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Thursday, April 7, 2016

Y-chromosome DNA from an Iberian Neandertal

Open access at the AJHG:

Summary: Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

Mendez et al., The Divergence of Neandertal and Modern Human Y Chromosomes, AJHG, Volume 98, Issue 4, p728–734, 7 April 2016, DOI:


andrew said...

Notably, TMCRA date for modern humans and Neanderthals by Y-DNA, mtDNA and autosomal DNA are all older than the oldest widely accepted date of archaeological evidence of Neanderthals, which makes sense considering that we are sister species, rather than derived from Neanderthals. The TMRCA dates are in lines with the time when H. Heidelbergus was in existence and neither modern humans nor Neanderthals existed.

Krefter said...

Am I reading this correctly, he had R1b-P312 :) Quick someone tell Maju.

Krefter said...

The sample is 49,000 years old, so contemporary to ust-Ishim.

Karl_K said...


You are right, he did have R1b-P312.

But it is just a coincidence. The authors didn't know that name was already taken. They will probably have to rename it nR1b-P312.

Aram said...

Where did common ancestor of Homo Sapiens and Neanderthalians originated?
If in Africa then why there was no Neanderthalians in Africa?

Karl_K said...


Homo heidelbergensis – also Homo rhodesiensis – is an extinct species of the genus Homo that lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago.

This species would have been the ancestor of both Neanderthals and Modern Humans, but seperately. There is no need for Neanderthals to have been in Africa.

ryukendo kendow said...
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ryukendo kendow said...
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Rob said...


Before launching into nitty gritty, I'm not sure if this article- which Dave featured a while ago- is of interest

And yes, weights are the way to go. Better than cardio ;)

Rob said...


shifting from the other thread back, is there a way you can compare Srubnaya to BB in their overall composition?

Anonymous said...


Simos de los Huesos was proto-Neanderthal. They used to be considered H. Heidelbergensis. As Chris Stringer said, this may even mean that H. Antecessor was the common ancestor.

Anonymous said...


*Some* paleoantropologists consider H. Rhodesiensis and H. Heidelbergensis the same. Not all. Furthermore, as I said previously: H. Heidelbergensis was found to be proto-Neanderthal. At least the Spanish ones.

Karl_K said...

"This may even mean that H. Antecessor was the common ancestor."

It is probably impossible to work it all out without genetics and many more samples, and even then it would be complicated.

But it doesn't change anything. The common ancestor could have been in either Europe or in Africa or both.

Alberto said...


Yes, I certainly agree with the argument about polygamy being too costly in most situations, and only in some economies being a viable option. And it'd be interesting to investigate if early IE could afford it or not with their economies once out of the steppe.

But the other argument is important in this case too. Whatever early IEs had was a recipe for success, not one for disaster. Generalized polygamy within a closed community would almost inevitably lead to the kind of internal struggles you describe. Only having an external source for extra wives could make it feasible (if cost itself was not a problem), and at the same time give a very important breeding advantage.

Not that I strongly argue for it, especially if you might have a better explanation already.

Alberto said...


Using the more simple model so it can be more easily compared to the Bell Beakers I posted earlier:

Looks like Srubnaya is less Euro_MN and more Yamnaya (EHG + Kotias). If you want to check other finer details let me know.

Anonymous said...

@ Karl_K

Maybe it is impossible. However, pure on physical evidence (teeth, to be specific) people predicted the large Neanderthal admixture in Oase 1 and were proven right by DNA.

I give it a chance, given enough finds.

batman said...


If you exclude the historical records reflecting the 'chiefdomes' of ancient antiquity, also known as kingdoms and etnicities, one may speculate freely around the subject-matter of ancient cultures and their respective systems of procreation, breeding, reproduction and growth - to produce the ancient civilizations and etnicities we know, as well documented, historical realities.

If we include the classical sources, such as the old, IE annals from Ireland to India, we have to admit that they all rely on the semantic content of words like "gens/gentes", "etnos" and "aets" - producing "nationes", "demos", "populi", "chudi", "teuti", "tjodi" and "volk".

Thus the question remains; How did these "gentes" aka "aets" aka etnicities actually come about? How did they occur and how did they evolve?

