Neanderthal allele located in non-African modern humans

This should be of some interest:

Fernando L. Méndez et al., A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea. AJHG 2012. Pay per view (for six months) ··> LINK [doi:10.1016/j.ajhg.2012.06.015]

Abstract

Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.

According to Wikipedia, STAT2 is a gene which offers immunity against adenoviruses, which are related to respiratory illnesses (common cold, pneumonia, bronchitis...) and some other common diseases like conjunctivitis or gastroenteritis. Most infections are mild and require no specific treatment.

This suggests me that the selective pressure was quite weak, if any at all, so its introgression is most likely the product of a fluke and not selection. However it is not totally impossible that in the past some viral strain was particularly deadly causing adaptive selection.

(Slashed out text is edited: wrong notions)

Whatever the case it is also interesting to take a look at SNPedia, which lists five SNPs in this gene:

• Rs1883832 - whose T variant is almost exclusively non-African
• Rs4810485 - whose T variant is also almost exclusively non-African
• Rs2066808 - whose T variant is dominant outside Africa but also somewhat common in Africa
• Rs1927914 - whose T variant is dominant outside Africa but also somewhat common in Africa
• Rs10983755 - whose A variant is almost exclusive of East Asians

I can only imagine (as I have not got access to the paper, so I can't double check)  that the introgressed haplotype includes the first two SNPs in their T variants (see below). If so, the Neanderthal allele should cause: increased risk of osteopenia in women, some increase in the likelihood of lymphoma, among other things (arthritis, asthma?) which I'm not sure about. I do not see any indication of the haplotype being beneficial in any way but you tell me. 

Hat tip to Jean.


Update: I just got a copy of the paper, so I share these key figures:

We can see in them that the genomic positions at 55,030,689, 55,030,712 and 55,036,471 do not seem to correspond with the SNPs listed in SNPedia (so my previous inference was wrong, it seems).

We can also see in the map how the haplotype N is distributed in what would seem to be random founder effects.

There is a chance that the Denisova variant (haplotype D) is found in some Papuans but being described by just a single transition this is not certain.

As you know I dislike molecular-clock-o-logy, which I consider close to pseudoscience but considering that there has been some paper recently claiming (as they usually do: as if it was rocket science instead of a mere educated guess) low divergence ages for Neanderthals and H. sapiens, I feel almost obliged to mention that this paper estimates the haplotype divergence at some 500-731 Ka., what, after correcting for the usual under-estimate of the Pan-Homo divergence, can be consistent with the classical archaeological understanding of the Neanderthal-Sapiens divergence before a million years ago, with the spread of Acheulean and H. heidelbergensis.

The Xavantes as genuine unmixed Native Americans

Xavantes (cc Agência Brasil)

A new paper proclaims that Xavantes appear to be one of the less mixed and or more genetically distinctive Native American people of present day.

Patricia C. Kuhn et al., Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture. PLoS ONE 2012. Open access ··> LINK [doi: 10.1371/journal.pone.0042702]

Abstract

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

The Xavantes, comprising today some 10,000 people, have suffered repeated hostility from the Western civilization in Brazil since centuries ago. In spite of all they have managed to remain proud and distinct.

Fig. 2 three-dimensional global PCA with emphasis in American populations

Fig. 3 (edited by me: only the labeling): neighbor-joining global tree

Ample analysis of the genetics of European (Ashkenazi) Jews

A new paper on European (Ashkenazi) Jewish genetics is available:

Ehran Elhaik, The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. arXiv 2012. Open access. [arXiv:1208.1092v1 [q-bio.PE]]

(Supplemental material available HERE). 

The author prefers to use the term European Jews to that of Ashkenazi, because Ashkenaz is traditionally Germany and this may imply certain assumptions about the origins of this population, i.e. the Rhineland model, which he intends to contrast with the Khazar model and what he calls the Judean model. 

No intention exists in all the paper of investigating the Anatolian model, by which Western Jews would be descendants, in essence, not so much of Iron Age Jews from Palestine (Judean model) but neither from Europeans, be them Western (Rhineland model) or Eastern (Khazar model), but rather of Hellenistic converts from areas like Cilicia or Cyprus.

This alternative model is clearly supported by autosomal genetics, in this and previous papers. However haploid genetics seems to point to different sources.

In the paper, European Jews were roughly subdivided into Eastern (Belorussia, Latvia, Poland, and Romania) and Central (Germany, Netherland, and Austria) European Jews: EEJ and CEJ respectively in the graphs. They show some but not well defined structure however.

