August 28, 2012

Paleolithic Europeans may have been substantially Neandertal-admixed

In Oetzi the Neandertal Champion, I suggested a way to determine whether the higher Neandertal admixture in Oetzi suggested by Sams and Hawks is due to his Near Eastern Neolithic or European Paleolithic ancestry.

The basic idea is simple: first build a map of Oetzi's ancestry with a tool that distinguishes between the Near East and Europe. I did this with my West Eurasian cline (weac2) calculator. The output of this procedure is to calculate admixture proportions for Oetzi across the genome. In some windows along his chromosomes, he will appear to be 100% Atlantic_Baltic (European-centered component), in others 100% Near_East, and in some intermediate, or possessing some other component. At each window we have an Atlantic_Baltic and a Near_East admixture score.

Secondly, we need to calculate a score of Oetzi-Neandertal (Vindija) similarity in the same window. I used the Neandertal data from the Harvard HGDP, and my own copy of the Oetzi genome which I've created by intersecting a SNP file provided by Andreas Keller with the Stanford HGDP set of SNPs. In the end I combined Oetzi and Vindija in a common set of 37,320 SNPs, removing all SNPs with missing alleles. One could get more SNPs by not taking these various intersections and working with full genomes, but this set of SNPs suffices for my purposes.

In any case, I used 0/1/2 coding and took the absolute value of the Oetzi minus the Vindija value, normalizing by dividing with the number of SNPs in each window. That was my Score variable, and the lower the value the more Oetzi matches Vindija.

The idea is simple: does Oetzi tend to appear "Near_East" or "Atlantic_Baltic" in places along his genome where he is close to Neandertals?

I limited myself to windows where there were at least 10 SNPs common between Oetzi and Vindija, as well as windows where the sum of Atlantic_Baltic and Near_East was at least 95%, so there was good evidence that these two components were responsible for the whole diploid pair of segments. A total of 1,128 windows remained. The results are as follows:

Cor("Near_East", Score) = +0.082
Cor("Atlantic_Baltic", Score) = -0.079

These are small, but significant, and we should remember that relative levels of Near_East and Atlantic_Baltic vary for reasons unrelated to Neandertal ancestry in most of the genome. Here is a plot of the Score variable for the 1,128 windows, ordered from high-to-low:
There is a group of windows with particularly low Score, so perhaps these represent the strongest evidence for Neandertal ancestry in Oetzi. Any such ancestry may mostly consist of small segments, so my not-so-dense sieve formed by the small number of studied SNPs is probably missing a lot of Neandertal segments that may turn up with full genome comparisons.

In any case, the median Atlantic_Baltic for all windows is 46.48%, and the median Near_East one is 52.78%. But, let's see how these numbers look when we consider the lowest quantiles of Score (=more Neandertal matching):



These numbers kinda speak for themselves. Of course, it is wrong to equate Near_East = Neolithic and Atlantic_Baltic = Paleolithic. On the other hand, the assumption that these two components possess a greater relationship with the Neolithic farmers and the Paleolithic Europeans respectively, seems justified.

So, it seems that in regions where Oetzi matches the Vindija genome, he tends to be "Atlantic_Baltic". The implication is that Paleolithic Europeans were more Vindija-like than incoming Neolithic ones from the Near East. Oetzi may have been more Neolithic farmer than Paleolithic hunter-gatherer across his whole genome, but the situation is reversed for regions suggestive of Neandertal ancestry.

The idea that Upper Paleolithic Europeans were admixed with Neandertals is not new. Its most recent prominent champion is Milford Wolpoff (figure on the left is from one of his most recent works, showing a Copper Age European male (top) sharing features with La Chapelle Neandertal (middle) at the exclusion of Herto (an archaic H. sapiens from Ethiopia), indicating a degree of continuity from Neandertals to more recent Europeans.)

Just how Neandertal-admixed were the Paleolithic Europeans? If Hawks is correct in his claim that Oetzi was ~5.5% Neandertal, and given that Oetzi appears to have been overall more than 50% incoming farmer and less than 50% local hunter-gatherer (conservatively), then it is easy to conclude that even ~10% Neandertal for Paleolithic Europeans may not be too far from the truth. We'll have to see what their actual ancient DNA looks like to confirm the hypothesis found in this post.

Finally, since it's my custom to resuscitate old physical anthropology when it matches modern observation, here's Carleton Coon's 1939 Races of Europe, from his "Statement of Aims and Proposals":
At any rate, the main conclusion of this study will be that the present races of Europe are derived from a blend of (A), food-producing peoples from Asia and Africa, of basically Mediterranean racial form, with (B), the descendants of interglacial and glacial food-gatherers, produced in turn by a blending of basic Homo sapiens, related to the remote ancestor of the Mediterraneans, with some non-sapiens species of general Neanderthaloid form. The actions and interactions of environment, selection, migration, and human culture upon the various entities within this amalgam, have produced the white race in its present complexity.
I'd say that if these results are confirmed by subsequent research, then "bullseye" is a good way to describe the above passage.

