January 31, 2013

Fundaments of curry found in Indus Valley Civilization

Turmeric (Curcuma longa)
(CC by J.M. Garg)
[Updated on Feb 8th, based on details arisen in the discussion, see comments]

While modern curry is an amalgamation of many influences some of its foundations may have been used already in the South Asian Chalcolithic and Bronze Age civilization (contemporary of ancient Egypt for example), known variedly as Indus Valley Civilization (IVC) or Harappan culture. 

Key curry ingredients, namely turmeric and ginger, have now been found in pot and cow teeth remains from the impressive South Asian first civilization, suggesting that the fundamentals of modern Indian cuisine were already there some 5000 years ago.

A carbonized garlic clover was also found. Garlic is another key component of curry.

An interesting revelation is that rice grains were among the findings, indicating that the farming of this oriental cereal had already reached India by c. 2500 BCE and was popular enough to make it not just to the modern rice-farming regions of East and South India but also as far as Pakistan.

Source: Slate (via Pileta).

Million years old human remains from Eritrea

Fragments of a human skull dated to some one million years ago have been found at Muhuli Amo, Eritrea. They are probably correlated with a previous finding of hundreds of Acheulean tools. 

The skull fragments found
Sources: The Archaeology Network, Pileta, Noticias de Prehistoria[es].

Maps of lamp usage in Paleolithic SW Europe

Illustration by Arturo Asensio
Decorating Altamira Cave
As I have briefly mentioned before David Sánchez has a most interesting series of articles (in Spanish language) these days, at his blog Noticias de Prehistoria - Prehistoria al Día, dealing with the usage of oil lamps in SW Europe (France, Iberian Peninsula) in the Upper Paleolithic. If you are familiar with Spanish language (or willing to use an online translator), you can read them at the following links: PART 1, PART 2 and PART 3 (update: part 4 is now also online).

To be most synthetic I will essentially borrow the excellent maps which shall give us a glimpse of the spread and time frame of this illumination fashion in the region:

Lamps found in France with chronology and type of site (Beaune & White 1993)
Lamps found in Iberia (by David Sánchez)

It must be mentioned, following the original articles, that the lamps of Iberia have all been found inside caves (while in France the locations are more diverse) and also nearly all them belong to the Magdalenian period. The exceptions are Bolinkoba (8), which is from a Solutrean chronology, La Trinidad de Ardales (1), which has no context, and a possible ill-documented lamp from Lezetxiki (14), originally argued to be of either Aurignacian or Mousterian context. 

Even if you don't understand Spanish, I would suggest to take a look at the original articles for the many illustrations of a varied array of lamps.

Native American gigantic mound was built in just 90 days

Map of the earthworks
The Poverty Point earthworks (Louisiana, USA), are a very large construction dated to c. 3200 years ago. Among the various parts of the impressive complex is Bird Mound, which spans 50,000 square meters and needed almost 300,000 cubic meters of earth to be built. 

This huge task was previously thought to have been accomplished in a long time, however new research of the layers indicates the opposite: that it was finished in just three months, what apparently required thousands of people passing baskets of earth in "bucket brigade" style.

"Given that a band of 25-30 people is considered quite large for most hunter-gatherer communities, it's truly amazing that this ancient society could bring together a group of nearly 10,000 people, find some way to feed them and get this mound built in a matter of months," Kidder says.

One caveat is that they surely were not "hunter-gatherers" but at least part-time farmers but it is still an impressive feat.

Source: Eureka Alert (via Pileta). 

Lineages of West Asia compared to Africa and Europe

Just a quick mention of this new paper on the matri- and partilineages of West Asia:

Danielle A. Badro et al., Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0054616]

Abstract

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Maybe most interesting is this map:

Figure 1. Geographic distribution of mtDNA haplogroups.
Frequencies distribution from the current study and from the published data [30], [31], [35][48] as reported in Table 1.

A very important issue with this map is that "Malians" and "Burkinabe" are actually Tuaregs from those countries (samples taken from Pereira 2010), hence their large fractions of Eurasian lineage H (H1 in fact). Also I am a bit perplex at the large portions of "other", which in the region considered can only be: L4, L5, L6 (all them small lineages from Africa and Yemen), R0(xH,V), N1, W, X and M1 (important in West Asia and some parts of Africa - I wonder why they are not listed on their own right) and maybe some other very rare lineages.

Regarding Y-DNA (and also largely mtDNA) the study focuses on statistical comparisons, not providing any comprehensive table nor map of haplogroup distribution. However for those interested in data mining the whole list of haplotypes (with purported haplogroup) of this study is available in table S2.

Horse genetics (autosomal DNA)

Barb horses
(CC by Notwist)
Yet another paper on horse genetics is available these days.

Jessica L. Petersen et al., Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0054997]

Abstract

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Regardless of what the authors claim, previous studies have suggested dual origins (steppes and local domestication at or near Iberia) or even multiple ones for modern horses and this paper's data does not say otherwise but actually reinforces this notion. For example let's have a look at their fig. 1 (duly annotated by me):



Ignoring by the moment the Latin American breeds, which stem directly from the root of the tree, the oldest division is between the Iberian breeds (Lusitano, Andalusian) and all others, which in turn split in two groups, both scattered in Europe and Asia (different parts of Asia however). This would seem to confirm the dual origins theory. 

