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Monthly Archives: March 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)
 
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Posted by on March 12, 2011 in Central Asia, population genetics, Siberia, Y-DNA

 

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.
 
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Posted by on March 12, 2011 in Chalcolithic, Ireland, Iron Age, Neolithic, UK

 

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:

Abstract

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.  

 

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.
 
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Posted by on March 11, 2011 in dolphin, Genetics, human evolution, 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.
 

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.
Braaains!
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.
 
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Posted by on March 10, 2011 in Genetics, human evolution

 

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).

Components

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.

Diversity

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.