June 24, 2015

Oase1 had a Neandertal ancestor no earlier than ~200 years before his time

Several important conclusions of the discovery that Oase1 had a Neandertal ancestor 4-6 generations before his time (37-42 thousand years ago):
  • This is a smoking gun that modern humans interbred with Neandertals, following up on the publication of the Ust'Ishim and Kostenki-14 genomes; these two had longer Neandertal chunks than modern humans, from which it was estimated that their Neandertal admixture happened more than 50,000 years ago, roughly what one gets when looking at Neandertal chunks in modern humans alone. The Oase1 has even longer Neandertal chunks, and Neandertal admixture happened in its very recent past. 
  • So, it seems that Neandertal admixture was not a one-off event but is bracketed at least by the period 50-40 thousand years ago and happened in at least two places: Europe and the Near East.
  • The fact that the earliest European sample (N=1) has a recent Neandertal ancestor indicates that Neandertal admixture in the earliest Europeans cannot have been extremely rare or non-existent; if it were, the chances of finding one with the first try would be extremely low.
  • It is unlikely that Neandertals were killed off by modern humans immediately after the arrival of the latter in Europe, as the Oase1 is dated well after the arrival of modern humans to Europe.
  • Modern Europeans don't seem to be particularly related to the population of Oase1. After one substracts contamination and Neandertal admixture, what is left over is actually closer to East Asians than modern Europeans. But, it's equally close to East Asians and European hunter-gatherers. This can be explained if modern Europeans have ancestry from the mysterious "Basal Eurasians" via the Neolithic farmers.
Why did the Neandertals (and the significantly-Neandertal admixed AMH like Oase1) disappear? My bet is on the Campanian Ignibrite eruption.

Nature (2015) doi:10.1038/nature14558

An early modern human from Romania with a recent Neanderthal ancestor

Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel, Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich & Svante Pääbo

Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Link

19 comments:

German Dziebel said...

"After one substracts contamination and Neandertal admixture, what is left over is actually closer to East Asians than modern Europeans. "

Good try but to be exact, Oase is closer to modern Amerindians (and of course MA-1) than to modern Europeans, modern east Asians or even Ust-Ishim or Kostenki (Extended Data Table 1).

Groggard said...
This comment has been removed by the author.
andrew said...

"It is unlikely that Neandertals were killed off by modern humans immediately after the arrival of the latter in Europe, as the Oase1 is dated well after the arrival of modern humans to Europe."

At 37,000 to 42,000 years ago with the best estimates of the disappearance of Neanderthals in Romania favoring the older dates, Oase1 is still soundly within the Aurignacian era, which was the first wave of modern humans in Europe and with dates estimated ca. 47,000-41,000 (calibrated radiocarbon dating) to 45,000-35,000. Modern human arrival in this part of Romania could easily have been just 2,000-3,000 years old when Oase1 died.

Also, just because some modern humans arrived at the early end of the Aurignacian doesn't mean that others didn't join the party in the middle or end of that time period, particularly given the fluid movements and small units of social organization for hunter-gatherers.

The distance that ancestors of a hunter-gatherer in Romania could hail from four to six generations earlier is considerable. Certainly, locations from Italy to Turkey would be within the realm of the plausible, and the Caucasus to Syria to Spain would be within the realm of the possible.

Admixture itself, of course, is proof of some period of co-existence, and conventional wisdom seems to be that in any one place there was at least a thousand years of co-existence.

I think that the 6% to 9% figure may have particular significance because that is right around the level of admixture at which a mixed race individual can "pass" for a member of his or her majority ancestry.

It would be interesting to see if there is any way to discern any biases in the Oase1 genome that favor a male or female Neanderthal ancestor. For other reasons, I think the evidence favors a scenario in which Neanderthal hybrid individuals who have descendants living today overwhelming were the product of a male Neanderthal and a female human giving birth to a female hybrid individual. It might be possible to look at the specific loci of the Neanderthal components to see if this possibility is statistically favored.


terryt said...