However there are two more elements to consider: on one side the Northern Iberian breeds (apparently even older than the Southern ones, per Warmuth 2011) are not being considered here. 

The other element to ponder is the most strange position of the three Latin American breeds. As there were no horses in America at the arrival of Europeans, the origins of such anomaly must be in the Old World, meaning probably that these breeds retain genetics of even older populations. These could be the already mentioned Northern Iberian breeds but they are said to have some admixture from Berber horses (or Barb) as well and this population (argued to be very old) has not been subject to any genetic study as of now.

Hopefully future studies on the matter will consider these issues.

Statistical analysis of HVS-I (mtDNA) in Niger-Congo populations

Not sure that the paper has much interest but it affects a region with not too many studies and is open access so a brief mention may be appropriate.

Valeria Montano et al. The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation. BMC Evolutionary Biology 2013. Open accessLINK [doi:10.1186/1471-2148-13-24]

Abstract (provisional)

Background

When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study.

Results

By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas.

Conclusions

Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling. 


One of the problems I find to their approach is the use of only the deprecated HVS-I (control region) of the mtDNA, along with absolutely no list of inferred haplogroups (not even in the supplemental materials apparently). Based on just HVS-I data, then they proceed to make statistical analysis of all sorts, which may have some interest but is not my cup of tea, really. Maybe someone else may find use for this stuff however.

January 29, 2013

Technological revolution in African Acheulean some 800,000 years ago

Well, maybe the title is a bit of a hype but something like that seems to be the most relevant finding on the Acheulean of Konso (SNPP region, Ethiopia): that the technique stood the same for a million years and then, some 800,000 years ago, became more refined in which was apparently one of the first technological leaps of archaic Humankind. Specifically it is the edges of the handaxes (the archetypal Acheulean finding, which may have been more a knife of sorts than a true axe) which became more refined and apt for its cutting purpose.

Yoyas Beyene et al., The characteristics and chronology of the earliest Acheulean at Konso, Ethiopia. PNAS 2013. Open accessLINK [doi:10.1073/pnas.1221285110]

Abstract

The Acheulean technological tradition, characterized by a large (>10 cm) flake-based component, represents a significant technological advance over the Oldowan. Although stone tool assemblages attributed to the Acheulean have been reported from as early as circa 1.6–1.75 Ma, the characteristics of these earliest occurrences and comparisons with later assemblages have not been reported in detail. Here, we provide a newly established chronometric calibration for the Acheulean assemblages of the Konso Formation, southern Ethiopia, which span the time period ∼1.75 to <1.0 Ma. The earliest Konso Acheulean is chronologically indistinguishable from the assemblage recently published as the world’s earliest with an age of ∼1.75 Ma at Kokiselei, west of Lake Turkana, Kenya. This Konso assemblage is characterized by a combination of large picks and crude bifaces/unifaces made predominantly on large flake blanks. An increase in the number of flake scars was observed within the Konso Formation handaxe assemblages through time, but this was less so with picks. The Konso evidence suggests that both picks and handaxes were essential components of the Acheulean from its initial stages and that the two probably differed in function. The temporal refinement seen, especially in the handaxe forms at Konso, implies enhanced function through time, perhaps in processing carcasses with long and stable cutting edges. The documentation of the earliest Acheulean at ∼1.75 Ma in both northern Kenya and southern Ethiopia suggests that behavioral novelties were being established in a regional scale at that time, paralleling the emergence of Homo erectus-like hominid morphology.

Fig. 4. Handaxe refinement through time. Upper, dorsal; Lower, ventral.
From left to right, two each are shown from KGA6-A1 (∼1.75 Ma), KGA4-A2 (∼1.6 Ma), KGA12-A1 (∼1.25 Ma), and KGA20 (∼0.85 Ma). In each pair of handaxes from the respective sites, near-unifacial (left) and more extensively bifacial (right) examples are shown (except with the KGA20 handaxes, which are both well worked bifacially).

I am a bit intrigued by the all-covering work style of the last handaxes, which remind somewhat to the later MSA technology, which belongs already to Homo sapiens. Our species may have also evolved in that very area of the Nile Basin, with the oldest specimen known being from nearby Omo River.

Of course that there are hundreds of thousands of years in between and of course that the peculiar orography of the Rift Valley is susceptible of offering archaeological findings from old much more easily than other areas but still...


Other sources: Pileta, NBC News.