I'd say that the core of the paper's interest is in the following graphs:

1. Autosomal PCA:

Fig. 3 PCA scatterplot of West Eurasians (click to enlarge)

Again, as in previous analysis, including mine, Western Jews, in this case the European or Ashkenazi subgroup appears to cluster near Cypriots, suggesting a Southern Anatolian main origin (Tarsus area) very likely. However this region (ancient Cilicia) is still to be directly compared with Jews (I know it's just it's fine tuning but still when you have a theory, you'd like to see it reality-checked).

Another possibility would be hat this clustering is an artifact, assuming diverse origins homogenized by Jewish endogamy since the Middle Ages. But the fact that all three Western European subpopulations (Ashkenazi, Sephardi and Moroccan) tend to cluster over there (when they do not behave as fully distinct, as happened to me with all but Sephardites earlier this year).

Not shown here is fig. 7 that lists proportions of shared IBDs with West Asian and Caucasus populations (only): Caucasians are highest (roughly 9%), followed by Palestinians (c. 7%), while most groups are at c. 5% (except Lebanese who are at c. 3%).

In general this data supports some but limited Palestinian connection and a much more northernly origin of Western (or at least Ashkenazi) Jews. This is consistent with previous data (see below).

2. Haploid or uniparental relations:

Fig. 7 Relative affinity of (A) mtDNA and (B) Y-DNA of European Jews

Note please that the map is awfully drawn in some key details, for example the dark areas in Kurdistan correspond in fact to Lezgian (from Daghestan, in the NE Caucasus) and another one I don't discern well but that begins with I and hence must be an Iranian or Indian group, not Kurdish. The center of the "Kurdistan" affinity hotspot must be hence much farther NE, in Daghestan or Azerbaijan.

So by uniparental lineages, European Jews do appear as a mixture of Western (strongest in Y-DNA) and Caucasian lineages (strongest in mtDNA), supporting both the Rhineland and the Khazar hypothesis in a combined way. However no comparison with Cypriots nor Southern Turks was made, and these are the populations to whom Western Jews show most direct affinity by autosomal DNA, being Cilicia one, if not the largest, hotspot of the Jewish Diaspora in the Roman Era, a most likely realistic origin for

See also previous analysis:

• My own amateur analysis: (Sephardi) Jews in the context of the Levant and Anatolia
• Discussion on Behar 2010 at Leherensuge (my old discontinued blog)
• Discussion on Atzmon 2010 at Leherensuge

 

Claim first known lighters from Palestine Neolithic

A new study claims that cilindro-conic artifacts and holed items found in Yarmukian Pottery Neolithic sites (6th millennium BCE) are the first known fire-making artifacts and not, as had been argued previously, ritual or cultural objects such as idols or game boards.

Naama Goren-Inbar et al., The Earliest Matches. PLoS ONE, 2012. Open access ··> LINK [DOI: 10.1371/journal.pone.0042213]

Abstract

Cylindrical objects made usually of fired clay but sometimes of stone were found at the Yarmukian Pottery Neolithic sites of Sha‘ar HaGolan and Munhata (first half of the 8th millennium BP) in the Jordan Valley. Similar objects have been reported from other Near Eastern Pottery Neolithic sites. Most scholars have interpreted them as cultic objects in the shape of phalli, while others have referred to them in more general terms as “clay pestles,” “clay rods,” and “cylindrical clay objects.” Re-examination of these artifacts leads us to present a new interpretation of their function and to suggest a reconstruction of their technology and mode of use. We suggest that these objects were components of fire drills and consider them the earliest evidence of a complex technology of fire ignition, which incorporates the cylindrical objects in the role of matches.

Rather than matches I would use the analogy of lighters if any because matches by definition have a chemical head that burns with friction, while lighters can have many designs and traditionally often used, like these, friction to ignite a wick or tinder (example). 

The kind of fire-making the authors suggest resemble more the style used by Bushmen and other peoples in which a stick is energetically rolled inside a small plank, until it achieves enough heat by friction to set some tinder alight. 

Often friction is generated just using the hands but in other cases the string of a bow is used instead (right). 

This last seems to be what the authors suggest to have been the case with the strange artifacts:

Fig.3 - Fired-clay cylindrical artifacts

Fig. 6 - Kfar HaHoresh limestone artifacts interpreted as fire boards

In support for their case the mention that the Egyptian hieroglyph for fire is a fire drill with the bow method, precisely their suggested method, based on some grooves arguably made by strings, however I could not confirm this extreme because the Internet is full of all things pseudo-Egyptian and basic introductory pages to the most complex Egyptian hieroglyph writing system (similar in the general concept to Chinese script, for instance) do not go that far. 

