November 30, 2012

Ice and "complex organic materials" on Mercury's poles

This is one of those perplexing astronomical news that make history and I can't but mention. US scientists have found, with the help of scout satellite MESSENGER,  that not just suspected Mercury's polar water ice (in shadowed craters) is indeed that but also that confusing dark regions around it are complex organic materials, possibly darkened by the intense solar radiation that bathes the small inner planet. 

The team found that the probe's reflectance measurements, taken via laser altimetry, matched up well with previously mapped radar-bright regions in Mercury's high northern latitudes. Two craters in particular were bright, both in radar and at laser wavelengths, indicating the possible presence of reflective ice. However, just south of these craters, others appeared dark with laser altimetry, but bright in radar.

This confused scientists for a while but eventually they realized that the puzzling regions actually hold water ice at a meter's depth into the soil, where the heat of the sun can't reach so easily. 

Radar-reflectant regions (ice) show in yellow

The most interesting part however is that the astronomers are almost certain now that the dark material must be complex organic matter, darkened by the extreme solar radiation.

Is there life in Mercury? 

Source: Science Daily.

Ref studies: 
  1. David A. Paige, Matthew A. Siegler, John K. Harmon, Gregory A. Neumann, Erwan M. Mazarico, David E. Smith, Maria T. Zuber, Ellen Harju, Mona L. Delitsky, and Sean C. Solomon. Thermal Stability of Volatiles in the North Polar Region of Mercury. Science, 29 November 2012 DOI: 10.1126/science.1231106
  2. Gregory A. Neumann, John F. Cavanaugh, Xiaoli Sun, Erwan M. Mazarico, David E. Smith, Maria T. Zuber, Dandan Mao, David A. Paige, Sean C. Solomon, Carolyn M. Ernst, and Olivier S. Barnouin. Bright and Dark Polar Deposits on Mercury: Evidence for Surface Volatiles. Science, 29 November 2012 DOI: 10.1126/science.1229764

November 29, 2012

Asturian internal genetic barriers for both uniparental markers (revised)

¡Bumped because of correction and updates that markedly change the original!

Formal correction (Nov 29):

All what I said about not testing for G2a seems incorrect because one individual with this lineage was reported in the Oviedo district. This leaves 21 F(xG2a,K) individuals (15 of them from the Avilés district, making 20% of the local gene pool) in the mystery zone. They could still be other G subclades (but rare in Iberia or elsewhere in Europe), H (but normally thought as restricted to Roma People in Europe) or F* (F-other). 

Some rare F clades have been reported in Europe before but never in such large numbers, I believe. Sadly the authors mention for comparison old (2004-06) studies of the Caucasus, etc. which appear not to have tested for G, leading me to think (with the help of awfully presented, or rather hidden, raw data) that they had not tested for G2a. 

The seem to have done it after all. Thanks for noticing to Jean.

Follows original entry and update (bottom) with haplogroup frequencies (based on the work of Jean Lohizun, who sorted up the raw lists into something you can at least count).

_____________________________ . . . _____________________________

Original entry (Nov 28):

This new paper on the genetics of Asturias (Iberia) seems to be of limited interest because the authors only appear interested in statistical inference, instead of properly reporting basic data as primary social service of their publicly paid research effort. They also seem dead set into not testing for well known Iberian lineages like Y-DNA G2a (or even G, never mind discerning subclades of E) something that was already obvious in their previous attempt with mtDNA, and seem oblivious to some of the most important work on the population (haploid) genetics of the Iberian Peninsula such as Adams 2008.

Still it may be of interest for data miners but be warned that all the haplogroup data is only available as long unsorted PDF lists in the supplemental material (mtDNA list download, Y-DNA list download).

Antonio F. Pardiñas et al., Assessing the Genetic Influence of Ancient Sociopolitical Structure: Micro-differentiation Patterns in the Population of Asturias (Northern Spain). PLoS ONE 2012. Open access → LINK [doi:10.1371/journal.pone.0050206]

Maybe the only highlight of the study is that the authors infer some genetic barriers within Asturias, especially segregated seem to be the coastal district of Avilés (3) and the mountain miner districts so-called Southern Oviedo and Caudal (5, 9), also including the Narcea (2) district for matrilineages (mtDNA). Meanwhile the largely Galician-speaking Eastern district of Eo-Navia (1) appears segregated only for patrilineages (Y-DNA). 

Figure 2. Map of Asturias showing the SAMOVA group division coupled with the inferred barriers to gene flow.
Panels show results for the mtDNA data (A) and NRY data (B). Thin lines indicate division in the SAMOVA analysis but no actual barrier inference, while inferred barriers between groups are shown by strong lines. Bootstrap value for each of the barriers is shown next to it and only those with values equal or higher than 70 are shown.

The authors find hard to understand the genetic distinctiveness of Avilés district and talk wildly about "basal F" (probably G2a but why did not you test for that?!) Haplogroup G is relatively rare in Asturias but common for example in Portugal or Ibiza, being surely an indicator of Neolithic-derived settlement (found in ancient DNA from Occitan and Catalan Cardium Pottery sites and is also the lineage of the famous Alpine mummy Ötzi, probably also of Cardial ancestry). However, as you may know, no Cardium pottery is known so far to the North or West, so it may indicate a post-Neolithic resettlement of some sort. 

