For what they were... we are

Neanderthals crossed the sea at least once

2012-02-29T20:25:00.000+01:00

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

2012-02-29T19:35:00.001+01:00

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).

Abstract

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.

On and around with Ötzi's genome

2012-02-29T12:20:00.002+01:00

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

2012-02-29T09:23:00.000+01:00

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.

Copper findings in Kerala reinforce the concept of Chalcolithic India

2012-02-27T20:22:00.000+01:00

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.

Basque mtDNA

2012-02-26T21:56:00.004+01:00

I finally today put my hands on the latest study on Basque matrilineal genetics:

Doron M. Behar et al., The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times. AJHG 2012. Pay per view.

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

Notes:

(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:

Basque-specific mtDNA lineages (on U5b and J1c, argued to be also signals of post-Glacial colonization from SW Europe).
Category 'Basque origins'.

Oldest toy car is from Kurdistan c. 5500 BCE

2012-02-26T13:32:00.000+01:00

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.

Sources: Sunday's Zaman[en], Pasado y Futuro[es], Pileta de Prehistoria[en].

Intelligence genes more elusive than Higgins' boson

2012-02-26T06:18:00.000+01:00

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.

Maternal ancestry of Jamaicans

2012-02-25T13:31:00.000+01:00

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:

Michael L. Deason et al., Interdisciplinary approach to the demography of Jamaica. BMC Evolutionary Biology 2012. Open access.

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.

Late West European Neanderthals had very low matrilineal genetic diversity

2012-02-24T20:51:00.001+01:00

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.

Abstract

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.

The Gravettian culture in Central Europe

2012-02-24T09:04:00.001+01:00

Even if five years old, I have just stumbled (at Aggsbach's Paleolithic Blog) on this very nice and extensive paper on the Gravettian of Central Europe, and it seems to me a must-read for anyone with some interest in Upper Paleolithic Europe or in general in the origins of Europeans.

Jiří A. Svoboda, The Gravettian on the Middle Danube. Paleo 2007. Freely accessible (in English and French).

I'd say that the first sections are the most interesting ones, notably for the non-specialist reader. In them the author ponders the origin of Gravettian, concluding that it cannot be derived from early Upper Paleolithic cultures like Bohunician or Szeletian and that it must be instead an intrusive culture from West Asia (links to the older Ahmarian culture of the Levant).

The Kozarnikian group of Bulgaria's Kozarniki cave may signal the migration through the Balcans.

Once in Central Europe, the Early Gravettian or Pavlovian indicates discontinuity again by occupying different sites to those used by their predecessors, and also with different settlement tactics (large open air axial settlements in low altitudes and near rivers). Another difference is that burial then became a common feature, allowing us to find their remains much more easily (the famous "Crô-Magnon" type individuals).

The time-frame for this Pavlovian facies of Moravia and nearby areas of Austria and Poland is mostly 27-25 Ka BP (uncalibrated C14), with older dates only in Willendorf (Austria). A contemporary non-Pavlovian Early Gravettian site is Bodrogkeresztúr-Henye in East Hungary (c. 29-26 Ka BP).

The Early Gravettian is followed an Upper Gravettian of Central-East European scope (often described as Eastern Gravettian, as it extends into Eastern Europe). The author calls it Willendorfian-Kostenkian.

Finally an Epigravettian exists after c. 20 Ka BP, however Svoboda considers that this is a misnomer and more proper for the Mediterranean variants, which are more congruent with classical Gravettian typology, and proposes the name of Kasovian (on an Ukrainian site with a good stratigraphy for this period). This Kasovian would be in fact an hybrid of Gravettian and Aurignacian influences and begs for a comparison with the Badegoulian culture of Western Europe, sometimes considered the precursor of Magdalenian.

The latter sections deal with landscape and burials.

Human Y-chromosome stable, not going extinct anytime soon

2012-02-23T03:30:00.001+01:00

Years ago it was claimed (Aitken & Graves 2002, ppv) that the human Y-chromosome was in rapid decay and would vanish in some five million years. Today I read at BBC and Nature (article) that this won't happen after all, being in fact quite stable.

Jennifer F. Hughes et al., Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 2012. Pay per view.

The main finding seems to be that the comparison with chimpanzee Y chromosome alone was misleading and that further comparison in the simian tree (rhesus macaque) actually found Y chromosomes very similar to those of our species.

The macaque Y contained just one gene that humans have lost, and that gene resides on a particularly unstable portion of the Y. The human Y has grown much longer than the macaque’s, but the genes were mostly the same.

From the Net: 'Evidence of Massacre in Bronze Age Turkey' (Past Horizons)

2012-02-21T01:13:00.000+01:00

Determining social relationships between populations in the past can be difficult. Trade can be inferred from evidence such as pottery with foreign designs, or non-local foods. Warfare can be determined from the presence of mass graves or cemeteries of adult males displaying trauma, or weaponry showing signs of frequent use. However, trauma is not always a sign of conflict with external populations. It can also reflect the normal struggles of daily life or even interpersonal violence within the community.

Skeletal collections with trauma found from the Neolithic period in Anatolia suggest that injury was caused by daily activities and lifestyle, rather than systematic violence. However, shortly after this period there is an increase in trauma associated with violence that may suggest an increase in stress within and between populations in this area. In order to examine this conclusion, a new article by Erdal (2012) looked at the skeletal remains of a potential massacre site from the Early Bronze Age in Turkey.

... full story at Past Horizons.

Tassili-n-Ajjer rock art is at least 9000 years old

2012-02-19T22:20:00.002+01:00

Tassili-n-Ajjer, the famous rock art site of the Central Sahara has been dated to 9-10 millennia ago or older, using OSL techniques.

Sources[fr]: Pileta, Hominides.com.

Academic ref. (PPV): Norbert Mercier, Jean-Loïc Le Quellec et al., OSL dating of quaternar y deposits associated with the parietal art of the Tassili-n-Ajjer plateau (Central Sahara), Quaternary Geochronolog y (2012), doi:10.1016/ j.quageo.2011.11.010

______________

Note to readers: I am going to attempt to at least limit posts that deal with too many unrelated issues. So expect more of these shorter snippets. I hope is best for all.

Echoes from the Past (Feb 17)

2012-02-17T13:23:00.000+01:00

And again a quick look to many things which have been showing up around the Net these last few days:

Neanderthal society

Bryan Hayden has a very interesting (and freely accessible!) paper at the Oxford Journal of Archaeology on reconstructing Neanderthals society, which was apparently much like ours for similar conditions (small operative bands of 12-30 people linked in larger ethnic and/or clannic groups through seasonal meetings and general social networks). M. Mozota has a quite interesting review at his blog as well for those who can read in Spanish.

Natufian Mesolithic Syrian site dug

The site of As-Suwayda (or Sweida), dated to c. 14-9 thousand years ago, had 12 circular huts, two of which were more complex, suggesting to some the beginnings of social stratification (or could be communal buildings?) The two more complex (not larger) huts were located to the south of the village and show, one, inner divisions and an internal elevated platform, and, the other, external platforms and a trench. All huts are 4-5m. round.

The Natufian culture is one of the beginnings of sedentarism, as their members lived largely on recollection of wild cereals, although it is generally understood that there was no productive agriculture yet.

··> Servicio de Información y Noticias Científicas[es].

Neolithic driven by aridification in South Asia

D. Fuller at Indian Ocean Corridors discusses how an increasingly drier climate may have aided the expansion of agriculture in the Indian subcontinent:

The significant aridification recorded after ca. 4,000 years ago may have spurred the widespread adoption of sedentary agriculture in central and south India capable of providing surplus food in a less secure hydroclimate.

Relevant paper: Holocene aridification of India (C. Ponton et al. 2012, PPV)

Chalcolithic oxen traction in Iberia

A very interesting article in Spanish language by J.M. Arévalo discusses the use of animal traction in the Chalcolithic of Mucientes in the Northern Iberian Plateau during the 3rd millennium BCE (c. 2830-2290 BCE). Article available at Periodista Digital[es] and Asociación los Dólmenes[es].

The production, use and export of threshing teeth, made on flintstone at Cantalejo, emphasizes the almost necessary use of ox traction (horse domestication is unclear for the period while oxen remains are consistent with such kind of work). Interestingly the article is accompanied by an image of what may well be the oldest preserved wheel in Europe (Ljubljana, 4th millennium BCE, many centuries before Indoeuropean arrival, pictured).

Other archaeology/prehistory

Nerja rock art will be directly dated: the calcite layer over them will be dated so the doubts on authorship may be clarified. ··> Pileta[es].

East Asturian Magdalenian cave sites Tito Bustillo and El Buxu were used by the same group ··> Pileta[es].

Rock art found at Paleoindian site in Clarke Co., Virginia (USA) ··> Clarke Daily News.

England's Neolithic submerged town had market street ··> BBC.

The IVC seal represents a goat

Rare Indus Valley Civilization seal found at Cholistan (Punjab) ··> Dawn.

20 megalithic cairn circles and an apparent fortification from the Iron Age found at Andrah Pradesh, India ··> Firstpost.

Conservation plan to protect the Hill of Tara (Ireland) ··> The Meath Chronicle.

Spanish language specialized open access e-magazine Trabajos de Prehistoria vol. 68, no. 2 is available.

Human genetics

You may want to take a look at the latest exploration of Northern Europe's autosomal genetics by Fennoscandia Biographic Project, using the most advanced analysis tools available (it seems): as always Scandinavians are somewhat distinct within Western Europe but Finnic peoples are a world on their own.

Other genetics

Rice varieties indica and japonica may have been independently domesticated (paper): Independent Domestication of Asian Rice Followed by Gene Flow from japonica to indica (Chin-chia Yang et al. at MBE, PPV).

Archaeological looting alert in Ptolemais, Libya

2012-02-16T22:56:00.000+01:00

The Hellenistic city of Ptolemais (also known as Ptolemaida, Tolmeta and Tolmeitha) is being looted in an extensive and well organized manner. According to Ojos para la Paz[es] (Eyes for Peace):

Witnesses have declared that right now the coasts are being used for illegal trafficking. Also foreign bulldozers are visible, as well as digs and ships that look like fishing ships. Asking the locals what is going on, they say that there is people digging and do not want to be bothered. They are unknown people. In the excavated places men carrying vases to the ships can be seen. It is obvious that they are looting this site. We know that right now Libyan archaeological remains are being sold in Egypt and other countries.

Sorry, comment moderation was a mess

2012-02-12T13:26:00.001+01:00

I must say that for some reason Blogger did not send any notice of your comments this week, so they got stuck in a queue that I was not even aware it existed.

They have been already published but I want to apologize for the delay. I was kind of surprised that there were no comments at all but well... I just expected to get a mail each time a comment arrived and that was not the case at all.

In any case comment moderation is over and hopefully will not need to be used ever again.

Sorry and thanks for your patience.

Echoes from the Past (Feb 12)

2012-02-12T13:21:00.000+01:00

Some more links for you.

I'm also lifting the temporary comment moderation filter, hopefully lessons have been learned and no more such measures will be needed. Thanks for your patience.

Prehistory of Europe

Pileta: Más sobre Unas focas pintadas por neandertales podrían ser la primera obra de arte...[es] - Salaman mentions that lack of economic resources do not allow to research further by the moment the possibility that the Nerja seals could have been drawn by Neanderthals.

Pileta: Catalogan pinturas de Altamira que son 15.000 años más antiguas que los bisontes[es] - Some Altamira paintings are found to be 15,000 years older than the famous bisons. This may make them the oldest rock art in Europe (with permission of Nerja and comparable to Grotte Chauvet). No images of the early Aurignacian art are available yet but it is coincident with a trend to reclassify European rock art as of earlier age and Aurignacian period, as discussed here, but mostly not as early as in this case (before 30 Ka BP).

Neanderfollia[cat] offers us some interesting maps of the MP-UP transition in Europe:

Mapa de jaciments Chatelperronians (Chatelperronian sites)
Mapa de jaciments Aurinyacians (Aurignacian and Proto-Aurignacian, but not Bohunician, sites)

Prehistory of South Asia

AIOC: Lithic continuity & innovation in Holocene South India - D. Fuller introduces a new paper (ppv) on the Holocene industries of India (pictured below).

AIOC: Sourcing the 'lost Saraswati' river: new geological evidence - the same author, discusses how the lost Saraswati river does not match the Holocene geology of the subcontinent but could correspond with that of the Pleistocene.

AIOC: A widening range of textiles on Harappan trading ships

Paleodiet

How to feed a pregnant Neanderthal (AVRPI) - the almost always interesting archaeologist Julien Riel-Salvatore discusses several papers on the apparent myth of high protein Paleolithic diets.

Genetics

Max Planck Institute Leipzig | A High Coverage Denisovan Genome - The Denisovan genome is available for all to explore (the researchers however request courtesy if used for academic publication).

Ultraconserved regions of the genome do not seem to have any particular importance:

PLoS Genetics: Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila (open access).

Linguistics

Il tente de décrypter l'ADN de la langue basque (SudOuest)[fr] - Basque cultural journalist Hasier Etxeberria prepares a documentary on the various theories on the origins of the Basque language.

Psychology and Biology

Brains may be wired for addiction

Preference for fatty foods may have genetic roots

Why do cells age? Discovery of extremely long-lived proteins may provide insight into cell aging and neurodegenerative diseases

Tiny primate 'talks' in ultrasound - our distant Pinoy wild cousin, the tarsier, is not as silent as was thought, they just talk in ways we can't hear.

What elephants want: Ranging and raiding in Asia and Africa | EveryONE - elephants in fragmented habitats need more land, they also follow the lead of the old ones when raiding crops.

Splitting hairs with the Neanderthal affinity

2012-02-08T12:53:00.000+01:00

John Hawks published today an interesting albeit potentially misleading exercise of comparing (known) Neanderthal DNA (Vi33.16) to moder humans by HGDP samples.

The first graphic is a for example a very visual representation of why geneticists have concluded that there is a percentage of Neanderthal admixture in non-African humans, a striking visual synthesis of the results of Green 2010 with other modern samples:

It is easy to see for all in this graph that if the median shared Neanderthal variants in Africans is c. 626,000, while in Eurasians is c. 644,000 (visual estimates), then there is something going on and admixture is the most likely explanation.

A simple cross-multiplication exercise shows that the admixture apportion using these medians would be c. 2.9%. However a cautionary use of a higher figure among the African variability range (likely not caused by admixture but retained ancestral diversity) such as 630,000 yields 2.2%.

Green 2010 and later reanalysis by the NGP team estimated 2.4% (although they initially talked of 1-4%), all of which illustrates how is not easy to come with an exact percentage figure and that some uncertainty remains and must remain by the very nature of the exercise and the samples involved.

Splitting hairs

But of course we love to split hairs, at least a bit. I must admit I did it myself back in the day with the handful of samples used by Green et al. originally. Then I was asking rhetorically: are Chinese slightly "more Neanderthal" than other Eurasians?

Not quite because of the uncertainty implied in all the comparison is the real answer: the apparent differences are too small to be significant.

And this more or less what Hawks ponders in his article. As you can see above Europeans appear now slightly more Neanderthal than East Asians. However the difference is actually trivial: approx. 1000 base pairs, what is a variance of 0.12 percentile points of that approx. 2.4% (Hawks writes 'half-percent' when talking of intra-European differences of the same range, but he must be measuring something else than I am: 0.005x2.4%=0.012%, maybe he meant 5%... of that 2.4%? Unsure and, as he does not allow comments, I can't ask).

However, in spite of formally acknowledging this insignificance of the differences, he goes on to state the following unlikely hypothesis:

At present, we can take as a hypothesis that Europeans have more Neandertal ancestry than Asians. If this is true, we can further guess that Europeans may have mixed with Neandertals as they moved into Europe, constituting a second process of population mixture beyond that shared by European and Asian ancestors.

While it's not absolutely impossible, the data does not support any meaningful extra admixture in Europeans but actually what it does support is the lack of any significative difference through Eurasia. IF there was any extra admixture in Europe (or better West Eurasia, what's the obsession with Europe?) it is not detectable and hence was surely hyper-minimal.

We are therefore before yet another case of wishful thinking, of which I have stumbled upon several, much more severe cases in the las weeks alone. The illusion of a Neanderthal admixture or assimilation or even full continuity into, specifically, modern Europeans (usually West Asia is totally ignored even if it was there where most of the Sapiens-Neanderthal interaction must have taken place) is an obsession difficult to put aside for some I am learning.

