May 02, 2016

Neandertal ancestry, going, going, ..., gone (?)

A deluge of new data from Upper Paleolithic Europe will give us all a lot to think about. It is incredible that Neandertal ancestry seems to have decreased over time in Europe (Oase1 is off-cline with lots of extra Neandertal ancestry from a recent genealogical Neandertal in the family tree). The functional form of the decrease seems pretty well approximated as linear.

The authors write:
Using one statistic, we estimate a decline from 4.3–5.7% from a time shortly after introgression to 1.1–2.2% in Eurasians today (Fig. 2).
This is remarkable because it shows  that most of the Neandertal ancestry of the earliest AMH in Europe was gone by the Mesolithic. It really seems that Neandertal genes were bred out of the gene pool over time. Will this trend continue into the future? Perhaps only minute traces of Neandertal DNA will remain in humans in 10,000 more years. Some of Neandertal DNA may yet prove to be neutral or beneficial, so at the limit the percentage may be more than zero. Nonetheless, the historical trend does suggest that modern humans inherited mostly genetic garbage from Neandertals and evolution is more than halfway through the process of getting rid of it.

As a corollary, there may have been other episodes of archaic admixture that are no longer detectable. Perhaps our modern human lineage has repeatedly admixed with other species, but traces of those admixtures are long gone by the action of natural selection. The reason for our relative homogeneity as a species may not be that we avoided intermixing with others, but that, sadly, most others had not much that was beneficial to offer to our ancestors.

Nature (2016) doi:10.1038/nature17993

The genetic history of Ice Age Europe

Qiaomei Fu et al.

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.



Matt said...

To add to this, the purifying process seems to be paralleled in a Neanderthal that had admixture from Sapiens (Hawks -

In a way, poor fitting parts may make more sense as an idea than garbage (because selection in Neanderthal seems to have treated AMH ancestry as garbage as well).

More than anything, this makes me question our methodology for finding divergence dates between Neanderthal and AMH lineages. It seems like in light of this, its more possible than Neanderthals had admixture from Sapiens ancestral Homo Out of Africa, which was cleansed from them in a similar process to what we see here. If you can go from 5% - 2% in 50,000 years, and possibly thence to 0% in another 50,000 years...

We would have thought this would not be the case, on neutral ancestry, yet this finding shows that it may have been the case.

Another thing here might be whether we would find a lot more Denisovan ancestry in ancient Oceanians.... and whether the differences in Neanderthal ancestry between Eurasians and Africans and different Eurasians are associated with between population fitness (or perhaps only with within population fitness).

szopen said...

What about the possibility that neanderthal ancestry dropped, because the population with higher neanderthal ancestry were conquered by subsequent waves of newcomers?

Mark Moore (Moderator) said...

Need more measurements but do I see a noticeable dip there about 13K ago? Four preceding measurements above the grey line, then two way below it. I can't see graph well enough but maybe someone who did can tell me if those measurements came from the Iran/Turkey area?

eurologist said...


First I thought migration could account at least for some of these findings, but it appears that the study rejects this interpretation in favor of deselection.

I am glad to see that that the early (>14,000 years) presence of R1b in Europe, especially in Italy, that some of us suspected, now has been confirmed. Similar ages for light eye color are encouraging compared to misguided and unsophisticated attempts of sweeping under the rug what we know about the vitamin D/ calcium balance versus folic acid preservation (i.e., people living farther north (generally, at higher or lower latitudes) must have lighter skin to survive, unless they have a diet full of vitamin D and/ or calcium).

It is interesting to do a little bit of history of science, on this. Almost every single time ancient haplogroups are recovered, they are much earlier (where found) than expected. Thus, there is overwhelming evidence that haplogroup timing is and has been systematically underestimated.

In the end, I think this paper is asking more questions about European Ancestry than it can answer.

War Lord said...

"We were surprised to find haplogroup R1b in the ~14,000-year-old Villabruna individual from Italy."

LOL When will they leave all those ridiculous age estimates placing the origin of European R1b to the Neolithic? It's the signature of the Aurignacian and it is 40 000 years old. The only key problem is, when R1b-S116 separated from R1b-U106. Was it during the pre-glacial times or during the Mesolithic/Neolithic? I am betting on pre-glacial times, because the history of R1b-U106 is tightly tied with I1a/I2a1b.

