March 30, 2011

Evolution news: punctuated speciation and the fittest wins only sometimes

We all (except a handful of fanatics) agree that evolution happens. What is not fully clear are the details of how it happens. These days two new researches challenge some conceptualizations and support others instead.

Evolution is not constant but punctual.

That is what Stephen A. Smith (left) and colleagues have discovered when analyzing the phylogeny of angiosperms (flowering plants). They found that the conceptualization of evolution as punctuated rather than constant seems to be correct, and also that the characteristics of a new taxon evolve in a single population or root species before diversification (radiation) occurs.

The research has been published in the American Journal of Botany (open access) and a synthesis appears at Science Daily.

Perfectly fit? Maybe not needed.

A simplistic school promotes the idea that given enough evolutionary time in a simple ecological niche only one competitor will survive: the fittest one.

However this does not seem to be the case. Research by Robert E. Beardmore and colleagues, published in Nature (ppv), vindicates previous research in which optimal efficiency coexists with suboptimal one:

The fit use food well but they aren't resilient to mutations, whereas the less efficient, unfit consumers are maintained by their resilience to mutation. If there's a low mutation rate, survival of the fittest rules, but if not, lots of diversity can be maintained.

Full story at Science Daily.

March 25, 2011

Texan evidence of pre-Clovis North-Americans

Clovis (L) and Buttermilk (R) toolkits
Several news sites have announced today what is arguably the first consolidate archaeological evidence of human population of North America before the emblematic Clovis culture: the Buttermilk Creek culture of Texas, dated to c. 15,500 to 13,200 years ago.

This site adds to others more or less accepted ones from North and South America, clearly establishing that the colonization of the double continent happened at least several millennia before the emblematic Clovis culture, which is dated around 13,500 and 13,000 years ago.

Source: Science News.

March 20, 2011

Archaeonews from South Asia

The latest Archaeonews bulletin is full of interesting information on South Asian prehistory, from Nepal to Kerala:

Nepal mountain burials

27 people buried in caves at c. 4000 meters above sea level have been found in the Himalayan country and dated between 3000 and 1500 years ago. 

67% of the bodies were defleshed, a mysterious burial practice, which may relate to a contemporary Tibetan one (sky burial) or, alternatively,  Zoroastrian rituals (who in the past defleshed the bodies and fed the meat to animals - nowadays they feed the whole bodies to vultures in special grounds). 

Full stories at República and National Geographic.

Kerala Megalithic dome

A new Megalithic tomb has been found at Kodiyeri with a curious pillar (left), a similar dome is recalled to have been found 40 years ago (but nobody seems to know its destiny anymore).

Full story at The Hindu.

Kerala claims oldest non-African Paleolithic site

With and age of 1.83 million years at the deepest layer, Bukit Bunuh may be one of the first homes of our cousins Homo erectus (or H. georgicus or...), when they migrated to Asia.  The site was apparently chosen for its excellent ecology that would have provided our cousins with all they needed for a living: fresh water, hunt, plants and stone to make handaxes. 

The site also shows more recent inhabitation dates of 40,000 and 30,000 years ago which surely belong to modern humans.

Protection from UNESCO as World Heritage Site has been requested. 

Full story at University Sains Malaysia and Asia Research News.

Note (Mar 31):

I wrote earlier in regards to this Indian site: Also, maybe more in detail, at Ancient Indian Ocean Corridors (by archaeologist Michael Petraglia, who includes a link to a relevant paper in press).

But this one is actually another site, in nearby Tamil Nadu, with a confirmed age of 1.6-1.4 million years on a more careful (and hence credible) measure. David Sánchez has an excellent review of this finding and its implication in Spanish language today.

Violence among early Scotland farmers

Early farmers of Scotland died violently... but then they were buried in a monument, the Tomb of the Eagles (left), at Isbister.

Out of 85 burials in this tomb, 16 have clear evidence of head trauma caused by weapons. Some of these injuries were healed but others not, meaning that they were killed by them (or related violence).

The tomb's age is of c. 3000 BCE, a few centuries after farming began in the area.

Full story at Daily Mail.

Also in Scotland it has been announced the discovery of rock art that could be Neolithic near a recently discovered chambered tomb (dolmen) at South Ronaldsay, Orkney, reports Orknejar.

Original source: Stone Pages Archaeonews bulletin.

March 15, 2011

Provenzal genetic data... and weird speculations

The following paper offers some information on the genetics of Provenzals and some specific populations of Turkey (Foça, Izmir) which is compared with older studies (on Turkey and Greece) to reach quite unfathomable conclusions:

I'm split on this paper: on one side it does provide some interesting data and makes some common sense claims (like Provence having been little affected by Neolithic expansion direct colonization) but then you stumble upon absurd ideas, such as Cardium Pottery stemming somehow from "Anatolia":
Using putative Neolithic Anatolian lineages: J2a-dys445=6, G2a-M406 and J2a1b1-M92 the data predict a 0% Neolithic contribution to Provence from Anatolia.
There is absolutely no reason to be looking at Anatolia: the Neolithic wave that arrived to Provence did not originate in Anatolia but in the Western Balcans. It is very possible that Anatolia was the ultimate origin of Greek Neolithic and this was in turn at the origin of Cardium Pottery Neolithic somehow, but the real origin of the Neolithic wave that arrived to Provence must not be looked for in any case in Western Anatolia - that is a total nonsense.