Hawks is still quite serious and scientific and knows the ropes of genetics quite a bit and, therefore, he does not insist on that too much, showing different angles and comparisons that are interesting albeit unsupportive of his outlined hypothesis. However he does not abandon that unlikely boat so obviously sinking.

I am realizing that it is much harder for some Eurocentric multiregionalists to abandon their old Neanderthalist hypothesis than I would have expected. After all the genetic data is there for all to see and I must say that Hawks provides us with highly informative eye-candy here, which clearly supports the Neanderthal admixture episode and the uniformity of it across the various Eurasian populations.

Yet he seems blinded by the C.I. variation, which is caused, no doubt, mostly or only by local founder effects and/or drift (after the Neanderthal admixture episode).

Illusion of African Neanderthal admixture

A good example is again provided by Hawks himself:

Yorubas here appear some 2000-3000 BPs more Neanderthal than Luhyas. Even Hawks admits to be puzzled by this result, which is obviously attributable to mere ancestral diversity within Homo sapiens (but not for him). He expected the opposite result: that Luhyas, who live in Kenya, would be more influenced by Eurasian back-flow into Africa and display some greater Neanderthal affinity.

Actually this comparison does not just illustrate well how such small ranges of variation are normal and a remnant of ancestral diversity within the species (most probably) but also illustrates how Dienekes' hypothesis about Neanderthal admixture being in fact internal structure of Homo Sapiens before the migration out of Africa (or even after, because he has also argued for a greater role for Arabia and what not) is a total fantasy.

Thanks for the interesting and beautiful graphs, Dr. Hawks, but I cannot agree with your hypothesis because I see zero support for it in your own data. I think you have a clear case of splitting hairs syndrome, probably a symptom of repressed multiregionalist grudge (Eurocentric Neanderthalist variant).

Comment moderation

2012-02-08T04:21:00.000+01:00

Sorry but I am implementing comment moderation for a short while. Some people do not seem to understand that this is my blog and that ultimately I set the rules here, with permission of all-powerful Google and Interpol.

Some people do not seem to understand that this is not a forum in the classical sense (I allow free comment for the most part but there are better such spaces and, if there are not, go create one yourself) and that hijacking one comment after another to promote a personal obsession even if is within anthropology, without even bothering to write their own materials (for example in their own blog, which is after all nothing but a personal or group notebook - accessible or not, that's optional).

It makes zero sense for someone to show up here and expose a whole hypothesis in fragmented form in the comment section. Yet that is what TerryT has been doing for way too long. With time I have realized that he's being really abusive and sentences like "I'm just trying to put you on the correct track" are totally representative of his self-righteous stand, intellectual stalking of me personally and his abusive hijacking of the discussion threads of this blog.

This temporary moderation is directed towards Terry and nobody else. I intend not to publish a single comment by him anymore unless he first does his damn homework and publishes his hypothesis in an easily accessible way and understands that you can't go around doing that to people, that we have our personal space even online and that disagreeing is normal and not a reason for pseudo-intellectual proselytism of the worst kind.

As exception and in order to allow himself to defend his name, he can post here as long as it's on topic: his disciplining and his abuse of me and my blog (not anything about mtDNA stems or whatever other scientific opinion matter, that he will have to post at his blog).

I really hate doing this but either I block his comments before publication or I react to them angrily or I censor him after publication what feels bad (I have done with some other pseudo-intellectual stalkers). He has been repeatedly warned and yet he has forced me to take this action by ignoring all red lights once and again.

Hopefully the comment moderation will be lifted soon. Sorry for the inconvenience.

Maju.

Echoes from the Past (Feb 2)

2012-02-02T20:46:00.005+01:00

Lots of links that I think of interest but I do not have time, knowledge or enough discipline to deal with in greater detail.

Truly sorry about the format (or lack of it); I'm drowning in information.

Middle Paleolithic

Olduvai Geochronology Archaeology project

PLoS ONE: Why Levallois? A Morphometric Comparison of Experimental ‘Preferential’ Levallois Flakes versus Debitage Flakes (open access)

Pigmento de ocre neandertal de 250 mil años de antigüedad[es] (ochre pigment used by Neanderthals some 250,000 years ago), also: Neanderthals used red ochre much earlier than previously thought

Levallois core and flake (replica)

Neanderthals and their contemporaries engineered stone tools, anthropologists discover, also Modern flint expert 'reverse engineers' Neanderthal stone axes - and says our ancestors were clever, elegant engineers

La Cueva de Nerja podría albergar las pinturas más antiguas de Europa[es] Nerja Cave (Andalusia) holds which are possibly the oldest rock art of Europe (which must be of Neanderthal-made if the dates are correct). Also: Las pinturas rupestres más antiguas del mundo podrían tener 43.000 años de antigüedad y ser obra del Hombre de Neandertal según unas nuevas dataciones de Nerja[es] and Cave paintings in the Nerja Caves are much older than thought and also Más sobre el sensacional descubrimiento de la cueva de Nerja[es].

Neanderthal-made rock art?

Upper Paleolithic & Epipaleolithic

El joven de la cueva del Mirón fue enterrado hace 18.500 años[es] (the young man of El Mirón cave, Asturias, was buried 18,500 years ago)

Una sentencia da la razón a Zeleta S.L. y pone en peligro a Praileaitz[es] (tribunal puts Praileaitz cave, Basque Country, at even more risk)

Neolithic & Chalcolithic

Diverging Trajectories? Forager-Farmer Interaction In the Southern Part of the Lower Rhine Area and the Applicability of Contact Models (Luc Amkreutz) - Academia.edu (you need an academia.edu account to view, very interesting anyhow)

Archaeologists uncover oldest evidence of ploughing in Czech lands

Russian fish trap findings

Halladas en Rusia trampas de pesca de más de 7.500 años de antigüedad[es] and 7500 years old traps found in Russia and Complex Fish Traps Over 7,500 Years Old Found in Russia.

Diversidad LBK y relaciones entre Neolíticos y Cazadores-Recolectores[es] (LBK diversity and relationships between Neolithic and hunter-gathererer peoples).

Modelos generales del Neolítico versus datos arqueológicos[es] (general modeling of Neolithic versus actual archaeological data)

The Mesolithic–Neolithic transition in southern Iberia 10.1016/j.yqres.2011.12.003 : Quaternary Research (ppv - proposes some Neolithic colonization/influence in Iberia via North Africa), also: Una tercera ruta de expansión del Neolítico explicaría los rasgos de identidad en el sur de la Península Ibérica[es] (a bit skeptic I am of some of the claims)

Rare monument find leaves wind farm in doubt

Seeing Beneath Stonehenge | Exploring the Stonehenge Riverside project with Google Earth

Ancient popcorn discovered in Peru

Debating early African bananas

Denuncian la destrucción de una tumba del Neolítico en un monte de Redondela (Neolithic tomb destroyed at Redondela, Galicia).

Metal Ages and History

Malta inscription

Rare Cuneiform Script Found on Island of Malta

«Tartessos no era un pueblo de catetos. Eran sensibles y técnicamente capacitados»[es] (Tartessos was not a redneck people: they were sensible and technically capable - there's been some Tartessos conference these days in Andalusia, with nothing new).

Aparecen en Liédena los restos de un poblado de la transición entre la Edad de Bronce y la de Hierro[es] (settlement from the Bronze-Iron ages' transition discovered in Liedena, Navarre)

'Available for rent: The Acropolis of Athens'

Excavation of Bosnian Sun Pyramid given green light (remember the Bosnian "pyramid"? - it is back!)

Human genetics and evolution

PLoS ONE: Y Chromosome Lineages in Men of West African Descent (open access)

Fig. 2 - PCA (BAM stands for Bamileke)

New Genetic Research Suggests Link Between Earliest Native Americans and Southern Siberia. The relevant paper: AJHG - Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians (ppv for 6 months)

Following genetic footprints out of Africa: First modern humans settled in Arabia and the relevant paper: AJHG - The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa (ppv for 6 months)

Master controller of memory identified (this is kind of scary: they wiped out memories in mice!)

Study Reveals Possible New Key to Human Evolution (synapsis making in early childhood allows for extreme learning)

Low IQ & Conservative Beliefs Linked to Prejudice and Social conservatives have a lower I.Q.? (probably) and the relevant paper: Bright Minds and Dark Attitudes: Lower Cognitive... [Psychol Sci. 2012] - PubMed - NCBI (ppv) and a related accessible 2011 paper: political-orientations-intelligence-and-education.pdf

Bonobos' unusual success story (like humans bonobo males are more successful at mating with relatively low testosterone levels).

Chimp 'X factor': Extensive adaptive evolution specifically targeting the X chromosome of chimpanzees, also: Extensive X-linked adaptive evolution in central chimpanzees

Other

Biologists replicate key evolutionary step

Mouse to elephant? Just wait 24 million generations

Isolated Amazonian tribe makes uncomfortable contact

Egyptian autosomal genetics in the regional context (quick 'Admixture' run)

2012-01-30T13:28:00.011+01:00

[Important caveat: apparently both Egyptian samples are from the Delta region, the one most affected historically by Eurasian influence. The one labeled Egypt or Egypt (1) is Henn's sample (n=18), while the one labeled egyptan (sic) or Egyptian (2) is Behar's (n=12)].

Some readers questioned whether the strong Iberian affinity apparently found in Egypt in the previous Admixture run focused on North Africans was actually masked Highland West Asian or otherwise non-Peninsular Arab West Asian influences. I was initially skeptic because I had expected by default that Saudi Arabs would represent better all possible West Asian influences than Iberians.

I was mostly wrong as shown here.

Methods: I just run Admixture for K=4, K=6 and K=8 on a selection from the 1000 Genomes sample, following GNXP's instructions and using the following populations: both Egyptian samples (n=18 and n=12), plus 10 individuals from each of the following populations: Spaniards, Moroccans, Maasai, Ethiopians, Saudi Arabs, Palestinians, Turks and Kurds. The selection of Maasai and Ethiopians to represent Tropical Africans was made because previous research (mine and Henn's) showed these two being, of the available samples, the ones to best represent ultra-Saharan influence in Egypt specifically.

Results: I am showing only the K=8 results because the lower K levels do not seem overly informative (if anyone wants them, feel free to ask).

1. The K=8 graph:

2. The K=8 numerical apportions (same as above but in figures, minimally edited by me to improve visualization):

3. The K=8 ADMIXTURE summary, showing Fst distances between components ('pops'), minimally edited to improve quick understanding (component 'ethnic' labels):

Highlights:

Egypt:

There is (and I could eventually detect) an Egyptian-specific component, of West Eurasian affinity (look at the Fst table), what implies that it's surely descendant of the pre-Neolithic Egyptians of Asian origin. Paleolithic Egyptians that I presume existed based on other genetics (mtDNA X1, M1 and such), as well as Eurasian-like iconography like the Qurta rock art, similar to materials from SW Europe and Anatolia (but admittedly the Egyptian Paleolithic, with a few exceptions, is not well known on archaeological grounds being such a sedimentary and then desertic area overall, and also because archaeology in Egypt has been largely focused on the quite impressive pharaonic period).

This Egyptian-specific component represents 29% of one sample but only 19% of the other one, being also of some relevance in Ethiopia (9%). This and other differences between the two samples suggest some structure to be unveiled within Egypt but I lack the means (diverse enough samples) to do it. Anyhow the two samples are only somewhat different.

Besides this component, Egyptians show a diverse array of external influences, possibly Neolithic immigrants (?). The most important ones are the Kurdish or Highland West Asian component (17-20%) and the two Arab components together (14-25%) but others (Berber, Palestinian, East African) are also quite influential. The Iberian influence was largely a mirage (although still weights 4-8%).

East Africans:

Among the other populations, the most interesting finding of this run is that the Maasai appear, unlike in other research, to be 96% themselves (but still less distant from Eurasians than the average Tropical African, which is in the Fst=0.2 range), with at most residual admixture from Eurasians (mostly Egyptian/Palestinian). Ethiopians in turn appear here as somewhat admixed Maasai, with North African (mostly Egyptian) and peninsular Arab influences. However my previous relevant exercise showed that, at sufficient K-depth (or with a different sample strategy), Ethiopians eventually converge in their own specific and dominant genetic cluster (91%), which, as in the Fulani case, is similarly distant (and not too distant) to West Eurasians and Tropical Africans, indicating (I understand) very ancient homogenized intercontinental admixture. It surely requires an specifically designed run to understand these matters well enough.

Arabian-Egyptian (Arab 2) very distant component:

Also notice the Arab 2 extremely distant Fst values, in the >0.2 range. On first impression I thought they were the Maasai component for that reason but nope. We may be here before another OoA remnant, which is very relevant in Arabia peninsula and also in the second Egyptian sample (c. 12% in both cases) and totally absent in Iberia instead.

In any case, it is again evident that different sample strategies can produce quite different results and therefore it is good to look at these matters with an open mind and many complementary perspectives.

Update: K=4 and K=6 graphs, for the record and because some kind of speculation may have some use for them:

Update (Feb 1, after realizing that both samples are from the Delta):

The finding of an Egyptian-specific component may be even more relevant further South. If some areas of the Delta have retained some 30% of this component, it's probable that it'd be even better preserved towards the interior. On the other hand I'd also expect more Tropical African influence further South but that should be at least balanced by a significant decrease of (post-)Neolithic West Asian influences.

Of course only real samples will provide real answers.

Annnouncement of study claiming that Baztanese are genetically continuous since at least 6000 years ago

2012-01-22T05:30:00.000+01:00

Sorginetxoa dolmen (Baztan) (source)

Sadly enough the paper does not seem to be available anywhere yet but it was announced on Thursday to the press that a new study by the BIOMICs department of the University of the Basque Country (UPV-EHU), the same who delivered the recent research on the genetics of the Basque diaspora, claims to have found that modern Baztanese (and by extension modern Basques) are direct descendants of the people living there 6000 years ago (and maybe even earlier).

From what has been published in the media, the conclusions appear to be an exercise of molecular-clock speculation but it's also possible that rare lineages have been detected or that the authors are linking the results of their research with aDNA extracted elsewhere.

In any case I must remain cautious until the study is effectively published. This is just a heads up for whatever it may come.

Sources (all in Spanish):

Thanks to Neandertalerin for the mention.

'Portuguese Prehistoric Enclosures' blog: what a great find!

2012-01-21T05:23:00.002+01:00

I just stumbled, lead by a note at Pileta, with a most fascinating archaeological blog that goes by the name of Portuguese Prehistoric Enclosures. Where the term enclosure may be a cattle pen... but it may well mean a big city or more commonly a walled village of some size.

I'm almost drooling like a Pavlov's dog before the huge amount of information that this Portuguese archaeologist, A.C. Valera, is sharing with the World... and in English! As he mentions in his post #13, the phenomenon of enclosures in the Iberian peninsula has remained largely a local concern having almost no international projection.

Just yesterday, he produced a wonderful map of the known enclosures of Portugal, which is located in a separate page (and will be updated as needed).

I will probably use that blog in the future as source for my own posts but by the moment I am overwhelmed by the large amount of information that has been published and that I knew nothing or almost nothing about until now. So I'll just list by the moment some eye candy for you to follow the corresponding link (in the caption) if that's what you wish:

004 - Fraga da Pena walled enclosure

008 - Santa Vitória ditched enclosure

009 - Leceia walled enclosure

016 - Castro de Santiago walled enclosure

030 - A long way from home (imports)

039 - Burning rituals

044 - Enclosures and funerary context: Perdigões recent evidence

049 - The first wood henges in Iberia

050 - Castelo Velho walled enclosure: a milestone

054 - Santa Justa walled enclosure

057 - Beaker and ditched enclosures

068 - Plurality of funerary practices in ditched enclosures

070 - Neolithic ditches and rectangular houses

072 - Águas Frias ditched enclosure

Also very interesting (although in Spanish language) is this video on the archaeological findings of Marroquíes Bajos, Jaén (from 028 - Going public on large enclosures):

Remember: Portuguese Prehistoric Enclosures blog.

