Monthly Archives: August 2012

East Asians now claimed to be "more Neanderthal" than Europeans

Unlike what John Hawks had apparently found a few months ago but similar to what I thought apparent from the original Green et al. data back in 2010. 
Mathias Meyer et al., A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 2012. Pay per view ··> LINK [doi: 10.1126/science.1224344]
Denisovan ancestry is claimed now to be only found among Aboriginal Australasians (Papuans) but then again the data in the supplementary material (freely accessible) seems, to my untrained eyes, to allow for a thin Denisovan genetic influence in all Eurasia. 
I withhold my judgment because there seems to be a lot of sensibility to methodology in this hair-splitting excercise. John Hawks however has written a lengthy article trying to explain why both results appear contradictory regarding which levels of Neanderthal admixture. I would not bet much for his explanation however: I’d rather suspect that the methodology is not sound enough to estimate very thin admixture, so they are getting contradictory results in the uncertainty zone, what is just logical – even if a Schrödingerian kind of logic, of course.
Another finding is that Denisovans were apparently quite endogamous had very low diversity for modern standards, specially in the short bloc zone (ancient bottleneck) but also in the long bloc one (recent endogamy)*.


*Red text was updated, slashed out text was removed after first publication.


Comment moderation enabled

Sorry but some very specific individuals are insisting in being annoying and violating the few rules of respect and common sense in spite of repeated warnings.

Hence I have enabled comment moderation for some time as dissuasive tool.

My apologies to all readers and commenters of good will, who I know are the vast majority.

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Posted by on August 30, 2012 in blogging


Scotland: Maeshowe Chambered Cairn in 3D animation

Orknejar reports on a 3D video-animation of this important megalithic monument, considered a major piece of which was probably a major religious complex in the Chalcolithic (Late Neolithic), located at Orkney:

See also (older news and reports):


Autism does not have genetic causes

Not a single SNP was found to influence the development of autism spectrum disorders in an ample GWAS study:
Richard Anney et al., Individual common variants exert weak effects on the risk for autism spectrum disorderspi. Human Molecular Genetics 2012. Open access ··> LINK [doi: 10.1093/hmg/dds301]

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.
A synthetic report on this paper may be found at The Spitoon.
This study seems to effectively discard any major genetic influence in autism and forces us to look again for environmental clues like environmental pollutants, pregnancy conditions, early parental care (such as breastfeeding), vaccines, etc. in order to understand the causes behind these problems. Per Wikipedia:

Environmental factors that have been claimed to contribute to autism or exacerbate its symptoms, or may be important to consider in future research, include certain foods, infectious disease, heavy metals, solvents, diesel exhaust, PCBs, phthalates and phenols used in plastic products, pesticides, brominated flame retardants, alcohol, smoking, illicit drugs, and vaccines.

Common pollutants, notably many common plastics, pesticides, etc., are high among the likely causes of the disorders, as well as many other modern diseases.

Posted by on August 29, 2012 in health, human genetics, mind, psychology


Bronze Age rock art in Azores

The claim, even if very unexpected, seems legitimate enough to have been made by the President of the Portuguese Association of Archaelogical Research (APIA), Dr. Nuno Ribeiro, within a conference titled “pre-Portuguese human presence in Azores, myth or reality?”
Among the findings cataloged in the last few years Ribeiro mentioned building remains that seem prehistorical, a Roman era inscription, a rock art site in Terceira island and several megalithic structures. Only in the last year, five tombs of the hypogeum kind and three sanctuaries also dug in the rock were located. All the findings are still pending radiocarbon dating however but the style of the rock art is similar to Bronze Age ones from Iberia. 
However red tape by the regional government is blocking further research: in 2011 for lack of financing and in 2012 for not being withing the frame of a legal decree.  The archaeologist denounced that all these extraordinary findings are therefore in state of abandonment. In one case, works in the local airport, carried without the corresponding archaeological survey, may have damage a site.
These findings strongly suggest that the navigation skills of Bronze Age peoples of the Eastern North Atlantic (Western Europe, NW Africa) were much more advanced than we usually admit.
Source: RTP[por] (h/t Pileta).
See also these articles in English language at the Portuguese American Journal: art1, art2.