We know way too little as of yet to explain the exact process of cultural transference from West Asia (Anatolia specially) to the Balcans (Thessaly in particular) and from Thessaly to the Adriatic, where the cultural elements are so distinct anyhow. There is no particular reason to expect any arrival directly from Anatolia into Italy or SW Europe in the Neolithic. Any such migration would have been dampened in two filters: one in Greece and another one in the Adriatic Balcans.

From my ongoing (and slow) work of summarizing  European Neolithic in maps:

Here you can see in brown the first area of Cardium Pottery Neolithic: Dalmatia, Montenegro, Coastal Albania, most of Bosnia, Italy (in a second moment)... It has a precedent in Otzaki (Thessaly) and a derived influence in Biblos (Lebanon) but by no means can it be linked to "West Anatolia" of all possible places.

Universities and grants should require that any geneticist doing historical population genetics hire a prehistorian for assessment, sincerely.

Still there is a very interesting amount of data that is of interest, summarized (as I said before) in figure 2 specially. This is an extensive table that I cannot reproduce here with enough resolution without some previous work. So for reason of its relevance and novelty I'll focus on the Y-DNA data of Provence (n=51, only attested lineages shown):

  • E1b1b1b1a2 (V13): 4%
  • E1b1b1b1c (M123): 2%
  • G(xG2a3a) (M201): 8%
  • I1 (M253): 2%
  • I2(xI2a2,I2b) (M438): 4%
  • J1 (M497): 2%
  • J2a4h1a (DYS445=6): 8%
  • J2a4b(J2a4b1) (M67): 2%
  • R1a1a (M198): 10%
  • R1b1b2 (M269): 59%

Up 26 to 30% (depending on how you evaluate I2*) of the genetic pool is "Eastern Mediterranean" in Provence. E1b1b1b1a2 (V13) is probably from Albania or other Adriatic areas (see Battaglia 2009). That can also be argued to be the case for all the other "transmediterranean" lineages, which agrees well with a Neolithic origin of all them. However it is not impossible that these Neolithic arrived in batches and with intermediate stops in Italy for example or, why not, in Phocaea in some cases. 

But the research falls very short from demonstrating what they claim to demonstrate. If they have demonstrated something at all they have failed to explain it properly. So the only interest of this paper is the raw data, which adds to other such data to be integrated into a careful and comprehensive exploration of all (and not just some) data with proper prehistoric assessment. 

It is in any case important to understand that under the Neolithic colonization hypothesis, E1b1b1a2 should not be expected to originate neither in Anatolia nor in Greece but in Albania, Montenegro and Dalmatia. And, if anything, in Greece rather than Anatolia. Attributing European Neolithic directly to Anatolia or West Asia in general is not an acceptable assumption but a wacko fetish that should be discarded altogether.

March 14, 2011

Early farming was inefficient compared to foraging

Early farming was only able to generate some 60% of what foraging (hunting and gathering) did, according to new research:

Samuel Bowles, Cultivation of cereals by the first farmers was not more productive than foraging. PNAS, 2011. Pay per view (depending on world region and time).


Did foragers become farmers because cultivation of crops was simply a better way to make a living? If so, what is arguably the greatest ever revolution in human livelihoods is readily explained. To answer the question, I estimate the caloric returns per hour of labor devoted to foraging wild species and cultivating the cereals exploited by the first farmers, using data on foragers and land-abundant hand-tool farmers in the ethnographic and historical record, as well as archaeological evidence. A convincing answer must account not only for the work of foraging and cultivation but also for storage, processing, and other indirect labor, and for the costs associated with the delayed nature of agricultural production and the greater exposure to risk of those whose livelihoods depended on a few cultivars rather than a larger number of wild species. Notwithstanding the considerable uncertainty to which these estimates inevitably are subject, the evidence is inconsistent with the hypothesis that the productivity of the first farmers exceeded that of early Holocene foragers. Social and demographic aspects of farming, rather than its productivity, may have been essential to its emergence and spread. Prominent among these aspects may have been the contribution of farming to population growth and to military prowess, both promoting the spread of farming as a livelihood.

A news article is also available at PhysOrg.

Is the alternative explanation correct?

I find this discovery most interesting because the assumption has generally been that automatically farming was more productive than the old human way of life: foraging what Nature had to offer. 

Yet this assumption did not explain why farming had not evolved earlier or why the, generally very pragmatic, peoples of the World, did not adopt it earlier, as they were no doubt aware of how gardening could be done.

It reminds me somewhat of the very much comparable misunderstanding on the transition from the Bronze to the Iron Age: iron had by then been known for very long but it was brittle in comparison with bronze, quasi-bronze (copper and arsenicum) and even the old good flint stone. Actually I read somewhere recently that another good old friend of humankind, obsidian, makes such great blades that compete favorably with steel scalpels.

Things are not so simple: steel began to be developed (as sweet iron is not really good for most uses) after tin resources began to fail in the Eastern Mediterranean, as the communications with Atlantic Europe (where most tin mines were back then) may have collapsed when the two classical Iberian civilizations, El Argar and Zambujal (VNSP), did as well for reasons not well understood and not too relevant to discuss here. 
It was therefore problems in the bronze industry, so critical for the military of the time, what pushed steel technology ahead, inaugurating the Iron Age.

Molino neolítico de vaivén
Seed milling was done long before Neolithic too
Therefore I'd like to consider what may have caused people to adopt farming instead of just continue foraging, as they had done successfully until that time. We know that farming was preceded by a period we call Mesolithic and that is characterized by intensive foraging of wild cereals or other foraging behaviors that somehow announce the advent of farming or herding. 

