Monthly Archives: February 2012

Neanderthals crossed the sea at least once

New research has found that the Ionian islands of Lefkada, Kefalonia and Zakynthos were never united to land, what implies that the Mousterian findings (probably Neanderthal-made) belong to peoples who crossed from the mainland, almost necessarily on boat or raft of some sort (they could have swam in theory but hardly with kids and all the family, you know).
Source and more data at New Scientist (found via Pileta).
Reference paper: G. Ferentinos et al., Early seafaring activity in the southern Ionian Islands, Mediterranean Sea. Journal of Archaeological Science 2012. Pay per view.

The rich are rich because they are greedy and cheat

There’s a new study out there set to open some minds to reality:
Raul K. Piff et al., Higher social class predicts increased unethical behavior. PNAS 2012. Pay per view (free in six months or already depending on global region).


Seven studies using experimental and naturalistic methods reveal that upper-class individuals behave more unethically than lower-class individuals. In studies 1 and 2, upper-class individuals were more likely to break the law while driving, relative to lower-class individuals. In follow-up laboratory studies, upper-class individuals were more likely to exhibit unethical decision-making tendencies (study 3), take valued goods from others (study 4), lie in a negotiation (study 5), cheat to increase their chances of winning a prize (study 6), and endorse unethical behavior at work (study 7) than were lower-class individuals. Mediator and moderator data demonstrated that upper-class individuals’ unethical tendencies are accounted for, in part, by their more favorable attitudes toward greed.

They even justify their unethical behavior because for them greed is somehow ethical, something good (as Reagan would memorably state in his reign), justifying almost everything (while for the rest of us it is obviously not). 
I wonder if there is a greedy gene and if we could inactivate it with genetic engineering. Of course I also wonder if such thing could be ethical… but sounds better than guillotine, right?
In the media: The Independent, Kaos[es].
Other great discoveries of modern psychological science: conservatives are quite scared, and progressive and open minded people are generally smarter.

Posted by on February 29, 2012 in psychology, Sociology


On and around with Ötzi’s genome

As you’re probably more than aware by now there’s a new paper on the market (yeah, 32 bucks – but worry not that I already got my hands on it) on the most loved mummy of Europe: Ötzi the Iceman.

A. Keller et al., New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nature 2012. Pay per view.

The most notable conclusion would seem to make Ötzi closest in all to Sardinians or more like   Corsicans, at least by Y-DNA. This one has been described now as G2a-L91, what is per ISOGG 2012 G2a2b (although the authors use the old nomenclature G2a4) and is most commonly found in Southern Corsica and the Corsican-speaking parts of Sardinia (Gallura).
The autosomal DNA has been compared with an all-Europe sample (the Behar 2010 one, I think based on the nomenclature used), to which a Sardinian sample was added. The result (right) does suggest a Sardinian (or Corsican) affinity of Ötzi.
Notice please that in the supplemental material the Ötzi dot achieves three different positions depending on the level of refinement: while all place Ötzi to the bottom left corner, he’s exact position varies quite a bit – it’s not like PC analysis (nor genetics overall) is rocket science, you know.
Also another caveat I have with this kind of analysis is that all it says is that Sardinians and Ötzi are very negative for both PC components, th Northern and the Eastern ones. The only association at the bottom left corner is a negative one: neither Nordic nor Greek, and this is not too informative.
Yes, the Y-DNA points to an association with Corsica (rather than Sardinia), what reinforces the suggestion posited by the autosomal DNA basic (but negative) analysis, still it would be nice if the authors would have bothered to do some ‘Admixture’ type of analysis as complement. 
At the moment all we have is a negative: Ötzi, who belonged to a Cardium Pottery derived cultural group (Bocca Quadrata or La Lagozza, can’t recall right now) and bears a quite clear Neolithic marker such as Y-DNA G2a, shows up as strongly non-Balcanic, unlike most modern Italians (Europe S sample).

It looks odd indeed… but it might be explained if we assume that from that time on, secondary (post Neolithic) Bronze Age flows from the Aegean (and Central Europe) altered gradually the genetic composition of Italy. This is supported by archaeology as far as I know: even before Mycenaean Greeks, the Aegean was influencing Southern and Central Italy more and more. This trend was reinforced in the late Bronze Age (Mycenaean colonization in the South, Etruscan migration in the Center) and the Iron Age (classical Greek colonization of Magna Graecia).

Before the Romans Italy was all or most of the time a recipient of cultural influences (from the Balcans, from SW Europe and from Central Europe) and did not, as far as I can tell, export culture except as secondary trampoline (the Cardium Pottery Case notably). Excepting the Cardium Pottery case, it acted more as a buffer between West and East and dead end than what its central Mediterranean position would suggest. Even in the Heraklean myth, original Greek version, the route to the fabled Hesperides does not go through Italy but North Africa. Only later, as the Romans rose to prominence, was Hercules made to journey back through Italy, something not specified in the original version. 
I’m saying all this because it may explain why the Europe S (Italy) component tends so strongly towards the Balcans (and to lesser extent Northern Europe) but neither Ötzi nor Sardinians do, even if they look Neolithic-blooded to some extent.