The paper also provides some PC analysis in relation to Europe but fails to explain properly which are each of the various Asturian "groups" (which seem to correspond to clusters by thin lines in the map above - maybe digging in the supp. material... but worth it?)

Figure 3. PCA plot of mtDNA haplogroups of Asturias and other regions of Iberia, the British Isles and Mainland Europe.

Figure 4. PCA plot of NRY haplogroups of Asturias and other regions of Iberia, the British Isles and Mainland Europe.

En fin: a confusing paper that could have been much better or at least user-friendly with some little extra effort and better focus. Still worth mentioning, I guess. 

See also: Asturian mtDNA (on a previous paper by the same team) and category: Iberia

 ______________________ ... ______________________

Update (Nov 29): haplogroup count

Based on lists made by Jean Lohizun.

  • E: 22
  • F*: 21
  • G2a: 1
  • I: 5
  • J: 12
  • K*: 9
  • R*: 8
  • R1b1a2: 106

Mitochondrial DNA:
  • HV*: 2
    • HV0*: 9
      • V: 5
    • (within HV4):
      • HV4a*: 5 
        • HV4a1a: 3
      • HV4b: 2
    • HV6: 1
    • HV12b: 13
    • H*: 12
      • H1*: 1
        • H1a*: 1
          • H1a3: 4
        • H1b: 1
        • H1c*: 6
          • H1c3: 3
        • H1f: 2
        • H1h: 4
        • H1j: 3
        • H1x: 1
      • H2a2*: 50
        • H2a2b: 4
          • H2a2b1: 9
        • H2a5b: 1
      • (within H3d):
        • H3d: 6
        • H3f: 6
        • H3g: 12
        • H3h: 3
      • H5: 13
      • H6*: 10
        • H6a1a1a: 1
      • H7a1: 1
      • H9a: 1
      • H10a1: 4
      • H15: 3
      • H20: 1
  • JT*: 1
    • (within J):
      • J1*: 1
        • J1b1a1: 7
        • J1c*: 4
          • J1c1: 5
          • J1c2: 12
      • (within J2):
        • J2a1a: 1
        • J2a2: 1
        • J2b1a: 5
    • T*: 3
      • T1: 1
        • T1a: 9
          • T1a2a: 1
      • T2*: 2
        • T2b*: 16
          • T2b3*: 2
            • T2b3a: 1
        • T2c*: 2
          • T2c1b: 1
        • T2e*: 2
          • T2e1: 4
  • (within U):
    • U1a2: 1
    • U4*: 2
      • U4a1*:2
        • U4a1d: 3
      • U4a3: 1
      • U4b3: 1
    • (within U5):
      • U5a1*: 4
        • U5a1a1: 1
        • U5a1b1*: 1
          • U5a1b1e: 1
      • U5a2: 2 
      • U5b*: 1
        • U5b1b1*: 1
          • U5b1b1e: 1
        • U5b1d: 5
        • U5b1f: 2
        • U5b1g: 1
        • U5b2a1a: 1
        • U5b2a1b: 1
    • U6*: 2
      • U6a:1
    • (within U8):
      • U8a: 1
      • K*: 1
        • K1*: 1
          • K1a*: 2
            • K1a1: 1
            • K1a3a: 3
            • K1a4c: 6
            • K1b1a2: 2
        • K2*: 1
          • K2a: 1
  • R9*: 1
    • R9b2: 1
  • (within N1):
    • I*: 1
      • I1a1: 1
      • I2a: 1
    • N1b: 1
    • N1e'l*: 1
  • W*: 1
    • W1: 1
  • (within X2):
    • X2b: 1
    • X2d: 1
  • (within M):
    • D4k: 1
    • M1*: 1
      • M1b1a: 1
  • (within L3(xM,N)):
    • L3f1b4a: 5
    • L3x: 1
  • L2a: 1
  • L1b: 1

Roma orignis and the Y-DNA haplogroup H1a1a-M82

The origins of the Roma people of Europe and West Asia are better understood each day.

Niraj Rai et al., The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations. PLoS ONE 2012. Open accessLINK [doi:10.1371/journal.pone.0048477]


Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.

Figure 1. The most parsimonious route of prehistoric expansion of Y-chromosomal haplogroup H1a1a-M82 and the recent out-of -India migration of European Roma ancestors.
Figure 2. Phylogenetic network relating Y-STR haplotypes within haplogroup H1a1a -M82.

I don't feel I can say much more. Just, as usual, to insist in taking the proposed age estimates with caution.

Epipaleolithic Sicilian had mtDNA haplogroup HV1

Besides sequencing this individual's ancient DNA, the study focuses on discerning the earliest stable occupation of the island and the diet of its inhabitants.

Marcellino A. Manino et al., Origin and Diet of the Prehistoric Hunter-Gatherers on the Mediterranean Island of Favignana (Ègadi Islands, Sicily). PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0049802]

The authors argue that this occupation of Sicily could be the oldest stable one and that it happened because of the formation of a land bridge because of low sea levels soon after the Last Glacial Maximum (but actual bathymetries hardly support such land bridge, so soon after the LGM they needed boats again to cross the dangerous Strait of Messina). However some Aurignacian artifacts are known and believed to be of older chronology. 

They also argue that, based on the N/C isotopic ratios, these peoples had a mostly carnivore land-based diet. This leaves me quite perplex because the Nitrogen-15 values are much higher than those of foxes (a mostly carnivore animal) and that is usually considered a signature of feeding off sea mammals. 