Out of Africa migration was coincident in time with an internal expansion in Africa of mtDNA L3

2012-01-20T05:15:00.006+01:00

Ethio Helix mentions today a rather interesting study (potentially, as it is behind a paywall) on the expansion of mtDNA L3 in Africa and its relation with the migration Out of Africa of L3-derived lineages M and N.

Pedro Soares et al., The expansion of mtDNA haplogroup L3 within and out of Africa. Molecular Biology and Evolution, 2011. Pay per view.

Abstract

Although fossil remains show that anatomically modern humans dispersed out of Africa into the Near East ∼100–130 ka, genetic evidence from extant populations has suggested that non-Africans descend primarily from a single successful later migration. Within the human mtDNA tree, haplogroup L3 encompasses not only many sub-Saharan Africans but also all ancient non-African lineages, and its age therefore provides an upper bound for the dispersal out of Africa. An analysis of 369 complete African L3 sequences places this maximum at ∼70 ka, virtually ruling out a successful exit before 74 ka, the date of the Toba volcanic super-eruption in Sumatra. The similarity of the age of L3 to its two non-African daughter haplogroups, M and N, suggests that the same process was likely responsible for both the L3 expansion in Eastern Africa and the dispersal of a small group of modern humans out of Africa to settle the rest of the world. The timing of the expansion of L3 suggests a link to improved climatic conditions after ∼70 ka in Eastern and Central Africa, rather than to symbolically mediated behavior, which evidently arose considerably earlier. The L3 mtDNA pool within Africa suggests a migration from Eastern Africa to Central Africa ∼60–35 ka, and major migrations in the immediate postglacial, again linked to climate. The largest population size increase seen in the L3 data is 3–4 ka in Central Africa, corresponding to Bantu expansions, leading diverse L3 lineages to spread into Eastern and Southern Africa in the last 3–2 ka.

As always, take the age estimates with lots of spices: they are just educated guesses which will vary wildly depending on the assumptions made a priori, like the usually under-estimated time for the divergence of the Pan-Homo genera, etc.

But otherwise the paper appears very much coincident with what Behar and myself (based on his data) could have inferred, including a NW African specificity of L3k, it seems.

Frequency maps by subhaplogroup:

A: L3a, L3i, L3h, and L3x combined, B: L3f, C: L3e, D: L3b, E: L3d

Their reconstruction of the spread of L3:

For many more details, you should visit Ethio Helix' original entry: The Mother of Mothers!

PS- As contrast to Ethio Helix' "too white" (in my opinion) selection of Ethiopian portraits, I have located some real women from non-Semitic Ethiopia, which may give a better idea of how the women of the L3 clan looked originally:

Hamer girl (from the SNNPR):

Gumuz mother (from the Benishangul-Gumuz region):

Nuer woman with their characteristic scarifications (from the Gambela region and nearby South Sudan):

Oromo woman (from Oromia, the largest region of Ethiopia):

Extremely ancient introgression in Papuans

2012-01-20T04:49:00.006+01:00

Melanesians

Neanderfollia mentions today[cat] new genetic research that has found unusual diversity in gene OAS1 among Papuans. They contend that this is caused by extremely old introgression that they estimate in more than three million years (more than the age of the genus Homo).

Fernando L. Méndez et al., Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Molecular Biology and Evolution 2012. Pay per view.

Abstract

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

This is what I have been arguing since December 2010: "denisovan" admixture in Australasian and SE Asian aborigines stems from Homo erectus (diverged from our line at least 1.8 Ma ago) or even maybe a most distant cousin (maybe H. floresiensis, argued by some to be more archaic than H. erectus in key elements like the wrist or toes).

Yet I am a bit skeptic of the age estimate, because, unless the H. floresiensis australopithecine hypothesis could be confirmed, the date is out of bounds for Humankind proper and creates many conceptual challenges, which are admittedly hard to swallow. While the "australopithecine hobbit" hypothesis would fit this scenario, it remains hard to swallow that the two genus would still be inter-fertile just a few dozen millennia ago and then again, why would archaic admixture come from this remote relative and not the much closer H. erectus, which we know lived in East Asia until rather recently.

Finally I am in general very skeptic of age estimates as such and their ability to be able to inform more than they confuse. Normally I find them too recent but the opposite (too ancient) can also happen, I imagine. They are in any case just estimates: educated guesses and nothing else.

Update:

Got a copy of the paper (thanks again) and I would say that these two figures are of special interest:

Fig. 2 - Median joining network of OAS 1 haplotypes

Fig. 3 Geographic distribution of the deep lineage in A) Old World populations and B)
South East Asians and Oceanians.

I find particularly notable that the haplotype has been found at very low frequencies in South Asia and nowhere else West of Wallace Line. It can be backflow but may also be indicator about the possible location of the admixture event.

Certainly nothing seems to suggests in these or other maps (1, 2) of "Denisovan" admixture that the episode could have happened in Altai or nearby areas as some readers, stubborn proponents of obsolete migration models, have insisted on. Instead all the evidence suggests that the admixture episode happened in SE or otherwise Tropical Asia, whether deep in Indonesia or more towards the mainland is debatable indeed.

See also:

Neanderthal gene flow found in modern humans (on Green 2010)
Exploring the Neanderthal admixture episode (version 1)
Denisova hominins, Neanderthals, Melanesians and so on... (on Reich 2010)
Explaining 'Denisovan' and also 'Neanderthal' admixture: the simplest scenario (where I first hypothesize that H. erectus and also maybe a relative of Neanderthals like the Hathnora hominin, could be the actual culprits).
Is X-DNA lineage Neanderthal?
Denisovan admixture widespread beyond Wallace Line, non-existent elsewhere - but then:
Minimal Denisovan admixture in SE Asians.
'Denisovan' admixture may actually be from H. erectus.

Artistic styles of the rock art of the Cantabrian Strip

2012-01-18T23:28:00.004+01:00

Doe of Arenaza

While it is always a pity that scientists allow modern artificial borders such as the one between French and Spanish states, to restrict their research, the information obtained can still be full of interest in spite of this undeniable handicap. This is the case of this delightful paper (only available in Spanish language) on the style and chronology of rock art in the Cantabrian Strip (Northern coast of the Iberian Peninsula):

Aitor Ruiz Redondo, Convenciones gráficas en el arte parietal del Paleolítico cantábrico: la perspectiva de las figuras zoomorfas [Graphic conventions in the rock art from Cantabrian Paleolithic: the perspective of the zoomorphic figures]. Trabajos de Prehistoria 2011. Freely accessible.

The author reviews previous work on the stylistic differences of the rock art of the area concluding that there are three clearly distinct stylistic groups:

Fig. 4 Multivariant analysis

The three groups have not just stylistic differences but also some geographical and chronological variations:

My visual synthesis (on top of fig. 1: map of sites mentioned)

Animal type indicated only where more than 60% of all figures per tab. 1

In spite of the clear stylistic differences group 1 and 2 overlap in time, specially after considering the wide error margins of dates based mostly on accretion layers (I'm showing above only the most overlapping ones, for reference). They also overlap in the dominant motif, which is the doe (less importantly also horses in group 1, buck deer in group 2 and bison in both). These groups are considered to belong to the Gravettian or even Aurignacian periods.

On the contrary, group 3, which is the most stylistically advanced, post-dates the rest by at least the full span of the Last Glacial Maximum. According to Ruiz, there are at least six millennia between these groups and the Magdalenian rock art, which is the most famed one because of the full perspective and great realism achieved. Contradicting previous work, he suggests that there was no rock art in the region in the Solutrean and Early Magdalenian periods.

Fig. 7 - comparison of three proposed timelines (right: Ruiz Redondo)

While the author thinks that the difference between groups 1 and 2 is chronological, I fail to see the evidence clear. Instead a geographical difference is rather obvious (see map above), with group 1 concentrated in Asturias and Western Cantabria and group 2 in Eastern Cantabria and Western Biscay.

Group 3, which is much better dated than the others, is clearly dominated by the bison, painted almost obsessively, as in the famed Altamira ceiling. Another important animal is the goat, usually painted in black, as well as the horse.

Santimamiñe rock art

There are more interesting articles (all in Spanish however) in the same magazine: Trabajos de Prehistoria (hat tip to Pileta).

Echoes from the Past (Jan 18)

2012-01-18T14:19:00.001+01:00

Again lots of short news and hopefully interesting links I have been collecting in the last weeks:

Lower and Middle Paleolithic

Cova del Gegant Neanderthal jaw

Catalonia: Neanderthal mitochondrial DNA sequenced for the first time. The sequence, obtained from a jaw from Cova del Gegant (Giant's Cave), is fully within normal Neanderthal range ··> Pileta de Prehistoria[es], NeanderFollia[cat], relevant paper[cat] (PDF)

Castile: Stature estimates for Sima de los Huesos (Atapuerca) discussed by John Hawks.

Upper Paleolithic and Epipaleolithic

Romania: stratigraphies and dates revised by new study (PPV) ··> Quaternary International.

Andalusia: oldest ornament made of barnacle's shell (right) found in Nerja Cave ··> Pileta de Prehistoria[es], UNED[es], Universia[es].

England: Star Carr dig to shed light on transition from Paleolithic to Epipaleolithic ··> short article and video-documentary (32 mins) at Past Horizons.

Basque Country: archaeologists consider a barbarity that only 65m are protected against the quarry at Praileaitz Cave (Magdalenian) ··> Noticias de Gipuzkoa[es].

Yemen: 200 tombs said to be Paleolithic discovered in Al Mahwit district, west of Sanaa. Tools and weapons were also found. Other thousand or so artifacts from the same period were found in the Bani Saad area ··> BBC.

Peruvian rock art

Sarawak: Niah Cave being dug again for further and more precise data on the colonization of the region by Homo sapiens ··> Heritage Daily.

Siberia was a wildlife-rich area in the Ice Age ··> New Scientist.

Peru: 10,000 years old cave paintings (right) discovered in Churcampa province ··> Andina.

Neolithic and Chalcolithic

Iberia and North Africa: Southern Iberian and Mediterranean North African early Neolithic could be the same process according to new paper (PPV) ··> Quaternary International.

Galicia: Neolithic and Metal Ages remains to be studied for DNA ··> Pileta de Prehistoria[es].

Texas: very informative burnt hut reveals clues of the natives of the San Antonio area c. 3500 years ago.

Mexico: 2000-years old paintings found Guanajuato ··> Hispanically Speaking News (notice that the photo appears to be act of shameless journalistic low quality, being a European bison painted with European style, probably from Altamira).

Metal ages and historical period

Croatia: oldest known astrological board unearthed at Nakovana (Roman period). The cave was probably some sort of shrine back in the day, maybe because a striking phallic stalagmite. Besides the ivory astrological device, lots of pottery has been found as well ··> Live Science.

The best preserved fragment depicts the sign of Cancer (full gallery)

Basque Country: Iruña-Veleia affair: Basque autonomous police does not have means to test the authenticity of the findings. The Commission for the Clarification of Iruña-Veleia asks for the tests to be performed in one of the few European laboratories able to do that ··> Noticias de Álava.

Cornwall: replicating sewn-plank boats of the Bronze Age ··> This is Cornwall.

India: cremation urn from the Megalithic period excavated in Kerala ··> The Hindu.

Human genetics and evolution

The six flavors

Centenarians don't have any special genes ··> The Atlantic.

Fat is a flavor: newly discovered sixth flavor in human tongue identifies fat (and usually likes it) ··> Science Daily.

Hominin tooth found in Bulgaria dates from 7 million years ago ··> Daily Mail.

Anthropology (senso stricto)

The journey of the Tubu women: fascinating documentary in Spanish language about these trans-Saharan trader women available at Pasado y Futuro[es].

Small capuchin monkey bands fight as well as large ones because members are more motivated and have many less defections, even in peripheral conflicts ··> Science Daily.

Other

Horse genetics again ··> new paper at PLoS Genetics.

Fig. 4 - Phylogenetic tree of extant Hippomorpha.

North African autosomal genetics (again)

2012-01-14T14:26:00.000+01:00

Two weeks ago I performed almost the same exercise here at this blog but now a paper with academic seal of proficiency has been published at PLoS Genetics:

Brenna M. Henn et al., Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genetics 2012. Open access.

The basic results are very very similar if not outright identical to what I achieved. And that is because the sampling strategy was also very similar. If anything Henn and colleagues used a broader sample of Tropical African populations.

From Fig. 1 (click to expand)

The choice of North African populations is exactly the same as mine (actually the samples I used are from a previous paper by Brenna Henn, who is making a great job in exploring African genetics, and must be the same as in this paper) exception made that I included 10 HGDP Mozabites also. The choice of West Eurasian populations is different but does not seem to produce any relevant difference in the result. The main differences are in the choice of Tropical African samples, which does produces some differences.

Tunisian Berbers' endogamy

But first of all let's explain what happens with the weird Tunisia sample:

... the Tunisian Berber population displayed an excess of pairs of individuals sharing 200–1200 cM IBD. This bimodal distribution indicates that many 1st and 2nd cousin genetic equivalent pairs were present in this sample, even though donors declared themselves to be unrelated during the sampling process. Analysis of long runs of homozygosity (ROH) indicate that the Tunisian population averaged almost twice as much of their genome is in ROH than other North African populations, 230 Kb versus 120 Kb respectively (Figure S3). The pattern of ROH and pairwise IBD in the Tunisian Berbers is likely the result of endogamy due to geographic isolation or cultural marriage preferences.

That's why they perform so weirdly, relating always to themselves almost before any other affinity. This fact makes them a poor and mostly uninformative population.

Different sampling strategy, somewhat different results

As I say, the main difference between my sample strategy and Henn's (and the result produced) is in Tropical Africa: I used Ethiopians, Mandenka and Fulani; Henn used also Fulani and then also West and East Africans but different ones. I found apparent Mandinka (West African) admixture in NW Africa (and almost no East African/Ethiopian one), Henn found apparent Luhya (East African) admixture instead (and almost no West African one).

I don't know yet how these two apparent different findings may conciliate but the difference of findings is in itself interesting, outlining the strategy of future research.

Something that is quite obvious as Henn uses such a broad Tropical African sample is that many of the components discerned are just one for each Tropical African population. This is interesting, underlining the immense genetic diversity of Africa, but not very informative in regard to North Africans.

That (and the fact that I went down to K=11 - and even K=12 but this one was uninformative) is probably the reason why I, with a smaller peripheral sample, could detect what I believe that is a very old layer of North African specificity.

So the sampling strategy (both sample choice and number of individuals in each sample), as well as the K-depth reached can affect the results of these analysis of the population genetic structure. There is almost always a different approach that can produce complementary information as result.

Back to Africa but when?

But overall the results are very similar: the bulk of North African genetic affinity is with West Eurasia and not so much Africa as such. That is the most obvious result and indicates that the Out-of-Africa migration had an important backflow which affected several parts of Africa but very specially the North.

Nothing unexpected, at least for me. But it really hits a blow to those who, quite lightly, associate Y-DNA and overall ancestry: if there is Y-DNA and mtDNA contradiction, as is the case in North Africa, where most of the patrilineages are African but most of the matrilineages are of Eurasian origin, in most cases the mtDNA is right and the Y-DNA is nothing but a varnish.

The main exceptions seem to be areas of sustained male inflow across generations, notably some parts of Latin America. But this kind of sustained industrialized migration pattern is unlikely to have ever existed in prehistory or even pre-Modern history anywhere.

Anyhow, interestingly, the authors make an interesting exercise to find out estimate times of Eurasian arrival. The result is forewarned with reasonable precautions:

Since this model neglects migration, we expect our results to form a lower bound on the population divergence time, as similar levels of population divergence would require a longer separation in the presence of migration.

So at least this old:

Fig. 3 (edited to correct a color typo) - click to expand

Although these divergence time estimates may not be precise, as they do not adequately model ancient migration, they do suggest that the population divergence between the ancestral Maghrebi population and neighboring Mediterranean populations occurred at least 12,000 ya and indeed more likely predated even the Last Glacial Maximum.

It is interesting anyhow that the Fst distance to Europe are lower than to Arabia and that the window for a possible migration from Europe can well fit with the Oranian genesis c. 22,000 years ago, which I am pretty sure that is related with Iberian Gravetto-Solutrean: Oranian was back in the day called Iberomaurusian for a reason and, regardless of revisionisms, the Oranian dates for the West are quite older than those of the East - never mind that at least 25% of North African mtDNA (and maybe 10% of Y-DNA) is of European (and most likely Iberian) derivation and that European affinity remains apparent, distinct and important (specially in Algeria and North Morocco) even after North African specific components have become obvious and dominant.