So far modern genetics seem to have established that both neanders and cro-magnon practized patrilinearity. Same result reoccurs on the mesolithoic and neolithic sites where a number of y-dna is sampled.

Trielles may be a neat example, where the males honored with a complete burial were of the same G2-line.

A wwider look at the Eurasian aDNA seem to draw a map where various regions are dominated by specific hg. For some reason they seem to overlap with known cultures from EN - as hg G is concentrated in SW Europe, hg H in SE/Middle East, hg J in SE and India, hg I in NW Europe and hg N in NE Europe and Northern Asia.

With the LN we got a new economy establishing itself on the juicy grasslands of western Eurasia, where the Holocene winter could be mild and the cattle feeding itself, outdoors, all the year around.

As the Holocene optimum set forth, and the humidity rose along with the median temperatures, this economy became very productive - as the yet uninhabittable tundras, steppes, praeries and meadowlands of western Eurasia became fertile.

Following this period is a rapidly increasing ability to digest milk and diary. This increase can be linked to the LN agricultures. Both can be linked to the origin and growth of two brand new dynasties - ran by the descendants of the brothers R1a and R1b, respectively. (To an amateurs eye it seems to be some correlation between lactase-persistance and hg I, as well.)

To explain the occurance, growth and spread of these specific R-lines - along with the "bovine" cultures - we need a common origin and a consequent tradition of patrilinear inherritance.

Thus we may explain the process leading from an "extended family" - defined by the male-line - as a stem growing into a branched three of "tribes", held together at the core by the chrown family-line, serving their roy-all task as "Pater Familias".

As the seeds of the king-line is spread around the land it would branch out, horisontally, in four steps - to reach every household of the "extended family" - also called "aet" and etnicity.

Since the stem-family is the direct descendant of the first family (of its kind) - they would be the nature-given centre of the secondary and tertiary settlements of the family. As their numbers grew they were obviously populating continental areas, as "branches from a stem". Thus the bifurication-area of R1a/b is a key to understand the origin of bovine agriculture.

As with the older y-dna the R1a/b would define "extended families" - as in 'etnicities'. As with the older y-lines they would evolve through a organization defined by the laws of time and nature - which made the stem-family the natural head of the etnicity, as is refelcted in the historical kingdoms and cheifdoms, defined by their "common ancestry" - as the origin and basis of a common language, economy, culture and history.

batman said...

rk - moreover:

To explain this process our historical sources describe a five-cast society, with the stem-family as the first and thus "royal". To create an entire aet the male head of the stem-family had to produce a ring of sons around himself - forming a "second cast" (dukes) - that could reach the major regions of the land. Within their respective regions these princes were to produce a number of sons who would become local cheiftains ('earls', 'knights'), known as the third cast or the "middle nobility".

Parts of their duty was apparently to produce a royal grand-son as the head of every farm in their respective village/community - also known as the "lower nobility", adressed as "Sirs", "Ceorls", "Peasants", "Farmers", etc.

As this connected every farm, village and region by descent, the entire land could develop into a stable, growing population - gouverned and ran as "one, big family" - developing both in quantity as in quality, throughout millennia.

Thus the local nobility - as grand-grand-sons of the king, would be the sole producves of the children of each and every farm - creating the fifth cast of the royal seed-line - and thus the "pyramidal" society.

Pr. consequence all kids born would be grand-grand-children of a prince - and thus a direct descendant of foregone king, just like the ruling king.

An agnatic, pyramidal breeding-system would make all members of society a cousin to everybody in his/hers village. This nativity is also known from the regional, three-cast, (tri-ball) societies" that survived locally, after the fall of the ancient, five-cast civilizations. (Thus troval societies of relative descent could later ally as 'sprachbunds' and trade-partners, as well as unite as a 'federation' of 'clans'.)

A more solid constitution and a more rational beuraucracy - than the brotherhoods and sisterships of an extended family - is actually hard to find. To keep the old system intact there where three premises:

1. Patrilinear preference.
2. Agnatic inherritance.
3. Polygamic reproduction.

If a productive farm need and feed 30 persons, every Farmer (Ceorl/Peasant) would have to produce 30 children, in order for the farm to maintain its basic production and its traditional functions within the village, region and kingdom. If half of the farm-family were women - and they were soley in charge of the female side of the reproduction - the new Sir Peasant would risk mating with a number of the girls of the farm he inherrited.