Figure 3. Carbon and nitrogen isotope composition of bone collagen from Mesolithic humans and fauna of Grotta d’Oriente.

See also: Magdalenians did eat sea mammals (at my old discontinued blog Leherensuge).

Y-DNA survey of Tamil Nadu

Fig. 1 - Sampling sites
Warning (Dec 1): table 2 was so messed up that I had to postpone most of the commentary on this important paper. Please disregard this entry and head to the new, much more extensive and correct version HERE.

Always welcome to find more about the genetics of India, surely one of the key geographical nodes of prehistoric human expansion (and, of course, a huge region with interest of its own right).

Ganesh Prasad Arun Kumar et al., Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System. PLoS ONE 2012. Open accessLINK [doi:10.1371/journal.pone.0050269]

The authors took special interest into sampling tribes, some of which are still foragers and a reference for all kind of anthropological research of South Asia, all Eurasia and even beyond. They also sorted the various populations into groups or classes based on socio-economic reality (and language in some cases) rather than the, arguably overrated, varna (caste) system. See table 1 for details.

The bulk of the data is in table 2, an edited and annotated version of which I include here (two columns, R2 and SD, were transposed in the original, I resized for optimal visualization and annotated wildly to highlight most important clades, etc. - that's how I read papers, rather than paying too much attention to the wording or beliving blindly all what geneticists say on age estimates and other educated hunches):

Annotated and corrected version of table 2 (click to view in optimal size).

As I'm not totally sure that the tabulation (even after correction) is right, I'm going to withhold judgment. Hopefully it'll be corrected soon and we can analyze the data properly.

Update (Nov 30): I wrote to the authors on the issue and got prompt reply. Apparently the shifted column is that of J2-M172 and not R2 as I thought first, but instead of a simple swap all columns since J2a1 shifted one place to the left (so  all that K* is actually L1, all that R* is actually R1a1, etc.)

I am very interested on what this paper seems to have found and therefore I will wait a bit for the formal correction (which is apparently in wait for PLoS ONE editors to perform only) and write on the matter anew. Because, if nothing else, the high levels of F* and C among hunter-gatherer tribals seem very important.

November 28, 2012

Ivory worked in Andalusia 4800 years ago was from West Asia

The revolutionary ivory hoard
It has been reported today that workshops in the Chalcolithic (and Megalithic) site of Valencina de la Concepción (near Seville, Andalusia) used ivory imported from West Asia, belonging to tusks of the extinct Syrian (or also Assyrian) elephant (the westernmost variant of the Asian elephant, Elephas maximus). 

Until today it was generally believed (by default) that the ivory used in Chalcolithic crafting was from North Africa, however the (also extinct) North African elephant was a variant of the African species Loxodonta africana. 

While trade with Northern Europe (amber) was acknowledged as a matter of fact but was strongly supported by cultural elements (Megalithism), as well as by the unmistakably Nordic amber which washes to the beaches of the Baltic and German Sea, trade and cultural connections with the Eastern Mediterranean were considered speculative at best.

This discovery, which traces the first (indirect?) trade with West Asia to some 4800 years ago appears to demolish almost single-handedly the usual notions about Western European Chalcolithic (c. 3000-1800 BCE) by which contacts with the Eastern Mediterranean were considered speculative or even unlikely. There seems to be a glass bead in Eastern Iberia but nothing else that could support consistently contacts with anywhere East of Italy or Lybia. Only nearing the Bronze Age (which may begin c. 1850 BCE in the most developed parts of Iberia) such connections could be taken for granted (and yet mostly because of cultural rather than material imports). 

However the late Megalithic burial types of the Chalcolithic (tholos, artificial caves, etc.) which partly replace the classical dolmen in the areas we could well call more civilized (parts of Southern Iberia and Languedoc), has been argued in the past to be conceptual imports from the Eastern Mediterranean (places like Kurdistan and Cyprus, where tholoi were used first for housing apparently). But a time gap of a whole millennium (or more) made it all a bit hard to accept and the competing theory of the architectural concept of false dome (tholos) being invented twice became rather mainstream. 

The finding has been reported in the Acts of the Congress on Ivory and Elephants, which took place in Alicante and it's also said to be published in the Journal of Archaeological Science (but I can't find it so it may well be awaiting publication). The research has been carried by academics from the University of Huelva, the German Archaeological Institute and the Valencina Museum. 

View Larger Map

November 27, 2012

Ethiopian haploid genetics

Ethio Helix mentioned yesterday a doctoral thesis on Ethiopian haploid DNA:

Christopher Andrew Plaster, Variation in Y chromosome, mitochondrial DNA and labels of identity within Ethiopia. The Center of Genetic Anthropology, University College of London, 2012 (doctoral thesis) ··> LINK (PDF).

The study deals with the anthropology, ethnology and linguistics of the African state, and especially with the haploid genetics (although more in detail with the Y-DNA side of the matter than with mtDNA). It is very much worth reading for anyone interested on the anthropology and population genetics of Africa and in particular the Horn region.