Update: much more than just the edges but a whole technological paradigm change:

I was not really appreciating the whole extent of the technological revolution implicit in these changes. I just took note (reading too fast, too many things to do) of the edge refinement but Va_Highlander has correctly called my attention on that it was a much more ample and complex change in the whole technology of stone flaking and not just the edges, maybe even a whole jump in our mental capacities:

In contradistinction to the >1.2-Ma assemblages, the younger ∼0.85-Ma Konso Acheulean is characterized by considerably refined handaxes. Some of these handaxes are refined to the extent that they would qualify as approaching “three-dimensional symmetry” (i.e., symmetric not only in plan view but also in cross-section form) (Fig. 4 and Fig. S2). Some suggest that manufacturing 3D symmetric tools is possible only with advanced mental imaging capacities and that such tools might have emerged in association with advanced spatial and navigational cognition, perhaps related to an enhanced mode of hunting adaptation. It has been pointed out that purposeful thinning of large bifacial tools is technologically difficult, even in modern human ethnographic settings. In modern humans, acquisition and transmission of such skills occur within a complex social context that enables sustained motivation during long-term (>5 y) practice and learning.
 

In light of the above information, it is of interest that our metric analysis shows that there may be a fundamental difference between the handaxe technologies of >1.2 and ∼0.85 Ma. Whereas refinement of handaxe shape did occur from ∼1.6 to ∼1.2 Ma, this refinement did not result in tool thinning and advanced 3D symmetry.

Whale remains reinforce the notion of Magdalenian being linked to sea mammal predation

First it was the whale bone spear point of Isturitz (Basque Country), then the isotope evidence of sea mammal based diet of a Magdalenian individual from Kendric Cave (Wales) and now direct evidence of whale remains in the cave of Nerja (Andalusia). The evidence mounts up for a quasi-Inuit lifestyle of at least some people of the Magdalenian culture of late Upper Paleolithic Europe.

Esteban Álvarez Fernández et al., Occurrence of whale barnacles in Nerja Cave (Málaga, Southern Spain): indirect evidence of whale consumption by humans in the Upper Magdalenian. Quaternary International 2013. Pay per viewLINK [doi:10.1016/j.quaint.2013.01.014]

Abstract

A total of 167 plates of two whale barnacle species (Tubicinella majorLamarck, 1802 and Cetopirus complanatus (Mörch, 1853)) have been found in the Upper Magdalenian layers of Nerja Cave, Mina Chamber (Maro, Málaga, southern Spain). This is the first occurrence of these species in a prehistoric site. Both species are specific to the southern right whale Eubalena australis, today endemic in the Southern Hemisphere. Because of Antarctic sea-ice expansion during the Last Glacial Period, these whales could have migrated to the Northern Hemisphere, and reached southern Spain. Whale barnacles indicate that maritime-oriented forager human groups found stranded whales on the coast and, because of the size and weight of the large bones, transported only certain pieces (skin, blubber and meat) to the caves where they were consumed.

The barnacles
According to the authors, this is the first case of consumption of whale meat and blubber ever documented in Europe. 

The hearth where the remains were found is dated to c. 14,000 years ago. 

Previous evidence from this prolific Andalusian cave have previously informed of consumption of seafood and fish, along with rabbits and the occasional goat, a tradition that dates to Neanderthal times in that region. 

A perplexing curiosity is that one of the whale kinds identified is the southern right whale, which was not known to have lived so far north at all (its main habitat is the Antarctic seas with some extension towards Brazil and the Mozambique Strait). I wonder if it is a case of misidentification and the species is either the North Atlantic right whale or an extinct relative of both.

Sources: Materia[es], Pileta[es].


PS- And what was the blubber used for (besides eating)? Our friend David Sánchez coincidentally just published two successive and quite interesting articles (in Spanish) at his blog on the lamps of the Upper Paleolithic: 1st part, 2nd part.

A particularly beautiful lamp from Lascaux (Dordogne)


Update (Jan 29): another finding of whale consumption in Magdalenian contexts unknown to me until now (h/t David) is from Las Caldas (Asturias). One of the two co-researchers is the same as the lead author of the Nerja paper → direct PDF link.


Update (Feb 22): David again added more interesting information on the matter of possible whaling in the Magdalenian period by pointing us to Colchón Rodríguez & Álvarez Fernández 2008, where they discuss (in Spanish) the presence of sea mammal remains in the cave of Las Caldas (Asturias): a seal tooth (pierced as to be part of a necklace or similar decoration), a pilot whale tooth (only initially worked), a sperm whale tooth (fully sculpted into low reliefs of whale and bison) and also several whale and other sea mammal bones used for tool-making (they made spear points on whale bone, as was documented years ago for Isturitz in the same period) and some mollusks, notably the shell of a whale barnacle (Coronula diadema).

Las Caldas (locator map) is some 20 Km. inland nowadays, in the Magdalenian period maybe 30 Km. or so. The whale barnacle suggests that whale meat was moved all that distance from the coast.

January 26, 2013

Epipaleolithic finds near Oxford, England

One of the arrowheads found
Archaeologists have found the remains of people living at Didcot (Oxfordshire, England) some 9000 years ago. Previous research had found Neolithic materials almost only but now a clear layer of hundreds of flint tools and weaponry and hearth remains has been unearthed and dated. 

January 23, 2013

Tianyuan, mtDNA B and the formation of Far Eastern peoples

The genetic study of the ancient man of Tianyuan is already online, as I commented yesterday in a quick update.