All Africa autosomal analysis at Ethio Helix

I want to call your attention at the very interesting autosomal analysis of all Africa at Ethio Helix today. Surely Africa is too big and too diverse to be captured well enough in a single pan-continental analysis but there is still a lot to learn from that study.

Leave a comment

Posted by on February 29, 2012 in African genetics, autosomal DNA


Copper findings in Kerala reinforce the concept of Chalcolithic India

Pottery found at Ramakkalmedu
The finding of copper beads, used for ornament, in Megalithic burials of Ramakkalmedu (Kerala) reinforces the idea of India also having a Chalcolithic period, intermediate between Neolithic and Iron Age. Until recently however the paradigm was one of Neolithic being directly followed by Iron Age.
Anyhow, in Europe often the notion of Chalcolithic, rather than just usage of copper and other soft metals (gold, silver), implies more the growth of social complexity and the first stages of civilization (much like Neolithic doesn’t anymore mean the use of polished stones but farming instead). 
Whatever the criteria used (not all authors agree), the beads excavated in Kerala are fine quality jewelry, and seem to imply a gradual advance of the Chalcolithic from the Deccan Plateau and ultimately from the Harappan civilization of the Northwest. 

Source: The Hindu.


Posted by on February 27, 2012 in Chalcolithic, India, South Asia


Basque mtDNA

I finally today put my hands on the latest study on Basque matrilineal genetics:
I have to commend the paper because the detail achieved is unprecedented, owing to a good and ambitious sampling strategy and testing for not just the whole hypervariable region (both HVS-I and HVS-II) but for 22 coding region markers as well. As result they have found a number of rare haplogroups and others that are common among Basques but apparently not elsewhere.

Fig. 1, showing the detailed sampling strategy

They have therefore achieved an unprecedented depth in the analysis of mtDNA H among Basques and neighboring populations but they pay no attention to other haplogroups. In this sense I have missed slightly more attention to U(xK), which is an important Basque haplogroup, second only to H, and the lack of proper tabulation of the results other than for haplogroup H. This made me dedicate most of this Sunday to manually tab the information, which I believe is important knowledge to share and discuss.
But first the pearl of this work, the discovery of novel Basque-specific sublineages of haplogroup H. They are detailed in table 1:

Table 1

But there is even more data in the supplemental materials, however it is not well organized (specially all the non-H sequences: merely tabbed in PDF format) and requires some hard work to put together. As said before, I dedicated some long hours to that task and I came up with the following data:

A. Gascony:

Bearn (n=56):

  • H1: 11 (20%)
  • H2a: 2 (4%)
  • H3: 3 (5%)
  • V: 3 (5%)
  • HV: 2 (4%)
  • U: 16 (29%)
  • K: 6 (11%)
  • J: 4 (7%)
  • T: 2 (4%)
  • X: 3 (5%)
  • Singletons: H5’36, H6, H9, H59

Bigorre (n=48):

  • H1: 9 (19%)
  • H3: 2 (4%)
  • V: 4 (8%)
  • U: 11 (23%)
  • K: 5 (10%)
  • J: 2 (4%)
  • T: 4 (8%)
  • Singletons: H2a, H6, H14, H67, HV, R0, K, I, X, W, C

Chalosse (Dax district) (n=60):

  • H1: 9 (15%)
  • H2a: 4 (7%)
  • H6: 2 (3%)
  • H13: 4 (7%)
  • H74: 2 (3%)
  • V: 5 (8%)
  • HV: 2 (3%)
  • U: 13 (22%)
  • K: 3 (5%)
  • J: 5 (8%)
  • T: 3 (5%)
  • X: 3 (5%)
  • Singletons: H3, H4, H5, H8, H42

B. Northern Basque Country:

Lapurdi/Baztan (Lapurtera dialectal zone) (n=58):

  • H1: 15 (26%)
  • H2a: 2 (3%)
  • H3: 3 (5%)
  • H4: 2 (3%)
  • V: 8 (14%)
  • U: 13 (22%)
  • J: 8 (14%)
  • T: 2 (3%)
  • Singletons: H5, H6, H24, K, X

Lapurdi/Lower Navarre (Benafarrera dialectal zone) (n=73):

  • H1: 24 (33%)
  • H3: 4 (5%)
  • H5: 2 (3%)
  • H20: 2 (3%)
  • V: 6 (8%)
  • HV: 6 (8%)
  • U: 13 (18%)
  • K: 2 (3%)
  • J: 5 (7%)
  • T: 2 (3%)
  • X: 4 (5%)
  • Singletons: H2a, H6, H42