Personally I find most interesting the fact that there seem to be some correlations between Y-DNA and mtDNA. The author mentions that there is such correlation in diversity but it seems apparent that there is some more than just that, as should be obvious for example in the following graphs:

Population codes are:
  • AF Afar (Cushitic, Afar region: 2)
  • AM Amhara (Semitic, Amhara region: 3)
  • AN Anuak (Nilotic, Gambela: 6)
  • ML Maale (Omotic, SPNN region: 10)
  • OR Oromo (Cushitic, Oromia: 8)

What I have in mind is, first of all, that those populations who have the most Eurasian (F-derived) Y-DNA lineages also have the most Eurasian (N, M) mtDNA ones. However there is noticeably greater apportion of mtDNA from Eurasia than Y-DNA - and most of that excess corresponds to mtDNA M (all of it M1).

In a simplistic scenario in which one or several waves from Eurasia would be the only element to consider, we would expect similar apportions for male and female lineages or even noticeably more immigrant Y-DNA. This is not the case and therefore it is perplexing.

After some thoughts on the matter I realized that the situation is similar, mutatis mutandi, to the one of North Africa. This probably means that the cause of both anomalies can well be the same: a relatively recent (Epipaleolithic?) expansion of Afroasiatic-speaking peoples with mostly African male lineages (typically E1b1b-M215). But notice that in North Africa also J1 (ultimately from West Asia) appears to be also important in the Afroasiatic phenomenon, as it is in the Horn (and certainly in West Asia), making the situation even more complex for interpretation.

In this regard it is worth mentioning that haplotype networks from this study show that while the Amhara and Oromo J1 is intermingled and diverse, the Afar J1 forms a very tight cluster, strongly suggestive of an ancient founder effect.

Another such apparent correlation could be Y-DNA E1 and E1b1a7 with specific subclades (?) of mtDNA L0/L1 (probably L0) and L2. At least the apportions are almost identical among the Anuak (but not among other groups, hence why I suggest specific subclades to be determined).

It is a pity that no more fine detail was achieved with mtDNA, especially the more purely African part of it, i.e. L(xM,N). Much better detail is provided instead for the once-backmigrant M and N derived lineages (table 5.9), from which I highlight the following (only >5% shown):
  • All M is M1 (overall: 10%, AM 17%, OR 13%, AF 9%, ML 6%)
  • R0(xHV) reaches 11% among the Amhara (all R0: 15%)
  • N1 reaches 7% among the Afar
  • U(xK) reaches 6% among the Afar (all U: 9%)
  • K reaches 6% among the Maale (all U: 9%)
  • The Anuak seem the most purely African population among this selection with only 3% of M1 and 0% N. 
I would seem that even the Omotic, the most remote Afroasiatic branch according to linguists (some even consider it a distinct family), have some Eurasiatic genetic influence. However I'd say that this influence is at least largely pre-Neolithic and has been subject to deep reshaping by internal African dynamics as suggested above. Still Neolithic and even maybe post-Neolithic layers of West Eurasian deposition are also apparent in the structure - always in my understanding.


Ethio Helix has updated with extra information not included in the thesis.  Notable is a graph with much greater detail on the Y-DNA haplogroup distribution.

The E1* block is now split between a number of E1b1b subclades and some important dose of E1b1c, which is the dominant lineage among the Maale (and hence maybe among other Omotic peoples). Among the E1b1b sublineages, the Afar are relatively dominated by E1b1b1e, while the Maale have an important bloc of E1b1b1c1 and the Oromo appear dominated by E1b1b1a1b.

The B bloc is also split in several subclades, all them only relevant among the Anuak (most of it B2a and most B2a within B2a1a.

It is also quite notable that some J(xJ1,J2) has been found among the Maale. For reference on this rare paragroup, I'll mention that another niche of J* is the nearby island of Socotra (74%, probably a verly local founder effect and specific lineage to be described) and there is also some J* reported among peninsular Arabs, some Turks, Greeks, Jews and a few others - but otherwise most Y-DNA J either belongs to J1 or J2.

Elephant hair density helps cooling

The low density of elephant hair has been demonstrated to help cooling:

Conor L. Myrvhold. What Is the Use of Elephant Hair? PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047018]

At low densities, hair has almost no effect on air flow and does not trap an insulating air layer near the skin, but the extended hair acts as a pin fin that increases thermal exchanges with the surrounding air. Thus, as the hair density decreases from that of very furry animals, a break-even point is reached where the hair function switches from an insulator to a heat exchanger. This break-even point occurs at a density of about 0.3 million hairs/m2 [26] for thick hair covers with creeping flow in between (recall that 1500 hairs/m2 is about the maximum density of elephants). For comparison, the hair density of the human head is about 2 million hairs/m2 (see Methods and Discussion S1).

These heat dispersal properties were already known for plants (leaf hair, cactus' spines) but it is the first time to be demonstrated for an animal, more specifically a mammal like us. 

Figure 1. Pictures of elephant hair on the top of the back of an Asian elephant, (A) and an African elephant’s head (B).
The presence of hair on elephants was first noted by van Leeuwenhoek [30]. Photos taken by Conor L. Myhrvold in the Woodland Park Zoo, Seattle, Washington, from outside of the elephant enclosure, with permission from the Zoo.

I searched online for hair density on human body (the question we all have in mind, right?) and I could only find a commercial reference (I'd appreciate a better one if you know one). Still it seems that the hair density on tights and legs (and therefore probably on most of the body) in humans is 50 hairs/cm², what translates as 0.5 million hairs/m², somewhat (but not a lot) above the threshold mentioned above.

