Cow lineages in Europe, Africa and creole America

Another paper on bovine mtDNA adds important information to better understand the major matrilineage of domestic bovine cattle: haplogroup T1.

Silvia Bonfiglio, Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1. PLoS ONE 2012. Open access.

Importantly, Bonfiglio made a significant effort in sampling Egyptian and Ethiopian cattle, as well as some Latin American breeds. Not a single haplogroup outside of T1 was found, unlike in Europe where P, Q and R lineages do exist, suggesting some level of hybridization with wild aurochsen. There is however some uncertainty as for the exact phylogeny of haplogroups T1e (European) and T1f (Euro-Egyptian), which could also be branches of T1'2'3, as illustrated in fig. 1:

click to expand

The authors conclude that, soon after domestication in West Asia, bovine cattle spread to both Europe and Africa, where experienced secondary expansions, as evidenced by at least one lineage (T1d) looking East African by origin. 

That is also probably the case of T1c (Euro-Egyptian but more diverse in Egypt) and T1b (also most basally diverse in Egypt), which is the origin of the African-derived American "AA" haplotype of Paraguayan cattle, which is within this lineage.

Dated to 15,000 BP or older (source)

Update(Jun 10): There is abundant evidence in form of rock art and some remains at Jebel Uweinat, Qurta and Wadi Qubaniya supporting presence of wild taurine cattle in NE Africa since at least 15,000 BP. This allows for a possible semi-independent domestication event in Africa for bovids (h/t to Marnie).

See also:

• Category bovine genetics.
• A. Beja-Pereira et al., The origin of European cattle: Evidence from modern and ancient DNA. PNAS 2006.

Mitochondrial DNA H found in Epipaleolithic Basques (and Greeks?)

Definitely the spread of mtDNA H in Europe is older than Neolithic.

First we had the reports on abundant mtDNA H in Upper Paleolithic Morocco and Epipaleolithic Portugal, based only on HVS-I, what is admittedly confusing, and never properly published either one. All this was used by the gurus of Neolithic replacement to deny them any validity at all.

However, a few weeks ago we got notice of a study that found mtDNA H in two caves of Cantabria, dated to the Magdalenian period. That alone should have put the Neolithic replacement theory to rest but, of course, faith is blind and irrational, and some seem to be grasping for the proverbial straws... even if themselves do not know which are or where can those imaginary straws be found.

Reality checks sometimes do hurt, I know.

For whatever doubts that may still persist, today I have got notice (h/t Jean) of yet another paper that found mtDNA H in pre-Neolithic europeans. In this case in proto-Basques from Western Gipuzkoa and, less clearly, proto-Greeks from Argolid.

Marie Lacan, La Néolithisation du bassin méditerranéen: Apports de l'ADN ancien. Doctoral thesis (Biologie, Santé, Biotechnologies (BSB)), 2011. Freely accessible as PDF (in French language only).

Dr. Lacan (I really hope she earned her gallons with this quite impressive paper) first ponders in a quite balanced manner on the issues surrounding the Neolithic colonization of Europe on light of modern and ancient DNA. Then, she goes straight to solve the problem by properly testing several individuals from several Epipaleolithic caves from Southern Europe.

That direct and ambitious approach pays off:

The ages of the conclusive results are:

• Linazeta cave, dated to 6230-6100 cal. BCE (more than 1000 years before any Neolithic), Deba, Gipuzkoa (more info in this paper) - H(xH1, H3)
• Franchthi cave, Koilada, Argolis (dates from final Mesolithic to final Neolithic) - H(xH1,H3). 

The dates of Franchthi are inconclusive but in the case of Linazeta it is most clear. Specially if we add to it the recent findings in Cantabria (two individuals from two different Magdalenian sites) and the previous, less conclusive, findings in Portugal and Morocco. 

The conclusion can't be more clear: in SW Europe at least, mitochondrial haplogroup H existed since at least Magdalenian times.

