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Monthly Archives: October 2012

New mtDNA age estimation paper claims post-LGM expansion dates for most relevant lineages

In Europe as in Africa and Native America.
You know that I’m very much refractory to molecular-clock-o-logy because it implies many a priori speculations and assumptions that probably make the results to be wrong and yet these results are presented as if they were the genetic equivalent of the proverbial “rocket science”, when they are nothing but educated guesses, often contradicting each other.
Still I think that this paper is worth mentioning for two reasons:
  1. It gives age estimates that are clearly pre-Neolithic for most lineages, rebuking certain fanatic school that pretends to impose their clearly unfounded ideas of mass demographic replacement in the Neolithic and in a single direction, with a simple pattern. It is always good to have that kind of counter-arguments at hand.
  2. The paper is freely available (open access) in spite of being published by Nature (in an open access  dedicated magazine titled Scientific Reports).
Hong-Xang Zhieng et al., MtDNA analysis of global populations support that major population expansions began before Neolithic Time. Scientific Reports (Nature) 2012. Open access ··> LINK [doi:10.1038/srep00745]

Abstract

Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

Importantly, these age estimates must be considered as minimal ages (everything else assumed correct and equal) because the mutation rate used in at least some of the calibrations (Soares’ rates) is clearly too fast, with even Dienekes (a former hardcore defender of very short chronologies and hyper-fast mutation rates) admitting to it as of late.
I quote from Dienekes:

Soares et al. were cautious, and they assumed an earlier Human-Chimp split than had been favored until then. However, a new paper by Langergraber et al. have used direct observation of the autosomal mutation rate and of ape generation lengths to argue for an even earlier Human-Chimp split: at least 7-8 million years ago, and as many as 13 million.

Which  is something I am quite glad that people has begun realizing because I was saying that more or less, in many different ways, since 2008 (refs.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, etc.) And it was not just me because I was mostly reflecting what many scholars were finding here and there, publishing and seldom being listened to.
So these post-LGM dates are at best minimal dates, most probably requiring corrections that range between +15% and +85% (avg. +50%) per the Langergraber figures.
So for example, the authors estimate a 10-18 Ka window for the main expansions in Africa and Europe, that could well be a 15-27 Ka window in fact (max. 10-33 Ka.)

Figure 4: European expansion lineages from median-joining network
Blue, GBR; purple, FIN; yellow, CEU; cyan, TSI; green, IBS.
However mtDNA specifically has other major issues, absent in nuclear DNA (autosomes or Y chromosome): that the mutations happen so spaced in time for the whole mitochondrial DNA chain, which is very short, that the main factor is not the molecular tic-tac but population dynamics.
I should write more extensively on this matter but D. Pierron already did for me in 2011 (discussed here).
As I understand this problem of extremely unequal mtDNA lines, these irregularities are mostly caused by relatively large populations in which mutational change is effectively stopped by mere drift. As most women in the population experience no mutation in their mtDNA, the mutants have all the tickets to see their novel, derived, lineages drifted out by their relatives with a conservative one.
So in my understanding mtDNA “clock” must only be counted (if at all) from the root and not, as is usual, from the ends. This is a total game changer because counting from the root, H must be slightlty older than U, while counting from the ends that is impossible.
I never count mtDNA from the ends even if I know that most geneticists and aficionados do because I find such a procedure totally thoughtless, a mechanical imitation of a method that works for longer DNA chains which accumulate mutations in every generation, quite unlike mtDNA, which is much more stable.
En fin, the paper provides us with another opportunity to reconsider the highly speculative but incredibly popular field of molecular-clock-o-logy. It also provides some nice MJ networks of many haplogroups, which speak on their own, one of which (Europe), I used to illustrate this entry.
 