I'd dare suspect that this means that human body hair (vellus) is for most people thermally neutral but then I wonder how it works with sweat, which is a key part of our tropical thermo-regulatory natural design. Elephants and plants do not sweat (although they do get wet on occasion), so it may well work somewhat different for them.

That seems to be an interesting challenge to explore.

Visual etymological

Spanish archaeological blog Asociación los Dólmenes reports today[es] that a curious and somewhat obscene finding is at the roots of the modern city of Seville (known as Hispalis in Roman times). The finding of a phallic relief on the entrance of one of the oldest buildings of that city, at the port, has open a debate on whether the city has its origins in whore house (as could be normal for a harbor) or are we talking instead of a building-protector deity apparently of North African origins (where is found in many public buildings).

But regardless of the exact meaning of the icon, the depiction of an erect virile member with avian legs made me think of the origin of colloquial Spanish and English words for penis: cock and polla (Sp. chicken, fem.) Obviously Romans were not thinking of T. rex, right?

What about other languages? Berber, Portuguese, Catalan-Occitan, French, Italian? 

PS: The image actually has a lizard-like tail what should get us all a bit perplex because the closest thing that comes to mind is a dinosaur but Romans could not know anything about dinos, could they? 

This is the kind of argument used to reject the authenticity of some archeological findings like in the Iruña-Veleia case, where conjectures about the plausibility or not of this or that text (the non-existent Descartes - is Miscart) or letter (Z for example) have been used as alleged proof of falsification

Whatever the deep logic behind this icon, it's not weirder than gargoyles or centaurs, is it?

November 23, 2012

Ancient pig genetics

For some a religious taboo but for most a staple food, pigs have been in our farms and kitchens for many millennia now. 

It has been known for long that pigs are just the domestic variety of the Eurasian boar (Sus scrofa) but which populations specifically has been a matter of some debate. Now we know that East Asian pigs were domesticated locally (see appendix) but in the West it was found recently that European pigs have European boar lineages, while West Asian pigs in many cases do not. Previous studies determined that early European pigs were of West Asian ancestry but that by c. 4000 BCE all lineages were local.

This new study explores lineage diversity in ancient West Asian pigs from Anatolia, Kurdistan, Armenia, Georgia and Iran.

Claudio Otoni et al., Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. MBE 2012. Open accessLINK [doi: 10.1093/molbev/mss261]


Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or appeared so as a result of admixture between introduced pigs and European wild boar. These pigs not only replaced those with Near Eastern signatures in Europe, they subsequently also replaced indigenous domestic pigs in the Near East. The specific details of these processes, however, remainturnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria and Turkey. Our results firstly reveal the genetic signature of early domestic pigs in Eastern Turkey. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, nearly 1,000 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the demographic and societal changes during the Anatolian Bronze and Iron Ages. 

Probably most interesting is figure 1, which synthesizes the new findings:

(click to expand)

Fig. 1. A spatiotemporal depiction of ancient pig haplotypes. Rows represent eight chronological periods and columns pertain to sites organized along a longitudinal axis from west to east. Approximate locations of the archeological sites from which the samples are derived are shown as numbered circles on maps beneath the horizontal axis. Asterisks indicate directly AMS-dated samples. The question mark signifies not enough material was available for AMS dating. Slashed boxes indicate samples on which GMM analyses were performed. Pie charts to the right of each row summarize the haplotype frequencies for each chronological period across all sites. Columns pertain to one or two sites except for two columns that consist of several sites: Armenia (Sevkar-4, Areni-1, Khatunarkh, Shengevit, Lchashen, Tmbatir, Pilorpat, Beniamin, Tsakaektsi) and Iran (Qaleh Rostam, Qare Doyub, Qelīch Qōīneq, Dasht Qal’eh, Doshan Tepe, Malyan, Mehr Ali, Chogha Gavaneh and Gohar Tepe).

All shown West Asian lineages (Y1, Y2, Arm1T and Arm2T) belong to the NE2 clade, a related NE1 clade (common in Southern Iran, Iraq and Egypt, as well as Georgia) was not detected. See fig. 2 for details.

Early European domestic pigs all belonged to the Y1 haplotype, later replaced by the European ones, as mentioned above.

_________________________ . _________________________

Appendix: East Asian pigs were domesticated from local boars

Some references:

November 21, 2012

More on the Paleolithic of Nefud (Arabia)

The Nefud or An Nafud is a desert that sits on the North of Arabia Peninsula. Last year, tireless archaeologist Michael Petraglia published a paper on a newly found archaeological culture from that, now so arid, region (see here) dated to c. 75,000 years ago.

Location of the Nefud site of Jubbah (fig. 16 of present study)

It was pay per view however. This new release he has chosen instead the open access journal by default, PLoS ONE:

Michael D. Petraglia et al., Hominin Dispersal into the Nefud Desert and Middle Palaeolithic Settlement along the Jubbah Palaeolake, Northern Arabia. PLoS ONE 2012. Open accessLINK [doi:10.1371/journal.pone.0049840]


The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.