I would not anyhow discard the game board notion myself but your call.

Research continues in Santimamiñe Cave (Basque Country) and produces some new information

Littorina littorea
(winkle, magurio, faocha)

Santimamiñe Cave, near Gernika, has one of the most complete archaeological records of all Europe, from Chatelperronian to Iron Age with the only exception of Aurignacian, including some Magdalenian rock art, although not as spectacular as in other sites.

Research continues however and these days a new hearth, at the innermost human habitation area of the cave, dated to c. 12,000 years ago (end of the Upper Paleolithic) has been discovered with tools and food remains that should help us to better understand the way of life of our ancestors.

They ate stuff like deer, goats, bisons, aurochsen, game, salmon, sea snails (winkles) and sea urchins.

The hearth belongs to the Late Magdalenian culture and, for what chief archaeologist Juan Carlos López Quintana says, they are probably contemporary with the artwork located deeper in the cave, in a small hidden room.

Part of the Santimamiñe rock art

The research continues at good pace financed by the Chartered Government of Biscay, having made the work of some 20 campaings in just eight years. They expect to reach the Early Magdalenian layers by 2020 or so. It's a methodical work. 

Follows video in Spanish:

Sources[es]: ETB, Pileta.

'DNA in Forensics 2012' meeting at Innsbruck

In spite of the strange name the materials are all about population genetics, a main interest of mine and this blog, and that's why I mention it.

I'm not sure if all the names mentioned in the full program (PDF) will be partaking (or if it is just the materials to be discussed) but, if so, the meeting will be full of high profile geneticists.

The meeting will take place in September 6-8 at Innsbruck, Austria.

Short version of the program:

Thursday, Sep 06

Registration (10h00 - 14h00)

Welcome (14h00 - 14h30)

Richard Scheithauer (Innsbruck, Austria)
Mechthild Prinz (New York, USA)
Lutz Roewer (Berlin, Germany)
Walther Parson (Innsbruck, Austria)

Session I: Forensic aspects of the mitochondrial phylogeny
Chair person: Walther Parson. 14h30 - 16h30

Session II: Applications of mtDNA analysis
Chair person: Lourdes Prieto. 17h00 - 19h00

Friday, Sep 07

Session III: Updating the Y chromosome phylogeny
Chair person: Lutz Roewer. 09h00 - 11h00

Session IV: Applications of the Y chromosome phylogenetic approach
Chair person: Daniel Corach. 11h45 - 12h45, 14h00-15h30

Session V: Next generation Y-STRs
Chair person: Manfred Kayser. 16h00 - 18h30

Social Evening

Saturday, Sep 08

Session VI: New technologies in haploid marker analysis
Chair person: Peter de Knijff. 09h00 - 10h30

Session VII: Biostatistics of lineage markers
Chair person: Michael Krawczak. 11h00 - 13h45

For more details, see the dedicated website. 

(Hat tip PrinceDuadha).

Iruña-Veleia scandal: four years later archeometric analysis will finally be made

The crust clearly indicates that they are anything but recent

It is an order by the tribunal, on request of the defense, who have insisted from the beginning that the exceptional graffiti found in Iruña-Veleia, which include images and short texts in both Vulgar Latin and early Basque (plus some other stuff), are genuine and not any hoax. 

The archeometric analysis will be performed at the Institute of Cultural Patrimony of Spain, a reputed institution with sufficient capability to perform the much needed analysis. Previously the court had asked two different police corps to perform the analysis but both had to admit that they could not do it. Supporters of the truthfulness of the findings had even offered to pay the analysis from their own pockets, proposing several European laboratories for that purpose. 

Meanwhile the influential clique of mostly linguists, led by the infamous Lakarra and Gorrochategui tandem, who claimed that the inscribed shards were false only because they would clash with their own pet theories, have been pretending that no scientific test can prove anything here: only their own self-serving opinions count. 

Sources[es]: Noticias de Álava, Iruina.

For background on this shameful story of cronyism and pseudoscience inside the Basque academic and political establishment, see category Iruña-Veleia:

• in this blog.
• in my old discontinued blog (Leherensuge).

Some of the shards previously posted in these blogs:

Tartessian script in Veleia

NIIV = NEU (I or me in Basque)

NIIVK CORDV MM (?) - click to expand

SIINIICA -
SOCRATIIS
VIRGILIO
MISCART (?)

NIIVRII ATA = neure ata (my father in Basque, modernly father=aita)