Epigenetics and IQ variability

A new study on monozygotic (identical) twins with clear IQ differences finds that epigenetic methylation of certain genes may be the cause:
Chih-Chieh Yu, Genome-Wide DNA Methylation and Gene Expression Analyses of Monozygotic Twins Discordant for Intelligence Levels. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047081]

Abstract


Human intelligence, as measured by intelligence quotient (IQ) tests, demonstrates one of the highest heritabilities among human quantitative traits. Nevertheless, studies to identify quantitative trait loci responsible for intelligence face challenges because of the small effect sizes of individual genes. Phenotypically discordant monozygotic (MZ) twins provide a feasible way to minimize the effects of irrelevant genetic and environmental factors, and should yield more interpretable results by finding epigenetic or gene expression differences between twins. Here we conducted array-based genome-wide DNA methylation and gene expression analyses using 17 pairs of healthy MZ twins discordant intelligently. ARHGAP18, related to Rho GTPase, was identified in pair-wise methylation status analysis and validated via direct bisulfite sequencing and quantitative RT-PCR. To perform expression profile analysis, gene set enrichment analysis (GSEA) between the groups of twins with higher IQ and their co-twins revealed up-regulated expression of several ribosome-related genes and DNA replication-related genes in the group with higher IQ. To focus more on individual pairs, we conducted pair-wise GSEA and leading edge analysis, which indicated up-regulated expression of several ion channel-related genes in twins with lower IQ. Our findings implied that these groups of genes may be related to IQ and should shed light on the mechanism underlying human intelligence.

The list of genes with a detectable effect is as follows:

Table 2. List of genes having the same tendency of expression level in most twin pairs.

It’s worth noticing that a recent study (Chabris 2012) reviewing the literature found that most or maybe even all alleged genetic influences in intelligence are probably false positives (discussed here). Therefore is probable that many (most?, all?) differences in intelligence are caused by environmental influences, often manifested in epigenetic modifications like the ones detected in this study.
 
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Posted by on October 18, 2012 in epigenetics, human genetics, intelligence, mind

 

Intriguing North African Neanderthal admixture paper

This new study aims to quantify Neanderthal admixture in North Africans in order to evaluate the unlikely but popular-in-some-circles hypothesis that the signature of Neanderthal admixture in non-African Homo sapiens could be caused by structure in Africa prior to the migration into Asia and beyond (“ancient African structure model” hereafter).
It does seem to add evidence against the “ancient African structure model” and, incidentally, in favor of the mainstream interpretation that North Africans have large amounts of West Eurasian ancestry (questioned without clear base in some Africanist circles). However it also arrives to some odd results regarding East Asian Neanderthal admixture which are not addressed at all in the study.
Federico Sánchez Quinto et al., North African Populations Carry the Signature of Admixture with Neandertals. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047765]

Abstract

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal’s genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

Europeans and Africans
First of all they take a look at the structure of European and African populations regardless of Neanderthal ancestry, which is probably of interest on its own right:
Figure 1. Results of the ADMIXTURE analysis (k = 4) with North African populations
Sadly, the Tunisian Berbers who define the North African polarity, taken from Henn 2011 and 2012, are a recognized (by Henn herself) as a highly endogamous population that behave a bit weirdly. I do not think that in this specific context they are distorting the results significantly (compare with my own exercise earlier this year) but I do think that the sample should not be used anyhow.
Otherwise we can see that:
  • There are both West Asian and European components in North Africans (the red “Tunisian Berber” component is also probably of West Eurasian ultimate origin, from my previous work, where I carefully looked at FST distances among components – however some nuances, like a probable pre-OoA* residue in North Africans are not evident in this analysis, which is too shallow).
  • There is some African (mostly North African) ancestry in Iberia (more towards the West, as we know from other studies).
  • There is some minor West Asian ancestry in Europe, consistent with a less important penetration in Neolithic (and maybe also post-Neolithic) times.
  • There is Tropical African ancestry in North Africans as well (even if the Luhyas are probably not the best proxy).
Neanderthal blood in North Africans
The main goal of the paper is however to estimate Neanderthal ancestry in North Africans, with the following results:

Table 2. Estimates of Neandertal ancestry in North African populations, along with European, Asian and Sub-Saharan African groups. [Notice that GIH is mislabeled, it actually means: Gujarati Indians from Houston].