Azores are located far away into the North Atlantic Ocean (CC by Tyk)

Posted by on August 28, 2012 in Azores, Bronze Age, Megalithism, navigation, Portugal, rock art, sea


Early Neolithic boat and row fragments found in Korea

The remains were originally uncovered in 2005 in Ujin but only now it seems to have reached the international media. They are made of camphor wood and are stratigraphically from the Early Neolithic period (c. 8000 years ago). 

What remains of the boat is 3 meters long and 60 centimeters wide,
whereas the original ship is thought to have been at least 4 meters

The artifacts show how advanced carpentry was already in that period.
Sources and more details: Yahoo Groups: Austric, Korea Times, Yonhap, Delta World, Pileta[es].
Oldest Korean farm
In a related news item, the remains of the oldest known Korean farm were unearthed at Goseong earlier this year.
See: PhysOrg.
The site of the farm: lines indicate habitation or farming (white earlier, blue later)

Posted by on August 27, 2012 in archaeology, East Asia, Korea, navigation, Neolithic


Asturian mtDNA

Rock art from Asturias
A reader sent me a copy of a recent paper on the matrilineages of Asturias (in the northern parts of the Iberian Peninsula and part of the important Upper Paleolithic province known as the Franco-Cantarbrian region).
A. Pardiñas et al., Mitochondrial diversity patterns and the Magdalenian resettlement of Europe: new insights from the edge of the Franco-Cantabrian refuge. Journal of Human Genetics 2012. Pay per view ··> LINK [doi:10.1038/jhg.2012.100]
The authors identify what I understand is a false problem and try to find a solution but, as I see it, the whole matter lacks merit because instead of focusing on specific lineages like H, H1, H3, V, J or T2b (for example), they just discuss general haplotype diversity, what is pointless. 
Worse: they do so based only on HVS-I, which can only be considered a very mediocre proxy for actual lineage estimations, specially where haplogroups like H are dominant – because HVS-I usually says nothing or almost nothing about H and many of its subclades. 
So most of paper is just much ado about nothing, so to say. However the researches made an effort to quantify Asturian haplogroups (always with the limitation of using only HVS-I) and these results are of some interest, being the only reason why I mention this paper.
The mtDNA haplogroup (and paragroup!!!) frequencies of 429 Asturians (from various cities, all with Asturias-born maternal grandmother), based on HVS-I sequences, are as follows [haplogroup – absolute number (percentage)]:
  • R0 – 251 (58.5)
    • R0a – 1 (0.23)
    • HV -250 (58.3)
      • HV* – 2 (0.47)
      • H – 225 (52.4)
        • H* – 101 (23.54) 
        • H1 – 58 (13.5)
          • H1* – 53 (12.35)
          • H1a – 5 (1.17)
            • H1a – 1 (0.23)
            • H1a3 – 4 (0.93)
        • H2 – 14 (3.26)
          • H2a2b – 13  (3.03)
            • H2a2b* – 2 (0.47)
            • H2a2b1 – 11 (2.56)
          • H2b – 1 (0.23)
        • H3 – 30 (6.99)
        • H5 – 8 (1.86)
        • H6 – 11 (2.56)
          • H6* – 9 (2.10)
          • H6a1a1 – 2 (0.47)
        • H7a1 – 2 (0.47)
        • H9a – 1 (0.23)
      • HV0 – 17 (3.96)
        • HV0* – 8 (1.86)
        • V – 9 (2.10)
      • HV4 – 6 (1.40)
        • HV4a* – 3 (0.70)
        • HV4a1a – 3 (0.70)
  • U – 64 (14.92)
    • U* – 2 (0.47)
    • U1a2 – 1 (0.23)
    • U2’3’4’7’8’9 – 33 (7.69)
      • U4 – 11 (2.56)
        • U4* – 4 (0.93)
        • U4a – 7
          • U4a1 – 6 (1.40)
          • U4a3 – 1 (0.23)
      • U8 – 22 (5.13)
        • U8b – 4 (0.93)
        • K – 18 (4.20)
          • K* – 11 (2.56)
          • K1 – 7 (1.63)
            • K1a – 5 (1.17)
              • K1a1 – 2 (0.47)
              • K1a5 – 1 (0.23)
              • K1a11 – 1 (0.23)
            • K1b1a – 2 (0.47)
            • K1c2 – 1 (0.23)
          • K2b1 – 1 (0.23)
    • U5 – 23 (5.36)
      • U5* – 4 (0.93)
      • U5a – 11 (2.56)
        • U5a1 – 9 (2.10)
          • U5a1* – 7 (1.63)
          • U5a1b1 – 2 (0.47)
            • U5a1b1* – 1 (0.23)
            • U5a1b1e – 1 (0.23)
        • U5a2 – 2 (0.47)
      • U5b – 8 (1.86)
        • U5b1 – 7 (1.63)
          • U5b1* – 3 (0.70)
          • U5b1d – 4 (0.93)
        • U5b3 – 1 (0.23)
    • U6 – 5 (1.17)
  • JT – 93 (21.68)
    • J – 45 (10.49)
      • J* – 27 (6.29)
      • J1b1a1 – 8 (0.23)
      • J2 – 10 (2.33)
        • J2a1a – 1 (1.86)
        • J2b1a – 9 (2.10)
    • T – 48 (11.19)
      • T* – 5 (1.17)
      • T1 – 11 (2.56)
        • T1a* 10 2.33 (1.20–4.22)
        • T1a2a 1 0.23 (0.01–1.29)
      • T2 – 32 (7.46)
        • T2* – 2 (0.47)
        • T2b* – 20 (4.66)
        • T2b3a – 1 (0.23)
        • T2c – 3 (0.70)
        • T2e* – 1 (0.23)
        • T2e1 – 5 (1.17)
  • N1 – 6 (1.40)
    • N1* – 1 (0.23)
    • N1b* – 2 (0.47)
    • I – 3 (0.70)
      • I* – 1 (0.23)
      • I1a – 1 (0.23)
      • I2a – 1 (0.23)
  • W – 3 (0.70)
  • M1 – 3 (0.70)
    • M1* – 2 (0.47)
    • M1b1 – 1 (0.23)
  • D4g1 – 1 (0.23)
  • L3f1b4a – 5 (1.17)
  • L2a – 1 (0.23)
  • L1b – 1 (0.23)