Qiaomei Fu et al., DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 2013. Open accessLINK [doi: 10.1073/pnas.1221359110]

Abstract

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Mitochondrial DNA

Part of fig. 1
And the old guy (or is it a woman?) happened to carry the matrilineage (mtDNA) B, more specifically B4'5, defined by a relatively long deleted block at positions 8281-8289 (this excludes B6 now linked with R11 and also the other relative of all them R24, see PhyloTree for details). However within B4'5 the lineage could not further be resolved within the modern haplogroups, so it is neither B4 nor B5 but a third branch of the same haplogroup. 

The authors actually talk of "haplogroup B" but they explicitly mention a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289) as well as a substitution at position 16,189, what makes it unmistakable B4'5 per the current PhyloTree build.

The tree to the right illustrates this fact, placing Tianyuan man's lineage hanging directly from the root of this haplogroup that, beyond reasonable doubt, coalesced somewhere in East Asia (probably SE Asia, with Laos and Hainan being good references judging on diversity) some time before this person lived and died near what today is Beijing. 

What does it tell us? Really nothing new, at least within the parameters I have been managing: it confirms that the expansion of mtDNA B4'5 was already happening back in that time and that it had reached more or less its current area of expansion in East Asia (American and Oceanian B variants expanded later, of course). It also implies that its ancestors R and N, which experienced important successive expansions in the course of the colonization of Eurasia by our species had expanded  at an even earlier date (again nothing new to me but a nice confirmation anyhow).

On the other hand, this person's particular matrilineage went eventually extinct later on. This again does not tell us too much because it is something to expect with the course of time, especially at low population densities, as was the case in the Paleolithic. He can still be ancestral to modern peoples in the area and elsewhere but not by a purely mother-to-daughter line - at least not that we know. 


Chromosome 21 autosomal DNA

Because of the poor state of the DNA, the researchers had a difficult time sequencing it (technical details in the paper), however they managed to reconstruct a good deal of chromosome 21, which they used to compare with modern humans and also with Neanderthals and the so-called Denisovans

The result places Tianyuan closer to modern Far Eastern populations than to the rest of modern humans. This clearly indicates that the process of division in various more or less homogeneous subcontinental-sized populations was already somewhat advanced. 

Fig. 2. Maximum-likelihood tree relating the chromosome 21 sequences of the Tianyuan individual, 11 present-day humans, and the Denisovan genome. The most strongly supported gene-flow event is shown in yellow. Bootstrap support for all internal edges is 100% except for the edge putting Tianyuan outside the four Asians, which is 31%. The scale bar shows 10 times the average standard error of the entries in the covariance matrix.

While it is generally acknowledged that Papuans cluster at very deep level with East Asians, the authors are not fully persuaded of the exactitude of this tree, particularly in this aspect. They declare:

We note, however, that the relationship of the Tianyuan and Papuan individuals is not resolved (bootstrap support 31%). Further work is necessary to clarify whether this reflects the age of the Tianyuan individual relative to the divergence between modern human populations.

The caveat is particularly relevant because the colonization of New Guinea is at least as old as 49,000 years ago, some ten millennia before Tianyuan, what does not fit too well with the tree at that level of detail, assuming (as I do) that modern Papuans are direct unmixed descendants of those early settlers. Papuans do carry at high frequencies a related matrilineage (P also basal descendant from R) but that is also true of modern Europeans and they appear more distant in the tree above.

A good contrast to understand better the difficulties in getting a good picture from autosomal DNA, especially one so old, is table 1:


Here we can appreciate the differences and proximities by another measure. The closest compared modern person to Tianyuan man is a Karitiana, followed closely by the Han and, surprisingly, by the Sardinian and the French, and only then the Dai and Papuan. 

The distance of the Karitiana to Tianyuan man is still greater than that with not just the Han or the Dai but also the Europeans. However this can be argued to be because Native Americans must have a deep dual East Asian and West Eurasian origin, the latter via Altai (Y-DNA Q, mtDNA X2).

Let's check the Han then, who are not believed to have any meaningful West Eurasian admixture. Curiously the paradox happens again: the Han is somewhat closer to Europeans by this measure than to Tianyuan, and even their comparison with the Papuan shows up slightly less differentiated. 

This is admittedly harder to explain but we can conclude that either (a) this method can only grasp affinity/divergence to some degree or (b) that the Tianyuan partial genome indicates a very preliminary level of continental differentiation. Or (c) both. Of course time is the main cause of genetic differentiation and by no means we can imagine that such an ancient individual would be too similar to his modern plausible descendants but, on the other hand, all (including Tianyuan mtDNA) indicates that the process of continental differentiation was already well developed 40,000 years ago (most European ancestry must come from people living in Europe or West Asia back then) so we can either blame subtle flows like Siberian migrations that have kept both genetic pools somewhat closer than in pure isolation or we must assume that the measure is not too exact.



Admixture with other human species

The paper also deals with Denisovan and Neanderthal admixture, finding that Tianyuan man was within the modern range for both parameters in East Asia. 