(But, I will not refrain from spoiling the fun a little bit, by pointing out that the potential high similarity of UP Europeans with the Vindija genome may be due, at least in part, to gene flow from UP Europeans-to-European Neandertals in that particular specimen. Now, it may be that such gene flow may have gradually made the European Neandertals more modern-like, and thus facilitated their eventual full absorption into the gene pool of subsequent Europeans. But, we don't know that for sure. A second Neandertal genome, preferably a pre-contact one will be the decisive factor in determining the direction of gene flow conclusively.)

18 comments:

Crimson Guard said...

Coon in his later work had moved away from his old TROE era scheme and from any notable Neanderthal ancestry in modern ancient/Europeans:



"FROM ABOUT 30,000 TO 10,000 YEARS AGO, the Upper Paleolithic Europeans lived in the lee of the ice from Spain to Russia. They buried their dead as the Neanderthals had done, and they wore fitted garments. From a grave below the permafrost at Sungir, about 142 miles(200 km) east-northeast of Moscow, a male skeleton dated at 22,000 years ago was disinterred in 1964. It showed traces of a fur shirt and trousars and bracelets and beads of mammoth tusk and the perforated canine teeth of arctic fox.

The Upper Paleolithic Europeans were modern Caucasoids. During their span of 20,000 years, their bodies changed physically very little if at all, for their adjustments to their environment left nothing to be desired. The famous "Old Man of Cro Magnon" was not a giant, as often depicted, but only 5 feet, 6 inches(168.4 cm) tall. The mean stature for twelve adult male skeletons was 5 feet, 8 inches 173 cm). The tallest 5 feet, 11 1/2 inchs(182cm), and the shortest was 5 fet, 3 inches(160cm). The five female skeletons recorded had a mean sature of 5 feet, 1 inch(155.5 cm) and a range from 5 feet, 1/2 inch(154 cm) to 5 feet, 2 inches(157.5 cm). This sex difference in stature varies closely with that in head size, as we shall presently see.

The limb bones of these people were rather slender, like those of Mount Carmel people, and their hands and feet were normal for slenderly built Europeans. We know this from negative silhouettes made by spraying pigment out of bone tubes over hands held against a cave wall, and from footprints found on cave floors.

There is little evidence that the Upper Paleolithic Europeans absorbed the Neanderthals that preceded them. Why the Neanderthals faded away is a mystery. One may postulate that they succumbed to diseases brought by their successors to which they had no genetic immunity, just as smallpox and tuberculosis decimated the American Indians; or one can suppose that they were hunted down by the invaders(which has also been done in modern times); or perhaps they died of crowding or of grief. (Is it possible that, because of phonemic limitations, they could not learn their invaders' languages? Or only with a poor accent?)

About the fate of the Upper Paleolithic hunters there is no mystery. They did not vanish with the mammoths on whose flesh they feasted and from whose ribs they built large oval houses on the steppes of Russia. They survived the Pleistocene, and their descendants in Europe and in Asia became Mesolithic salmon-seiners, Neolithic villagers, Bronze Age warriors, and Iron Age Vikings. They followed the reindeer to the edge of the ice, and, when it melted, they remained there. They were restless. After they had learned agriculture and cattle breeding from others like themselves who had come from the east, they expanded, migrating southward and eastward in many waves. One of those waves reached India and later spread to many other parts of the world.- "Racial Adaptations: A study of the origins, nature, & significance of racial variations in humans" by Carleton S. Coon, 1982

Annie Mouse said...

Vindija is in my opinion substantially admixed with Homo sapiens (skull similarities). It is impossible at this stage to distinguish true neanderthal from sapiens in it. It is IMO a lousy standard for neanderthal genetics.

The Vindija you see in Oetzi may be neanderthal or sapiens. Impossible to say until we get a true unadmixed Neanderthal genome.

Annie Mouse said...

Erp. I did not notice the end comment. Trash the last comment which was redundant.

Africa Gómez said...

Wow, this is so cool, your blog is science in the making. I went to a local museum in the summer displaying a 4,000 yr old chieftain, Gristhorpe Man, and I noticed his strong superciliary arches. I took photos, but this reconstruction speaks for itself. http://www.culture24.org.uk/history%20%26%20heritage/archaeology/art81754
Unfortunately, the way the - complete! - skeleton found in an oak tree coffin was treated thereafter means that there is little hope for ancient DNA. I can't wait to see what new Neandertal and paleolithic genomes tell us.

andrew said...

Kudos on the clever methodology, which squeezes more hypothesis testing information from the same data.