In this study, they report the oldest known Arabian occupation by any kind of humans c. 211,000 years ago:

Though so far a small excavated stone tool assemblage, the recovery of 28 artefacts in a deposit dated to 211±16 ka represents the oldest reliably dated occurrence in the Arabian Peninsula. We tentatively associate this assemblage with the Middle Palaeolithic on the basis of the age of the technology and the recovery of two Levallois flakes. Although we cannot be certain of the species that manufactured the artefacts, we note that the lithic assemblages were produced at a time corresponding with the origin of Homo sapiens in Africa based on mitochondrial DNA [40] and nuclear genomic [41] age estimates and fossil finds [42], [43]. The early JQ-1 artefacts also correspond with the upper age range limits of the Acheulo-Yabrudian and the Zuttiyeh fossil, potentially indicating the presence of archaic hominins [44] in Arabia, and possibly early representatives of the Neanderthals [45].
However the main findings are still from the 75,000 years old layer, whose cultural affinities and possible maker species are pondered. The most visually accessible result is a PC analysis:

Fig. 17 (Jebel Qattar and Jebel Katefeh are the Jubbah Lake sub-sites)

Notice how the Jubbah sub-sites (the two Jebels) fall between two Levantine Mousterian sites: El Wad and Tabun C, attributed to Neanderthals. So it is very likely that this colonization represents an expansive attempt by West Asian Neanderthals. 

Possibly related is the also recent finding (Delagnes 2012) of Mousterian in Yemen, dated to c. 55,000 BP. Therefore it would appear that after the expansion of Homo sapiens in Arabia, eventually leading to the colonization of Southern and Eastern Asia, as well as Near Oceania, there was an expansive tendency of Neanderthals as well, which may have helped to partly erase the genetic remnants of the out-of-Africa episode in the most fertile parts of Arabia Peninsula.

November 20, 2012

Very fast double change in Earth's polarity 41,000 years ago

Some 41,000 years ago is not only the age of the Campanian-Ignimbrite eruption and the sudden arrival of people with Aurignacian culture (most probably Homo sapiens) to the heartland of Paleolithic Europe: the Franco-Cantabrian region, sealing the fate of our Neanderthal cousins.

Some 41,000 yeas ago is also, we are told now, the date of the latest polarity reversal of planet Earth.

Researchers from the German Research Centre for Geosciences (GFZ), Norbert Nowaczyk and Helge Arz, have found that around that date, any hypothetical compass would have been for some 440 years (est.) completely lost. Some of that time the compasses would have pointed South and the rest the magnetic field was so messed up that failed its normal role of protection against solar radiation, which  was then surely rather dangerous for life on Earth.

The North Pole went mad, then the Phlegrean Fields erupted

Sources and more details: GFZ, PhysOrg, Before It's News.

Reference study: Nowaczyk, N. R.; Arz, H. W.; Frank, U.; Kind, J.; Plessen, B. (2012): "Dynamics of the Laschamp geomagnetic excursion from Black Sea sediments" Earth and Planetary Science Letters (pay per view), 351-352, 54-69. doi:10.1016/j.epsl.2012.06.050

Ancient DNA from Eastern Europe and Sardinia

A very interesting doctoral thesis has been known these days (h/t Jean). The thesis by Clio S. I. Dersarkissian (directed by A. Cooper and W. Haak) includes novel ancient mtDNA from North Eastern Europe (Karelia and surroundings) specially and also some Scythian and Sardinian burials from the Metal Ages.

Clio Simone Irmgard Dersarkissian, Mitochondrial DNA in ancient human populations of Europe. University of Adelaide, 2011 (thesis). Freely accessible ··> LINK [identifier:]

The most interesting findings may be those from Karelia:
  • First pre-Neolithic mtDNA H in Northern and Eastern Europe and one of the few findings strongly confirmed in such haplogroup before Neolithic. It clearly reinforces the already well established notion that mtDNA H existed in Europe before the Neolithic.
  • U2e - which might well be descendant or otherwise related to the U2 of Kostenki.
  • C1 - suggesting pre-Neolithic Siberian influences in Northern and Eastern Europe. The specific sublineage (named as "C1f") has not yet been sequenced elsewhere.
There are some more interesting data regarding ancient NE Europeans, Scythians and Sardinians but let's see that by parts.

Epipaleolithic peoples from Karelia and Northern Russia

Possibly the most impacting findings of this paper are those regarding two Epipaleolithic sites in Karelia (Uznyi Oleni Ostrov) and nearby parts of Northern Russia (Popovo, in Russia proper but not far from the Karelian border), as well as one more recent site from Sápmi (Lapland).

As I mentioned above, the U2e and C1 ("C1f") findings are unusual and suggestive of ancestral connections with Kostenki (Early Upper Paleolithic site from Southern Russia with U2 mtDNA) and Central Asia and Siberia. In fact an overall comparison with modern populations, shows strong affinities with West Siberians and Uyghurs for these Epipaleolithic Karelians.

Instead the Bronze Age Sami site shows more generic or distributed Siberian affinities, although there are populations in West Siberia (Nenets?) that also fit well with that mtDNA genetic pool. Bashkirs show similar affinity to both ancient populations (see ch. 1, fig. 3 - p. 103).

Not shown here are the results for the 18th century Sami site of Chalmny-Varre, which look a very modern Sami mtDNA pool, dominated by V7e and complemented by U5b1b1 and U5a1. 

Confirming the existence of mtDNA H in pre-Neolithic Europe

I really want to underline this, because certain influential people have been dead set into denying the existence of mtDNA haplogroup H in Europe altogether before the Neolithic. Why? Because they have a theory (a hypothesis more properly speaking) and they can't accept to be wrong about it.