This is very important because it ratifies the mainstream model of two minor admixture episodes: (1) with Neanderthals at the exit from Africa and prior to the Great Eurasian Expansion (so all non-Africans, including Tianyuan man, have very similar levels of Neanderthal admixture today) and (2) with a relative of Denisovans (Homo erectus?) maybe in Indonesia affecting only (or almost only) the aboriginal peoples of Oceania (and Filipino Negritos but not the other so-called Negritos from Malaysia or the Andaman, who are not particularly related anyhow).

(As a side note notice that the Denisovan-like gene flow into Papuans in fig. 2 appears to hang not from the end of the branch but from a very high position, suggesting it was a relative and not the known Denisovans of Altai themselves who became admixed into Papuans and other Oceanian populations, probably a relative living in the route to Australasia).


Update: Marnie just published a mention of a previous work on Tianyuan 1, which focuses on the isotopic evidence for a fish-based diet. 

January 21, 2013

Ancient North Chinese from 40,000 years ago closely related to modern locals

Tianyuan Cave (source)
The information is sketchy as of now but the news in the press indicate that an Homo sapiens from Tianyuan Cave, near Beijing, whose fragmented remains were discovered in 2003, was closely related to modern East Asians and Native Americans. 

The paper is not yet online but the information released to the media strongly suggests that East Asians were already distinct from other populations some 40,000 years ago. This would seem to be based on the sequencing of the mitochondrial DNA and the explicit mention of Native Americans indicates that the lineage must be A, B, C or D (X, the fifth and less common matrilineage of Native Americans, is not found in East Asians, with some exceptions from Siberia, so we can exclude it safely). 

Ancient DNA from cell nuclei and maternally inherited mitochondria indicates that this individual belonged to a population that eventually gave rise to many present-day Asians and Native Americans, says a team led by Qiaomei Fu and Svante Pääbo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

This would seem to discard some adventurous hypothesis floating around about tremendous demographic changes in the Paleolithic and afterwards, at least for this region. Probably not even when "mode 4" technology arrived to the region (from Altai) c. 30,000 years ago. 

In other words: the seeds of modern populations were already there c. 40,000 years ago in East Asia (and surely also in most other regions) and, even if they may have changed somewhat, they have remained the same at least to some notable degree.

Furthermore, the autosomal DNA also seems to have been sequenced to at least some degree because the researchers state that Denisovan and Neanderthal genetic inputs are at the same levels as modern North Chinese (i.e. some 0% and 2.5% respectively):

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003, carries roughly the same small proportions of Neandertal and Denisovan genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

Or in the words of the Max Plank Institute:

The genetic profile reveals that this early modern human was related to the ancestors of many present-day Asians and Native Americans but had already diverged genetically from the ancestors of present-day Europeans. In addition, the Tianyuan individual did not carry a larger proportion of Neanderthal or Denisovan DNA than present-day people in the region.

This also seems to discard models implying Denisovan admixture happening in Siberia or NE Asia and would indirectly support my own hypothesis of admixture with Homo erectus (for which Denisovans, plausibly an Erectus-Neanderthal hybrid, would be just a proxy) in or near Indonesia.

Sources: Science News, Max Plank Institute.


Update (Jan 22): the paper is already online and is open access (cool!)  I don't think I have time to discuss it today but will do tomorrow without doubt (other than the sky falls on my head, you know).

January 19, 2013

Y-DNA of Moldovans

Moldova is the easternmost generally recognized sovereign state in Europe speaking a Romance language. Achieving its independence from the Soviet Union in 1991, Moldova saw part of its territory segregated in the mostly unrecognized Republic of Transistria (multiethnic, under military control of Russia). There was some talk about joining the related Republic of Romania but this plan seems to have been abandoned for now.

Alexander Varzari et al., Paleo-Balkan and Slavic Contributions to the Genetic Pool of Moldavians: Insights from the Y Chromosome. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0053731]

Abstract

Moldova has a rich historical and cultural heritage, which may be reflected in the current genetic makeup of its population. To date, no comprehensive studies exist about the population genetic structure of modern Moldavians. To bridge this gap with respect to paternal lineages, we analyzed 37 binary and 17 multiallelic (STRs) polymorphisms on the non-recombining portion of the Y chromosome in 125 Moldavian males. In addition, 53 Ukrainians from eastern Moldova and 54 Romanians from the neighboring eastern Romania were typed using the same set of markers. In Moldavians, 19 Y chromosome haplogroups were identified, the most common being I-M423 (20.8%), R-M17* (17.6%), R-M458 (12.8%), E-v13 (8.8%), R-M269* and R-M412* (both 7.2%). In Romanians, 14 haplogroups were found including I-M423 (40.7%), R-M17* (16.7%), R-M405 (7.4%), E-v13 and R-M412* (both 5.6%). In Ukrainians, 13 haplogroups were identified including R-M17 (34.0%), I-M423 (20.8%), R-M269* (9.4%), N-M178, R-M458 and R-M73 (each 5.7%). Our results show that a significant majority of the Moldavian paternal gene pool belongs to eastern/central European and Balkan/eastern Mediterranean Y lineages. Phylogenetic and AMOVA analyses based on Y-STR loci also revealed that Moldavians are close to both eastern/central European and Balkan-Carpathian populations. The data correlate well with historical accounts and geographical location of the region and thus allow to hypothesize that extant Moldavian paternal genetic lineages arose from extensive recent admixture between genetically autochthonous populations of the Balkan-Carpathian zone and neighboring Slavic groups.