Another conclusion is that several different groups have moved north in Eurasia at separate times, and from different regions, only to die out (haplotypes at least). Y-DNA of Ust-Ishim, Oase 1 and Kostenki have become extinct. The same could basically be said of MA-1's Y-DNA. The same is true of mt-DNA of Ust-Ishim and Oase 1, and even Tianyuan.

eurologist said...

"However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe."

I don't see the logic of this statement. Obviously, this individual is closely related to the first people who made it into Europe, some of whom very likely got there directly, without first sampling the Levant and surroundings. And from uniparental DNA we know they came from the eastern subcontinent and/ or SE Asia. Clearly, extant East Asian have as much diverged from that original population as Europeans have - so one would not expect any closer relationship from the get-go. Then you add 40,000 years of divergence and West Asian ("Basal Eurasian") admixture - and com to the conclusion that people like Oase1 could have contributed 50% - 80% to various modern Europeans.

Grey said...

"Why did the Neandertals (and the significantly-Neandertal admixed AMH like Oase1) disappear?"

I think they had genes that were important for survival in the far north (or the far interior away from the coast) and when they interbred those genes crossed over to AMH so they lost their advantage

but only gradually - I think they or at least heavily admixed versions may have survived quite late in the coldest mountains leading to the various legends.

David Jacobson said...

The European population was surely disrupted by the maximum of the last ice age. A discontinuity between earlier and later European populations should be no surprise. The relationship between people in Romania and in East Asia suggests a wider then expected distribution of people with East Asian genes. Those results suggest skepticism about the kind of thinking that has located the main event of modern humans and Neanderthals in the Near East. They suggest even more skepticism about thinking that wants to imagine some simple pattern of European settlement by the initial expansion of early farmers. Europe has been peopled by thousands of years of human migrations. Resettlement by hunter gatherers at the end of the ice age surely was one kind of event. Expansion of farmers was another. Those surely have been supplemented by a variety of migrations across Central Asia, across the steppe lands North of the Black Sea, and into Europe through a variety of routes. The last two thousand years show many examples of those kinds of movements. Evidence is accumulating for a number of bronze age examples. People knew how to walk and how to use boats
even earlier. There is no prospect of identifying all these migrations and their consequences even with whole genomes from a modest set of ancient bones.

aeolius said...

The question arises as to why there was or is a general sense of the rarity of mating of Neanderthal and AMH. Perhaps it arises from the same source as racism.
An examination of the former might give a disproportionate understanding of the latter.

jeddom said...

Dienekes, I hope this is not too far off topic, but what would happen in a case of microchimerism occurring in the ancient remains being sampled, i.e., if the organism being genetically tested contained two distinct cell lines, due to one of many possible medical reasons? Would one or the other be ruled out as 'contamination'?

For example, what if a 40,000 YBP female AMH-Neandertal hybrid, in addition to her own DNA had a cell colonization of cells from her fetus, which contained a different percentage of Neanderthal ancestry?

How would this situation be interpreted under current conditions?

epoch1970 said...

This is more interesting than most people think. I refer to remarks om several boards and forums.

It clearly demonstrates that Neanderthals weren't killed off or competed away by Anatomical Modern People. And since this example seemed to have had very little if any descendants alive in current day Europe it may be evidence that whatever fate struck Neanderthals also struck the first modern humans in Europe.

Alexandros HoMegas said...

Its the Neanderthal admixture the makes Europeans and Asians more intelligent? I've read some time ago that jews have higher Neanderthal admixture.

Tobus said...

@German:Oase is closer to modern Amerindians (and of course MA-1) than to modern Europeans, modern east Asians or even Ust-Ishim or Kostenki (Extended Data Table 1).

