Monthly Archives: January 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

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). 

Posted by on January 31, 2013 in America, Native Americans, USA


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]


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.
Leave a comment

Posted by on January 31, 2013 in African genetics, mtDNA, West Asia, West Eurasia, Y-DNA


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]


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.

Leave a comment

Posted by on January 31, 2013 in horse genetics


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)


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.


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.


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.

Posted by on January 31, 2013 in Africa, African genetics, mtDNA