Judging from the Y haplogroups, the allegedly mysterious Near Easterners expanding 14 500 years ago are actually just I-M170 people expanding from a refugium in Southern Europe, although I suspect that I2a1b in Sweden and Luxembourg 6000 BC is an error. It should be I2a2!

What is truely surprising is the number of C1 and M in Europe during the Upper Paleolithic. Well, it is not such a surprise, if we admit that they were brought from Central Asia by the Aurignacian people, but such a high frequency in those few samples, and C1 instead of C3, and C1 among the Gravettian people (who should be I-M170)...

Athena said...

I just keep staring at Oase1, it really is such an outlier. In a sense, we're lucky to have found any genomes of that age that ARE so admixed. Going to this talk tomorrow ( and I will be interested to hear how Oase1 is explained under a 'no interbreeding' model.

Brian H said...

It might not *all* be garbage. Some of it might be formerly useful genetic information that has become steadily obsolete with time/changing environment. Either way it might appear to be be decreasing more or less isotonically with time.

capra internetensis said...


I don't agree that the haplogroups almost always end up being found earlier than expected. People were expecting to find J and E all over the Neolithic, but they seem to have arrived in force much later.

There is old R1b1a-L389* and R1b1c-V88 in Italy, so finding a sample of R1b1-L754* is not really surprising, indeed Gioiello predicted it. It is unexpected for people who thought R1b was far away to the northeast at this time and only arrived later, but that was just a hypothesis based on rather flimsy evidence. There is no conflict at all with the estimated age of the haplogroup itself (if you look at the Y-Full tree, L754 level is their L278 level).

@War Lord

can't tell if joking.

norim said...

Online access to this article has been provided by the content sharing initiative:

Anonymous said...

Also you don't even mention the 14,000 year old r1b y-dna found in Italy!

Hector said...

Wow, one errant ~15000 years old R1b was found in Europe and Eurocentrists are reviving the hope that R1b originated in Europe and perhaps K2b or P itself, not too far from Europe.

So many C's found in pre-Bronze Age Europe must be quite disturbing and now some of them are inventing the idea D is the true East-Eurasian lineage while C and F derived ones are introgression from "Caucasoids"(whatever that means).

Just hilarious.

Joyce said...

R1b in Europe expanded just a few thousand years ago from a few men and I doubt that it is a signature of blue eyes or light skin or any very ancient cultures. The iceman of Italy had blue eyes(probably deep blue)but darker skin and he did not have R1b. You can see Africa from Italy which is hardly a low light zone. It is hilarious to read the fragile ego of some men hanging on their precious Y which has nothing to do with phenotypes by itself. Because of the condition of Europe in Ice age, most of Europe was settled relatively late, so Europeans and Middle Easterners and North Africans share a lot of y and mtDNA. Ice Age "Europeans" seem unrelated to current Europeans, according to ancient DNA.

Adrian Purcell Heathcote said...

Joyce, amazing that you commented without knowing anything about the contents of the paper. It shows that Ice Age individuals HAVE contributed ancestry to modern day Europeans and that that the gene pool of Europe was stable from 37,000 to 14,000 years ago, when there were changes related to the Villabruna Complex.

As to your comments about fragile egos and the Y chromosome, it sounds as though you might be the one with the fragile ego. And perhaps it should be fragile since you are so manifestly ill-informed.

Unknown said...

"So many C's found in pre-Bronze Age Europe"

I'm not sure why it would be disturbing to anyone without a personality disorder almost as severe as your own, but if you actually bothered to read the papers, it'd be pretty obvious that none of them are calling European C 'East Eurasian'. It was a pre-intra-Eurasian-divergence haplogroup that essentially disappeared in West Eurasians.

eurologist said...


"I don't agree that the haplogroups almost always end up being found earlier than expected. People were expecting to find J and E all over the Neolithic, but they seem to have arrived in force much later."

Not sure who those people were, but they surely were largely fools.
I am more thinking about central European G subgroups, or R in Siberia or now in Europe, for example.