Most interesting is without doubt the list of haplogroups:

Table 2 - Kharahasani is located to the South and Sofia to the North, the Romanian and Ukranian samples are both from nearby regions (Romanian Moldavia and Transistrian Ukranians).

My notes (see ISOGG for nomenclature):
  • The high diversity of haplogroup I (also in nearby Romania and Ukraine), including I1-M253, I2a1b-M423 and I2a2-M223 is consistent with the wider region being, arguably, ancestral to this lineage. However "Low Germanic" I2b does not show up, as doesn't "West Mediterranean" I2a1a nor Anatolian-Caucasian I2a*.
  • Among Neolithic-specific inputs, which are particularly important in the Balcans, Moldovans show notable (13%) presence of E1b1b1a1-M78 variants, especially the well studied E1b1b1a1b-V13, related now even by ancient DNA to European Neolithic flows. They also have some (2%) E1b1b1b2a-M123, an Eastern and NE African lineage found at low frequencies in Southern Europe.
  • Another clearly Neolithic lineage is G2a-P15, found among Moldovans only at very low frequencies (more common in the context of the Mediterranean Neolithic it seems).
  • Not yet documented by aDNA but also likely Neolithic in Europe is haplogroup J, found in Europe mostly as J2 (originating in Highland West Asia) but also, mostly in the Balcans, as J1 (originating maybe in Palestine). Moldovans show both at low frequencies (4% each).
  • Almost all the rest belongs to the largest European clade, R, mostly its Eastern variant R1a1a-M17 (30%). Western R1b1a2-M269 makes up 16%. 
  • Minor clades are H (Romani), T (South and West Asian, with extensions into East Africa and, thinly, in Europe), N (NE European and North Asian) and Q (probably from West Asia).
In the PC analysis (fig. 2, not shown) Moldovans appear intermediate between Balcanic and Central-Eastern European populations but rather leaning towards the latter.

In spite of their historical and ethno-linguistic connection Romanians and Moldavians do not appear to be particularly related in the genetic aspect:

The genetic relationship between Moldavians and Romanians deserves special attention, since these two groups speak practically the same language and share many cultural features. It is reasonable to assume that Moldavians and Romanians inherited genetic lineages, shared with other Balkan populations, from Vlachs who, in turn, received them from Paleo-Balkan tribes. However, Moldavians and Romanians do not form a cluster that would have separated them from the neighboring populations. Indeed, in the space of multi-dimensional scaling based on the RST distances between STR haplotypes, Romanian populations appeared scattered among the Balkan populations and did not cluster with the Moldavians (Figure 3). According to the AMOVA analysis, the degree of within-group differentiation among Moldavian and Romanian populations was significantly greater than genetic differences between either Romanians or Moldavians and the group comprised of the Balkan populations (Table 3). Moldavians and Romanians also appear dissimilar on the diagram of binary lineages (PC plot, Figure 2). Thus, sharing nearly the same language is not accompanied by specific genetic similarity between Moldavians and Romanians. Furthermore, Italian populations that share the Romance/Latin language with Moldavians and Romanians, show little genetic similarity with them. These results agree with previous genetic studies suggesting that the genetic landscape of southeast Europe had been formed long before the modern linguistic/ethnic landscape was shaped [16], [48].

Instead the genetic affinities of Moldovans lean strongly towards their Slavic neighbors from Eastern and Central Europe:

In contrast to Romanians and most other Balkan populations, Moldavians show a clear genetic similarity to western and eastern Slavs. This is strongly implied by haplogroup R-M17, which dominates the paternal lineages of the Slavs and is broadly represented in Moldavians. (...)
The noteworthy domination of R-M17 chromosomes in Moldavians compared to Romanians is due to the R-M458 subclade. Haplogroup R-M458 likely has its roots in western/northern Poland, where it has its greatest modern concentration and microsatellite diversity [49].

This supports my impression of R1a1a1b1a1-M458 being not spread by Slavic migrations (it is very rare among Balcanic Slavs but has an notable presence in Greek Macedonia instead) but much earlier, plausibly by Indoeuropean migrations which had a major sub-center in Poland in the Chalcolithic period.

Mitochondrial DNA of some Slavic peoples

With emphasis on haplogroup H5 and H6.

Marta Mielnik-Sikorska et al., The History of Slavs Inferred from Complete Mitochondrial Genome Sequences. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0054360]

Most interesting is maybe table 1 (right), which lists two Polish populations (Kashubia, at the Baltic coast, and Podhale: the Carpathian piedmont), Ukrainians and Czechs.

We can see here that the most common lineages among these Slavs are not different from other European populations, namely H*, H1, U5a, U5b and also the, arguably Neolithic, lineages J1 and T2. I find relevant in this sense that there is a significant amount of T(xT1,T2) among Kashubian Polish especially.

Another point of interest is the minor presence of North and Central Asian lineages A, C, D and G, for which the authors present an elaborate rationale:

... we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1).