The results for Africa and West Eurasia are more or less within expectations, what is very anomalous however is the East Asian results of c. 200% Neanderthal ancestry (relative to CEU) but let’s leave that for later.
We could well discuss however why, if North Africans are some 80% West Eurasian by ancestry their detected Neanderthal admixture is so low (c. 50-60%). It may well be a matter of diverse ancestral influences (not all West Eurasia is Europe), and would be consistent maybe with the relatively low amounts of Neanderthal admixture found in Indians (GIH, 84%). Sadly the Qatari sample was not tested for Neanderthal admixture, which would have been interesting on its own right and also in relation to North Africa
Whatever the case this is the authors’ map of estimated North African Neanderthal ancestry relative to Euro-Americans (CEU, which have c. 2.4% Neanderthal ancestry):

Figure 3. Neandertal genetic introgression in North African populations as a fraction of that found in Europeans [colored bars represent K=4 apparent ancestry as above].

Maybe the most interesting population here is MOS (Southern Moroccans) which in my December 2011 Admixture analysis of North Africans appeared to show significant amounts (14.4%) of a very distinct component that I judge as Aterian remnant (in other populations not higher than 1.5%).
While the authors think that the findings are supportive but can’t totally prove that the Neanderthal admixture appearance is real and original from Eurasia, I find the very low Neanderthal admixture signal in Southern Moroccans as very clear evidence that pre-OoA structure (which is preserved as minority component in this population apparently) that the Neanderthal admixture signal has nothing to do with any pre-OoA North African specificity. 
Otherwise South Moroccans should show a neutral signature and not this outstanding depression of Neanderthal admixture. There are surely other factors at play there (greater Tropical African admixture, lower European admixture) but this “Aterian” component should be high in Neanderthal signature if there was any pre-OoA African structure at all. 
Some people may want to cling to the proverbial burning nail, maybe arguing that the Neanderthal-like structure was in Egypt and not NW Africa. Not only that looks too much like the West Asian admixture episode that the mainstream theory argues for but it also ignores the cultural and anatomical similitudes between NW African Aterian peoples and those from Palestine in the context of the likely window for the archaeologically supported OoA: 125-90 thousand years ago. 
So, in my understanding the results of this paper are quite supportive of the mainstream (Asian admixture) model, rather dismissing the African structure counter-hypothesis, even more than the authors themselves admit to. 
European degrees of Neanderthalness?
I am sure that some readers will have noticed that there is an appearance of greater Neanderthal values among Basques (129% rel. to CEU) and Iberians (115-118%). However the differences are very small and not more marked than, for example North Tunisians (138%).
Considering the other issues that the results of this paper imply, I cannot really argue that these differences are meaningful at all. However they sparse data shown for other parts of West Eurasian would be consistent with greater Neanderthal admixture in Europe than in West Asia (and the corresponding gradation in Europe depending of Neolithic ancestry), with an apparent highest value in a population usually considered as a Paleolithic continuity genetic refuge: Basques.
But only further data and specific analysis can confirm or question this appearance. 
East Asian extremely high Neanderthal values
This is what is totally puzzling in this study and what can really bring to question all other conclusions. The authors appear to find that East Asians (CHB, CHD, JPT) have values of Neanderthal admixture that are double than those of West Eurasians. 
This clashes with all we know. In fact one of the findings of Green 2010 was that all Eurasian-derived populations have similar Neanderthal admixture values, c. 2.5%, with lesser population or individual variations only. This has only been confirmed once and again in successive studies, for example John Hawks earlier this year, who actually claimed that Europeans held slightly more Neanderthal admixture than East Asians.
Then why do the Sánchez Quinto team find such brutal East Asian Neanderthal admixture values? No idea. They don’t even mention the matter in all the paper. And that is a big flaw, which can only cause readers to doubt the whole paper or even the methodology altogether. 
Any ideas?
_____________________________________________________
*OoA: Out of Africa, it refers to the human migration episode and related founder effect (bottleneck) which populated Asia and its peripheral minor continents (Australasia, Europe, America) with our species, Homo sapiens. It is a critical episode in human prehistory and probably the time when most if not all Neanderthal admixture happened. But, in principle, already in Asia.
 

