to show some admixture with Denisovans, though maybe a third or fourth of that of Melanesians.

Affinities of the Denisova tooth, chronology of the Denisova cave.

In Supplementary Information 12, the authors deal with the possible paleo-anthropological affinities of the Denisova tooth (a molar), finding that it is closest in morphology to those of Australopithecus sp., H. habilis, African (but not Chinese) H. erectus and (oddly enough) Oase 2 (a H. sapiens that does not cluster with the rest of our species in this aspect).

Indonesian H. erectus is also very close if it is a second molar but not if this is a third molar. 

H. sapiens (other than Oase 2), H. neanderthalensis, Chinese H. erectus, H. georgicus (Dmansi), H. antecessor/heidelbergensis (Atapuerca) do not cluster in any case.

In this section, they also deal with the radiocarbon chronology of the site, concluding that:

... we propose the following scenario: a first hominin occupation of the cave more than 50,000 radiocarbon years ago by the Denisova hominins, and a second occupation during the Upper Palaeolithic, at 30,000 years BP or later, probably by modern humans.

Feel free to discuss.

Update (Dec 23): Denisova mtDNA "modern"?

Dienekes mentions today that Niccolo Caldararo has published an article at Nature (freely available as PDF) suggesting that the Denisova mtDNA sequence may be corrupt. If this would be true, then the sequence would be that of a H. sapiens.

This could explain some of the anomalies in the autosomal NJ tree and related age estimates, that would make Chinese and French (for instance) diverging by more than 500,000 years, what is totally absurd.

However, considering that a very similar sequence was successfully sequenced also for the tooth, this claim seems less likely.

Still many questions remain open because there are issues such as the divergence estimates for various H. sapiens, specially Eurasian H. sapiens, that just do not make any sense at all. So I'd say it's best to lay back a bit and wait patiently for more brilliant insights, which will no doubt come.

Update (Dec 25): see this new review for a more elaborate review of mine on this matter, including some intriguing hypothesis I am launching, partly on feedback provided by commenters.

December 22, 2010

New paper on mtDNA U6

With focus on chronology and what I think it is a quite interesting analysis of this matter: they calibrate on archaeological grounds, with several anchor points, what is a clear advance in comparison with the "chopper industry" methods used so far.

Frequency of U6: A - sample sites, B - U6 C - U6a, D- U6b

Background: The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene.

Results: Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East.

Conclusions: A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6’s European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast.
An intriguing element is that the chronology of the exclusively Canarian (Guanche) lineage U6b1 seems quite older than the (sketchy) evidence for colonization of the islands, suggesting that either this colonization was older than we know from archaeology or that the lineage coalesced first in mainland North Africa, where it has vanished since then (or is yet to be found). This paper suggests 4.8 Ka (2800 BCE) while the archaeological record only reaches to the 6th century BCE.

The chronology for a greater expansion c. 20 Ka ago is consistent with the main Upper Paleolithic culture of the area, the Oranian (or Iberomaurusian) culture, which has oldest dates in the NW of the region and, as I have argued elsewhere, is also responsible for the expansion of haplogroups H and V, which surely joined the genetic pool of North Africans because of Iberian influence (Graveto-Solutrean).

This is not however the estimated age of U6 overall, which is estimated in 33.5 Ka, roughly consistent with previous estimates (34-36 Ka).

The authors reject the theory of Maca-Meyer by which U6a would have expanded from East Africa (the Nile) westwards:
The case for the postulated “U6a1” movement from East Africa back to the Maghreb advanced by Maca-Meyer et al. [20] is not favoured by our inferredphylogeny, as the 16189 transition does not identify non-monophyletic groups. Indeed, the only sub-clade which seems to have a preferred distribution in East Africa (three individuals from Ethiopia) falls within U6a2, with only coding-region diagnostic mutations at positions 6359 and 11204 (dating to 13.4 ± 4.0 ka).