To the extent that one can be reasonably confident of an elevated Cro-Magnon descent Neanderthal admixture hypothesis, moreover, one can use that to provide an estimate of the Paleolithic contribution to the modern European genome that is methodologically independent of, for example, estimates based on proportions of uniparental lineages and mutation based dating of particular uniparental lineages.

This is a tool available not just for Europe as a whole, but for targeted subpopulations. For example, it provides an independent means to estimate the extent to which the Basque are derived from Franco-Cantabrian refugia.

Used in a different way, it allows simple admixture analysis of populations to serve as a way of targeting for further analysis modern populations that have a higher than average likelihood of having elevated levels of Neanderthal admixture relative to the baseline.

A next step along that line would be to compare which specific Neanderthal SNPs are found in populations with different levels of Paleolithic admixture. If Paleolithic Europeans acquired Neanderthal admixture in Europe after a first round of Neanderthal admixture found in West Eurasians, then one would expect individuals with elevated levels of Paleolithic admixture to have particular Neanderthal SNPs not found in other West Eurasians.

Indeed, one might even be able to break up the private Paleolithic SNPs with the other SNPs and do a LD analysis to provide some insight into the relative dates of admixture periods testing the hypothesis that wave one ought to be something like 100kya to 75kya, while wave two ought to be something like 45kya to 30kya.

Elevated Paleolithic admixture also continues the context in which we can start to bring the sociology of race to bear when evaluating alternative narratives of the intergroup interactions between Paleolithic and Neolithic modern humans. Higher levels of Neanderthal admixture in Paleolithic modern humans, even if it has no adaptive or functional component, would have enhanced the extent of patently obvious racial differences between the two groups at first contact. Very few people unadmixed members of one population would be able to "pass" for members of the other population. One would stick out in a group of people from the other populations like a Nigerian man in Beijing. The mixed paternity of mixed Paleolithic-Neolithic individuals would likewise be obvious. I don't know precisely what implications this would have for the group interactions, but surely these realities would play a meaningful part in any scenario of how they actually did.

Average Joe said...

It would be interesting if Carleton Coon turned out to be closer to the truth than many of his critics.

mooreisbetter said...

I don't mean to reduce to an absurd degree the debate on whether archaic sapiens intermixed with local modern sapiens, BUT:

The debate for me has always come down to this:

The traits of archaic populations that mirror precisely the traits in regionally varied modern populations cannot be explained by selection.

Put simpler, with examples:

Asian archaic species had "shovel shaped" incisors. There is no real evolutionary purpose for shovel-shaped teeth. Many modern Asians have shovel-shaped incisors. The notion that such a trait evolved twice, and East Asia generated selective pressure toward it, is absurd.

In Europe: Neandertals had big noses and long heads. Many Europeans have big noses and long heads. In fact, the "nasal bridge touching the forehead" is a trait only found in some Europeans and nowhere else. Again, the notion that there was some kind of double evolution (first to Neandertals, then to moderns) in Europe, is wacky.

All that leaves is substantial admixture. Dienekes, your high figures certainly sound plausible to me.

Ponto said...

It would be good to strengthen the hypothesis that modern Northern Europeans are more Mesolithic European in ancestry when true Mesolithic Europeans are tested not just from north of the Alps but from Greece, Italy combined with results from the Near East and North Africa.

Presently all the dna results from Mesolithic Europeans are young, from the interface of the commencement of farming in the regions where the hunter/gathers were selected for testing. The Swedish farmer woman buried under a Neolithic Dolmen was born in the same region that her hunter/gather companions were found. They could all have been due to recent immigration, the farmer woman's people from the Mediterranean/North Africa/Near East and the hunter/gathers from east of the Caspian Sea. Older samples of true UP Europeans and true Neolithic farmers are needed otherwise the results are just a lot of speculative hot air.

terryt said...

"I'd say that if these results are confirmed by subsequent research, then 'bullseye' is a good way to describe the above passage".

I read Carlton Coon many years ago and I admit I have been heavily influenced by his ideas. So the conclusion in your current post is no surprise to me.

"I will not refrain from spoiling the fun a little bit, by pointing out that the potential high similarity of UP Europeans with the Vindija genome may be due, at least in part, to gene flow from UP Europeans-to-European Neandertals in that particular specimen. Now, it may be that such gene flow may have gradually made the European Neandertals more modern-like, and thus facilitated their eventual full absorption into the gene pool of subsequent Europeans".

I'd say you are almost certainly correct with that. A combination of factors is the most likely scenario. Nothing in biology is simple.

"A second Neandertal genome, preferably a pre-contact one will be the decisive factor in determining the direction of gene flow conclusively"

Both directions would be my guess.

Fanty said...

"Many Europeans have big noses and long heads."

I dont know modern figures, but only maps that are 50 or more years old.