They also suggest that the L2a1l2a, found among the Polish, is of Ashkenazi Jewish origin. L1b1a8 found in Polish and Russians belongs to the wider L1b1a, recently argued to be European-specific.

Another point of notice may be the rare HV0(xV) found at significant frequencies among Ukranians (4.5%).

But the authors make a particular effort to discern within haplogroups H5 and H6, which they find of particular interest. H5 might be (with doubts) of Italian origin and they consider its coalescence age (on the dubious molecular clock estimate methods) as clearly pre-Neolithic.

Based on these speculative methods they argue that several Slavic-specific clades within H5 may be contemporary in origin with U4a2, common in Central and Eastern Europe. They consider both to be roughly from Early Neolithic times.

Figure 1. Complete mtDNA phylogenetic tree of haplogroup H5.
Legend:
Green: Polish, Czech, Slovaks, Ukrainians and Russians
Red: German, Dutch and Austrians
Yellow: Italians and Spaniards
Blue: Irish, British, Danes and Finns
Magenta: Tunisia
→ Black: Levant
Grey: USA
White: unknown geography
If they are correct in their interpretation of the tempo of H5, the hypothesis of H sublineages migrating Northwards, from Southern to Central Europe, within Neolithic would seem to gain some support.

However H5 is less common in the Czech Republic and Austria than in Poland or Ukraine and the Neolithic colonization of Poland should have gone via the Czech Republic and, previously, Austria. Of course we cannot reject upfront a founder effect specific to Poland but what about Ukraine, which was almost totally oblivious to the Balcano-Danubian Neolithic phenomenon?

The other focus is H6, which is found almost only among Ukranian and Czechs of the four target populations. Generally speaking H6a and the most rare H6c are European, while H6b is Central and West Asian. In spite of its extreme rarity, the authors detected H6c in three individuals (one Czech, one Pole and one Slovak), all non-Slavic H6c are from Central-West or NW Europe (or from unknown locations). This seems to define H6c as a rare Northern-Central European haplogroup (excluding Eastern Europe apparently).

The remaining H6 samples sequenced in our study belong to different H6a subclusters being identified as singletons (H6a1a*) or as members of subclusters H6a1a4, H6a1a9 and H6a1b3. Subcluster H6a1a9 is novel, comprising of two haplotypes found in Russians and Ukrainians. Subcluster H6a1b3 is also interesting because it contains, except for European individuals of unknown origin, a founder haplotype of Czech origin and two Polish haplotypes.

Figure 2. Complete mtDNA phylogenetic tree of haplogroup H6 (legend as above).

L0k lineages found in Zambia

Only the abstract is available to me as of now:

Chiara Barbieri et al., Ancient Substructure in Early mtDNA Lineages of Southern Africa. AJHG 2013. Pay per view (6 month embargo, then freely accessible) → LINK [doi:10.1016/j.ajhg.2012.12.010]

Abstract

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

See also at my old discontinued blog Leherensuge:

Notice from these last that both L0k and L0d have minor presence in Arabia (L0k2 in Yemen, and now it seems also in Zambia, and L0d3, shared between Khoisan and Kuwaitis).

January 17, 2013

Very skeptic on claim of Neolithic flow from India to Australia

I feel quite skeptic about the claims held by this paper but in any case it is worth mentioning.

Irina Pugach et al., Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 2013. Pay per view (6-month embargo, then freely accessible) → LINK [10.1073/pnas.1211927110 ]

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India. 

The evidence for this claim is all derived exclusively by statistical inference on autosomal DNA. Suspiciously enough, even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration. 

Additionally c. 4000 years ago Southern India, the alleged origin of the genetic flow, was already immersed in a flourishing agricultural economy and it looks very strange that the migrants, people who were exchanging crops with Africa for example, would not carry a single element of this new economy to the island continent. Of course this inconsistency could easily be fixed by merely arguing that the molecular clock estimates used tick too quickly, which is a general problem anyhow and therefore no real surprise.

If the hypothesized migration happened earlier, in the Epipaleolithic or Late Upper Paleolithic, then it would also be easier to explain that, with smaller populations, genetic drift could have caused the extinction of whatever Indian uniparental markers that the migrants carried with them initially. It still causes my eyebrows to rise instinctively. 

Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists. 

The only techno-cultural burden that the migrants might have brought with them to Australia would therefore have been the dingo, but this dog has lots of relatives in Island SE Asia, where the authors could not detect any significant Indian admixture.

So the hypothesis looks weak to me. Let's see the evidence they present:



Above we can see the ADMIXTURE K=4 result, probably not the optimal one (which would probably produce an Australian-specific cluster (mostly but not fully masked as Papuan) and surely two different Indian ones, partly masked as European and Onge affinity) but the one the authors decided to show us as evidence for their hypothesis.

Not only this is surely not the optimal clustering level but also Australian Aborigines are comparatively undersampled, while Indian weight is overwhelming. This is a clear example of how NOT to design a scientifically useful sampling strategy for ADMIXTURE-like comparisons like this (because oversampled populations tend to overshadow the rest just by the weight of numbers). 