So, in the Fertile Crescent, there was for a time, since about the end of the Ice Age, a focus on a pre-farming type of foraging. As I have not read the paper yet, I do not know if Bowles has factored this period in his equations. As for me, I'd think that this kind of foraging (maybe already associated to some early gardening practices) we call Mesolithic, seems to respond to an ecological pressure of some sort, no doubt related to the then ongoing climate change. 

Another issue I am pondering is that, even before cereal farming was fully developed in Palestine, herding of sheep and goat was adopted in Kurdistan, followed by cow herding in Anatolia (near the well-named Taurus mountains). Maybe herding had to be developed in order to make farming effective? Cattle (be it bovine or ovi-caprine) provides nutrients in form of manure and, goats specially but not only, can also be used to clear up wild vegetation areas, while pigs are great to plow the fields.

So I am wondering if animal domestication was a condition to make cereal (and pulse and flax) farming an economically effective way of life. 
Honestly I prefer a true economic explanation rather than one based on very conjectural preferences about sedentarism, and this may be made up of:
  • The push factor of climate change at the end of the Ice Age
  • The pull factor of animal domestication, increasing the yields of agriculture until it became economically worthwile
What do you think?

March 12, 2011

Y-DNA of Khazaks from Altay Republic

Not very clear which is the motivation behind or the peculiar interest of this paper but it should add to the data resources anyhow:

Matthew C. Dullik et al., Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions. PLoS ONE 2011. Open access.

The data adds to and is compared with previous research (several papers) on Kazakhs from Eastern Kazakhstan. Central and Western Kazakhstan remain pretty much unexplored.

There are some difference in the respective Y-DNA pools but they seem to originate in differential founder effects and not specially in admixture with Altays. Notably:
  • Altay Kazakhs are higher in C(xC3c) (24%) and lower in C3c (39%) than other Kazakhs.
  • They are also higher in O3 (26%)
  • They are also higher in G and J (9%) altogether

SW Altayan Kazakhs may be admixed patrilinearly with native Altayans, while SE Altayan Kazakhs do not show such affinity. This difference may be caused by sampling in a Christian Khazak community living side by side with Altayans and Russians.

Fig. 4 PCA (Y-DNA) of Central Asian and Mongol populations

It is interesting that while the genesis of the Kazakh nation lays historically in separation from Uzbeks, these two Turkic nations do not share almost any lineage.

The poor sampling of Kazahstan and even Kazakhs in China is admitted by the authors as a problem to properly understanding Kazakh genesis. As mentioned before most samples come from Eastern and SE Kazakhstan however most of the country remains unsampled.

Fig. 1  Kazakh populations sampled (5: this paper, * sample localities)
Population density in Central Asia (for reference)

Some curious archaeology news from the Atlantic Islands

Found via Archaeology in Europe and quite worth a mention here, I believe:

A Chalcolithic Age (late Neolithic by British standards) handbag preserved in bog. The piece of basketry to the left was part of a very extended design used by people, usually women, through the World since at least Neolithic times. The first such design is claimed to be from West Asia c. 4800 BCE, while this Irish specimen (from Tyford, Wesmeath) seems to have "only" 5000 years of age.

Full story at Irish Times.

Of similar age, 5500 years, is the first complete Neolithic (Chalcolithic by pan-European chronology) pot  found in Britain. The site of Didcot in Oxfordshire has also yielded well preserved Iron Age housing and other materials. 

Full story at BBC

Finally big myths are being shaken: Romans may not have built "Roman roads" after all. Iron Age Britons were already building them long before the Romans arrived. If that was the case in the then rather remote island, I presume it's probably also in other parts of Europe.

The Independent wonders, quite legitimately, what did the Romans do for us (if they did not build our roads)? In truth the notion of the Roman Empire as a force of culture and civilization may well be very much misplaced, after all, Romans learned everything but war from their Etruscan neighbors.

Human natural societies flexible and not primarily built on genetic kinship

Understanding hunter-gatherer societies is important because we are after all just paleolithic peoples dumped into Market Street. Our flexibility allows us to deal with this strange unnatural reality with some ease but this is not the context in which we evolved, not at all.

New research in this ancestral reality of us, embodied in a variety of surviving hunter-gatherer groups, provides some interesting results:


Contemporary humans exhibit spectacular biological success derived from cumulative culture and cooperation. The origins of these traits may be related to our ancestral group structure. Because humans lived as foragers for 95% of our species’ history, we analyzed co-residence patterns among 32 present-day foraging societies (total n = 5067 individuals, mean experienced band size = 28.2 adults). We found that hunter-gatherers display a unique social structure where (i) either sex may disperse or remain in their natal group, (ii) adult brothers and sisters often co-reside, and (iii) most individuals in residential groups are genetically unrelated. These patterns produce large interaction networks of unrelated adults and suggest that inclusive fitness cannot explain extensive cooperation in hunter-gatherer bands. However, large social networks may help to explain why humans evolved capacities for social learning that resulted in cumulative culture. 

A news article is also available at Science Daily.

What may seem a bit unexpected is how this social structure is not at all like any related primate group. Our closest relatives live in individual units (orangutans), in single-male dominated harems (gorillas), in patrilocal promiscuous communities (chimpanzees) and in matrilocal even more promiscuous ones (bonobos). 