An interesting paragraph, which I'd like to discuss is the following one (from the conclusions section):
The recently revised archaeological dates for the Aterian industry of North Africa emphasize that the makers of this industry do not appear to have left any imprint in the maternal lineages of present-day North Africans. The oldest arrivals amongst extant mtDNAs appear to be the U6 and M1 lineages, which date to 36.6 (24.9; 48.8) and 25.4 (17.9; 33.1) ka respectively [31]. As with U5 in Europe [11], the arrival time could be older in each case, since the haplogroups appear likely to have arisen within the southern Mediterranean region from haplogroup U and M ancestors, making dating the arrival time very imprecise. Nevertheless, the estimates seem to match best the appearance of the Upper Palaeolithic Dabban industry in Cyrenaïca, as suggested before [15,23].
I do agree that the antecessor of U6 (and maybe also M1) arrived in North Africa most likely with the Dabban industry and that the chronology estimates confirm that (roughly). However I disagree when they claim that Aterian industry left no genetic legacy. This claim is unfounded because they ignore the L(xM,N) lineages which make up some 25% of North African mtDNA and at least in many cases must be from a time frame older than the Dabban industry, as I discussed in my old blog.

Another substantial disagreement I have is when they claim that:
Aside from U6, North Africa was also the recipient of European, Near Eastern and sub-Saharan African lineages most of which most likely arrived in the Holocene. Haplogroups H1, H3 and V expanded in Iberia in the Lateglacial/postglacial [11,58-61], and evidently spread into North Africa from Iberia across the Gibraltar Straits, most likely in the early Holocene [62-65].
This comes from a calibration error, arbitrarily deciding that H1, H3, V and others (H4, H7) as having expanded only after the Last Glacial Maximum. In turn this stems from a fundamental misunderstanding of what archaeologically makes sense: that the only moment of clear contact between SW Europe and North Africa is at the genesis of Oranian culture, which shows clear influence from the peculiar Iberian Gravetto-Solutrean complex (and in turn Iberian Gravetto-Solutrean later shows influence from North African fashions, notably the back-tipped arrow or spear points). While there is lesser connection between Iberia and some scattered coastal spots of North Africa in the early Holocene (Neolithic) with the Cardium Pottery culture this cannot justify almost 30% of the North African mtDNA. There is a more important later "Iberian" influence in North Africa with the Megalithism, however it is hard to explain why these very late hypothetical colonists contributed so much in the maternal genetic pool and so little in the paternal one, not to mention that non-Megalithic Guanches (Canary Island natives) also show more (fossil) Y-DNA R1b and I (17%) than modern mainland North Africans (discussed here).

The reality of this situation will be better understood when DNA chronologists accept that the timeline of mtDNA H (and V) is older than usually accepted and comparable to that of U, if not even older. In any case my calibration point for these lineages (H1, H3, H4, H7 and V) is precisely the unique trans-Mediterranean connection episode that happened almost without doubt at the genesis of Oranian culture. It is the only safe calibration point, what means that these lineages were formed and consolidated in SW Europe prior to that expansion into North Africa, so they must be at least of Gravettian time-frame (which is c. 22 Ka for Mediterranean Iberia), because Solutrean proper had a very limited presence in this area (two nearby caves in Valencia), even if it gradually modified the strong Gravettian substrate (and was modified by it).

Horse had multiple domestication events (ancient equine mtDNA)

German researchers have successfully retrieved mtDNA from 85 ancient specimens from diverse Eurasian regions and periods, ranging from c. 12,000 BCE to the Middle Ages. They have found that most of the extant mtDNA diversity in the species existed before domestication.


Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.

The paper provides ample insight on the various haplotypes and where they are found first. Not all lineages are from the putative area of first domestication (the Eurasian steppe) but they are also from other regions (East Asia, mainland Europe, Iberia).

Fig. 2 - Ancient horse mtDNA haplotypes with timeline and region

They also researched primitive horse breeds. 39 haplotypes were confined to one of these breeds. Among them are notable those of the Iberian peninsula (Lusitano, Marismeño, Cartujano, Garrano), which appear to have roots in pre-Neolithic local wild horses. Similarly the Basque pony known as pottoka also has roots in ancient mainland European horses (X1, derived from D). [Correction (Apr 6 2011): Pottoka's matrilineage X1 is of apparent Siberian origins: C - only attested in one individual. X1 as such is only documented since the Iron Age, in mainland Europe].

Other primitive breeds with unique haplotypes are Arabian, Cheju, Akhal Teke, Sicilian Oriental, Yakut, Debao and Fulani. The authors argue that the Altai Mountains and the Takla Maklan and Gobi deserts were barriers partly impeding the genetic flow from the Eurasian steppe to East Asia, where several of these breeds belong.

Update (Apr 6 2011): see also to this more recent post: Horse's double origins, on new research supporting by means of autosomal DNA diversity the double origin in the steppes and SW Europe of modern horses.