It seems polygamy was needed - to create, develop and maintain the kingdoms of ancient antiquity - as specific y-lines and thus 'etnicities'.

batman said...

A two millenial old model of the five-cast society:

ryukendo kendow said...
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FrankN said...

@Alberto, Rob:
I have posted a few more comments in the previous thread. I personally would favour keeping all the nMonte-related result posting and discussion there. This thread is already filled by two unrelated, and both highly interesting, discussions.

rk e.a.: Very interesting thoughts! However, two annotations seem appropriate:

1) To the extent mythology reveals cultural orientations, it suffices to look at Zeus and Odin. They are both married, which doesn't inhibit them from regularly seducting or raping, and ultimately impregnating other women. Note also Heracles in this respect, who, in spite being Zeus illegitimate offspring, can make certain claims to his father's legacy. Greek godesses, OTOH, are also not just sitting at home waiting for their unfaithful husbands to return. I am less acquainted with Indian mythology, but it seems a similar pattern is present there as well.
In short - there is a twilight zone between monogamy and polygamy that IE gods appear to have explored quite extensively.

2) "[Women were] reliant on males for protein, iron and fats, and energy-dense, high-risk food like honey."
Actually, not so.
a) Virtually every eco-zone around the Globe except for the Arctic and possibly Australia, has evidence of intesively collected and typically early domesticated "energy-dense" sources of protein, fats and carbonhydrates (not sure about the "iron" part though):
- SEA/Oceania: Banana and coconut, exported to other regions at least as early as 5000 years ago
- W. Africa: Oil palm, shea butter, breadfruit
- Central Asia: Pistacchio, apricot
- Caucasus: Grapes, flax (as fibre evidenced already 35,000 years ago, most likely, the linseed was consumed as well)
- Mediterranean: Olive, Figs, Dates (the latter may go under "high risk", depending on the tree height)
- European UP/Mesolithic: Hazelnut evidenced as early as 25,000 years ago, predominating mesolithic assemblages from Portugal to the Hebrides and N. Norway. For Duvensee NE Hamburg (Maglemosian), it has been estimated that hazelnut provided for 40% of annual calory intake, a level comparable to EHG calory intake from cereals. Also worth mentionning are chestnuts (in parts of CE staple food well into the 18th century), acorn, water chsstnut, goosefoot, knotweed, blackberry, sloe, crab apple etc. Poppy was domesticated in the Western Mediterranean as oilseed, it reached the Rhinish LBK already as domesticated plant. Pollen analysis shows Sea Buckhorn (Vitamin C!)as the main scrub in European Ice Age taiga-steppes.
- NE America: Butternut, Maple (sirup)
- NW America: Hazelnut, pumpkin/melons
- Central America: Avocado, earliest gathering evidnce from 10,000 BC
- Andes: Peanuts (domesticated before 8000 BP), (sweet) potatoes
- Amazonia: Cashew - sugar-rich fruit, the "nut", actually a seed, serves as fat and protein source
- East Asia: Not sure here, that's more your terrain, rk. I'd tentatively put bamboo and the soy bean on the list.
- Siberia: Pine nut, various berries as Vitamin C source.
In fact, women could survive without men providing a decent piece of meat from time to time. Men not, without Vitamin C from sources collected (mostly) by women.

b) The "game changer" comes with poultry domestication, which makes eggs and meat easily available to women. While AFAIK East Asian poultry domestication hasn't yet been "time-stamped", there can be no doubt about its very early origin. Mesolithic NW European sites abound by duck bones (up to 50% of bone numbers, 20% of live weight), which has inspired quite some speculation about early domestication of the Mallard. Note here also ducks and turkeys among the few domesticated animals in pre-Columbus America.

FrankN said...

Correction: "40% of annual calory intake, a level comparable to EHG calory intake from cereals"
is meant to read "EEF calory intake from cereals". "EEF" might be slightly misplaced here, the 40% figure comes from estimates for Cucuteni-Tripolye.