So the old theory of migration from Iberia c. 22,000 years ago (maybe with some backmigration northwards as well) is not any colonial construct but something most probable, as indicate both archaeological and genetic data very consistently.

Less clear is whether there was a previous West Eurasian flow c. 40,000 years ago with the Dabban industries (so far only known in Libya, although unmistakably "Aurignacoid" in character). Genetically the main support for this first Eurasian backflow is mtDNA U6 (derived from Eurasian U), whose origin is probably in Morocco, where most of the basal diversity accumulates (and then around it, in Canary Islands and Iberia).

It is not impossible that the lineage might have arrived, still as undefined U*, via Europe, however the structure of the autosomal DNA, as illustrated in this study or in my exercise from December, evidences that the North African specific components (excepted the "Aterian" one) are most akin to West Eurasia (by much). So there was probably a first migration from West Asia c. 40 Ka. ago and then an Iberian layer overlapped.

This paper also suggests more recent migrations from Tropical Africa, although I am unsure if I can take their timeline conclusions at face value, specially regarding the East African component, that I imagine quite older (they suggest, table 1, just 25 generations ago, what I find most hard to believe for such a notable impact).

I would personally conclude that the North African genetic composition appears to be made up of:

A deep, quite diluted, 'Aterian' layer
A dominant North African specific layer of mostly West Eurasian roots
An Iberian or European layer (Oranian)
Maybe an East African (Capsian) layer (needs clarification but agrees with Y-DNA)
Maybe a lesser Arab layer and also maybe some recent Tropical African input

Caught in the act: lactose intolerant and lactose tolerant populations together but mostly unmixed in Chalcolithic Upper Ebro

2012-01-13T06:17:00.004+01:00

There is a new paper on ancient DNA from the southernmost Basque Country that has found the oldest known lactose tolerance alleles in prehistoric Europe:

Theo S. Plantiga et al., Low prevalence of lactase persistence in Neolithic South-West Europe. European Journal of Human Genetics 2012. Pay per view.

Context

The samples studied are the same (in part) as those from Izagirre and de la Rúa 1999, specifically 19 individuals from San Juan Ante Porta Latinam (Araba) and 7 from Longar (Navarre). In spite of both sites being inside Euskal Herria (Basque Country) as usually acknowledged, the are both very close to Logroño, capital of La Rioja autonomous region. I mention because this area of the Upper Ebro is at least somewhat distinct from the higher reaches of the core Basque Country and may not be representative of ancient (proto-)Basque genetics but rather of Ebro Valley populations.

It is easy to appreciate in genetic research as that of Adams 2008, that Aragon (I presume representative of the overall Ebro Valley) is markedly distinct from sub-Pyrenean neighbors like Basque Country or Catalonia, holding a much larger apportion of presumably Neolithic haplogroups of Transmediterranean origin (surely E, G, J and T, as well as maybe most of I), being more similar in this to Valencia, Ibiza or Western Iberia.

Paleo- and Epipaleolithic Basque Country

Similarly the Ebro Valley is a region of very early Neolithic settlement in which often no pre-Neolithic habitation is known to have existed. However the data I know for the Basque part of the Upper Ebro basin (X. Peñalver 1996), suggests an Epipaleolithic (epi-Magdalenian) settlement of most of Araba (but not the Ebro banks as such) and only the highland parts of Navarre (right).

It is therefore only in the Neolithic and later on in the Chalcolithic (term used sometimes loosely to indicate the late part of the Neolithic, when social complexity increases, regardless of the presence of copper, gold or silver), when the Upper Ebro, including that within conventional Basque borders is colonized.

These colonists may or not have been of aboriginal (proto-Basque) stock. In fact anthropometric estimates emphasize the presence of Gracile Mediterranean types in devastated La Hoya town, contrasting with the native Pyrenean type of apparent Paleolithic stock.

Chalcolithic and Early Bronze sites

Whatever the case, it is clear that the Upper Ebro valley is not the core of the Basque Country, located further north, but a border area which may have been colonized partly by people of exotic origins upon the arrival of Neolithic. Of course all this is open for discussion and further analysis of the available data.

[See also: Wikipedia: Basque Prehistory].

Findings

Luckily several readers have sent me copies of the paper (you people are awesome, thanks), and even some ideas on what is most interesting (not always the most obvious).

The findings are detailed in table 3:

The most important finding is also the most obvious: the lactose tolerance allele (or more specifically rs4988235 in its T variant, as there are others less famous such alleles) is found at the oldest known site in Europe and that is (in spite of all my previous caveats) in the Basque Country.

There is a similar aged site in Götland, Sweden (Mälstrom 2010), but the apportions are even lower (1/19 alleles or 1/10 persons had the CT combo). All other older of contemporary sites in Central Europe or nearby Occitania have yielded negative for what is nowadays a dominant allele in Western and Northern Europe. However there are many blanks: for example no Neolithic (never mind Paleolithic) British or Atlantic French or Portuguese samples have ever been tested for. In fact no Basque samples other than these either... so the question marks are still many.

The second finding is that the apportions are low, even if it is enough for lactose tolerance to kick in that a single T allele exists (classical Mendelian dominance), only 31% and 14% of the people sampled were lactose tolerant, meaning that (most probably) non-processed milk was rare in their diet. This is contradictory with the idea that the allele became common thanks to positive selection, after all these people had been herding livestock of various types for 2000-2500 years already (just in situ, i.e. not counting their likely ancestors in Italy, the Balcans or West Asia: add other 3000 or 4000 years maybe) and yet most were lactose intolerant (apparently).

This is something that the authors also find surprising, pondering that maybe its frequency levels may have risen more recently just because of cultural pressure. What?! Drinking milk became fashionable and you were stoned to death if you found it nasty? Hard to believe, honestly, and if you did not die from not drinking milk, there is no (or extremely low) selective pressure we can take seriously.

Two populations?

But the most striking finding, not even mentioned by the authors is the following: there are almost no heterozygous individuals in these samples: with two exceptions in the San Juan APL sample, people fall either to the CC (lactose intolerant) or the TT genotype. The percentage of heterozygous is much lower than that of the allele itself (11% vs. 26% in SJAPL and 0% vs. 14% in Longar).

I don't know how can you explain this but for me it is crying two populations that are still at the early stages of blending: one almost homogenously TT and the other almost homogenously CC.

Otherwise, if the admixture process would be advanced, there would be more heterozygous (CT) individuals than TT homozygous ones.

Which can be these two populations? Hard to say for sure but my natural intuition, knowing what I know about Basque Prehistory, is that the CC population would be made up of colonists of Mediterranean stock (possibly trans-Mediterranean: Balcanic, Italian or West Asian, as suggested by recent studies of mitochondrial DNA from Epicardial sites) who were quite obviously lacking the T allele altogether even if they were the ones to have the goats, sheep and cows initially.

These peoples left a legacy in the Ebro Valley and elsewhere in Iberia and Europe but they ultimately must have failed to become fully dominant and today their ancestry seems to be just a fraction of modern Western Europeans, seldom looking dominant even in the patrilineages.

The TT population must therefore be some other. Which one? In this context I can only think of the local aborigines rooted in the Paleolithic cultures of the area and described by anthropometric usages as of Pyrenean stock (I think Heraus would say Dinaromorphic Atlanto-Mediterranean but that's too long - incidentally he just posted on the phenotypes of Arabako Errioxa).

So this brings me to my fallback theory: the lactose tolerance allele is a mere fluke which became fixated randomly in pre-Neolithic populations just because (or maybe, speculatively, related to motherly lactation practices), eventually showing an unexpected use in drinking milk and eating desserts, what was nice for the development of Basque cuisine but mostly unrelated to survival.

Being able to enjoy rice pudding (as I'm doing right now) is probably the most clear advantage of the T allele

See also: Leherensuge: Actual lactase persistance more common than genes predict.

Update (Jan 19): a scanned paper by Belén Márquez et al., describes in detail the burials of SJAPL and Longar, both looking rather militarized (mostly adult males, abundance of arrow points and arrow injuries...)

'Denisovan' admixture may actually be from H. erectus

2012-01-10T03:45:00.002+01:00

H. erectus (fem.) reconstruction

Neanderfollia mentions today[cat] a new paper published at the moment only at arXiv that re-analyzes the data from Reich 2010 and related papers and concludes that the Denisovan admixture may well be original from Homo erectus, and not even individuals closely related to the Denisova cave specimens after all.

Peter J. Waddell, Jorge Ramos, and Xi Tan. Homo denisova, Correspondence Spectral Analysis, Finite Sites Reticulate Hierarchical Coalescent Models and the Ron Jeremy Hypothesis. Pre-publishing at arXiv (2012, freely accessible).

This article shows how to fit reticulate finite and infinite sites sequence spectra to aligned data from five modern human genomes (San, Yoruba, French, Han and Papuan) plus two archaic humans (Denisovan and Neanderthal), to better infer demographic parameters. These include interbreeding between distinct lineages. Major improvements in the fit of the sequence spectrum are made with successively more complicated models. Findings include some evidence of a male biased gene flow from the Denisova lineage to Papuan ancestors and possibly even more archaic gene flow. It is unclear if there is evidence for more than one Neanderthal interbreeding, as the evidence suggesting this largely disappears when a finite sites model is fitted.

The paper needs some style revision but is otherwise very interesting, even if it's largely an exercise of statistical analysis, often resulting somewhat arid.

Some excerpts:

(...) one of the most surprising features of the planner NeighborNet model is that it does not reverse the positions of Neanderthal and Denisova, so that Papuan could have a unique split with the Denisovan (as Reich et al. 2010 suggest the Papuan lineage received ~5% of its genes from that lineage). As we will see later, the apparent reason for this would seem to be that the distance from Denisova to Chimp is more strongly underestimated than that from Denisova to Papuan. The underestimation of the Denisova to Chimp distance could be due to Denisova harboring some very archaic alleles, or it could be sequencing error.

(...)

The decrease in frequency of the DP pattern on X, particularly when compared to the NP pattern (which is near autosomal average frequency on X) suggests the possibility of asymmetric gene flow in this introgression event. If so, it would seem that this might be most readily explained by greater survival and reproduction of the offspring of Denisova males impregnating the modern human female ancestors of Papuans rather than the other way around.

(...)

Note the high frequency of the DNP pattern, which may be due to the Denisovan relatives that mixed not being closely related to the Denisovan sampled.

(...)

It seems tempting then to think that a model of three independent out of Africa lineages, with three independent mixings with the same population of Neanderthals (plus the independent Denisovan mixing event), would fit markedly better than the present model.

This last bit I find hard to believe, notably because we know of no Neanderthals ever existing in East Asia. In addition it would be a very odd coincidence that all three arrived to the approximate same amount of Neandrthal admixture. It seems much more likely that these smaller differences have been fixated as the three populations diverged in the Greater Eurasian expansion, after the OoA initial migration, when they probably incorporated the Neanderthal ancestry. (My two cents anyhow).

In any case, their conclusions follow:

Discussion

Overall, the fitting shows that a hierarchical structured coalescent model with at least two introgression events between archaic humans and out of Africa Moderns leads to a substantial increase in fit. Overall fit however, is still far far worse than could be expected. It seems that to improve the fit a number of factors may come into play. Firstly, there are too many private NH, NF and NP [Neanderthal-Han, -French and -Papuan] patterns. Secondly, the latter of these, NP, seems markedly less than the former two. Thirdly, there may be too many sequencing/alignment errors in the present data to confidently move towards refining so many parameters and the overall fit. The marked improvement in fit when a finite sites model is employed is consistent with this. One model that may do a better job of describing the data with fewer parameters is independent mixing of Neanderthal genes with Han and French, but to a nearly identical total degree. Also, lesser mixing of Neanderthal genes into Papuan, made up for by a larger proportion of archaic alleles in Papuans coming from the mixing with an archaic that is only slightly closer to Denisova than to Neanderthal. This would in turn suggest that the mixing with Neanderthals was not purely right out of Africa and it was not a single event. Instead, there may have been opportunity for European ancestors to pick up Neanderthal alleles, in the unknown part of Eurasia they existed in prior to moving into Europe, ditto and independently for the ancestors of the East Asians, while Papuan ancestors moved fairly rapidly through the zone of classical Neanderthals and picked up most of their archaic genes in the Indonesian region. The form of this ancestral population may have been about equally related to Neanderthals and Denisovans, but may also have had an appreciable proportion of even earlier (e.g., Homo erectus genes) in its genome. This last point comes up in a number of analyses including the resampled NeighborNet and the finite sites model, but confirmation is difficult as the rate of sequencing / assembly error could be having a similar effect.

For background in this blog and its antecessor Leherensuge (from oldest to most recent):

Neanderthal gene flow found in modern humans (on Green 2010)
Exploring the Neanderthal admixture episode (version 1)
Denisova hominins, Neanderthals, Melanesians and so on... (on Reich 2010)
Explaining 'Denisovan' and also 'Neanderthal' admixture: the simplest scenario (where I first hypothesize that H. erectus and also maybe a relative of Neanderthals like the Hathnora hominin, could be the actual culprits).
Is X-DNA lineage Neanderthal?
Denisovan admixture widespread beyond Wallace Line, non-existent elsewhere - but then:
Minimal Denisovan admixture in SE Asians.

Echoes from the Past (Jan 9)

2012-01-09T08:11:00.001+01:00

Here you have the latest batch of rather interesting links:

Before prehistory

Over 65 million years, North American mammal evolution has tracked with climate change

Middle Paleolithic

Aterian tools

Shape Variation in Aterian Tanged Tools and the Origins of Projectile Technology: A Morphometric Perspective on Stone Tool Function (open access paper on Aterian tool morphology)

Neandertals and bears (John Hawks compares the range and recolonizations of brown bears in the Ice Age with those of human species)

Upper Paleolithic and Epipaleolithic

The 25,000 years-old necklace piece found this summer in Gipuzkoa could well have been used as sharpening stone[es] - also for background: Irikaitz archaeological site[es] and Irikaitz archaeological site -- host to a 25,000-year-old pendant

Pre-Neolithic findings at Vretsia-Roudias (Greece) and More on Pre-Neolithic findings at Vretsia-Roudias

Neolithic and Metal Ages

Stone Age temple found in Orkney may be more significant than Stonehenge and Orkney temple predates Stonehenge by 500 years - My apartment mate is often talking about how important the Orkney Megalithic religious complex must have been in its time to what I always reply that it's quite unexpected because it's such a remote place... I wonder if it was an important site for cod fishermen from all Western Europe or what.

Reconstruction of the temple complex

Prehistoric buildings hold an overlooked social complexity (a very curious report on the oldest known European stairway and its rather unexpected sophistication for a Neolithic context)

Ancient settlement excavations on Azerbaijan’s territory reveal interesting facts (village from 6000 years ago)

Megalithic burial urn excavated in Kerala's Idukki district (India)

China finds 3,600-year-old palace

Temple of Isis found near the theater of Italica[es] (Roman colony near modern Seville, hometown of emperors Trajan and Adrian)

Prehistory in the media

Spanish-speaking readers can now watch at YouTube the documentary/prehistoric fiction film 'Homo Sapiens: the perfect conquest' (Discovery Channel prod.): part 1 and part 2. The films contain many misrepresentations but also many actual facts and reasonable speculations and are therefore rather interesting to view (but take some things with great caution or eve total disbelief). Sorry but I do not know at the moment of an English-language version available online.