Also the authors tested two individuals from Santimamiñe cave, a site in Biscay with deep roots dating to the Gravettian culture and showing continuity of use until the Iron Age. This site is of particular importance to me personally because my paternal family comes from just a few kilometers away from there. These are also the oldest DNA sequences from Biscay, however they are already from the Neolithic period (c. 4000 BCE):

This, together with the Paternabidea findings, would confirm that Basques appear to have matrilineal continuity since at least the Neolithic, however this conclusion loses some relevance on light that this continuity now appears to have even deeper roots, into the Epipaleolithic at the very least, in line with the classical archaeological interpretations. 

Many details have yet to be unraveled but we can certainly conclude that the coffin of the Neolithic replacement theory has all the nails in it and is more than ready for  formal burial.

Another site dealt with in this ambitious paper is the Dolmen of Pierre Fitte, near Paris, dated to c. 2750 BCE (Seine-Oise-Marne culture, a local variant of both Danubian and Megalithic influences), which shows haplogroups K and K1 (HVS-I only) and Y-DNA I2a1 (two individuals).

The paper also discusses in some depth the previously researched necropolis of Treilles and L'Avellaner in the Mediterranean side of the region and quite clearly of likely trans-Mediterranean origins, a component of Neolithic arrival that nowadays is less important even if it has indeed persisted as minority element. 

See also: category ancient DNA (aDNA) and category European origins.

H. pylori also made it out of Africa

In our guts.

Out of Africa and back (to some extent) and also again out of Africa into West Eurasia where it mixed with the Eurasian component. All of which is identifiable also in more specifically human markers like Y-DNA or mtDNA.

Yoshan Moodley et al., Age of the Association between Helicobacter pylori and Man. PLoS Pathogens 2012. Open access.

Ethio Helix has an extensive review of the entry so I'll be most succinct here.

There are more nice images in the paper but this one above probably expresses it all:

• Hp Africa 2 is found among Southern African natives (Khoisan)
• Hp Africa 1 is found among West Africans and Bantus (with some penetration in the Khoisan stomachs)
• Hp NE Africa is found at the Middle and Upper Nile and Lake Chad
• Hp Europe is found also in West Asia and North Africa and shows clear signs of being a hybrid of NE Africa and Asia2 (so it's phylogenetic position is a blend of its parents')
• Hp Asia2 is from South Asia
• Hp East Asia and Hp Sahul (Australasia) need no further explanation

My main contempt is the insistence on unrealistic molecular-clock-o-logic age estimates, which are clearly miscalibrated because the migration out of Africa took place some 90-80 thousand years ago at the latest and not 55 Ka ago as they suggest with basis. Otherwise the pattern of flows must be as they described... but add at least 50% to all age mis-estimates to make sense:

It is interesting that no exogenous lineage from Neanderthals nor Erectus/Denisovans have been identified. Did we have sex but shared no saliva? Hmmm...

Review of Tropical Neolithic flows

Michael Petraglia at Ancient Indian Ocean Corridors blog draws our attention to a quite interesting review on the Neolithic of the various regions surrounding the Indian Ocean, all them of rather tropical climate:

Dorian K. Fuller et al., Across the Indian Ocean: the prehistoric movement of plants and animals. Antiquity 2012. Freely accessible. [→ updated link]

I strongly recommend full reading as I can only dedicate some space here and the study, while not really long, covers many diverse aspects of plant and animal domestication and translocation around the Indian Ocean. 

South Asia and Africa

First the authors deal with the issue of how the most important tropical crops of South Asia, which are mostly of African origin, arrived there. They conclude that the transfer took place at the very end of the Harappa (IVC) period, rather than earlier, even if it is confirmed that Harappa and the Persian Gulf (but not yet East Africa apparently) kept trading relations since much earlier. These African crops (millet and sorghum specially) were critical, as we know, in enabling the expansion of farming towards Southern India.

In return India gave Africa the zebuine species of cow, which, after hybridization, fueled the expansion of East African pastoralists into Equatorial areas.

This route between East Africa and South Asia is declared to be the precursor of the spice trade of later days:

The first hint of this spice trade comes from the findings of valued black peppercorns that were used to fragrance the nostrils of the deceased Pharaoh Ramses II (c. 1200 BC) (Plu 1985). This spice is endemic only to the wet forests of southern India (Asouti & Fuller 2008: 47), and in all likelihood was supplied by hunter-gatherer groups to coastal groups (Morrison 2002).