There are several analyses for LBK, based on isotope ratios, which I could look up if anybody is interested. From what I remember, Elbe-Saale LBK had a quite high share of plant food, including one woman "whose diet might be characterised as vegan".
LBK around Stuttgart (I don't recall whether the analyses actually referred to Stuttgart itself, or to nearby LBK settlements) was much more meat-based, with a considerable share of wild animal bones, and strontium analysis of cattle and human teeth pointing at transhumance. The male diet was much more meat-based than the female one. Female bones/joints indicated stress from bending/kneeing movements, male ones from one-sided throwing motions (typically the right arm).

I also recall an Israeli study of Late Natufian/PPN diets, with substantially higher male than female meat consumption, and a substantial share of hunting game bones in the overall bone assembly.

I guess it took some time for a hunting expedition to get hold of an aurochs, boar or deer stag that deserved to be taken home to the camp/village for joint feasting (and subsequent hide/skin processing). In the meantime, the men had to live on hares, hedgehogs, snakes or whatever else crossed their way, resulting in a more meat-rich diet. The same applies to seals/whales vs. herring, tuna vs. mackerel etc. The overall effect on male vs. female body size isn't particularly difficult to imagine - quantifying it is another issue, though.

A final thought: Seafood - mussels, oysters, crabs atl. We may have cultural variation here, and collection from cliffs exposed to high tides clearly ranks under "high risk". However, in general, this seems to fall more into the female than the male domain.

Rob said...
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Rob said...
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Rob said...
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Rob said...

@ Batman

Any explanation needs to be tailored to the specific period, region and culture in discussion. Any blanket theories which try to heap 'all R lines' into one explanation, especially if they uncritically analogize later Medieval models, are likely to be incorrect.

@ Ryu

Where do you want to start with your analysis ? Corded Ware or Yamnaya or BB ?
Maybe Yamnaya, given its the deemed predecessor of all (with some problems, IMO). But it makes sense to start there.

The problem with Yamnaya is that much of the excavations occurred as early as 100 years ago, when collateral disciplines like palaeozoology hadn't even been invented, and the excavations themselves were of variable quality. Moreover, much of the material (eg animal bones, etc) was apparently thrown away in the post-1990s era due to shortage of storage space, and funding, etc. So it is difficult to come up with very solid dietary conclusions, or demographic conclusions. But here is a start (let me know if you cannot get these)

* Egalitarian Pastoral Society Versus Nomadic Warriors? An Attempt to Reconstruct the Social Structure of the Yamnaya and Catacomb cultures. Эгалитарное пастушеское общество versus воины-кочевники? Попытка реконструкции социальной структуры
ямной и катакомбной культур. Elena Kaiser

* Pit-Graves, Yamnaya and Kurgans at the Lower Danube: Disentangling 4th and 3rd Millennium BC Burial Customs, Equipment and Chronology. V Heyd, et al (very good about finer periodization, and changes between early and later Yamnaya)

* The main development of early pastoral societies of northern Pontic zone: (pre-Yamnaya). Y Rassamakin (perhaps the most expansive overview of the pre-Yamnaya -> Yamnaya sequence)

* Pit graves in Bulgaria and the Yamnaya Culture. Kaiser, Winger.

* Immigration & Transhumance in the Early Bronze Age Carpathian basin. The occupants of a Kurgan, Gerling et al.

* Prehistoric Mobility and Diet in the West Eurasian Steppes 3500 to 300 BC. Pp 73 -> (for climate background)

* The Steppe and the Caucasus during the Bronze Age: Mutual Relationships and mutual enrichments." Natalia Shishlina (climate, demography, isotopic evidence)

* The Geographic Corridor for Rapid Climate Change in Southeast
Europe and Ukraine. Bernhard Weninger and Thomas Harper (Climate, demography)

* Multiregional Emergence of Mobile Pastoralism and Nonuniform Institutional Complexityacross Eurasia. M Frachetti (about the development of pastoralism in Eneolithic steppe, has some distinct data points on assemblage composition)

* The Black Sea and the Early Civilizations of Europe, the Near East and Asia. Ivanova (good overview of different areas of western steppe, and different demographies, metals, etc: west Black Sea, north Black Sea, east - Kuban - Caucasus region).

Sorry to bombard you, and perhaps you know all of them already. But I hope it might give some additional data points for your theories

batman said...

@ Rob,

What "Medieval models"...?

ryukendo kendow said...
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