Genetics

New PhyloTree build: the mtDNA tree of Humankind refined even a bit more. All this is new in build 13th:

Defining mutations updated: A2c, A2f, A2f1, A2h, A2i, A2p, A2r, A4c, A4d, A5b, B2g, B4g, B5a2, B5a2a, B5b2c, B6, C1b5, C1c1, C1c3, C4a1, C4a3, C7b, D1d, D2b1, D4b1b, D4e1, D4g2, D4g2a1a, D5a3a, D5c1, F1a2, F1a3, F1a4, F1e1, F1e2, F4a, F4a1, F4b, G1a2, G1b, G2a1e, G2b1b, G3b1, H13a2b, H13a2b1, H1c3, H2a5, H2a5a, HV1d, J1b, J1b1b1, J1b3, J1d, J2a1a1a, K1a1, K1a11, K1a1a, K1a1b1a, K1a1b1c, K1a1b2a, K1a3a1b, K1a4c, K1a7, K1a8, K1b1a, K1b1a1, K1b2b, K1c1a, K2a2a, L0a1b, L0a3, L0a'b, L0b, L1b, L1b1, L1b1a4, L1b1a6, L1c3b, L1c3b1, L1c3b2, L1c6, L2a1a2a1, L2a1a3, L2a1c2, L2b1b, L2b2, L2d, L2d, L2d1, L2d1a, L3b2, L3d1a1, L3d1c, L3d1d, L3e2a1b1, L3e2b3, L3e3a, L3f1b1, L3f2, L3h1a1, L3h1a2a, L3h1b1a, L3h2, L3i1, L3i1a, L3i2, L3k, L3x1, L3x2, L3x2a, L3x2a1, L3x2b, L4b, L4b1, L4b2a1, L4b2a2, L4b2b, M10a1, M10a1a, M19, M2, M24, M31b, M31b'c, M33a2a, M39, M6b, M7b, M7b1, M7b1'2'4, M7b2, M80, N2a, N9a2a, R0a2d, R0a2k, R7, R9c1, T1a2, T2a1a3, T2a1b1, T2b3a, T2c1b, T2f, T2g1, U2d, U3a, U3b2, U4b1b, U5a2d, U5a2e, U7, V9a, Z4, Z4a.

Newly added: A2f2, A2f3, A2h1, A2l, A2m, A2o, A2s, A2t, A2u, A2u1, A2w, A2x, A4e, A4e1, A4f, A5a3, A5b1, B2a3, B2c1a, B2c1b, B2c2, B2c2a, B2c2b, B4a1c1a, B4a2b, B4a4, B4b1a3, B4b1c1, B4i, B5a1c1, B5a2a1, B6a, C1b10, C1b11, C1b5a, C1b7, C1b7a, C1b8, C1b8a, C1b9, C1b9a, C1c1a, C1c4, C1c5, C4a1c1a, C4a1c2, C4a3b, C4c1, C4c1a, C4c1b, C4c2, C4d, C7a2, D1g, D1h, D1i, D1j, D4a1a1a, D4a3b1, D4a3b2, D4b1d, D4b2b2a, D4b2b2b, D4b2b2c, D4b2b6, D4e1c, D4e5a, D4e5b, D4g2b1, D4j3a1, D5b1d, D5c2, E1a2a, F1a3a, F1a3a1, F1a4a, F1b1a2, F1c1, F1c1a, F1e1a, F1f, F1g, F2b, F2c, F2d, F3a1, F4a1a, F4a2, G2a1c2, G2a1d1, G2a1d2, G2a1e1, G2b2b, H2a5a1, H2a5a2, H2a5b, HV14, HV4a1a, HV4a2a, HV4c, I6, J1b3a, J1b4, J1c2a, J1c2a1, J1c2c2a, J1c3d, J1c5d, J1c9, J1d1a, K1a13a, K1a14, K1a1b2a1, K1a2b, K1b1a2, K2a2a1, K2a3a, K3, L0a1a1, L0a1a3, L1b1a9, L1b2, L1b3, L1c3a1b, L2a1a3a, L2a1a3b, L2a1c1a, L2a1c2a, L2a1c4a, L2a1i1, L2a1m, L2a1m1, L2a1n, L2c1, L2c1a, L2c2b, L2c3a, L2c4, L2c5, L2e1, L3a1, L3b1a5, L3b1a6, L3b2a, L3d1b3, L3d1c1, L3e1d1, L3e1g, L3e2b1a1, L3f1a1, L3f2a, L3f2a1, L3x1b, M10a1a1, M11c, M2a'b, M2c, M31b1, M31b2, M52b, M6a1, M6a2, M7a1a9, M7b5, M7b6, M7b7, M7b8, M7c1d, M7c2b, M7c2b1, M7c2b2, M8a3a, N9a10a, N9a2a3, N9a4a, N9a4b, N9a7, N9a8, N9a9, O1a, R0a2k1, R7a'b, R9b1a3, R9c1a, T1a2a, T2a1b1a, T2b21, T2b3b, T2b4a, T2b6a, T2h, U1a1a, U3a1a, U3b3, U3c, U5a1g, U5a2c3, U5b1f, U6a3a1, U6d1a, U7a, U7a1, U7a2, U7a3, U7a4, U7b, U7b1, U8a1a1, U8a2, U8b1a, V9a1, W3a1b, W3b, W5a2.

Multiple rearrangements/additions within: B4c1b2, J1b1a, U5a2a.

Relabeled: A2r -> A2v, B5a1c <-> B5a1d, F1a'c -> F1a'c'f, L3j -> L3f2a1, N9a2a'b -> N9a2a, N9a2a -> N9a2a1, N9a2b -> N9a2a2.

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins (open access paper on dog's likely origins in SE Asia; see here for another recent study reaching similar conclusions)

Figure 3. Village and breed dog Y chromosome SNP-STR haplotype networks.

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome (open access paper)

Common Variants Show Predicted Polygenic Effects on Height in the Tails of the Distribution, Except in Extremely Short Individuals (open access paper on the genetics of height)

Variation within the Huntington's Disease Gene Influences Normal Brain Structure (open access paper finds brain-structure gene)

Controversy on open access publication

Elsevier-funded NY Congresswoman Carolyn Maloney Wants to Deny Americans Access to Taxpayer Funded Research

Ecological Society of America letter regarding #OpenAccess is disturbing

(Sephardi) Jews in the context of the Levant and Anatolia

2012-01-02T21:06:00.004+01:00

In June 2010, in rapid succession, we had the opportunity of learning from two papers which studied Jewish genetics in the context of wider samples.

The first one (Atzmon 2010 - PPV, discussed by me here) showed us, even if hidden in the supplementary material only, that the main Jewish cluster was extremely close to their "Turks and Cypriots" sample, specially to some of them (Cypriots apparently):

This central or pivotal group of Jews, marked as GRK+TUR and SYR, are the so-called Sephardi, which, in spite of their name (Sepharad means Spain) do not necessarily originate in the Iberian peninsula but rather share historically a pan-Mediterranean type of ritual, distinct from that of Ashkenazim and other Jewish populations (see also this article if you wish to understand better the complexity of Jewish ethnic divisions).

Just a few days later we got Behar 2010 (also PPV, discussed here), which did not deepen enough in the component analysis, in my understanding, but determined at least that Western Jews (Sephardi, Ashkenazi and Moroccan Jews) were of West Asian origin apparently.

However how exactly they related with West Asians was mostly unresolved (excepting that Palestinians have a lot of genetic distinctiveness and this was not shared with modern Jews nor nearly any other population at any meaningful level).

So, as I began toying around with ADMIXTURE, using the very basic but functional instructions by Razib, one of the ideas I had to explore were Western Jews (other Jewish communities seem to be derived from their host populations but Western Jews appeared as West Asian in these studies).

Extreme distinctiveness of Ashkenazim and Moroccan Jews

I doubted whether to retain the Ashkenazi and Moroccan Jewish samples or just work with Sephardites. In the end I retained them... but then I had to correct and start all over. Why? Ashkenazim specially cluttered the analysis with their extreme specificity (possibly because of some extreme bottleneck in their origins and/or inbreeding, although I can't say for sure).

The results were hardly a satisfactory answer for the question I meant to ask: how do Western Jews relate with the diversity of Anatolia and the Levant, the area where they probably originated? But rather placed these two communities as extremes in the area studied, as unlikely references rather than being referred to the wider native populations. Example:

Instead Sephardi Jews showed up as less strikingly monolithic and had been found in previous studies to be, quite obviously, central to the Jewish diaspora. So I decided to start all over retaining only Sephardi Jews, which should be enough to give the key answers about Western Jewish origins.

Analysis using only Sephardites

This analysis was more productive. The whole run is as follows:

The deeper K levels are not really too informative, specially not for the matter at hand, the origin of Sephardi Jews (and by extension all Western Jews probably). Probably the greatest interest is between K=4 and K=6. I decided to retain the last one as main snapshot:

The labels of the components in the last two images (bottom and right respectively) are a mere conceptual reference.

Kebaran (source)

Since K=2 there is an obvious distinction between Palestinians and the rest. This is coincident with what we find in Behar 2010 for example and what I have found in previous analysis: that Palestinians show a marked distinctiveness even in West Asia. My hypothesis is that they retain best a distinctiveness that may be as old as the Kebaran culture or even older. I understand that this means that, very possibly, Palestinians are the true descendants of historical Jews, Canaanites, etc.

Early PPNB (source)

However this analysis was not designed to discern Palestinian affinities but those of Jews, so I won't discuss this farther. Just to say that if the Palestinian pole is akin to Kebaran-Natufian-PPNA, then the other main detected cluster, shared abundantly by everyone in the region, could well be akin to PPNB.

In any case, the result is that, no matter how deep you go, Sephardi Jews are not clearly distinct from other West Asians, specially not from Cypriots and most often than not also not distinct from Turks. The main difference is certain very weak and slippery relation with Palestinian and other Levantines.

Particularly, component K5 (pop4 in the Fst table, blue in the bar graph), which I labeled as Palestine1, stroke as quite interesting. This component is most common among Palestinians (15% at K=6) but second most common among Sephardi Jews (5%), being smaller among all other populations analyzed. It is possible, I speculate, that this component is a remnant of a genetic link between the Palestinian population, long ago of Jewish religion and identity most likely, and the Diaspora Jews, most of whose ancestry seems to have other origins.

It would be, in this regard, most interesting to analyze genuine Palestinian Jews, descendants of those c. 10% Palestinians of Jewish religion who existed before the Zionist colonial project began, sadly even this notion of Palestinian Jewish has vanished or been erased, even if it was once common enough.

Regardless, in almost everything else, Sephardi Jews are identical to Cypriots and Turks, what suggests that my idea of Western Jews having originated not in Palestine but in the Hellenistic Diaspora, which was largely product not of emigration but of proselytism (and in this context early Christianity was just a Jewish sect of messianic character).

It remains to see how Ashkenazi and Moroccan Jews fit in this description. But while I had to renounce to analyze them, all the previous data strongly suggests that they are not too distinct from Sephardi Jews and should share at least partly that same origin, followed by intense bottlenecks.

_______________________________________

Update (Jan 11): before I forget, I must mention this other paper (that I did not know about) mentioned by PConroy in the discussion:

Avshalom Zoossmann-Diskin, The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms. Biology Direct 2010. Open access.

The author finds Easter European Jews (the bulk of Ashkenazim) to be of essentially European origin mtDNA-wise, with special mention to Italy.

North African genetics through the prism of ADMIXTURE

2011-12-29T17:33:00.010+01:00

I believe that with this exercise, which took me just a morning's time, I'm walking a path that has not been explored before: analyzing the autosomal genetics of North Africans on their own right, without being part of a larger context, be it African or West Eurasian or global. At least I'm not aware of any such paper nor self-research exercise in the blogosphere either.

Said that, I did get in the study five exogenous samples, in order to estimate possible external influences. These are: 10 Fulani, 10 Mandinka, 10 Ethiopians, 10 Saudi Arabs and 10 Spaniards. I did not alter the diverse HGDP North African samples (including two different Egyptian samples), except for two things: I removed the Moroccan Jews altogether and cut the Mozabite sample to 10 individuals, because of suspicion that their alleged isolation might distort the larger analysis.

More or less as I expected, at K=10, which was my preliminary goal, each of the exogenous ethnicities described one distinct component, while the other five components were North African specific.

What I did not expect at all was that Tunisians would show up as distinctive as they did (see below). I wonder if there is something special in that sample or if the measure applies to all (or most) Tunisians. Very strange and unexpected in any case.

In the end, concerned that I might be missing something of relevance, I made two more runs and one of them struck "genetic gold", it seems to me: a small South Moroccan component very distant from everything else, which might well be a remnant of the Aterian period or something like that.

Method: I used a fraction (as described in the previous lines) of the global HGDP sample following the method explained at Gene Expression to operate ADMIXTURE and associated programs (Plink, R).

Results:

K=2 - Without surprises: Tropical African vs. West Eurasian components.

K=3 - Big surprise: the first North African specific component is concentrated in Tunisia, not Morocco, not Mozabites... but Tunisians, uh?

K=4 - As another North African specific component (red, most common among Sahrawis, then Moroccans) shows up, the Tunisian component (green) retracts, so to say, to the Tunisian borders.

K=5 - Not happy with one, the algorithm finds a second Tunisian component, restricted also to that country. I'm as perplex as you may be.

K=6 - West Asian (Saudi Arab) and European (Spaniard) components diverge.

K=7 - Second (non-Tunisian) NW African component shows up. This one (turquoise) is most concentrated among Mozabites.

K=8 - A Fulani-specific component shows up. Intriguingly it is almost equidistant by Fst measure from the Mandenka and the Sahrawi components (0.105 and 0.115 respectively). All the North African specific components are much closer to West Eurasian ones than to the Mandenka component, so this might suggest a very old kind of trans-Saharan admixture, then homogenized in a single component.

K=9 - Not happy with one, the Fulani show a second component in a row. This one is neatly Tropical African (very distant from all and only somewhat close to the Mandinka component and the other Fulani component but at the 0.163 and 0.173 Fst values, which is also very distant). I imagine that this has to do with the Fulani L1b mtDNA lineage but never mind because the component will vanish again as we move on.

K=10 - A Morocco-centered component shows up here (green), also found in Algerians and Libyans. A distinct Ethiopian-specific component is also defined (influencing Egypt and Libya significantly and to much lesser extent also NW Africa).

K=11 - A small and very interesting component exclusive of South Morocco shows up.

(Note: at K=12 there is a third Tunisian component, go figure!, but I don't think that is informative at all so it's not shown).

Note: A reader suggested that some North Africans in these samples are heavily admixed with Tropical Africans, distorting the results in that aspect. I can't say but, if I manage to get working the program variant that should show individual instead of population bars, then we will find out.

Fst Distances at K=11:

Notice please that the South Moroccan component is extremely distant to all (Eurasians and Africans alike). I will speculate (as I have done before seeing this) that this component, now almost only restricted to Southern Morocco and heavily admixed, is a residue of the Aterian period and is related to a vaguely "Khoisanid" or equally vaguely "Mongoloid" phenotype found in the region.

Component apportions (numerical) at K=11:

Detail of K=11 graph:

Playing around with ADMIXTURE

2011-12-26T21:54:00.022+01:00

I decided to gift myself these Saturnalia with the basic knowledge of how to use the ADMIXTURE program. It is not easy but with the help of Razib's instructions, a good dose of patience and some computer savvy-ness I managed yesterday to have something done, even if not exactly what I wanted.

First of all I cleaned up the population file from all populations that have no apparent relation with West Eurasia and also a bunch of tiny minorities like Druzes, Bedouins, etc., which tend to be rather non-informative, and so on. I still retained a number of populations from all around Europe: several North Africans, even more West Asians and Caucasians and then also some peoples from Central Asia and Siberia. I committed two errors however: I removed most NW European representatives by taking out both the CEU (Utah Euroamericans) and North European samples and I accidentally retained two Caucasian Jewish populations.

Good enough for a draft, not good enough for the strategy I had in mind. I went all the way down to K=7 but I will show here only one panel, and only because it offers a perspective that my second attempt, today, did not achieve so neatly (different strategy, different results): to show a clear cut of the European and West Asian components:

example from a previous run: Europe - West Asia duality

We can see here four components:

Red: West Asian
Purple: European
Green: North African
Cyan: Siberian

North African genetic influence in Europe is almost trivial and concentrated in Iberia and the Balcans, although this influence is more apparent in West Asia. Siberian influence is also minor, excepting the Chuvash and to much lesser extent Russians and other East Europeans.

However West Asian influence is more important and concentrates in the Balcans and Italy. North Caucasian peoples are clearly West Asians genetically speaking, even if they technically live in Europe. In turn European genetic influence outside the subcontinent is concentrated along the Northern African coast, Asia Minor and Cyprus.

I'd say that the West Asian (red) component correlates quite strictly with the extent of demic replacement in the Neolithic (although, naturally, the demic wave would have been each generation more European and less West Asian).