"There is old R1b1a-L389* and R1b1c-V88 in Italy, so finding a sample of R1b1-L754* is not really surprising, indeed Gioiello predicted it."

Yes, Gioiello is one of the "some of us suspected" that I mentioned in my above contribution.


"Wow, one errant ~15000 years old R1b was found in Europe and Eurocentrists are reviving the hope that R1b originated in Europe and perhaps K2b or P itself, not too far from Europe."

I have ever seen anyone spouting such nonsense, and in particular not in this thread, so I think you are fighting ghosts. With the exception that parts of Kazakhstan are within Europe.

Hector said...

" it'd be pretty obvious that none of them are calling European C 'East Eurasian'."

Neither do any reputable papers from the West(as opposed to former Soviet Bloc) call Y haplo Q, past or present,a West Eurasian lineage.
But many here including you do that. There are even more of your deranged comrades on Davidski's blog.

Adrian Purcell Heathcote said...

A quote from the paper. This appears to be a refutation of part of the claim in the 2014 Lazarides et al paper

“A previous genetic analysis of early modern humans in Europe using data from the ~37,000-year-old Kostenki14 suggested that the population to which Kostenki14 belonged harboured within it the three major lineages that exist in mixed form in Europe today: (1) a lineage related to all later pre-Neolithic Europeans, (2) a ‘Basal Eurasian’ lineage that split from the ancestors of Europeans and east Asians
before they separated from each other; and (3) a lineage related to the ~24,000-year-old Mal’ta1 from Siberia. With our more extensive sampling of Ice Age Europe, we find no support for this.”

The mixing of these components then must have occurred later. The Yamnaya invasion is looking more and more significant but was also proceeded (is my guess) by long-term intrusions from the same general area.

Onur Dincer said...


I'm not sure why it would be disturbing to anyone without a personality disorder almost as severe as your own, but if you actually bothered to read the papers, it'd be pretty obvious that none of them are calling European C 'East Eurasian'. It was a pre-intra-Eurasian-divergence haplogroup that essentially disappeared in West Eurasians.

Exactly. The same with European mtDNA haplogroup M, which disappeared with the LGM.

Joyce said...

@Onur, and Hamar too

Good news!!! C is found on every continent at low frequency ( moderate in some ethnic groups), except Africa. C and mtDNA M survived, but the superior R1b must be found at every important archeological site or it must be the de facto inventor if not found. C is significantly older than R1b and it is neither Asian nor European and it is everywhere.

Joyce said...


I apparently did not comment on the article. I was here to satisfy my curiosity about human evolution and human genetics, but amused how some men believe that their Ys must be the signature for both phenotype and invention at some archaeological site. Einstein carried E and Napoleon too.

Joyce said...

Oase1 clusters with Amerindians, according to a plot of the same article on another website. His tribe probably went to America if they survived. New migrants from Middle East diluted the assumed Neanderthal genes of earlier settlers. Those genes might not be junk genes. There were probably "archaic" humans evolved in Eurasia, or how did 70% of humans with a different version of MCPH1 from the ancestral one? It was not from Neanderthals or Denisovans. I doubt that humans got it from an unidentified H. Erectus (about two third of human brain size).

Adrian Purcell Heathcote said...

"There are even more of your deranged comrades on Davidski's blog."

If you have a problem with Davidski's blog why don't you go and post there. And I think what your trying to insult -- and doing ineptly -- is not Eurocentrism but what could be called "R1a/R1b-ism". The idea that Indo-European Europe is entirely a matter of warrior R1a or R1b males pouring in from Poland. FWIW I find that idea rather stupid too, but I don't think denying it would make anyone anti-Europe, as you seem to be.

Maybe sort out exactly what it is you hate before spraying the internet with it.

Onur Dincer said...

@Hector and Joyce

I will never be ashamed of telling the truth, no matter how politically incorrect it is.

eurologist said...