A lot more research, with full coding region sequencing if possible, needs to be done in high “asterisk” haplogroups like H* (24%), H1* (13%), H3 (7%), H6*, HV0*, V, K*, U5*, J*, T1a* or T2b*. Hopefully next time.

Posted by on August 25, 2012 in European origins, Iberia, mtDNA, population genetics


Lactose tolerance favors obesity

While the lactose tolerance allele may have some positive health effects, notably because milk is one of the few good dietary sources of calcium, it seems to correlate also with some negative effects, namely obesity.
Ricardo Almon et al., Association of the European Lactase Persistence Variant (LCT-13910 C>T Polymorphism) with Obesity in the Canary Islands. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0043978]
Canary Islands, in spite of its subtropical geography, is one of the regions of the European Union where milk is most consumed, at levels comparable to Scandinavia. 
Although there is a strong correlation between being lactose tolerant and milk consumption it is not fully clear yet if it is excess milk consumption what makes people obese or an unknown collateral effect of the European lactase persistence allele.
Interestingly the correlation, very strong, is only found for obesity and not for being overweight:

Fig. 1 – BMI classification by LCT genotypes (LP: n = 330; LNP: n = 221)


Neolithic ship and obsidian cargo found near Naples

A sunken vessel has been discovered off the island of Capri (Campania, Italy), not far from Naples. The ship, whose details are unknown to me at the time of writing it, was tentatively dated to at least c. 5000 years ago, in the Neolithic (or earliest Chalcolithic) period. It carried a load of obsidian, a prime quality material for tools and weapons (which is said to produce sharper edges than modern surgical scalpels).
Sadly, I could not find much information on this most interesting discovery. I wonder if the obsidian was extracted from the Campi Flegrei at Naples Bay and who may have been demanding such a large cargo?

Archaeological map of Capri: red: Neolithic, yellow: Chalcolithic, other: later periods
(CC by Morn)

Sources: ANSA, Pileta.


Adaptionism (humor)

From the often great comic strip (cum video theater) Saturday Morning Breakfast Cereal:

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Posted by on August 24, 2012 in biology, evolution, Genetics, humor