As it is, this graph proves nothing but rather suggests that some Indian affinity is part of Australian Aborigine ancestral or founder specificity, when compared with Papuans. This may have many explanations first of which is a mere artifact by reason of a poor sampling and depth design of the experiment. ADMIXTURE is a powerful neutral tool, just a like a test tube or the Geneva particle accelerator, but what we do with it may well not be neutral, either by reason of mischievous manipulation or mere error.

In this case I find the test very poorly designed and executed. If I have some time later in the weekend, I may try to perform an alternative test according to my humble possibilities - I promise nothing however.

A complementary test that the authors perform used Tree Mix. As I have discussed elsewhere, TreeMix often produces very strange results and I do not consider it a reliable tool at all, but for whatever is worth here it is what they got:



While the purported migrations generated by the Tree Mix algorithm appear to suggest a secondary genetic flow from India to Australia (orange arrow at C) the data on which such result is based (D) only gives the most tenuous level (green) of extra genetic affinity between Southern Indians (DRA) and Australian Aborigines (AUA). Meanwhile the highly questionable algorithm identifies Dravidians and North Chinese (CHB) as being genetically very close (blue), when they are not in fact.

So what do I get from this paper? TreeMix' usual senseless noise and apparent mismanagement of ADMIXTURE, a powerful tool when used properly.

Less than inconclusive, I'd say. But your take of course.


Update: G Horvat (see comments) points me to Kumar 2009 (so far unchallenged at PhyloTree)  for a shared mitochondrial lineage between Australia and India, known as M42. This haplogroup has the following structure (each → indicates a coding region mutation according to PhyloTree, Kumar originally listed a few more):

    • → M42'74 
      • → M42 
        • →→→→ M42a (Australian Aborigines)
        • → M42b (India)
      • →→ M74 (South China, Vietnam, India)
This allows for a potential mtDNA backing of this purported connection, however it is a very small lineage and Kumar claimed that M42 coalesced long ago, in the context of the first colonization of Asia and Australasia by Homo sapiens:

The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. 

Yet the relatively long stem leading to M42a does allow for a later time-frame of arrival to Australia. Neolithic anyhow looks still most unlikely to me.


Update (Jan 18): Dingo DNA:

An important element to consider here are the origins of the dingo as the Australian wild dog is known. This dog variant suffered a strong founder effect upon arrival to Australia described mainly by two variants of the haplotype A29. This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia (either Indochina or China or both).

It is clearly not related to Austronesian expansion and could have arrived either within the early Neolithic of ISEA (arguably Austroasiatic in language) or even earlier. At least one of the papers I checked rather supports a pre-Neolithic introduction and certainly before the archaeologically supported age of c. 3000 years ago.

The Y-DNA of dingos also shows a strong founder effect (only two haplotypes, with overlapping but distinct distributions) and again the most obvious connections seem to be in SE Asia.

See (freely accessible):

Update (Jan 18): It is probably interesting also to mention that Australian Aborigines show no difference with Papuans in their overall amount of Denisovan ancestry. This also appears as contradictory with the idea of significant external admixture, which should have diluted at least minimally that Denisovan component (Indians have none).


Update (Apr 7): A new "working paper" has been published on this matter, sharing my critical stand towards the sloppiness of Puhach's team but still considering plausible a Holocene gene flow from India. I have commented in a new entry.

    Puctuated equilibrium, speciation and everything else

    I believe it is worth recommending the reading of this new review paper which discusses the various evolutionary theories en vogue, with emphasis in punctuated equilibrium, which is surely a very realistic model:

    Jaroslav Fregg, Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution. Biology Direct 2013. Open accessLINK [doi:10.1186/1745-6150-8-1]

    Abstract

    Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.

    Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation -- while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.

    The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.


    I don't dare to evaluate the paper but I do recommend reading it because it can help us to better understand what is going on when we talk of speciation, competition, evolution, dynamic equilibrium, etc. I picked up this quote:

    Approximately 35% of the substitutions (20-70%, depending on the studied taxon) was shown to occur in brief periods of speciation. It is worth mentioning that we are not aware of how many speciation events actually occur in the studied, seemingly unbranched lineages. Therefore, the published estimates of speciation associated substitution rates represent only the lower margin of the real figures.

    And the only figure, which illustrates how a highly diverse population/species can be stable and how evolution can happen and often does in bottlenecks instead:

    Most punctuational theories of evolution, including the evolutionary conceptions of Wright, Mayr, Carson, Templeton and Flegr (for comparison see Table 1), suggest that sexually reproducing species respond evolutionarily to selection (are evolutionarily plastic) only during speciation. The mechanisms of this type of evolutionary behavior of sexual species suggested by the various theories differ, for a review see [1]. For example, the genetic revolution model [2] implicitly and the frozen plasticity theory explicitly [3] suggest that a species is evolutionary plastic when its members are genetically uniform, i.e. only after a portion of the original species has split off, skirted extinction for several generations, and then undergone rapid multiplication (Figure 1).


    The paper uses the "open review" format, including commentaries from the reviewers and the replies by the author - this I find an interesting novelty which adds some value to the paper by pointing possible avenues for discussion or further research.