Blog will NOT get ads

In the end Google AdSense has resulted impossible to deal with. Their bots claim that I have copyright infractions in this blog but they don’t provide any details whatsoever, making impossible for me to be able to correct such vices. 
It was even suggested by some that the WP backup could be considered plausible copyright violation because there is another site with exactly the same content, go figure! Dealing with bots is worse than dealing with the worst bureaucracy apparently.
It has taught to me again this precious lesson: even if you wish to sell your soul, so to say, it’s most uncertain that customers will be available.
Thanks for your support in any case.
 
3 Comments

Posted by on October 17, 2012 in ads, blogging

 

Blog will get ads

(source)
Sadly I feel compelled to find economic resources in places I would not have tried before, so I have, after much procrastination, decided to include paid publicity in this blog via Google AdSense. I apologize to all readers for the bother and also because, in order to increase the site’s actual traffic, I have cut RSS feed to short format, what make you force to visit the blog more often and not just read on the RSS.
I really really really hate it but if I can make some $300 monthly out
of it (we’ll see but that’s what I have estimated based on what I could
read around the net for similar traffic as this blog already has), then I
must do it. If more, then the better, if much less, maybe not worth
it.  As far as I know (it’s all very obscure), I will get money based on both traffic and ad-clicks, specially the latter.
On the positive side I hope that, it motivates me to make this blog an even better site. 
I may also start a sidekick blog in Spanish language. Some people have in the past suggested me to do it but I was always reluctant because of the greater work it would be.  However, if I professionalize some of my blogs in the sense of expecting earnings from them, I can also think of that as a job and not anymore as just a hobby, so I can work more (and hopefully better) in them. 
Again my apologies for all the inconvenience. Feel free to discuss.
 
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Posted by on October 15, 2012 in ads, blogging

 

Claim oldest European ‘city’ in Bulgaria

From Pileta de Prehistoria

According to the Sophia Globe (h/t Pileta), the oldest ever city in Europe would have been located at Provadia (Varna province, Bulgaria).

The city is defined as such by medieval standards because it is a settlement surrounded by a wall, a very thick and solid one. However only a few hundred people (300-350) lived inside them, always according to Prof. Vassil Nikolov.
Nikolov attributes the city an age of 4700-4200 BCE, belonging to the context of Varna culture and related to the relatively well known Varna necropolis, probably the first princely burial of the continent.
However such an early age places the Provadia-Solnitsata city almost two millennia before any other known European city (Greek islands, Southern Iberia) and even 1500 years before Troy I, traditionally considered a major influence in the urbanization and Bronze Age of Europe.
Not even Egypt’s civilization is nearly as old; in all the wider region only some fortified cities from the Levant and Mesopotamia are as old and, excluding Jericho (c. 6800 BCE), none is significantly older. Even the oldest known Sumerian city, Eridu, was built only a few centuries before this Bulgarian city.
For more details, read the abstract (PDF) of Nikolov’s study (to be published?, where?)
Looking for more information on the matter I also stumbled upon this webpage by Dr. L. Nikolova, which discusses the Provadia settlement as a salt-exporting site, something that also seems to be the leit motif of Nikolov’s abstract.

Discussion
I am not really surprised by these findings because it has been known for some time that the area of Bulgaria was a very old center of civilization, comparable in age to Egypt (or, as it seems to be the case now, even quite older), probably evolving state and aristocracy structures first of all in Europe. It was probably the wealth of this realm and its successors which baited the Indoeuropean nomads into invasion later on (economic relations with the Volga are attested as early as this time). 
The only thing that really puzzles me is the age because when I first learned on these matters the time-frame appeared to be a thousand years more recent, more in agreement with other urbanizing and social-complexity developments elsewhere in Europe (Aegean, Iberia), Western Anatolia (Troy) and also Africa (Egypt). But well… I have to accept the dates estimated by the researchers, I just wish I knew a bit more about how these have been produced.