Instead humans form bands, typically of some 28 individuals, which are neither patrilocal nor matrilocal, and end up including people who are mostly not even closely related to each other. There it goes genetic egoism down the toilet!

This structure actually seems to integrate wider networks of relationships beyond the band, which (from other sources) is typically so flexible that it loses and gains members very frequently. Probably what this implies is ethnic (tribal) networks as main unit, however not even these are closed to strangers, not at all.

The research included some 5000 people from the following nations: Gunwinggu (Australia), Labrador Inuit, Apache, Ache (America), Mbuti, Aka (Africa), Agta and Vedda (Asia).

Update (Mar 17): Blackbird, who runs some interesting blogs on non-human animals you may want to check, mentions that our Pan sp. cousins, both chimpanzees and bonobos, may not be as gender biased as we used to think in regards on who moves and who lives in the established community. The following paper addresses this matter a bit and also includes an interesting analysis of haploid genetics among bonobos (all of which live in D.R. Congo):

Jonas Erikson et al, Y-chromosome analysis confirms highly sex-biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus). Molecular Ecology 2006. [doi: 10.1111/j.1365-294X.2006.02845.x]

He (Blackbird) suggests, and he may be right I'd say, that this ambiguity of locality is similar to what Hills observes for Homo sapiens and may therefore be a shared pattern among the super-genus.  

March 11, 2011

Dolphin mtDNA phylogeny

Tursiops truncatus brain size
Left to right: pig, dolphin and human brains
There is hardly any more iconic animal than the dolphin but there is also hardly any animal closer to us in a key identity element: intelligence. Lacking hands and living in water, dolphins have never developed some of the technological landmarks that we associate with human-like intelligence: fire management and tool creation, however their brains are, in comparison to body mass, very much our size, they demonstrate once and again to be very intelligent beings with some abilities (notably sonar perception and communication) rather beyond our comprehension. For instance only recently have we begun to understand that dolphin language is not framed in the mere two dimensions ours is but is actually tridimensional.

A few weeks ago, it came out in a discussion on "Neanderthals and us" whether dolphins, with their many different species, many of them (if not all) showing striking intelligence, could be a model to understand the relations between the various species of the genus Homo in the past. A problem, at least for me, is that we really do not know so much about dolphins either anyhow. Most documentaries are about the successful common bottlenose dolphin Tursiops truncatus or the also very successful and impressively bright orcas. But there are dozens of dolphin species.

In this sense it is very interesting to take a look at this new paper establishing a mitochondrial phylogeny on these sea mammals:

Particularly illustrative is the proposed phylogeny of figure 1:

It is notable that there are cases of hybridization (fertile hybrids!) in the wild as in captivity, of such different species as Turiops truncatus and Pseudorca crassidens, which would have diverged some 8.5 million years ago, roughly the (true) distance between chimpanzees (and bonobos) and us.

This really challenges the concept of species as defined in classical terms (absolute possibility of production of fertile hybrids) and reinforces the modern revised concept (normal reproduction in the wild).

Common dolphin noaaThe closest equivalent (always assuming all age estimates are correct) of "Neanderthal and us" (i.e. Homo ergaster and derived species by most accounts) in the tree above would be the relation between the long-beaked common dolphin (D. capensis) and the Indo-pacific bottlenose dolphin (T. aduncus). Just a little bit upstream and we get to the equivalent of all the Homo genus, while the overall dolphin relationships are in the range, as already mentioned of "Chimpanzees and us". 

Probably this phylogeny will not be of much use for comparison, more so as the various intelligence levels and other cognitive, linguistic or social adaptions of dolphins are ill understood at the moment, but it is still better than nothing and hence I felt it was an interesting reference to have in mind.

Prehistoric Aquitaine: exposition at Baiona (Bayonne)

The Basque Museum of Baiona (Bayonne in French) will welcome for two months the exposition Aquitaine préhistorique - Historiaurreko Akitania (Prehistoric Aquitaine), gathering some of the most fascinating stuff and information from European prehistory. 

Among the elements in this educative show are the famous Lady of Brassempouy (left) and more than 2,000 other  archaeological objects from the heartland of European Paleolithic.

For example this beautiful engraving of an auroch from Erango cave (Lower Navarre):

The exhibition will be at Baiona between March 22nd and May 22nd and has already been at Bordeaux' Museum of Aquitaine.

March 10, 2011

Lost genes make us what we are

Oddly enough it seems much of what we are as human beings is not because of new developments as about giving away old ones.

This is what new research claims:

Discussed also at Science Daily

Will furry freaks find their way back to whiskers now?
Some of these strategic deletions include the loss of a gene that forms the penile spine (John Hawks explains in detail what these spines are) of many other mammals. Similarly we lost the gene producing sensory whiskers. Both these losses are related to the androgen receptor gene (which we still have but whose function has been altered by loss of other related genes).

Many other key deletions have been detected in relation to steroid hormone signaling.


More interesting maybe is the loss of gene GADD45g, which limits brain growth. While the authors seem to agree that this deletion alone could not cause human large brain size and function, it does seem as it would be a central pillar of our brain development in any case.

March 9, 2011

African diversity and the possible origins of Humankind

There is a massive consensus nowadays on a shared origin of modern humans (Homo sapiens) in Africa (south of the Sahara), maybe some 200,000 years ago, regardless of minor hybridization episodes with other human species after the migration out of Africa.