Tropical Asian crops

Another section deals with the transfer of diverse crops between South and SE Asia (and even as far as New Guinea).

Indian pulses migrated to the East, while a number of other crops (areca nut, sandalwood, betle leaf and maybe banana) did in the opposite direction. The origin of mangos and lemons is also discussed and seems distributed between both regions. 

Many of these flows may have been from approximately the same time as the African-Indian connection, in the late 2nd millennium BCE.

The Malagasy connection

Finally a third layer of agricultural flows appear to connect SE Asia with Africa, the most notable being the banana, but also yams, taro and chickens. 

This one seems most likely related to Austronesian (Malay) flows in westward direction, leading to the formation of the Malagasy people and the colonization of Madagascar. 

In their journey westwards, the proto-Malagasy appear to have left some maritime vocabulary in Sri Lanka, SW India and the Maldives, where they also left their outrigger technology. A variant of this one, with two outriggers, is also widespread through East Africa, from Somalia to Mozambique and, of course, Madagascar. 

The Austronesians would have spread these crops and the chicken to Africa, bringing also possibly some commensals like the rat, the mouse and the Asian shrew, as well as a weed. Some of these may however been introduced in several episodes.

Claim that Danubian Neolithic people had classes

Or so is what new research has led many to think.

R. Alexander Bentley et al., Community differentiation and kinship among Europe’s first farmers. PNAS 2012. Pay per view (for six months or depending on your world region).

Abstract

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

Many details on the burials are freely available in the supplemental material. The necropolises (many individuals each) are from a diversity of sites between Slovakia and Alsace: Aiterhofen, Ensisheim, Kleinhadersdorf, Nitra, Souffelweyersheim, Schwetzingen and Vedrovice.

The key relevant finding seems to be that most males buried with adze have lower Sr87/Sr86 ratio in their tooth enamel than those buried without grave goods, suggesting that they were more likely be original from the more fertile loess lands than the others, the preferred location of Linear Pottery Culture sites (also Danubian Neolithic or LBK by its German acronym). 

Women overall also had lower Sr87/Sr86 ratio, suggesting that most had come from other less fertile districts. This last also implies patrilocality, surely dismantling the idea of Gimbutas of a matrilocal "Old Europe", which was already very much discredited (notice that this is not important in regard to her most important theory: the Kurgan model of Indoeuropean expansion, which is only very tangentially related to this matter). 

However my first impression is that drawing such radical conclusions from evidence which is only somewhat significant (I see many non-adze men who have below average strontium ratios and also a good number of adze men with high Sr ratios) and not at all absolute, seems a bit risky on first sight.

Whatever the case that is what they claim: that Danubians had classes or castes or some sort of social hierarchy and differentiation since the very beginnings. Sadly they have not researched what could have been a complementary source of information: DNA. 

Sources: Eureka Alert, Science, BBC, Pileta[es].

Western Danubian overlapped with pottery styles
that can be aboriginal or Cardium-derived
(source: Westward Ho!)

Climate change dried up the Sarasvati sending Harappans eastward to the Ganges

Before and after

That's what new research seems to claim: before c. 1900 BCE there was a stable moonson on the Thar Desert feeding what is now known as Ghaggar-Hakra River (seasonal) but mythologically referred to as Sarasvati River (a major hub of the Indus Valley Civilization or Harappa culture).

This, according to the researchers of Woods Hole Oceanographic Institution (WHOI) caused that people already living in the banks of that river had to emigrate eastwards towards the Ganges, where monsoons were still stable but where the fertility was not good enough to support large cities as in the West.

Source and more details at the press release and at WHOI.

See also: Dispatches from Turtle Island (Andrew has a nice review of some of the wider implications).

Another decorated cave discovered in Ardèche

The Ardèche or Ardacha region, so-named for a tributary of the Rhône, is one of the most important and older districts of modern human presence in SW Europe. Its importance was underlined with the discovery of the Grôte Chauvet, the cave of lions.

Now another discovery has been made in the same area with a decoration of what seems to be a horse head. The finding actually was made in 2011 by some speleologist but kept secret till it was researched preliminarily.

Sources[fr]: Pileta, France 3, Paleos Blog.