As to the new admixture appearing ~14,000 ya in the Villabruna Cluster, which has affinity to Near Easterners: it can of course not really be (what we currently think of) Near Easterners due to the lack of "Basal Eurasian" in Villabruna. I suggest a Balkan/ N Anatolian origin: firstly, we know that the Balkans were affected differently by the Gravettian movements/ transitions than the remainder of Europe. Secondly, the route between the SE Balkans and Anatolia was open, then (no Bosporus). Thirdly, a connection between the Balkans and Satsurblia (E Pontic/ Caucasus) is geographically quite plausible.

We desperately need ancient Balkan specimen.

eurologist said...

See also this new article perhaps confirming the isolation of a Basal Eurasian component in Southern Arabia:

Mark Moore (Moderator) said...


You did say "perhaps". I did not notice anything in there specifically tying R0 to the basal Eurasian genetic profile. I know that southern Arabia is where a lot of people think Basal Eurasian was hibernating, but where is the evidence connecting R0 to Basal Eurasian? Did I miss it or is this dot connecting which may not pan out?

YeomanDroid said...

I find it disturbing whenever people point out that R1b has been found in Upper Paleolithic Europe 14kya that it leaves the door open to assumptions and attacks about Eurocentrism and R1b-isms by stating a false narrative in order to support their own forced asserted opinions that R1b will never be found in Neolithic let alone Upper Paleolithic Europe.

A fact is pointed out and suddenly the fact pointing is an excuse to kill the messenger by stating the messenger is claiming something when in fact that is not the case. Instead, its rather dismissive and basically designed to shut out the fact R1b has been found in Europe 14kya and accuse the fact pointer of a dubious agenda - my only agenda is to find the truth. I'm not claiming this is the progenitor of all R1b in Europe, just merely pointing out that R1b is more widespread in early Europe than people were leading us to believe and NOTHING MORE!

What I found interesting is how ANE components may have been in Scandinavia >8000 years ago but not much attention is given to it. Perhaps not enough data but I expect the attacks to come just by pointing out this fact as well. What's next? Scientists actually corrupting the evidence of their discoveries to support agendas and a suppression of voices that are merely pointing out facts and wanting more answers. Tragic that this would be a thing in science accusing those of something that was never stated or claimed because they go against a view of the establishment or perhaps its just discriminatory agendas attacking R1b for whatever reason that may be.

Fun Fact: R1b was found 14,000 years ago in Europe. Deny it all you want, dismiss it as irrelevant all you want, and attack it all you want. It's here and there's nothing you can do about it but sulk in your tears of not being so right about everything you state! It is significant because it pointed out that many people were wrong when they said it (R1b) would never be found in Europe so long ago, as if Europe is some sort of exclusive club to specific HGs. Again, not stating the 14kya R1b found in Italy is a progenitor of anything but I do believe more R1b will be found with ANE components - meaning a Siberian origin, but coming to and fro into Europe as much as R1b pleased possibly entering through the Baltic/Scandinavian regions before 8,000 years ago - DEAL WITH IT!!!!!

shenandoah said...

What's so "sad" about feeling obligated by common sense to breed within your own species?

shenandoah said...

Why is limiting oneself to breed within one's own species "sad"?

Joe Lyon said...

Out of the entire genome of the Mystery Hominid (Homo Erectus soloensis), we only kept Microcephalin D...but it made a sweep of almost our entire genome. Same thing with the other hominids. We take what we need and we leave the rest.
The delusion is that we didn't do the same to members of homo sapien sapiens.
We likely have very little left that was mito Eve or Y Adam's contribution. Those two assimilated thousands of lineages of homo sapien sapiens too, and only kept what they needed- meaning they replaced what they had before.

Mark D said...

I know I'm late to this thread, but, for what it's worth - I'm not surprised by what surprises the authors, the Rib in 14,000 yo Italy. I've long been uncomfortable with all the Celts of the Atlantic Modal descending from steppe pastoral horsemen. I've thought for a very long time that R1b spread around the Med, that it was a littoral migration, possibly originating around the Black Sea and/or Caucasus and only the lack of ancient DNA on coastal areas subjected to flooding after the LGM would account for its absence so far. Moreover, there is an R1b isolate in interior Algeria unrelated to French colonialism. One doesn't have to subscribe to "Celtic from the West" to see that R1b could have spread around Italy and into Iberia, and then north to Gaul and the British Isles.