However it may not be so clear where in Africa exactly, if anywhere, are our shared origins. Earlier work on mitochondrial DNA (Behar 2008) suggested an East African origin, a result largely replicated by myself on the same data (with some lesser differences).

However now a new research paper on autosomal DNA suggests instead a Southern African origin, quite intriguingly:

The paper has some reasons for such claim but, after reading it, I really do not feel fully persuaded. Importantly, there is a huge critical sampling blank in the Upper Nile area, notably the tribal zones of Ethiopia and South Sudan, one of the leading candidate regions for the origin of Humankind. The East African sampling is somewhat restricted: two isolated huntergatherer ethnicities (Hadza and Sandawe), one Nilo-Saharan pastoralist nation (Maasai) and one Bantu farmer group (Luhya). Certainly it would have improved massively if two or three South Sudanese and Ethiopian peoples would have been included in this research (this Upper Nile area has the greatest basal diversity in mitochondrial DNA at several successive levels, much larger of what we find in Southern Africa or more southernly parts of East Africa, like Tanzania).


But well, this is what we have and this is what we get:

Above (fig. 1, click to view larger) we can see some of the runs in Admixture

Niger-Congo peoples retain quite an homogeneity all around Africa, reinforcing the idea of the Bantu expansion being largely a demic colonization (yet Mozambicans look different and in any case this matter should be explored separately and with proper sampling strategies: you can't just "jump" over all the Congo and Zambezi basins for example).

All other groups show their own distinctive components at k=8, and in some cases (Maasai) two different specific components. 

The distances between the various "purified" components (i.e. not the populations but the genetic components in them as shown in k=8 above) is dealt with in table 1. Interestingly the closest component to non-Africans (represented by Tuscans) is the yellow one (East Africa), followed by the purple one (Sandawe), the red one (West Africa) and the pink one (Maasai specific). This last component is suggested to be relatively close to some North African component but this is not shown in quantified form and the lack of sampling in the Upper Nile does not help in discerning this matter either. 

On the other hand the Hadza reveal themselves (their light blue component) as an isolated group with large Fst distances to all other components (less remote are East African, Sandawe, Pygmies and West Africans).

Instead, the less studied Sandawe (with mtDNA and Y-DNA similar to the Hadza, see table S3), reveal themselves as a well connected and highly diverse population (see below). They are genetically closest to the East African and West African components and the closest relative also of the Maasai-specific component.


The best representation of this is maybe found in fig. 2B:

Fig. 2B annotated by me

Look specially at the vertical axis where linkage disequilibrium (LD) is annotated (the horizontal axis shows distance from  a putative "origin" in Angola). Greater LD means lower diversity.

Fig. 2C
Among the annotations I made there are four grey square marks: they identify four populations that are "pure" (or almost) in the Admixture analysis above (k=8). I understand that the authors used components rather than whole populations when determining diversity clines (left) and that only explains the concentration of greatest diversity in Southern Africa and not in Gabon-Cameroon, where the Biaka and the Fang live.

Honestly, I got lost when they shifted from fig. 2B (where the Biaka and Fang are as diverse as the San peoples of Southern Africa) to fig. 2C (and 2D, where they used Fst data instead but produces similar results), where the diversity clines are concentrated towards Southern Angola mysteriously. This hat trick really got me baffled and unable to explain here what the heck is going on. I think that they decided to use genetic components instead of genuine populations but this can be argued to be an error because the ability of Admixture and such to discern such components as "absolute" is very much limited.

Back to fig. 2B (above), we can see that there are two implicit deviation groups from the 45 degrees line LD/hypothetical distance:
  • On one side: groups like the Sandawe, Maasai or Mandinka look highly diverse even if they are far away from Angola. Southern Moroccans can also be included in this group.
  • On the other hand, peoples like the Hadza, the Fulani and the Kaba are quite less diverse than expected, suggesting a more or less marked founder effect or other kind of bottleneck-like effect at the origin of these peoples. Tunisians are also quite less diverse than their neighbors and hence fall in this category, probably because they are less African than the rest (my best guess). 
The high diversity of Mandinka and Yoruba in West Africa, as well as that of Maasai and Sandawe in East Africa, appears to indicate a strong retention of ancestral diversity from before the Out of Africa episode in spite of them being agro-pastoralist groups (except the Sandawe). This strongly suggests that Neolithic spread at least largely by cultural and not demic diffusion, respecting to a great extent the ancestral diversity that existed before the arrival of domestication technology: there was no population replacement at that stage surely, even if a later process in the Iron Age (Bantu expansion) may have been indeed largely a demic colonization instead. 

In general, most Tropical African populations fall to the right of the 45 degrees line: they are more diverse than expected and they rather seem to follow a 30 degrees line, if anything. On the other hand North Africans fall along a purely vertical reference line (unrelated to distance to Angola), so that 45 degrees reference line is a bit of an artifact and we are here instead before two different curves instead with a discontinuity between them. 

Final remarks

In brief: rather inconclusive and asking for more data (specially from the Upper Nile) and better, more clear, analysis that can confirm the conclusions a bit more strongly (if appropriate).

Still an interesting and informative paper that will no doubt be referred to in future publications. Also, on occasion, people ask for references that illustrate how Africans are more diverse than non-Africans... well, this is a good reference for that as well.

It is important in any case to expand and intensify our knowledge of African genetics so critical to understand Human genetics overall and so ill researched so far. In this sense, this paper is no doubt an important step forward and I do welcome it for all the information it provides.