Zuberoa (n=61*):

  • H1: 16 (26%)
  • H2a: 3 (5%)
  • H5: 2 (3%)
  • HV: 3 (5%)
  • V: 2 (3%)
  • U: 14 (23%)
  • K: 5 (8%)
  • J: 9 (15%)
  • X: 3 (5%)
  • W: 2 (3%)
  • Singletons: H3, T

C. Southern Basque Country South (Spanish-speaking area since 19th century):

Araba (n=56):

  • H*: 2 (4%)
  • H1: 18 (32%)
  • H3: 6 (11%)
  • V: 3 (5%)
  • HV: 5 (9%)
  • U: 7 (13%)
  • K: 3 (5%)
  • T: 5 (9%)
  • J: 4 (7%)
  • Singletons: H58, N1, X

Central-Western Navarre (n=64):

  • H1: 10 (15%)
  • H3: 12 (19%)
  • H7: 2 (3%)
  • V: 7 (11%)
  • U: 10 (15%)
  • K: 2 (3%)
  • J: 3 (5%)
  • T: 7 (11%)
  • I: 2 (3%)
  • Singletons: H*, H2a, H5, H27, H42, H49, H81, N1, X

North-Eastern Navarre (Erronkari-Salazar): (n=55)

  • H*: 2 (4%)
  • H1: 9 (16%)
  • H3: 5 (9%)
  • H42: 4 (7%)
  • V: 6 (11%)
  • U: 17 (31%)
  • K: 2 (4%)
  • T: 6 (11%)
  • J: 3 (5%)
  • Singleton: K

D. Southern Basque Country North (Basque-speaking area in 20th century):

Biscay (n=59):

  • H1: 17 (29%)
  • H2a: 6 (10%)
  • H6: 2 (3%)
  • H53: 3 (5%)
  • V: 2 (3%)
  • HV: 3 (5%)
  • U: 9 (15%)
  • J: 6 (10%)
  • X: 2 (3%)
  • Singletons: H*, H14, H17, H24, H86, T, N1, I, K

Gipuzkoa (n=57*):

  • H1: 19 (33%)
  • H3: 7 (12%)
  • H17: 2 (4%)
  • V: 3 (5%)
  • U: 12 (21%)
  • K: 2 (4%)
  • J: 5 (9%)
  • T: 2 (4%)
  • X: 2 (4%)
  • Singletons: H2a, H14, W

Gipuzkoa SW (n=63):

  • H1: 24 (38%)
  • H2a: 3 (5%)
  • H3: 3 (5%)
  • H6: 2 (3%)
  • V: 3 (5%)
  • U: 16 (25%)
  • K: 2 (3%)
  • J: 3 (5%)
  • T: 2 (3%)
  • Singletons: H4, H58, HV, X, L3’4

North-Western Navarre (n=53):

  • H1:10 (19%)
  • H2a: 3 (6%)
  • H3: 8 (15%)
  • H4: 2 (4%)
  • H5: 3 (6%)
  • V: 3 (6%)
  • U: 12 (23%)
  • T: 4 (8%)
  • J: 5 (9%)
  • Singletons: H24, HV, W

E. Southern Basque Country – West Biscay (Spanish speaking since old):

Enkarterriak (n=21):

  • H1: 5 (23%)
  • H3: 3 (14%)
  • H15: 3 (14%)
  • HV: 3 (14%)
  • U: 2 (10%)
  • Singletons: H4, H24, H87, K, X

F. Spain (areas once within the Basque ethno-cultural area):

Northern Aragon (n=29):

  • H3: 5 (17%)
  • H4: 2 (7%)
  • HV: 3 (10%)
  • U: 5 (17%)
  • K: 2 (7%)
  • J: 6 (21%)
  • T: 3 (10%)
  • Singletons: H42, V, X

Northern Burgos province (n=24):

  • H1: 2 (8%)
  • H3: 4 (17%)
  • U: 8 (33%)
  • K: 2 (8%)
  • T: 2 (8%)
  • J: 2 (8%)
  • Singletons: H*, H4, V, L2

Cantabria (n=19):

  • H1: 7 (37%)
  • H3: 3 (16%)
  • H5: 2 (11%)
  • J: 2 (11%)
  • Singletons: H27, H30, U, K, T

La Rioja (n=52):

  • H*: 2 (4%)
  • H1: 13 (25%)
  • H3: 7 (13%)
  • H5: 3 (6%)
  • U: 8 (15%)
  • J: 4 (8%)
  • T: 5 (10%)
  • K: 3 (6%)
  • Singletons: H10, H13, H30, H51, H58, R0, I


(1) * Sample size of Zuberoa is listed as 62 and Gipuzkoa as 56 but after checking and rechecking I’m pretty sure that one individual has swapped populations. So I’m assuming that n(Zuberoa)=61 and n(Gipuzkoa)=57 for all apportions. 