You still don't get D-stats German? The Z-score is an measure of statistical significance - you need a Z-score of at least 2 and preferably 3 to show an affinity. Results like you are referring to with a Z-score of 1 or less mean that the reported score is *not* significant, and should be treated as a zero result. A rerun with a different outgroup or a different SNP set will likely give a different set of relative "affinities" - like we see when EDT2, the same run with transitions removed, gives very different results.

What these "zero" results in EDT1 show is that all modern and ancient pops form an outgroup to Oase, and the other (significant!) results show that all are closer to K14 and UI than to Oase. This is consistent with the results from the UI paper, which strongly suggest that UI represents a population ancestral to all modern Eurasian populations.

Tobus said...

@Alexandros HoMegas: Its the Neanderthal admixture the makes Europeans and Asians more intelligent?

Native Americans, Aboriginal Australians, Polynesians and South East Asians also have this same Neanderthal admixture, yet have a low average score on IQ tests - in some cases as low or lower than sub-Saharan Africans with zero Neanderthal mixture. Socio-economic factors are largely (if not totally) responsible for the idea that Europeans and Asians are "more intelligent" than other populations.

eurologist said...

"And since this example seemed to have had very little if any descendants alive in current day Europe it may be evidence that whatever fate struck Neanderthals also struck the first modern humans in Europe."

Again, while the paper makes similar statements, it does not provide any evidence for this.

Grey said...

"The question arises as to why there was or is a general sense of the rarity of mating of Neanderthal and AMH."

I don't think it was rare at all.

German Dziebel said...

@Tobus

"Z-score is an measure of statistical significance."

Nobody has ever shown anything different from what was presented with a different set of SNPs. But this is beyond the point. I'm not interested in debating your continuing pseudoscientific nonsense. Just one thing to say to close it off for good: what you just wrote is bad news for East Asians as they become sheer statistical noise. The only statistically significant connection is between all those ancient Europeans and Amerindians.

raphael petit said...

Here are the Globe 13 results (from Genetikers) for this first modern Western European that show high values for African (20%) and Asiatic components :

DODECAD /GLOBE13:

•24.46% South_Asian
•14.60% East_Asian
•12.10% North_European
•9.93% Australasian
•8.36% West_African
•7.60% West_Asian
•5.85% Palaeo_African
•4.80% East_African
•4.52% Southwest_Asian
•3.49% Mediterranean
•2.13% Arctic
•1.36% Amerindian
•0.80% Siberian

And Oracle results (using Fst):

1 ColouredWellington_Sch 26.3
2 Brahmins_from_Uttaranchal_M 30.2
3 Uygur 35.2
4 Uzbeks 36.0
5 Hazara 36.5
6 Burusho 37.1
7 Tajiks_Y 37.3
8 Bnei_Menashe_Jews 37.5
9 Cochin_Jews 38.0
10 Brahmins_from_Uttar_Pradesh_M 38.1
...
42 Puerto_Rican 45.4
....
54 Yemenese 47.3
...
57 Turks 47.6
...
60 Romanians 47.8

90 Algerian_D 50.3
...
138 French 55.6

Interestingly, the closest modern Europeans to this first "Romanian" are...Romanians

Globe4 results for information:
•39.07% European
•37.09% Asian
•20.75% African
•3.09% Amerindian

Srivatsan Kannan said...

Dear friends,
Im Srivatsan from Chennai, India. I know nothing of genetic science. My cousin recently tested his Dna. I have the raw data file with me. We're from iyengar - brahmin caste. The Aryan migration theory has always intrigued me. Can anyone help me analyze the results & throw some light on our ancestry ?
Thank you

Srivatsan Kannan said...

Dear friends,
Im Srivatsan from Chennai, India. I know nothing of genetic science. My cousin recently tested his Dna. I have the raw data file with me. We're from iyengar - brahmin caste. The Aryan migration theory has always intrigued me. Can anyone help me analyze the results & throw some light on our ancestry ?
Thank you