March 4, 2011

California islands' settlement confirms coastal colonization of America

The finding of three settlements in Santa Rosa and San Miguel islands off the coast of California confirms a sea-oriented cultural context of the first settlers of America, including clear coastal navigation capabilities, as they must have crossed nothing less than 10 km of open sea to reach the island.

The peoples, who inhabited the island some 12,000 years ago, at the end of the Ice Age, also had technology that seems oriented to the exploitation of the marine resources, with a highly refined kind of workmanship, very different in any case to that of better known Clovis and Folsom cultures from the North American interior.

In spite of the fact that much of the places where these peoples lived are now underwater, the archaeologists were able to document the exploitation of varied sea resources. The quite unique crescent-shaped arrow projectiles, a special design for bird hunting, had been documented without context before in continental coasts but never in such amounts nor associated to so many bird bones.

Also, until now no reliable dates existed.

California Channel Islands locator (Wikimedia Commons)

Source: Science Daily (another version of the same story can be read at BBC, including a more complete photo of the toolkit).

March 3, 2011

Childhood and death in Neolithic and Bronze Age Iberia

The reference Andalusian archaeology blog Pileta de Prehistoria mentions these days two papers of at least some interest on infantile burials in Bronze Age La Mancha and in Neolithic Catalonia. Both papers are freely available online in PDF format, however they are, with the exception of the abstract, in Spanish language, what is surely an inconvenience for many readers. In any case:

The spectacular motilla (motte-and-bailey) of El Azuer was mentioned in this blog in December, in a post that I largely used to put these forts in their space-time context.

They are pretty much technical papers with a lot of details on inferred health and other bio details of the infants (and adults) buried in these sites.

Bronze Age La Mancha (El Azuer)

An interesting detail is for instance the presence of some burials in giant jar (pithos) in El Azuer, a Greek cultural borrowing that I thought until now as restricted to El Argar cultural area and that, in El Azuer, underlines how these fortifications of the Manchego semidesert belong fully to the Argarian political area, being probably in their time a marche of the more or less centralized state that must have controlled all SE Iberia from Castelló to Granada and that was strongly influenced (as is obvious in the pithos burial fashion) by Mycenaean Greece.

Nájera-Colino 2010 fig. 18

Above we can observe the mortality curve in El Azuer, expressed as percentage of all deceased people (solid line) and as percentage of death expectations per age segment (dashed line). Instead of absolute ages, age segments are used instead: Infantile I (age: 0-6), Infantile II (age: 6-12), juvenile, adult, mature and senile.

It is quite evident (and confirmed in text) that almost half of all deaths in El Azuer happened among children (49%), mostly very young children (inf. I). Only the mature segment (above 40?) reaches similar mortality ages. Even among survivors of what was without doubt a quite harsh childhood, most died without reaching old age. However they could expect to reach maturity if they had experienced puberty.

The main cause of death among children are infectious and parasitic diseases, stimulated by malnutrition. Diarrhea, still today one of the main causes of infantile death worldwide, is speculated to have been one of the main killers in El Azuer as well but illnesses proper of infancy are also considered, as they usually leave no markings in the skeleton. 44% of the children show signs of ill-health, often until their deaths. 

Impressive air view of El Azuer fortress (from the paper)

Nutritional aspects are analyzed specially in regards to children diet however the presence of several adults in the high protein segment (along with some breastfed children) is highly suggestive of some class differences. If we are to linearly interpret class from the amount of protein intake among adults (what makes some good sense, specially in a rather homogeneous site such as this fort), we can conclude from fig. 20 (page 92) that:
  • 21 adults belong to the low protein segment or low classes
  • 9 adults belong to the middle protein segment or middle classes
  • 5 adults belong to the high protein segment or upper classes
It is easy to imagine that the low classes were servants, the middle classes soldiers (or their wives) and the upper classes aristocrats but we do not know enough of Argarian (proto-Iberian) social structure to be certain.

Excluding the six infancy I deaths in the high protein segment, surely all being breastfed at the moment of their deaths, all other dead children under the age of 6 are females with low protein profiles, probably the malnourished daughters of servants. I count five of them.

Things are a bit more balanced in the infancy II (6-12 y.o.) segment, where most casualties belong to males (5, versus 2 females and 3 unknown) and in some cases to the middle and high protein segments (but all from phase III). Still the apportions are clearly unfavorable for the lower classes.

Detected pathologies are all restricted to infants and, excepting two toddlers, to the low protein segments. So it is easy to conclude that in El Azuer (and probably in all the Argarian area by extension) malnutrition, illness and early death were largely concentrated among the low classes.

Catalan Neolithic

Instead the Catalan (Neolithic) burials describe a quite different picture: only 23% of deaths belong to children (both segments plus perinatal), which is less than half the observed figure for El Azuer. On the other hand most people (46-51%) died in adulthood, with only 10% reaching maturity.

In Catalonia it is also notable the almost total absence of caries, with only one woman showing them in more than one piece and no infants having them at all. Instead several individuals show dental deformations indicating major malnutrition or illness, very possibly the cause of their deaths.

Besides, the populations of the lowlands and the highlands in Baix Llobregat  specifically show quite different nutritional profiles with the latter eating largely meat, allegedly from hunt, which still made a good deal of the diet in the hills.