Today's strategy

Today I decided to be more methodical and also to reduce population numbers in order to speed up the process. I decided to only keep one North African and one Siberian populations (Moroccans and Selkups) and to reduce a lot the West Asian and Caucasian array of samples (I retained: Palestinians, Kurds, Turks and Georgians). I retained all non-Caucasus European populations, including the omissions of the previous day: CEU and North Europeans.

However I cut all samples to 10 members. Actually Belarus (only 9) and another unknown sample by error have just 9 but that should not affect the results. I doubted about retaining higher numbers for larger populations like North Europeans, Russians, French and Spaniards but in the last moment I chose not to (next time I probably get in 20 of each instead of just 10). In any case the smaller number of samples allowed me to go faster with the runs and reach deeper levels quite easily.

And I went on with the runs, getting this:

... and this:

The color code is a bit crazy and absolutely un-cool but I have managed to figure that it gives red to pop0 and then similarly spaced hues until blue or magenta. I'd rather prefer if the program was able to keep the same color for each comparable component but that seems to require human intervention (dyeing).

I decided that it was best to spend my time putting them side by side as above (also human intervention).

Points of interest

K=3

As in the previous trial, the first detached populations were North Africans (Moroccans) and Siberians (Selkups). Nothing unexpected. The Siberian component is clearly more distant than the North African one from the main component (European in this case, because the West Asian specificity is masked between Europe and North Africa once the samples have been reduced).

Fst (components):

Siberian-Berber 0.131
Siberian-European 0.112
Berber-European 0.054

It's clear (and is consistent along runs) that North Africans (Berber for short) are much closer to Europeans than Siberian natives (including the partly European Selkups). West Asians generally stay 50-50 between the European and North African components (because their specificity has not yet been unveiled because of the effects of sample size, smaller than usual).

I did not run K=2 but I imagine that it'd result in Selkups vs the rest, meaning East Asians vs West Eurasians overall.

I could express the distances in a neutral form pop0, pop1 as the program does but I think it's more confusing (I get confused myself), so maybe better to use a label and hope it is a good choice.

Most Fst distances are in the 0.040-0.070 range. I won't emphasize them.

K=4

The division of Europe into two components takes place at this stage. I decided to label them NE European and SW European because the latter is too influential in NW Europe and too low in the Balcans to be merely "South" (more presence among Northern Europeans than in Romania or Turkey), even if the NE component is more of a general presence. I wonder where they come from, if they are the produce of a duality in the early colonization of Europe, something like Aurignacian vs Gravettian or what? In any case both seem equally European and not originated outside the subcontinent. They are persistent across runs.

K=5

The West Asian specificity shows up, with focus in Georgia. West Asians finally stop looking like a mere amalgam of Europeans and North Africans and display their unique personality.

I insist in this being a mere effect of the sampling strategy: more West Asian samples would have caused this specificity to show up earlier in the runs (K=4) but, maybe more importantly, the European difference would have been the one eclipsed by the West Asian component. I actually have one example from yesterday's exercise:

counter-example from a previous run

Here Europeans and West Asians appear all mostly Green, which is primarily the West Asian component (and not the European one yet). While some North African affinity persists, this has nothing to do with the 50-50 eclipse of West Asian specificity that we can see in the main exercise.

This is a good example why we must beware of the exactitude of the components produced by these algorithms because often, differences in sample strategies and depth of analysis may show or hide critical insight.

K=6 - Slovenian Neanderthals or what?!

Since this level of analysis we get a small and quite puzzling new component that almost only exists in Slovenes and is not even dominant among them. Usually you don't get such a lesser component, much less shows up once and again in several K-depths. It is also just the third European-specific component, what the heck?!

The explanation may be that it is extremely distant from all the rest, so even if small it had little choice but surfacing.

The Fst distances of the Slovenian odd component are extreme: 0.312, 0.233, 0.241, 0.284, 0.239 with each of the other components. By comparison, the largest distance of the Selkup component is just 0.155, while the largest distance I got between World populations in an ad-hoc K=3 run was 0.195.

So this component, whatever it means, is significantly more distant to everything else in the region than continental populations are between each other. I can only think in massive local Neanderthal admixture but I know this is so weird and unlikely that a mere algorithm error is probably the truth.

If you have any idea... I welcome it.

K=7

New component: Palestinian!

K=8

An Orcadian component shows up (but vanishes at K=10).

K=9

A lesser Kurdish component shows up but it does not have the weird Fst distances of the Slovenian one, in spite of the first sight similitude.

K=10

The Orcadian and Kurdish components vanish (may they resurface in further runs? - I never run them). Instead Chuvash, Basque and a distinct Sardinian specific components show up.

I stopped here because it was taking longer and longer (some 50 mins for just this last run) and my patience is limited (specially when I have no clear goal).

This is the detailed spreadsheet snapshot of the exact distribution of the components at K=10:

click to expand

And the K=10 detail:

Mini update: the K5 detail, which is in a sense a simplified display of the same general scheme of things: showing the two main European components, one West Asian (Caucasus) component, the North African and the Siberian components:

Many doubts

The toy seems curious and I did at least manage to make it work at the basics. But I'd like to know:

How to sort populations so they show up in some logical order, like all Moroccan samples side by side and such.
Can I command Plink to retain populations instead of just remove them?
Where can I get other samples? I'm particularly interested in samples of SW Europe but really whatever will do: I'll follow the candy bait, I reckon.
How can I make the results show individual instead of whole-population bars?
How can I get the data (cross-ref-validation?) that indicates when the likelihood of meaning of a run is low or high.
Etc. (surely a lot remains in the ink jar - I just forgot)

Thanks in advance.

Update (Dec 28): Fst distances

Table of Fst genetic distances at K=10:

I marked with red stars the extreme (>0.2) Fst distances of the Slovene component, orange ones the those in highest quintile (after removing the Slovene oddity), which are all from the Siberian component, and green ones the lowest quintile Fst distances.

I also made an Euler diagram sketching Fst genetic distances between the various West Eurasian components:

Where Fst distances in the lowest quintile (after removing the Slovene oddity; <0.084) are shown with continuous lines and the second quintile (0.084-0.107) are shown with dotted lines. (Note: image corrected from first posted version, which had an error).

I think it gives an interesting impression of the possible relations between the various components, in which the NE Euro and Caucasian components (and to a slightly lesser extent the Basque one) seem pivotal, almost as if all the other West Eurasian components are peripheral outgrowths. The short Fst distance between NE Euro and Caucasus (or Highland West Asia) components already showed up in some of the analysis of Dienekes, raising some eyebrows, at least mine. However, as he does not use the smaller components, some of the correlations, notably that the Basque component is also in that pivotal zone, were not apparent at the time.

PS- highly tentative reconstruction of pop. history (excluding the Slovene odd component), based on average Fst (Fst(core))towards the "core" Caucasus/NE Euro components:

Fst(core)=0.125 - Divergence of Siberian/East Asian component (0.110 Chinese/CEU per Wikipedia): Eurasian expansion after the OoA.
Fst(core)=0.102-0.100 - Divergence of Sardinian (?) and North African components: Dabban industries?
Fst(core)=0.091 - Divergence of SW European component (Aurignacian?)
Fst(core)=0.084 - Divergence of the Palestinian component
Fst(core)=0.079 - Chuvash component
Fst(core)=0.065 - Basque component
Fst=0.060 - Caucasus and NE Euro divergence

A rough estimate of the possible Caucasus/NE euro divergence timing (by comparing the Fst values with those of presumably Aurignacoid divergences) would place it c. 24 to 30 Ka ago (depending on what values are used for the Aurignacoid divergence: 40 or 44 Ka ago and of which component is considered the SW Euro or the North African one). So I'd dare say that Basque, Caucasian and NE Euro components appear to have split ways (with all reservations) in the Gravettian period.

(Not sure how well it fits but this kind of maths would place the Siberian/East Asian divergence c. 55-60 Ka ago, a bit too recently IMO and the odd Slovenian component's divergence, if real, c. 110 Ka ago, weirdly old but H. sapiens rather than Neanderthal).

Echoes from the Past (Dec 26)

2011-12-26T12:40:00.005+01:00

Before the year is over, here there is a bunch of stuff I wanted to mention:

Lower and Middle Paleolithic

Humans may have originated near rivers - Technology & science - Science - LiveScience - msnbc.com - neither savanna nor jungle, beach (river banks) was the favored ecosystem even for old good Ardi, it seems.

Pileta de Prehistoria: 180 prehistoric sites located around Atapuerca[es] - not just Neanderthal ones: a bit of everything (located just outside Burgos city, Atapuerca is a key pass between the Upper Ebro basin and the Northern Iberian Plateau, which must have played an ecological and socio-political role always, and hence attracted people towards it).

77,000-year-old evidence for 'bedding' and use of medicinal plants uncovered at South African rock shelter

Upper Paleolithic and Epipaleolithic

ScienceDirect - Journal of Human Evolution : Stratigraphic and technological evidence from the middle palaeolithic-Châtelperronian-Aurignacian record at the Bordes-Fitte rockshelter (Roches d’Abilly site, Central France) - refines the dating for Chatelperronian (PPV paper).

Exceptional discoveries at Mas d’Azil - La Gazette Ariégeoise[fr] - not much info provided however.

The boulders at lake Huron were to trap the reindeer (caribou)

Remains found of the culture which inhabited Northern Chile 11,000 years ago - Terrae Antiqvae[es] - they exploited a quartz deposit for their tools in the middle of Atacama desert, which then was probably quite milder.

Divers retrieve prehistoric wood from Lake Huron - from 8900 years ago.

Simultaneous ice melt in Antarctic and Arctic at the end of the last Ice Age.

Neolithic and Chalcolithic

Turkey : oldest obsidian bracelet reveals amazing craftsmen's skills in the eighth millennium BC - CNRS Web site - CNRS

'Mother Earth' goddess figurine discovered at the Somme (France) - The Independent

'New' ancient monuments come to light at Knowth (Ireland) - Meath Chronicle

Pileta de Prehistoria: businessman Victorino Alonso on trial for destroying a Neolithic cave in Aragon[es] - I asked for death penalty back in the day.

El Neolítico en Europa: una simulación del proceso | Neolítico de la Península Ibérica - Iberian Neolithic - exposition and criticism in Spanish language of yet another paper simulating the Neolithic 'colonization' (Lemmen 2011).

Metal Ages and Historical periods

Bronze age man's lunch: a spoonful of nettle stew - The Observer

The Archaeology News Network: More on Bronze Age boats found in Cambridgeshire

Iruina blog: doubts about the ability of the Basque Autonomous Police to analyze the Iruña-Veleia pieces[es] - the Spanish Guardia Civil police force already declared themselves unable to do the tests. The defense asks to send the remains to one of the few international laboratories able to do the tests and has even offered to pay the cost of it. Also at Diario de Noticias de Alava[es].

Iruina: yet another study supports the autheticity of the Iruña-Veleia pieces, considering 'almost impossible' to falsify them so perfectly[es] - also at Diario de Noticias de Alava

An intimate look at ancient Rome - OregonLive.com - a journey through the hygienic practices of Ancient Rome.

The Archaeology News Network: Ruins of ancient city plundered in SW Iran

Scientists unlock the mystery surrounding a tale of shaggy dogs - Native Americans used dog hair for textiles (among other components).

The Archaeology News Network: Real Mayan apocalypse may have been their own fault -overexploitation of the jungle biome caused desertification.

Genetics

Some of these open access papers surely deserved a deeper look at... I did not have time or energies for that however.

PLoS Genetics: Ancestral Components of Admixed Genomes in a Mexican Cohort

PLoS ONE: Population Structure and Genetic Diversity in a Rice Core Collection (Oryza sativa L.) Investigated with SSR Markers - rice genetics and possible origins.

PLoS ONE: The Local Origin of the Tibetan Pig and Additional Insights into the Origin of Asian Pigs - pig genetics.

BBC News - Liking a lie-in in people's genes, researchers say - long sleeping is a genetic need: tell your boss next time you are late. I am among those who need to sleep 9-10 hours per day (normally) though I have also met people who only sleep 4-5 hours.

The Spittoon » Find Your Inner Neanderthal (I retract what I said before: the results are coherent, even if Africans still get too much too often I guess that's part of the margin of error. However there is another "free online" genetic test that is misleading).

Biology and psychology

Of mice and men, a common cortical connection - a nice comparison to better understand brain regions. To the right: F/M: frontal/motor cortex, S1: primary somatosensory cortex, A1: primary audtive cortex and V1: primary visual cortex. Mice have a much more developed somatosensory cortex (surely related to whiskers, smell, etc.) but a much less developed frontal/motor cortex (related to willpower and rationality).

Scientists Discover Some Keys to Human Brain Evolution | Popular Archaeology - exploring the past - and the relevant paper: PLoS Biology: MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

Maternal care influences brain chemistry into adulthood, animal study shows

Why aren't we smarter already? Evolutionary limits on cognition

Brain Scans Reveal Difference Between Neanderthals and Us | LiveScience - something about the sense of smell, not too clear.

Human skull is highly integrated: Study sheds new light on evolutionary changes

Primates are more resilient than other animals to environmental ups and downs - diversification and flexibility is the key to long-term success.

Battle of Andagoste (Kuartango, Basque Country) year 38 BCE

2011-12-23T19:04:00.002+01:00

Caliga showing the nails

Or should I say Caristian territory, year one of the Hispanic Era?

Actually it was probably the year before or maybe even two years earlier: 40-39 BCE according to the best estimations but the case is that a battle took place in the municipal territory of Kuartango, not far from Vitoria and Bilbao and the ancient city of Veleia, where many Basque and Vulgar Latin short inscriptions have been found.

I was totally oblivious to this historical-era archaeological episode until I read about it yesterday at Iruina[es] blog and then at Euskonews[es] (dated in 2006). It seems that some 1500 Roman legionaries (1200-1800, known by the size of the defensive castrum erected) were attacked and defeated by local tribal troops in what was the prelude to the Cantabrian Wars, a decade later.

The hill of the battle looks so peaceful now

While this prelude is poorly known to historians it must have been of some importance because Octavian (Augustus) declared the year 38 BCE as the first one of the Aera Hispanica, a chronology that was used in all Iberia (i.e. Hispania before the name was monopolized by the state of Spain) until the Late Middle Ages when the more cosmopolitan Christian calendar began to be used instead. And he did so because of the victories that he allegedly attained against the tribes of the North, campaigns of which little is known.

In that year of 38 BCE is known that M.V. Agrippa quelled an uprising by the Aquitani (Northern Basques and proto-Gascons). We can I guess speculate if this battle was caused by (or even cause of) the campaigns of Octavian in the South or that of his commander Agrippa in the North but I can only imagine that this is a trivial distinction and that both are one and the same crushing pressure of the Roman Empire against the Basque tribes overall.

Blue: Celtic tribes, Red: pre-Indoeuropean and hence presumably Vasconic tribes

The battle brings to question the myth of Southern Basques being submitted by Rome only or mostly by pacts and agreements. This myth is mostly based on the fact that Pompey camped at what is now Pamplona (Pompaelo) while his rival Sertorius (a supporter of Marius) did in Huesca (Osca), at the final showdown of the Sertorian War. However at that time the Romans battled with many diverse and circumstantial allies, alliances that might have been eroded by the time of this battle. Alternatively, different tribes may have held different relations with Rome and what applies (maybe) to the Vascones needs not apply to the Caristii or other tribes of North Iberia and Aquitania.

In any case the reconstructed battle depicts a siege of a roman military camp (castrum), maybe erected for the occasion, following the pattern of this image provided by Iruina blog:

The nails (clavos) are more than 600 used for caligae (military footwear), indicating where Romans lost a sandal and maybe their lives. The coins (monedas), weapons (armas) and slingshot ammunition (proyectiles de honda) may help give an impression of the details of the battle in and around the central fortification (núcleo) and also tell archaeologist of when the battle took place (for example these large shoe-nails were replaced by smaller ones in the Roman legions a few years later, the coins also allow for a quite precise estimate...) The overall estimate seems to be 38 BCE (+/-3 years) but the most exact claims are for the 40-38 BCE period in fact.