(2) Haplogroups in italic type are not named that way (or not named at all) in PhyloTree. I am confused by this and other nomenclature of this paper and so far haven’t got time to study what they might mean. Ideas are welcomed. 

(3) U means obviously U(xK). Just using the same terminology from the paper. Again, I haven’t got any time to explore how much of that U is U5b, U5a, U4 or other clades. This is in my opinion the greatest shortcoming of the paper: ignoring U almost completely. 

Based on this data, I elaborated some maps (official administrative divisions retained for reference, circle diameters are proportional to sample sizes):

Frequencies of mtDNA H1

Frequencies of mtDNA H3

Frequencies of mtDNA U(xK)

Frequencies of mtDNA J

Frequencies of mtDNA V

Notice that V is not as common among Basques as initially reported years ago.

See also:


Posted by on February 26, 2012 in Basque origins, Gascony, Iberia, mtDNA, population genetics


Oldest toy car is from Kurdistan c. 5500 BCE

The oldest toy car (right) is as old as 5500 BCE and was found near the North Kurdish town of Qoser (Kızıltepe). The car is worked on stone, has axles of different length and pre-dates Indoeuropeans by a lot. 
Previously the oldest known toy cars were from Turkmenistan (Altyndepe) or Mesopotamia, being dated to the fourth millennium BCE.
Other findings in the same site (also worked on stone) are dolls and whistles, the latter still able to produce sounds. These however could be more recent, from the fourth millennium.

Posted by on February 26, 2012 in archaeology, Chalcolithic, Kurdistan, Neolithic


Intelligence genes more elusive than Higgins’ boson

Havard University has issued a press release where Christopher F. Chabris, author of a yet unpublished paper on the matter, ponders the elusiveness of genes that could define intelligence. 
Twin studies have suggested that there is at least some truth to an association of intelligence (measured by IQ) with inherited genes, however now it seems clear that no individual gene is likely responsible of any notable influence on expressed intelligence. 
Chabris ponders that the genetic influence is probably the work of many genes acting collectively and not any single one of them, and also of the interactions of genes and environment.

What our results show is that the way researchers have been looking for genes that may be related to intelligence — the candidate gene method — is fairly likely to result in false positives, so other methods should be used.


Posted by on February 26, 2012 in Genetics, intelligence, mind


Maternal ancestry of Jamaicans

Jamaican slave revolt of 1759 (source)
There is a new study on the mitochondrial DNA of Jamaicans, shedding some light on the ancestry of this Caribbean nation:
I must certainly commend the historical introduction, which is not just comprehensive but also easy to follow and understand and well integrated with the information provided by the mitochondrial DNA findings. 
While there are a handful of lineages rooted in Native America or North of the Sahara (but not European), the overwhelming majority of the more than 400 Jamaican matrilineages studied in their HVS-I region have their roots in Africa. 
The most informative findings are however those about the regional origins within Africa of  the ancestors of modern Jamaicans. The Gold Coast and Bight of Benin regions (between Assini and the Niger Delta per fig. 1) are the main sources of Jamaican ancestry. Other West African regions (Sierra Leone, Bight of Biafra and West-Central Africa) were secondary sources only, while South and East Africa is almost not represented. 
This last appears to have surprised the authors, who expected more impact of the late slave trade based largely on the Indian Ocean coasts, similarly they seem a bit perplex by the relatively low influence of the Bight of Biafra, another major late source of African slaves. They argue that greater traveled distances may have hurt the chances of survival of people being transported from farther away (a documented fact) and that creole slaves, those born in the Caribbean, had much better chances of survival and even some chances of upward mobility.
See also: African ancestry of the Noir Marron of the Guianas, a previous example of the same approach cited in this paper. In that case however the bulk of the ancestry was from the Biafra area.

Posted by on February 25, 2012 in African Americans, African genetics, America


Late West European Neanderthals had very low matrilineal genetic diversity

According to the new paper, this diversity was lower than modern day Iceland, however it had been larger before 48,000 years ago.

Love Dalén et al., Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. MBE 2012. Pay per view.


Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mtDNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (<48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison to both eastern and older (>48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.

Other sources: Pileta[es], NeanderFollia[cat].
I do not have access to the paper so I remain in doubt about the details, however I wonder if this genetic bottleneck or founder effect may be related to the formation of Chatelperronian culture (oldest dates (ref: direct download): Grotte du Renne since c. 52 Ka calBP, Roc de Combe since c. 49 Ka calBP). It’d be interesting to know how these Western Neanderthal individuals correlate with the cultural mosaic of the MP-UP transition period c. 50-35 Ka BP.