Honey-colored flint cores (source)
In many cases the burials have valuable grave goods often imported from afar:  honey-colored flint from SE France, obsidian from the Central Mediterranean, jadeite from the Alps and locally extracted variscite. However the presence of grave goods varied a lot along time, being rare in the early Neolithic and increasing in the Chalcolithic (or late Neolithic). The honey-colored flint stone, often found in form of ready-to-work cores (which were imported that way from the mines) or large axes, underline the connections of Chalcolithic Catalonia with the once important Chassey culture (possibly of proto-Ligurian ethnicity), where this beautiful material had become extremely important in the socio-economical structure.

March 2, 2011

Tibetans are most related to Yi peoples

A new paper on Tibetan autosomal genetics holds some information relevant not just for Tibetans but for other East Asian and in general human peoples:

The generic place of Tibetans within Humankind

This is maybe the information of most generic interest, as it requires to map not just Tibetans and neighbors but also peoples from all over the world, notably Eurasia.

For this, figure 1 holds nearly all the relevant information. Some sub-graphs follow:

Above, the global Frappe structure results (A) place Tibetans clearly within East Asian populations (green) but show a distinctiveness of their own since K=6 (purple). In spite of sharing Y-DNA macro-haplogroup D with Japanese, Tibetans show no particular affinity with these (JPT).

In the East Asian specific results (B), at K=6, Tibetans again appear on their own, as do the other ethnic groups, except the Yi and Mongolians, who are subsumed within their neighbors to a great extent.

In the neighbor-joining phylogenetic tree (above), we can see that Tibetans again fall fully within the East Asian group (right fan). This structure is more interesting at this point for the global context anyhow because it can explain, for example, why in some cases West Eurasians and Africans may cluster together versus East Asians, depending on sampling conditions and probably the presence or absence of Indians (only some Pakistanis represent South Asia in this graph, as in so many others) as well as the numbers of sampled African (typically low because they are used as control only). If you draw a median line in this NJ tree, East Asians, in spite of their tight affinity with each other, fall to one half and West Eurasians and Africans fall to the other together.

Whatever this means, we can easily see that East Asians share an ancestral founder effect (including also Melanesians per previous research). However I must warn that this is more genuinely apparent in the HUGO consortium paper than here, because of the lack of Indian samples in this case. See here, here and here, for my own old entries in this matter (it is particularly clear in this graph).

By comparison only very homogeneous groups share such marked apparent founder effects, for example Europeans, West Africans, Pygmies, some (but not other) Indians. All these in the HUGO paper, in this paper instead, we can see again Europeans (but only represented by CEU, what is less meaningful), most Mozabites, most Bedouins, the other Levant populations (Palestinians, Druze and some Bedouins) and, very markedly, the Kalash.

However in the haploid genetic aspect East Asians do not seem so extremely "bottlenecked" as they do appear with autosomal genetics, not at all. In fact they host huge diversity within Eurasian haploid genetics. This is hard to explain, admittedly, but it clearly sends an alert signal for us to be extremely cautious and try to comprehend what really happened in this part of the World.

Tibetans are most closely related to the Yi

The term Yi (Nuoso in one of their languages, Lolo in Vietnam and Thailand) is a catchall term from Chinese ethnography to refer to an array of Tibeto-Burman-speaking peoples from Yunnan and nearby areas.

The close affinity between Tibetans and Yi in the context of East Asian populations is apparent when we apply the microscope, so to say, to the NJ tree (pictured above), as I did here:

It is easy to appreciate that, excluding the Mongol-Daur-Yakut loose group (suspect of minor West Eurasian admixture), the narrow East Asian founder effect split soon in three groups (of those shown here): Tibetans+Yi, the main group (Chinese, Cambodian and Lahu) and the Japanese - each of which diversified rapidly from those specific roots. 

However this result is not coincident with the HUGO consortium tree (different method: maximum likelihood), where Cambodians fall in a SE Asian specific group and Chinese in a distinct SEA/EA/America shared one. So, as always, be careful before rushing to conclusions based only on one paper's data.

High altitude genes have been selected among Tibetans

Here we have another of those rare cases of selective sweeps in humans: adaption to high altitude among Tibetans. Two genes have been found to produce this striking adaption to hypoxia and confirmed in this paper: EGLN1 and EPAS1. The authors suspect that other genes, notably ANGPT1, ECE1, and LEPR, are probably also involved in this adaption to such a demanding ecology. 

March 1, 2011

Paleo-Sardinian language: a relative of Basque?

Basque linguist J.M. Elexpuru discusses today at Noticias de Álava[es] the possibility that the lost pre-Romance language of Sardinia could be related to Basque, following the steps of Catalan linguist Eduardo Blasco Ferrer, who just published a book titled Paleosardo, le radici linguistiche de la Sardegna neolítica (Paleo-Sardinian, the linguistic roots of Neolithic Sardinia).

Ruins of a Sardinian nuraghe
Sardinia belonged to the Carthaginian Empire since the 6th century BCE and then passed to the Roman one in the 3rd century, remaining since then in the Romance linguistic area. However little is known of the history of the island before, except the famous nuraghe forts (similar to SE Spanish motillas) and that it was colonized (after some ill-known Epipaleolithic episode) within the Cardium Pottery culture in the Neolithic, probably from Central Italy.