There are Europeans with "long heads" but Europe isnt the place where that trait is extremely common.

those old maps claim:
Africans have long heads, middle easterners have long heads, south asians have long heads.

East Asians have short heads and central Asians have the shortest of all heads. Native Americans have medium lengh.

As for Europe, those maps claim South Italians, Iberians, British/Irish, Dutch, Scandinavians, Finnish, Balts and Russians to have long heads.

Shorts heads for French (northwest French medium), southern Germans (northern Germans medium lengh), Swiss, North Italians (southern Italians long), Austrians, Czechians, Slowakians, Hungarians and southern Poles (Northern Poles medium lengh)

The rest somewhere in the middle.

Of course Neandertals had extraordinary long heads, no homo sapiens can compete with.

I met people who claim long heads are a sign of a "Warrior race", "nobility", or "artisans". Or soldiers, police officers, fire fighters, sportsmen and other adrenalin junkies who try to get themselfs killed in a daily basis.

Short heads would mark farmers, craftsmen, Bankers and Merchants.

Others claim long heads are "Progressive".

Neanderthals must have been extraordinary "progressive" then. ;-)

There is one observation about head lenghes: In Europe heads become shorter since about 2000 years.

In East Asia, heads became shorter since 3000 years.
The warrior race fraction explains it by claiming the long heads get themselfs killed and the short heads hide under the table and survive.

wagg said...

Africa Gomez: "a 4,000 yr old chieftain, Gristhorpe Man, and I noticed his strong superciliary arches"

No need to go in a museum. There is a reason why the actors Ron Pearlman and Everett McGill were chosen as the main characters of "Quest for fire"... ;)

eurologist said...

As with the question of how much of the Neanderthal signal is African sub-structure and incomplete lineage sorting, the Denisovan genome may be useful, here. One could re-do the analysis only with those Neanderthal SNPs that match Denisovan. Not sure there would be sufficient left for the present analysis, but it should exclude anything mixed in from early European modern humans into the Neanderthal genome (because the Denisovan genome in its entirety does not show such a preference over other human populations).

Onur said...

Fanty, you make a lot of big claims but very rarely provide any proof or source for them.

Dieneke, I think you should tighten up the comment moderation rules of your blogs when it comes to the content of comments. I think it would be better for you to disable comment moderation rather than to apply such a loose comment moderation. That would significantly lessen your responsibility on comments published in your blogs. So my advice to you: either apply a strict comment moderation or disable it completely.

Creative said...

I have a question regarding Upper Paleolithic Europeans. Why did the Cro-Magnons specimens develop these square eye socket openings? For instance the “Old man of Crô-Magnon" , in contrast to many other Human skull forms. I am asking this because I also have these square eye sockets even though I don’t resemble a robust Crô-Magnon. I drift more in the Medish/Armenoid direction. The only thing different to the masses I noticed is that my eyes are a bit larger than average and much more deeper sitting in my skull, based on my impression.
According to a doctor who was examining my skull via X-ray because of a minor head injury, my Frontal Bone is thicker than average.
I understand that this is some sort of large game protection but I still don’t get why these
Evil looking square eye sockets developed.

pconroy said...

@Wagg,

Correct. There is also the Russian heavyweight boxer "Nikolai Valuev"

https://encrypted-tbn1.google.com/images?q=tbn:ANd9GcRNTN6_Rg8nD3DSljg2rGe0_ewtaFXmnf5LgRz_QurAMlbBwDIaOQ

http://www.erichufschmid.net/Neanderthals/Nikolai-Valuev.jpg

hamarfox said...

What would be the 'diluting' influence? Shouldn't modern UP-descended populations (relative to Neolithic ones) mirror this proposed difference in ancient admixture? Maybe you could make an entry about average Neanderthal levels (complete with spreadsheet) invarious European (and non-European) populations?

Ted Kandell said...

Dienekes, I thought of a simple test for true Neanderthal admixture among Europeans, and not just AMH admixture among Neanderthals:

Test for only SNPs that are derived among both Neanderthals and Denisovans.

These derived alleles must predate AMH and certainly any AMH admixture, They should not be from Incomplete Lineage Sorting, although perhaps they could be from a "Neanderthal-Denisovan-like" population in Africa. It should not be too difficult to tell which are Outside of Africa and which are not. (At least we can tell if they are missing among Paleoafricans, even if Neo-Africans have Eurasian ancestry.)

I'm sure with the new Denisovan 30x whole genome sequence you can find a large enough set of these derived Neanderthal-Denisovan SNPs to conduct a valid test. The main problem is determining the ancestral allele for all these SNPs.

You could certainly search for these derived SNPs in the "Neanderthal windows" you found, even those derived SNPs that were not tested but which are in full LD with other ancestral SNPs that were.

eurologist said...

Ted,

See my post from Wednesday. ;)