Update (Oct 10): photos and considerations on burial styles

Terrae Antiquae[es] has now a very extensive photo-gallery, of which I borrowed the following:

I must say that unlike the Varna necropolis burial which I initially used to illustrate the news, the burials shown here appear to be of the classical Neolithic flexed style (the lower part may be missing but the size of the pit and lateral deposition strongly suggest that.

I’m not just inferring from that and another photo but it was actually the burial style of all Balcano-Danubian Neolithic peoples and even some “Danubianized” Indoeuropeans later on: flexed lateral burial, so it is what should be expected in this context.

The extended position is actually typical of Paleolithic Continuity peoples, and the use of ochre is specially documented in Eastern Europe: Dniepr-Don Neolithic and related groups like Pitted Ware and the Early Bronze culture of Ezero also in Bulgaria but thousands of years after these layers.

At the Varna museum site however they do explain that the burials in what was surely a royal or otherwise princely necropolis are of two kinds: (a) 99 burials (mostly men) are in extended position (Paleolithic tradition), while other 67 (many of them women) lay on their right side in flexed position (Neolithic tradition).

This could point (my best guess here) to early penetrations from the steppe (Dniepr-Don culture), comparable maybe to those we see around the Baltic (Pitted Ware), all however anticipating and maybe preparing the way for what is probably the true Indoeuropean penetration of the Kurgan wave of cultures, which in most cases would return to the flexed burials… now in kurgan (tumulus).

However in Bulgaria the period of Kurgan invasions culminates in the formation of Ezero culture, which is the only one retaining extended burial with ochre, by that time already vanishing in the steppe and the Baltic.

 

Roman town of Iturissa found near Roncevaux Pass

Archaeologists at work (Berria)
It has been known these days that archaeologists of the Arazandi Society of Sciences, together with Italian colleagues, have located and partly dug the Vasco-Roman town of Iturissa, mentioned by several classical sources.
Iturissa was first mentioned by Ptolemy as a town of the Vascones, being then mentioned in two Roman itineraries as mansio (official Imperial inn) in the Asturica-ab-Burdigala (Astorga to Bordeaux) road, north of Pompaelo (Pamplona), controlling the Immus Pyrenaeaus (Roncevaux Pass, locally known as Ibaineta). 
The name Iturissa sounds totally Basque, possibly the latinized version of Iturritza (itur(ri)-aitza: spring rock?) but in any case something related to springs or fountains (iturri, often itur- in toponymy). Not too far from there for example there is a village known as Ituren, a similar sounding name. 
The modern towns in the area of Iturissa are however known as Auritz (Burguete) and Auritzberri (Espinal), with the current findings being from the area of Zaldua.
The campaign so far could only make some initial explorations, finding high quality foundations and walls and what looks like a very promising stratigraphic sequence. The researchers estimate that the whole town occupies several hectares.

Inscribed stones from Iturissa (Berria)
Cautionary note: 
I read at Rutas Arqueológicas de Navarra[es] that the town of Iturissa was dug in the 1980s, including a detailed map of it. However this settlement seems to be located further NW of the current dig, which is said to be in Zaldua, where the mausoleum and Roman bridge are the only things marked.

Related document (update):

Video (mini-documentary, 5 mins, mostly in Spanish, some Basque) of the finding and excavation of some Roman propagandistic milestones (millarii), which are the same stones shown above.

These were found at an almost forgotten path of Auritzberri known as bidezarra (the old path or road), which the people suspected to be an ancient Roman road but was just a popular belief… until now.

The discussed milestone reads: NOBILISSIMO CAES FLAVIO VAL CONSTANTIO P F AUG, i.e. to the holy (P[ius]) and happy (F[elix]) Emperor (Caesar) named Flavius Valerius Constatius Augustus, which should be Constantius Chloros.

Source: Iruña.