That hypothesis (very popular in some circles) states that European aboriginal hunter-gatherers were very radically annihilated by Neolithic invaders from West Asia (never mind that archaeology alone is much more complicated than that, they don't seem to like thinking too much, much less looking at the matter from all the angles).

And a central battle they have fought is denying the possibility that mtDNA H (he most common haplogroup today in Western Europe) existed in the continent before Neolithic. The whole haplogroup, in their imaginary reality, could only have arrived with the industrious (and seemingly quite genocidal) farmers from West Asia (who almost never even mixed with anyone aborigine, how odd).

Reality began questioning their findings since 2005 but back in the day only HVS-I or at best HVS-II (control regions of the mtDNA chain) were used, leading to inconclusive results, specially in regards to short-stemmed haplogroup H. So they could still deny and deny...

But, recently, two different new studies have found unmistakable mtDNA H in Magdalenian people from Cantabria and Epipaleolithic people from the Basque Country. The reaction of some such knowledgeable aficionados has been simply unbelievable: they have flatly rejected the results without any reason; these findings are simply too inconvenient truths for their conjectures to be accepted. They are so obsessed with their fantasies that they can't even accept mounting evidence against them: they have stopped being scientific and begun being fanatics.

Very sad, really.

This finding in Karelia adds to the mounting unquestionable evidence on the matter: mtDNA haplogroup H not only existed in pre-Neolithic Eruope but it was quite extended, roughly through the areas in which is today abundant (and not just SW Europe as I came to suspect for some time). However in most regions was still far less common than it is today (or even totally missing, as seems to be the case in Central Europe).

Said that, it is not too clear yet where does all the improved knowledge of ancient genetics lead us to but what is clear is that mtDNA H is older and specifically older-in-Europe than some (too many) people have been insisting on.

Also it seems more and more obvious that the popular Neolithic farmers did not define the modern genetic landscape of Europe at all. They certainly introduced lineages that surely did not exist before but their overall influence seems limited and it does look like, after an initial burst, they declined also quite abruptly.

This is something that has been in the news these days (but no paper yet) and that I observed also in 2009 in relation to some similar studies (see: here and here). The age that we begin seeing modern-like mtDNA pools actually varies a lot, for example:
  • SW Europe: Basque Country: Neolithic (at least) ··> Hervella 2009 (discussed here).
  • Central Europe: Elbe Basin: Bronze Age or Chalcolithic ··> Schilz 2006[de], Schweitzer 2008.
  • Far North Europe: Sápmi: some time after the Bronze Age and before the 18th century (this study).
  • Central Asia: Iron Age (see below).
I conjecture here that (before the Medieval agricultural revolution) Northern latitudes could in general support lower population densities, being also more susceptible to the effect of climatic fluctuations. But more data is needed before we can have some consolidated certainty.

In any case, I took some time to make a couple of updated maps of the European and North African (1) Late Upper Paleolithic (Magdalenian and Oranian cultures) known ancient mtDNA and (2) Epipaleolithic. With this last one I found some conceptual difficulties so I had to take decisions, which were:
  • A most recent date boundary of 4000 BCE (which already overlaps with Neolithic in most regions since 1500 or more years before). Actually the most recent sites are c. 4200 BCE from Lithuania and c. 4600 BCE from Navarre.
  • No inclusion of any Neolithic data even if contemporary. The only possible exception was Franchti Cave (Greece), which has a sequence beginning in the Epipaleolithic (or Mesolithic) but is largely Neolithic. The exact adscription of the sequenced individual is not known.

The results are:

Late Upper Paleolithic mtDNA from Europe and North Africa
R* and specially R*-CRS can well be H and have often been reported as such but we do not know for sure

Epipaleolithic mtDNA from Europe (until 4000 BCE)
R* and specially R*-CRS can well be H and have often been reported as such but we do not know for sure

Some of these data (and others from more recent periods) can be seen in the dedicated Ancient mtDNA maps page at this blog. It needs some updating however: not much time has passed since I created those maps but new findings do pile up quickly these days. 

Ancient Scythian mtDNA

Another point of interest of the thesis is the ancient Scythian tombs from the Don basin (Iron Age, proto-historical). The results show some greater Eastern genetic influence than modern peoples (Russians) do.

The results, which place ancient Scythians closer to modern Central Asians than to Eastern Europeans are consistent with other recent studies that show an inflow of Eastern Asian mtDNA lineages into Central Asia even before the Turkic invasions of the Roman period and early Middle Ages.

Bronze Age Sardinian mtDNA

Finally the thesis deals with Sardinians from the Bronze Age (Nuraghic period). The sites are both from the most central parts of Sardinia, so they may be more representative of an early refuge population than to the overall Bronze Age of the island but still they are curious and interesting:

Dersarkissian argues that this suggests continuity but with many doubts, partly because the source of the genetic data (isolated teeth) did not allow for any certain identification of individuals. Still the resulting mtDNA pool (no matter how you look at it) is not really modern but rather reminds of Central European and Mediterranean Neolithic sites. 

The may well be some of the last Neolithic immigrants, who, instead of replacing the hunter-gatherer aborigines all around (as some imagined too dearly) were the ones taking refuge in this turbulent period in the highlands of Sardinia.

Who knows?!