Rough chronology of the Roman takeover of the Cantabro-Aquitanian or proto-Basque area:

80-72 BCE Sertorian War. Pompey making camp at a Vasco town in 75 BCE is considered the foundation of Pompaelo (Pamplona)
56-51 BCE: conquest of Aquitania (within the context of the wider conquest of Gaul by Julius Caesar)
40-38 BCE: approximate date of the Battle of Andagoste
38 BCE: Agrippa defeats an Aquitanian uprising
38 BCE: decreed by Pompey to be the first year of the Aera Hispanica
29 BCE: Octavius proclaims World Peace (closes the gates of Janus) for the first time
29-19 BCE: Cantabrian Wars
27 BCE: Octavius becomes Augustus (standard beginning of the Roman Empire, previously known as Roman Republic).
23 BCE: Octavius proclaims World Peace for the second time
13 BCE: Octavius proclaims World Peace for the third time after a final campaign against the Alpine tribes (17-15 BCE)

On the origin of mitochondrial macro-haplogroup N

2011-12-12T08:25:00.006+01:00

The notion that the migration of Homo sapiens out of Africa had to pivot around West Asia has been deeply entrenched in our minds, partly because geographical common sense, partly because Eurocentrism, partly maybe because of the Judeo-Christian-Muslim religious background of most influential researchers historically...

However in the last years this idea has been challenged by the coastal migration theory that proposes a migration mostly along the coasts of the Indian Ocean rather than through the interior of Asia. This theory was first outlined by population geneticists, who needed to explain the facts of haplogroup distribution in Eurasia, not at all more diverse towards the West, as we could expect from the classical models pivoting around the Fertile Crescent, but rather towards the East and very specially in South Asia. Later it has been also corroborated, with lesser shadings maybe, by archaeologists who have sought material support in Arabia and India and found it.

While the origin of mitochondrial macro-haplogroup M in South Asia is seldom contested, that of its "sister" N is seldom agreed upon. The reason is that it is distributed somewhat evenly through all Eurasia, Australasia and even America.

This map, from the Metspalu 2005 paper (open access), illustrates the issue and how even renowned geneticists doubted not long ago on where to place the urheimat of the haplogroup:

The phylogeny has anyhow been refined in these six and a half years and you may notice that Australasia is not even included in the map, although it does play an important role, being surely more important than West Eurasia. In any case the map is illustrative of this state of confusion. Confusion that I will try (once again and hopefully for good) to dispel in this article.

The facts of mtDNA N

Macro-haplogroup N has 15 acknowledged basal haplogroups scattered through all Eurasia and Aboriginal Australia. They have diverse numerical importance but what matters to me here is how many mutations (coding region transitions, to be more precise) they are downstream of the N node. Why? Because this is surely indicative of the timing of their respective expansions in relation with N as such.

Looking at this measure we find the following classes of N sub-haplogroups:

Elder daughters: one coding region mutation downstream of N: N1'5, N9, N11, S and R. Notice that among these R holds a special place, not for any phylogenetic reason but because it has a scatter as wide as that of her mother N, suggestive of a very early coalescence and some sort of association between both expansions.
Two mutations downstream of N: N10 and O.
Four mutations downstream of N: N2 (incl. W), A and X.
Extremely long stems, rare clades without any known node under N: N8, N13, N14, N21, N22.

This distinction is not very important but I have always present in any case, because it implies that the various classes of subhaplogroups expanded at different moments after the N node. Notably there is a "pause" at the place of the third mutation and then after the fourth. So we can well imagine the expansion of N as a double explosion, first the two first categories and then the third and maybe the fourth.

Representing each haplogroup as a dot, where they might have coalesced (often a hunch within the local region), the result is as follows:

1.- Estimated coalescence of basal subhaplogroups of N

The size of the dots represents only the "class", that is: how many mutational steps they are under N, the larger the closer they are and the earlier they must have coalesced (according to the laws of probability). The peculiar macro-haplogroup R (whose approx coalescence location was estimated in the past and I will not explain here) has been painted of a lighter blue and given a slightly larger size.

I have also outlined the cloud of N expansion at mutational steps 1 and 2 (no difference), which are followed by an apparent pause at mutational step 3, as mentioned above. The cloud has been pushed northwards a bit in East Asia in order to avoid disputes on where exactly did N9 coalesce (it does not make much of a difference if you prefer Beijing over Shanghai for this clade's coalescence in the end).

Notice that this N cloud is almost identical as would be the M cloud (not shown but look here for a reference if you wish). Whether they were simultaneous or, as I think, N coalesced and expanded a bit after M did, their geography was the same: South Asia, East Asia and Australasia without distinctions. This T-shaped region (with the East on top) was the homeland of the first Eurasian (or more properly non-African) population of Homo sapiens (excepted those who remained in Arabia, which are another story).

The geographic origin of N

Alright, I have described the scatter of N subhaplogroups and the most likely sequence of the expansion but my main purpose here is to estimate the origin, the urheimat of N: where did the N matriarch, the ultimate matrilineal ancestor of all N people today, live?

I apply the statistical principle by which the derived basal haplogroups should tend to remain not too far away from the common origin. Being the most removed ones, exceptions and never the rule. It does makes sense, right?

Hence if we can estimate the centroid of the geometry described by the 15 haplogroups, we will have found the origin of N - or at least a raw estimate of it. There are several methods to estimate centroids but I chose to use the geometric one. In fact, for simplicity, I divided the subhaplogroups in three sets of five (so they all weight the same) and estimated their centroids by geometric decomposition. Then I estimated the centroid of the resulting triangle.

If I am correct the raw centroid of N is at the lower Mekong:

2.- Possible origins of mtDNA N (blue flowers): A - 'raw' geometric centroid, B - corrected against directionality.

I have argued on occasion that, in order to compensate for the directionality of the expansion, a correction can be applied to the geometric centroid or raw estimate of the origin. This correction should pull the origin towards the parent node, in this case L3 in East Africa (estimated here). How much? Maybe 1/4, maybe 1/3... this step, even if probably very reasonable, is a guess and not rocket science. Here I chose to use 1/4 and then look for the closest coast, which is that of Bengal - alternatively I can use a crooked line that follows the geography and get the same result (even less ambiguously Bengal again).

If I would have chosen a 1/3 value for the correction, it would fall in a more central part of India, if 1/5 in Burma surely. We can't be sure of where exactly that happened but we can be more than reasonably sure that it was between India and Cambodia.

And nowhere else: not in West Asia, not in Altai... thanks for the suggestions but I have heard that before... many times... always without a single piece of evidence nor well-reasoned backing of any sort.

The data says otherwise: around the Bay of Bengal or even further East maybe.

Getting R into the picture

I have said before (and is obvious for anyone interested on population genetics) that mtDNA R is peculiar. While it is not different phylogenetically from other subclades of N which are separated by just one coding region mutation, its geographic distribution is very different, because R, like its mother N, is everywhere.

In order to show it more clearly, I drew approximate origins of all basal R-subclades (in lighter blue). The size of the circles follows the same logic as do those of N above, representing only the distance from the mother node (R in this case, what means one step further downstream in relation with N), and hence a probable order of coalescence:

3.- Scatter of N (deep blue) and R (cyan) subhaplogroups. The flower indicates the possible common origin.

The scatter of R fits very curiously within that of N(xR). They do not overlap too much maybe and it looks on first sight like R could have pushed other N around to the margins of the common expansion cloud. However this does not seem to happen with M, so maybe another explanation is needed, like undifferentiated N and R traveling together, mostly under the leadership of the latter and causing different founder effects in different locations.

Whatever the case it is worth a good meditation, because it is possible that both haplogroups (mother N and daughter R) coalesced in rapid succession in a single region (Bengal probably).

Autosomal genetics of South Asia in the wider context

2011-12-09T00:28:00.001+01:00

Estonian geneticist Mait Metspalu has in the past performed leading research of the genetic pool of South Asia, so crucial to understand not just the subcontinental populations but all Eurasia as a matter of fact. Again he and his team provide us with valuable material to understand this region and its wider continental context:

Mait Metspalu et al., Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia. American Journal of Human Genetics, 2011. Open access. (doi:10.1016/j.ajhg.2011.11.010)

The authors added 142 samples from India to pre-existing catalogs and found that:

30% of SNPs found in Indian populations were not seen in HapMap populations and that compared to these populations (including Africans) some Indian populations displayed higher levels of genetic variation, whereas some others showed unexpectedly low diversity.

Reinforcing the generally acknowledged notion that India hosts very large, albeit largely untapped, genetic diversity.

Nothing really new in the wider picture but always worth reminding the basics (principal component analysis of Eurasians):

Supp. Fig. 12

Supp. Fig. 2 (part)

The Pakistan-India (ANI-ASI) duality

It may get a bit more interesting when they analyze the equivalent of Reich's Ancestral North/South Indian components (ANI & ASI), around which much speculation (sometimes quite wild) has built up.

These two components are apparent at both the PC analysis (PC2 and PC4) but maybe more clearly within the ADMIXTURE cluster analysis. The authors decided to use K=8 where I would have used K=13 (preferred by the combination of both check algorithms shown at Supp. Fig. 4 b and c) but the result is only different (for this purpose) in the inclusion or not of Caucasian populations in the ANI-equivalent component (k5 in the maps below).

Iranians are always included, as are Central Asians but quite less emphatically anyhow at K=13 than at K=8, as the affinity splits between the Baloch (ANI) component and the Caucasus-specific one. However Russians do not show any Caucasus-specific affinity and show instead strong influence of the ANI component, which seems to correlate well with Y-DNA R1a, specially once the Caucasus affinity is detached at K=13.

Whatever the case at K=8:

The authors do in fact make an effort to discern if the Baloch-ANI could represent the much discussed Indoeuropean (or Aryan) invasion (hardly doubted in the linguistic plane but not clearly supported in the genetic one). They conclude however that the arrival of the ANI component in South Asia should be much older, at least 12,500 years old, that is: clearly pre-Neolithic - and in any case not related to the Indo-Aryan invasion.

Barely outlined South Asian internal structure

It is interesting that at deeper K levels (K=18) a Gujarat-centered component (middle green), distinct from the two mentioned so far appears and takes a dominant role in most populations, particularly displacing the Baloch (light green) component:

Cut from Supp. Fig. 4a

I would like to encourage transcending the limitations of the chosen K=8 level of analysis and dive in the K=18 analysis found in the Supplemental Figures' PDF (fig. 4). As said before, the optimal level of analysis seems to be K=13 or maybe K=12, rather than the chosen one of K=8. Above K=10 in any case. However many of the improvements of greater resolution take place outside of South Asia, so for most purposes there is no difference (other than the inclusion or exclusion of the Caucasus' populations in the ANI bloc).

Something else that I miss here is a regional, South Asian specific (maybe with the inclusion of some West Asian and SE Asian controls), analysis. It may have offered interesting insights but it is just outlined, with just four South-Asian-specific components at K=18: more than enough for the pan-Eurasian analysis but surely quite limited to discern the details of population structure in South Asia alone.

Diabetes-related allele

One of the most specific findings of this survey is the detection of a group of alleles (at genes DOK5, CLOCK) that have been apparently selected for in South Asians but that has become harmful as diet and lifestyles change today, favoring type 2 diabetes.

Problems demonstrating positive selection

2011-12-02T14:31:00.000+01:00

This is a very interesting paper not because it offers any new striking discovery but because it brings to doubt previous ones and highlights the difficulties in demonstrating beyond reasonable doubt the functional selection in genes allegedly involved in pigmentation, which is one of the most clear differential adaptions among humans.

Johanna Maria de Gujter et al., Contrasting signals of positive selection in genes involved in human skin color variation from tests based on SNP scans and resequencing. Investigative Genetics 2011. Open access.

Importantly most of the discoveries challenged were made by the same team, what is a outstanding example of scientific commitment and self-criticism. Casting doubts and reducing certainty may not be what makes a Nobel Prize but it is how Science advances in fact.

Abstract (provisional)

Background

Numerous genome-wide scans conducted by genotyping previously-ascertained single nucleotide polymorphisms (SNPs) have provided candidate signatures of positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequence data. Four genes, OCA2, TYRP1, DCT and KITLG, implicated in human skin color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7-6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians and South Asians.

Results

Applying all commonly-used allele frequency distribution neutrality test statistics to the newly generated sequence data provided conflicting results in respect of evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. The application of Markov Chain Monte Carlo Approximate Bayesian Computation to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection as previously detected with sequence-based and some haplotype-based tests.

Conclusions

Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.

The Nubian techno-complex of Dhofar: yet another evidence for an early migration out-of-Africa via Arabia

2011-12-01T11:10:00.004+01:00

Jeffrey Rose and colleagues gift us with a beautifully written and delightfully detailed open access study on a culture of the Middle Paleolithic of Arabia: the Nubian techno-complex of Dhofar:

Jeffrey I. Rose et al., The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia. PLoS ONE 2011. Open access.

I strongly recommend reading this paper in full: it really deserves your attention.

The Nubian Complex: extension and origins

The Nubian techno-complex is a facies of the pan-African Middle Stone Age macro-culture (MSA for short), which is roughly equivalent in timeline to the Middle Paleolithic of Europe (and, as techno-culture, to Mousterian in this other context). A facies that is mostly concentrated in North Sudan and Upper Egypt (with the occasional Ethiopian site) and, now we get to know, in Dhofar (Oman).

Fig. 1 Nubian Complex occurrences

In Africa:

Late Nubian Complex assemblages have been found in stratigraphic succession overlying early Nubian Complex horizons at Sodmein Cave [11] and Taramsa Hill 1 [21] in Egypt; in both cases separated by a chronological hiatus. The early Nubian Complex roughly corresponds to early MIS 5, while numerical ages for the late Nubian Complex in northeast Africa fall in the latter half of MIS 5.

In Arabia:

For the time being, the apparent distribution of Nubian Levallois technology in Arabia is limited to the Nejd plateau and, perhaps, Hadramaut valley (Fig. 1). Archaeological surveys in central/northern Oman have not produced any evidence of Nubian Complex occupation [66], [68], nor have Nubian Complex occurrences yet been found in eastern [22], [69]–[71], central, or northern Arabia [72]–[74].

Fig. 10 Dhofar Nubian Complex' points

Note that the authors' concept of Nedj plateau does not correspond with that of Wikipedia, as they are obviously talking of the sites in highland Dhofar and not anywhere in Saudi Arabia (see map below).

The authors express their expectation that eventually other sites will be found within drainage systems along the western coast and hinterlands of central Arabia, linking Nubia with South Arabia. However it is also possible, I'd say, that the actual link is via the Horn of Africa, specially as Arabia has been quite extensively combed in recent years.

The Nubian techno-complex in Sudan appears to have evolved locally:

Taking into account its distinct, regionally-specific characteristics, Marks [2] notes that the Nubian Complex has no exogenous source and, therefore, probably derives from a local Nilotic tradition rooted in the late Middle Pleistocene (~200–128 ka). This supposition is supported by the early Nubian Complex assemblage at Sai Island, northern Sudan, which overlies a Lupemban occupation layer dated to between ~180 and 150 ka.

The oldest known Lupemban culture is dated to c. 300 Ka ago in Kenya and Tanzania.

The authors reject the presence of Nubian Complex tools claimed in the past for the Levant (Levantine Mousterian) and Persian Gulf (Jebel Barakah).

Previously to this work:

The first hint of the Nubian Complex extending into southern Arabia was documented by Inizan and Ortlieb [31], who illustrate three cores from Wadi Muqqah in western Hadramaut, Yemen, with Nubian Type 1 and Type 2 technological features. More recently, Crassard [32] presents a handful of Levallois point cores exhibiting Nubian Type 1 preparation from Wadi Wa'shah, central Hadramaut, Yemen.

Time frame and ecology: the wet MIS 5

The chronological reference of Marine Isotope Stage 5, time frame of the Nubian Complex, corresponds to a warm period between c. 130 and 74 thousand years ago, and corresponds very roughly with the Abbassia Pluvial, when the arid region of the Sahara and Arabia was quite more welcoming.

Fig. 3 Dhofar ecological zones and place names mentioned in text.

MIS 5 is divided in the following substages (figures are Ka ago and may vary a bit depending on source):

MIS 5a - 84.74 (wet)
MIS 5b - 92.84 (?)
MIS 5c - 105.92 (wet)
MIS 5d - 115.105 (?)
MIS 5e - 130.115 (very wet and warm: Eemian interglacial)

MIS 5 was followed by MIS 4, a cold and dry period triggered by the Toba caldera explosion (supervolcano).