However Dr. Elexpuru synthesizes this way the position of Blasco Ferrer:

... there was a migration from the Basque area in the Mesolithic (8000-5000 b.C.) which settled the island. There were surely other flows later on. Genetic research on mitochondrial DNA have revealed that haplogroup V, originary from the Basque-Cantabrian area, is very high in the central region. The language carried by the settlers, named Paleo-Sardinian by linguists, was the one spoken through all the Neolithic and Bronze Age in the island and still survived for some centuries to Roman domination in the central region, which was known as Barbaria. In some parts of the island the density of pre-Roman toponyms is well above 40%. 

He concludes mentioning some of the river and settlement names that are quite obviously Vasconic:  
  • River names: (h)aran, ardi, baso, berri, bide, ertz, goni (goi), gorri, iri, istil, iz, lats, lur, mando, on, orri, (h)osto, (h)otz, (h)obi, (i)turri, ur, zuri.
  • Village names: Aritzo, Ardaule, Asuni, Goni, Loiri, Luras, Olzai, Orgósolo, Ortueri, Osini, Turri, Ulassai, Uras, Uri, Urzulei...

I must say that all this would make better sense if Iberian and Ligurian could be somehow integrated in the picture. One reason is that haplogroup V is now known to be much more frequent and probably original not from the modern Basque Country nor even Gascony but from farther East: Catalonia probably. However now and again there are other rare or somewhat common lineages that appear shared between Iberia and/or the Basque Country and Sardinia (and sometimes also North Africa). 

One of the most common ones is Y-DNA I2a, a West Mediterranean and Pyrenean clade extremely common in Sardinia, which, if of Neolithic origin, would be the only such lineage quite frequent among Basques. But it could also be pre-Neolithic. 

Frequency of Y-DNA I2a, from Rootsi 2004

For the record, it was discussed  earlier in this blog (also here) the striking similitude of Basque and Sardinian (and some other European) carnival performances, all this in relation to the apparent paleo-European veneration of the bear and the continentally widespread shared root for this animal (hartz in Basque, almost the same in proto-Indoeuropean).

Also for the record I must mention that, in my not so humble opinion, the very word Sardinia seems to have a Basque etymology. Obviously it is derived from the pan-European word sardine but this term only makes etymological sense in Basque: sarda (fish school) + -gin (suffix of doing/making < egin) + -e/-a (nominative declension, like the article "the").  It needs of a loss of a syllabe (would make sardagina) but I still think it's plausible that sardine (and hence Sardinia) means school-doer or school-maker in Basque or a related language from old.

Whatever the case it is extremely difficult to deny the Basqueness of the toponyms listed above, even if I am sure that soon someone will come and contest such obviousness, based not on common sense but on twisted and ill-explained elaborations.

But what I still do not have fully clear is in which direction the Vasconic language spread. Of course the default hypothesis of an expansion from the Franco-Cantabrian region makes good sense but it is difficult to completely discard a Neolithic spread of the language family in the context of Cardium Pottery culture (and loosely related Atlantic ones, including Megalithism).

I also think that this Vasconic substrate is not something peculiar of Sardinia and that anyone who looks around with a keen eye and a half-decent knowledge of Basque language can't but stumble once and again on Basque-like toponimy all around the western half of the continent.

Article found via Ostraka Euskalduna[eu]

Basque language origins' 6th meeting: genetics and Basque origins

The 6th meeting of the Association of Basque Language Origins (Euskararen Jatorria Elkartea) will take place this May 7th at Gares, Navarre. Notably this gathering will have geneticists Stephen Oppenheimer and Antonio Arnaiz Villena as special guests.

Announcement and schedule are to be found at the blog Euskararen Jatorria (in Basque), but I'll reproduce the schedule here in English for the general interest:

9:30 Arrival, accreditation and book exposition
9:45 Welcome and presentation
10:00 Marian Martínez Pancorbo and Sergio Cardoso: Basque lineages speak of their past
10:45 Antonio Arnaiz: Basque genetics and linguistics: Iberian language in Veleia and Pamplona (in Spanish)
11:30 Break
11:45 Stephen Oppenheimer: the Origins of the British and the relevance for the Basque Country (in English)
12:30 Round table: the input of Genetics to understanding the origins of Basque language
14:15 Meal
17:00 Visit: Andelos, a Roman town and the Iberian script
18:30 Josu Naberan and Bienvenido Mascaray: the meaning of the sentences of 2nd century Andelos (in Basque)
19:00 200th birthday of Agosti Xaho: Aitor, the Cantabrian legend
19:30 Seberino Onaindia and Gabino Seijo: considerations on the Basque language (in Basque)
19:45 Last year of Iruña-Veleia in pictures. By Juan Martín Elexpuru, Dr. in Basque Philology and author of the book Iruña-Veleia euskarazko grafitoak (Iruña-Veleia: the Basque graffiti)
20:00 End of meeting

Cost: €45.00 (including meal and visit to Andelos), students and unemployed people: €30.00. 

Details of inscription at original post (in Basque).

Artistic impression of the two Europe-specific Y-DNA R1b major clades (details)

Selective sweeps lacking in human evolutionary history

There is a (quite mainstream) school in Genetics that just loves the idea of small genetic changes being so extremely adaptive that they quickly replace all or most other variants in frequency, clinging to fixation not by founder effect or drift but because of sheer adaptive power.

The followers of this school are plainly wrong. It was common sense before (I really never liked the idea at all: it's plain silly, overly simplistic, sensationalist, irrational) but now it has been reasonably demonstrated: selective sweeps are extremely rare in the human genome, while small, gradual, less important shifts, maybe in dynamic equilibrium... are the norm instead.

Full story at Science Daily.