November 19, 2012

Virtual visit to Iruña-Veleia

The Town Hall of Iruña-Oka  is the modern heir of the Vasco-Roman town of Veleia, known in medieval times as Iruña: the capital or the city, as happened with other Roman cities: Pompaelo, now Iruñea-Pamplona, Oiasso, now Irun, etc. 

As such, and on light of the continuous mismanagement by higher-level institutions (chartered government of Araba, Western Basque autonomous government), seems to have taken the matter of promoting and explaining the site on their own hands. 

To that effect, along with an already existing webpage with extensive information (in Spanish language mostly), the Town Hall has created a virtual visit site with panoramic views and reenacting illustrations ··> LINK

Needless to say that the Town Hall is not just the only institution taking Iruña-Veleia seriously nowadays but also the only one that seems to give official credibility to the finding of the exceptional graffiti (written in Basque, Vulgar Latin and other languages) performed by Eliseo Gil in 2006 and challenged by a powerful mafia of established linguists with enormous influences.

See also:

November 16, 2012

Some genetic support for South China origin of rice

CC by IRRI Images
I really miss Vietnam and other parts of Indochina (Cambodia, Thailand...) in this oh-so-Chinese study. Draw a line on a map and go to sleep...

Xin Wei et al., Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA. PLoS ONE 2012. Open access ··> LINK [doi]


China is rich of germplasm resources of common wild rice (Oryza rufipogon Griff.) and Asian cultivated rice (O. sativa L.) which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of O. sativa. However, the geographic origin and the domestication times of O. sativa in China are still under debate. To settle these disputes, six chloroplast loci and four mitochondrial loci were selected to examine the relationships between 50 accessions of Asian cultivated rice and 119 accessions of common wild rice from China based on DNA sequence analysis in the present study. The results indicated that Southern China is the genetic diversity center of O. rufipogon and it might be the primary domestication region of O. sativa. Molecular dating suggested that the two subspecies had diverged 0.1 million years ago, much earlier than the beginning of rice domestication. Genetic differentiations and phylogeography analyses indicated that indica was domesticated from tropical O. rufipogon while japonica was domesticated from O. rufipogon which located in higher latitude. These results provided molecular evidences for the hypotheses of (i) Southern China is the origin center of O. sativa in China and (ii) the two subspecies of O. sativa were domesticated multiple times.

The main interest of the study is to compare Oryza sativa (domestic rice) with O. rufipogon (wild rice and the ancestor of the former). It soon becomes obvious that both are the same species and that all O. sativa cluster with specific subpopulations of O. rufipogon (red rice, considered a weed):

Figure 3. Population structuring of O. sativa and O.rufipogon.

Complementarily a haploid phylogeny is studied and mapped by geography:

Figure 4. A map showing the sampled populations of O. rufipogon and the distribution of haplotypes.

From fig.2 we know that H1 corresponds to the haplotype found in O. sativa var. japonica (temperate climate variant) and that H2 and H3 correspond with the haplotypes found in O. sativa var. indica (tropical variant).

However notice how rare is the indica cluster in Tropical China O. rufipogon and that the exact combo only seems to show up in Hainan. For this reason, I would suggest future researchers to study the ancestor species also in Indochina, so we can understand better the origins of rice and particularly the indica variant, especially associated to Austroasiatic speakers now living almost exclusively in Indochina and parts of India.

The spears of Homo rhodesiensis

When I saw this image:

... I immediately discarded the news item. I said to myself: if those Canadian researchers can't reproduce a proper way to haft a Paleolithic spear, how can they know anything on the matter? Also I only occasionally comment on pre-Sapiens species and the paper is pay-per-view... so I had all the excuses not to comment. 

But in the end the report may be relevant even if the hafting techniques illustrated in that image are so totally wrong that it makes me angry (you don't tie a knife's edge, the points seem to be actually shaped so the wood goes around the base...)

Jane Wilkins et al., Evidence for Early Hafted Hunting Technology. Science 2012. Pay per view ··> LINK [doi:10.1126/science.1227608]


Hafting stone points to spears was an important advance in weaponry for early humans. Multiple lines of evidence indicate that ~500,000-year-old stone points from the archaeological site of Kathu Pan 1 (KP1), South Africa, functioned as spear tips. KP1 points exhibit fracture types diagnostic of impact. Modification near the base of some points is consistent with hafting. Experimental and metric data indicate that the points could function well as spear tips. Shape analysis demonstrates that the smaller retouched points are as symmetrical as larger retouched points, which fits expectations for spear tips. The distribution of edge damage is similar to that in an experimental sample of spear tips and is inconsistent with expectations for cutting or scraping tools. Thus, early humans were manufacturing hafted multicomponent tools ~200,000 years earlier than previously thought.

Raw examples of the points under discussion:

While these 500 millennia-old spears are not directly related to any hominin species, the general context almost necessarily implies that it must be Homo rhodesiensis, which is generally considered the immediate ancestor of Homo sapiens.

See for reference: Late human evolution maps (at my old blog Leherensuge), where I summarize the known paleoanthropology of the evolution of Homo spp. towards our kin and that of Neanderthals.

In synthesis: Homo rhodesiensis lived in Southern and Eastern Africa between c. 800,000 years ago (Saldanha Bay, South Africa) and the eve of our species c. 200,000 years ago (Omo, Ethiopia). Some of the late specimens (Lake Eyasi, Tanzania c. 240,000) are suspect of having transitional features towards us.

Direct sources: Noticias de Prehistoria[es], Eureka Alert.