In what regards to Dhofar:

... the monsoon increased in intensity during three intervals within MIS 5. Among these humid episodes, the last interglacial (sub-stage 5e; 128–120 ka) appears to represent the most significant wet phase within the entire Late Pleistocene, with rainfall surpassing all subsequent pluvials [42], [43]. Later, less substantial humid episodes associated with sub-stages 5c (110–100 ka) and 5a (90–74 ka) are also attested to in the palaeoenvironmental record. Uncertainties remain concerning the extent to which the climate deteriorated in the intervening sub-stages 5d (120–110 ka) and 5b (100–90 ka).

The increased humidity provided water security to all the region and is also correlated with plant and animal migration from Africa, what the authors think should almost forcibly make humans participant in this overall biological outpouring.

Out of Africa: the alternative routes

Dhofar mountains in monsoon season

The authors discard the Levantine route because of the techno-cultural isolation of the Shkul-Qafzeh group.

They acknowledge the conceptual debt to population genetics for unveiling the probable Arabian route Out of Africa, with particular mention to Behar 2008, who points to the possibility (that I have re-elaborated myself on my own means but on his data) of mtDNA L3'4'6 (and I'd say also L0) having left very indicative remnants in Arabia Peninsula. However they make unnecessary conceptual contortions in order to adapt archaeological knowledge to the molecular clock pseudo-science when it must be the other way around, if anything. No need.

In any case, and this is very important, they describe two different cultural groups in interglacial Arabia:

... we surmise that at least two technologically (hence culturally) differentiated groups were present at this time: Nubian Levallois in southern Arabia and centripetal preferential Levallois with bifacial tools in northern/eastern Arabia.

They also suggest that, after the arid MIS 4 parenthesis, South Arabia experienced another mildly wet period with the MIS 3 (since c. 60 Ka ago), which would have enabled:

... north-south demographic exchange between ~60–50 ka. South Arabian populations may have spread to the north at this time, taking with them a Nubian-derived Levallois technology based on elongated point production struck from bidirectional Levallois cores, which is notably the hallmark of the Middle-Upper Palaeolithic transition in the Levant [105], [106].

But the whole Persian Gulf and Arabian Sea area, not to mention East Asia, remains to be fit in (archaeologically speaking) if we are to understand this period's colonization of West Asia from the East (according to the genetic data).

See also:

In this blog:

Some key archaeological papers on the 'coastal route' (on Fields 2007, Bailey 2009 and Rose 2010)
Coastal route through Arabia 130,000 years ago confirmed? (on Armitage 2011)
Middle Paleolithic of Nefud (Arabia) (on Petraglia 2011)
The various options for the migration out of Africa (a review of all the former)

In external sites:

Update (Jan 11): I have received a copy of a related paper dealing with the relations of Hadramaut tools in the context of global Levallois technique. It is however too technical and inconclusive for me to discuss separately. Yet I do not see it being published anywhere online (PPV or open source or whatever), so I am just uploading it online (for a year) so you can download and read it yourself:

Rémy Crassard and Céline Thiébaut, Levallois points production from eastern Yemen and some comparisons with assemblages from East-Africa, Europe and the Levant.

Echoes from the Past (Nov 30) - The oldest rock art and other stuff

2011-11-30T11:19:00.002+01:00

Again, in short notice, a lot of interesting stuff. Most notably the portrait of the largest bird ever but also a lot of new info on Neanderthal (and Erectus!) Europe, the Iruña-Veleia archaeological scandal, etc.

First of all the giant duck:

Australian Aboriginal Rock Art May Depict Giant Bird Extinct for 40,000 Years : Living the Scientific Life (Scientist, Interrupted) - hat tip to David. The giant bird depicted at Niwarla Gabarnmung is not an emu but a Genyornis newtoni, the largest bird that ever existed. Its extinction date, c. 40,000 years ago, is the most recent possible date for the artwork therefore.

Middle Paleolithic

The origins of Neanderthals could be in Atapuerca

Pileta de Prehistoria: Atapuerca hominins could be a sister species to Neanderthals[es]. Actually much more is claimed in fact: that they are more related to Neanderthals than any other fossil known and that, for that reason and because of chronology, they are the best candidate to be the direct ancestors of Homo neanderthalensis.

Academic reference: Aida Gómez Robles et al., A geometric morphometric analysis of hominin upper premolars. Shape variation and morphological integration. Journal of Human Evolution 2011. Pay per view.

A possible issue is that the site of Atapuerca has provided such a huge number of hominin bones that it is very difficult to compare with even the whole collection of all other European sites.

Serbian Homo erectus in the age of Neanderthals

Excavations in Serbia Raising New Questions About Early Humans in Europe | Popular Archaeology.

They have found a Homo ergaster or H. erectus dated to before 110,000 (preliminary dating suggested 130-250,000 years). In this period it was believed that only Neanderthals lived in Europe already. Are these 'erectus' related to the equally mysterious occupation of Crete also before 130,000 years ago?

Update: the reference paper is this one (hat tip to Neanderthalerin):

Mirjana Roksandic et al., A human mandible (BH-1) from the Pleistocene deposits of Mala Balanica cave (Sićevo Gorge, Niš, Serbia). Journal of Human Evolution 2011. Pay per view.

Other MP:

BBC News - Moreton-in-Marsh Stone Age axe find leads to seaside theory - a Mousterian axe in England with a whole theory on the environment it was once used.

Upper Paleolithic

Qurta (Egypt) rock art is at least 15,000 y.o. << Antiquity

Beautifully preserved bulls of Qurta

Franchthi Cave revisited: the age of the Aurignacian in south-eastern Europe << Antiquity. The Aurignacian of Greece overlaps at both sides of the Campanian Ignimbrite Eruption c. 41,000 years ago.

Shell ornaments from Franchthi

New book in English talks about the Paleolithic of Galicia << La Voz de Galicia[es] - the book can be found online here.

Neolithic, Chalcolithic and Bronze Age

NEWS: Pits with celestial alignments discovered at Stonehenge « The Heritage Journal - more extended at the Birmingham Mail and The Independent.

Pileta de Prehistoria: "Guide to Galician Petroglyphs" presented[es] - the book (in Galician language) can be found here. It is notable that the authors emphasize the similitudes with petroglyphs from other areas, be them in the Iberian Plateau or in Ireland. Faro de Vigo[es] titles: 4000 years ago there was a single language that linked the British Islands and Galicia.

Iron Age

Iruña-Veleia scandal

New step in the legal and scholarly controversy on the exceptional findings at the Vasco-Roman site of Iruña-Veleia: state attorney demands physical tests to Basque Autonomous Police. Previously the defense had asked for them to be made by the Guardia Civil (Spanish military police corps, similar to the French gendarmerie or Italian carabinieri).

Various mentions in Spanish:

Also in relation to the Iruña-Veleia scandal Iruina blog tells us[es] (with video reports) that some scientists have exhausted their patience with the local politicians and tribunals and the abuses that they are inflicting on this most important archaeological site (not just for the history of Basques but also for that of the late provincial Roman Empire, including the origins of Romance languages and new religions like Christianity and Isianism) and have decided to bring the matter to the international arena, so the finger of shame would point to those guilty of unforgivable archaeological destruction.

Human genetics and biology

Maluku people are one genetically regardless of language:

Jason A. Wilder et al., Genetic Continuity across a Deeply Divergent Linguistic Contact Zone in North Maluku, Indonesia. BMC Genetics 2011. Open access.

1-China (Han), 2-Austronesian speakers (Maluku), 3-Papuan speakers (Maluku), 4-Highland New Guinea

Other:

Sandwalk: What William the Conqueror's Companions Teach Us about Effective Population Size - An interesting meditation on key concepts of population genetics, using the well known historical incident of the Norman invasion of England in 1066 that almost turned the Brits into provincial French:

Let's assume that there are 20 well-documented companions [of William the Conqueror]. Only one of these (William Mallet) has possibly passed on his Y chromosome to the present time and even that male line of descent is disputed. This is fully consistent with our understanding of genetics when you consider that most male lines are likely to die out in a few generations. Those that survive ten generations or so are unlikely to become extinct since there will likely be several male lines at that time.

So what were you saying about Genghis Khan?

Jaw size linked to diet: Could too soft a diet cause lower jaw to stay too short and cause orthodontic problems?

Babies show that sense of justice is hardwired.

Neolithic Basque (and Catalan, and Aragonese) mtDNA

2011-11-27T20:18:00.017+01:00

Important correction (Nov 29): the two papers mentioned did test for coding region markers, unlike what I mentioned earlier. The corresponding corrections have been inserted in the text in red color and the erroneous comments I made ~~stricken through~~. My deepest apologies.

It has lots of mtDNA H, of course, as does that of Portugal (both Epipaleolithic and Neolithic), approaching modern apportions.

Again hat tip to Jean for the finding.

This is a two years old paper that nevertheless has gone totally unnoticed by everybody (maybe because it is only in Spanish language?):

M. Hervella et al., Enterramientos en fosa en el Neolítico Antiguo en Navarra: evaluación de las evidencias arqueológicas mediante el estudio antropológico y molecular. Revista Española de Antropología Física 2009. Direct PDF link.

The authors tested not only for HVS-I haplotypes (~~not the ideal method but the cheap one and hence quite common, sadly enough~~) but also within the coding region and the locus 73 (defining R0) in the HVS-II region in the Ancient Neolithic necropolis of Paternabidea (Ibero, Navarre, near Pamplona) obtaining 9 useful results (out 13 individuals tested), of which seven were distinct haplotypes. The testing of coding region markers provides guaranteed haplogroups and not just estimates.

The results are:

That is above 50% H with very few Neolithic lineages (surely K, less clearly I, HV). Overall it is quite similar to modern apportions, as happens with the ancient mtDNA of Portugal (Chandler 2005).

Even if the adscription of what is probably CRS haplotype (ht2) to haplogroup H is sometimes questionable, the identification of other clear H (ht4) and H3 (ht3) haplotypes seems to clarify the matter quite a bit. I could not find the exact HVS-I sequencies, so I can't judge.

No individuals buried in the same tomb ("fosa") share haplotype.

Individual E1 was buried with a pot decorated with Cardium motifs, individual E2 had a necklace which included three variscite beads (semi-precious green stone very popular in the Atlantic Neolithic).

The necropolis of Paternabidea is dated to c. 6.090-5.960 ± 40 years BP. This is an uncalibrated C14 date, I understand, what should translate as c. 7000 real years ago or c. 5000 years BCE after due calibration, being one of the oldest Neolithic sites in the area (see this previous post for the regional Neolithic chronology).

Addendum: I think this is the right place to post this map that Argiedude sent me with the modern apportions of mtDNA haplogroup H1:

Author: Argiedude

This map seems to suggest a negative cline of this lineage from the sources of the Neolithic phenomenon in SE Europe and West Asia, a possible sign of having suffered some displacement by the newcomers. H3 is instead restricted to SW Europe.

For further info in mtDNA H past and present distribution see this entry at my old blog Leherensuge.

Update: Catalan and Aragonese Neolithic mtDNA

A complementary study on Catalan ancient mtDNA has been published these days, however under a paywall:

C. Gamba et al., Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers. Molecular Ecology 2011. Pay per view.

This are the results:

click to see larger (and legible)

In this case also coding region testing was performed, so the haplogroups reported are certain:

The information obtained from the HVRI sequence (table 4) together with the result of typing different diagnostic coding SNPs allows us to classify each Neolithic sample into its corresponding mitochondrial DNA haplogroup in the well-known mtDNA phylogeny.

X1 and K are likely to be Neolithic. N* is a mystery but unlikely to be Neolithic in principle. All the rest (H and U5) are likely to be pre-Neolithic.

It is notable that the most modern and also likely pre-Neolithic sequence is found in the Aragonese cave of Chaves (67% H, 33%K), farther from the Mediterranean Sea and the Ebro river, towards the Central Pyrenees.

Detail of the results of this study and others on ancient DNA can be found at Jean Manco's ancient DNA page (look here for Morocco and Canary Islands).

Update on Gamba's paper (Dec. 8th):

Argiedude (who remains without access to Google) wrote to me and clarified the following:

The reported X1 is X(xX2) in fact according to the published data (could be X1 but also X3, X4 or X*). However X3 used to be known as X1b until a few months ago, while X4 and X* are extremely rare.

H20a, which is actually the reported "H20" lineage is almost only found in Europe (notably Iberia). The sources are diverse but he lists: 5 from Spain (including one Canarian but no Moroccans), 2 Hispanics and no Portuguese/Brazilian. In addition he mentions some Sephardi Jews, while Mitosearch lists: 1 Greek, 1 Bavarian, 1 Sicilian, 2 Mexican, 2 Spanish. The oldest source on H20* and H20a being located in West Asia and Europe respectively is Richards 2000.

Update: a Paleolithic Basque mtDNA U5b1 from Aizpea?

Jean Lohizun also pointed me to this other ppv paper on immune polymorphisms. What is notable is that the free supplemental material, lists several mtDNA HVS-I sequences, most of which are from San Juan Ante Porta Latinam (a Chalcolithic Ebro river site already documented for mtDNA) but one is from Aizpea, an ill-known Epipaleolithic site from west-central Navarre. For this site they provide the following sequence: 051-093-189-192-270 (+16,000), which seems to lead to U5b1a'b'c following the latest PhyloTree build. But if you have a second opinion (two markers are missing), I'll be glad to read it.

Y-DNA of Basque diaspora in Western USA

2011-11-27T19:48:00.001+01:00

Hat tip to Jean for this finding.

Laura Valverde et al., Y-STR variation in the Basque diaspora in the Western USA: evolutionary and forensic perspectives. IJLM 2011. Direct PDF link. [DOI 10.1007/s00414-011-0644-8]

As the authors wisely assess the most important inference we can get from this study is how a colonial population diverges from that of the homeland. The Basque colony in North America is not too large (58,000 in all the USA), albeit significant specially in Idaho, Nevada and to lesser extent California (larger numbers but smaller apportion), and the origin is biased towards a single region: the Northern Basque Country (under French rule).

However the results show that they represent very well the ancestral homeland's haplotypes, only tested in the Southern Basque Country, diverging only somewhat:

Fig. 1 Median-joining haplotype tree: white European Basque (West), black American Basque

This is a good example of how a normal colonial population, even if reduced in founders and numbers, behaves in relation to the ancestral one: it retains most of the lineages. No marked founder effects are apparent anywhere.

Our results demonstrate a very high-level of conservation of the Y chromosome haplotypes characteristic of the European autochthonous Basque population among individuals of the Basque diaspora in the Western USA. No signs of founder haplotypes have been found...

Open sea fishing in Timor 42,000 years ago

2011-11-25T15:34:00.001+01:00

Ancient Timorese fishing hooks

A serious attention call today for all those who doubt that boating (or even mariner) skills of Paleolithic peoples could even exist at all. Timorese people were fishing tuna, a pelagic fish, requiring certain serious mariner skills, some 42 thousand years ago, roughly when their distant relatives were making their first incursions into 'the Neanderlands' of West Eurasia.

The ancient Timorese people who dwelt in Jerimalai shelter used elaborate fishing hooks, which are however dated to c. 23-16 Ka ago. These hooks were worked out of shells. With or without hooks, they fished a lot of tuna and parrotfish which are clearly dated to c. 42,000 years ago. These fish can't be captured from the shore.

Sue O'Connor et al., Pelagic Fishing at 42,000 Years Before the Present and the Maritime Skills of Modern Humans. Science 2011. Pay per view.

Abstract

By 50,000 years ago, it is clear that modern humans were capable of long-distance sea travel as they colonized Australia. However, evidence for advanced maritime skills, and for fishing in particular, is rare before the terminal Pleistocene/early Holocene. Here we report remains of a variety of pelagic and other fish species dating to 42,000 years before the present from Jerimalai shelter in East Timor, as well as the earliest definite evidence for fishhook manufacture in the world. Capturing pelagic fish such as tuna requires high levels of planning and complex maritime technology. The evidence implies that the inhabitants were fishing in the deep sea.

Media/blog articles: New Scientist, Adelaide Now, Dienekes.