May 13, 2015

Neandertal in the (immediate) family tree

Early European may have had Neanderthal great-great-grandparent
One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.

The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone's genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

15 comments:

Michael Boblett said...

I hear rumors about this man's Ydna. Anybody? Or shall we start guessing? Basal R, which is what I heard?

My Username Is Inigo Montoya said...

How plausible is it that these Neanderthal-enriched Europeans had their genomes subsequently diluted back proto-Eurasian levels by new OOA migrants?

eurologist said...

This makes perfect sense, given that late SE European Neanderthals look less archaic, and that early SE European and Levantine modern humans tend to have some archaic features.

A jumble of just a bit of Neanderthal DNA in most chromosomes, but a lot (~1/2?) in one, might indicate that the admixture was from a Neanderthal that him/herself had modern human admixture quite recently.

Of course, there were many Paleolithic entry ways into Europe - directly from the Levant, mixed from the Levant and a much more northern route north of the Black Sea (recently ~confirmed), an Anatolian route, and a northern route above the Black Sea, and then important changes in the Gravettian.

Still, hopefully the researchers can find sufficient markers to determine whether this Neanderthal DNA is more similar to Europeans than to Asians, or whether perhaps this particular individual and its group did not share much DNA with modern Europeans.

Slumbery said...

"...questions the idea that humans and Neanderthals interbred only in the Middle East..."

Was there such an idea? I thought the idea was that most of the extant Neandertal DNA is from that Middle Eastern interbred.

Grey said...

Only once never made much sense imo.

arch said...

"Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts"

The common thread tying together the gallery of Neandertal-centric familiars seems to be the Max Planck Institute.

I have seen this researcher openly affiliated directly with Max Planck in previous such 'discoveries' always centering around Neandertal genetics alleged in modern humans, however in this 'discovery' it appears that she is distanced from M.P., and assigned to a new scholastic point of origin.

The real immediate red flag for me here is that as before, the ancient human results are seemingly not even a matter for actual inquiry or concern, whereas the entire purpose and goal seems to be alone to attribute escalating 'Neandertal' ingress into modern humans, especially to find a route to assign such ancestry into European populations.

This was similar to the manner in which Planck centered a recent neandertal paper seemingly almost entirely around claims of preserved ingress into modern humans, while showing no apparent interest in any other facet of the issue, and making huge noise over the length of archaic segments when this was of no significance and utterly expected. It would have been exceptional if all segments were NOT showing less recombinant activity..

I would like to see a breakdown of WHO is funding Max Planck in this peculiar effort, what are the prime sources underwriting their lab and field efforts, and why.

This whole bizarre exercise is becoming similar to a car repair tech who does nothing 24/7 except talk about the 1973 AMC Gremlin, despite the fact that it is long out of production, no one owns, one, no one he talks to has ever had one, and none are in operation within a 100 county radius of his repair shop.

The material is ARCHAIC. It is not necessarily Neandertal in origin, and if it is Neandertal in origin, its not likely the ancestor of any modern europeans because it is not part of the modern Indo-Euro populations ancestry that we understand within our time frame as 'Europeans'.
It is infinitesimal statistically that this example or its genetic cohorts survived to produce descendants, and these would have been part of the pre-Indo peoples largely extinguished by Indo European population movements.

I think that if this material truly is Neandertal, the mark would be that it carries archaic segments in common with OTHER Neandertal tested remains, which are NOT in common (entirely) with other modern humans. The hybrid from 40k years ago would carry some segments lost in modern humans entirely over millenia due to random inheritance.

If instead, the subjects remains carry the same archaic segments common between extinct denisovans, neandertal and modern humans, it tells you pretty clearly that what this really is = archaic material in common between all populations descended from a ancient common ancestor --- which is what was clearly and UNDENIABLY the case all along for some if not most or even all of this material.

The promoters, planckers, etc, lose credibility with me because they have a single minded and seemingly extremely well funded tendency to go in only one direction, which is neandertal sexual ingress into modern europeans. PROVE IT. Better yet, prove a lot of stuff and add value to the WHOLE of ancient genetics instead of this same story seeking to 'dig up' a case to attribute neandertal sexual ingress into europeans for what appears to me to be a politically correct purpose, not one of scientific necessity.

My Username Is Inigo Montoya said...

@arch I wonder, what would be the value of proving Neanderthal introgression in non-Africans for any "politically correct purpose"? How is the alternative un-PC?

Grey said...

"The real immediate red flag for me..."

Mine was the (silly imo) idea that there was only one admixture event and then all the neanderthals (or other archaics) died off soon after.

If they were cold adapted then they would likely have survived latest in the far north or up in the mountains e.g. Himalayas, and/or heavily admixed populations would have survived longest in the far north or up mountains.

The possibility of much more heavily admixed hybrids possibly surviving quite late seems pretty interesting to me.

terryt said...

"This makes perfect sense, given that late SE European Neanderthals look less archaic, and that early SE European and Levantine modern humans tend to have some archaic features".

A fact that has long been totally ignored by those proposing minimal, or even no, mixing between Neanderthal and Moderns. To me mixing has long been obvious. What this paper suggests is that early mixes that developed on the margin of modern human expansion were replaced by later movements from some 'core' region, presumably somewhere in South Central Asia.

"might indicate that the admixture was from a Neanderthal that him/herself had modern human admixture quite recently".

I see no reason why that is not possible, perhaps even likely.

"It is infinitesimal statistically that this example or its genetic cohorts survived to produce descendants"

I think it is specifically stated that it did not leave any surviving descendants.

Mike Thomas said...

@ eurologist

"m the Levant, mixed from the Levant and a much more northern route north of the Black Sea"

Proven ? When & how ? I do t think it has actually, u less you're referring to the abortive colonisation pre-CI eruption ?

Arch
Interesting comments. Are u saying there's is a secret Neanderthal lobby? Ha ha . But in seriousness , is this PC agenda yr implying a move toward proving indiginism of modern europeans ?

eurologist said...

"I hear rumors about this man's Ydna. Anybody? Or shall we start guessing? Basal R, which is what I heard?"

Michael,

A bit early and a bit to far west for basal R, IMO. C, and probably G and F and perhaps IJ were around, locally. The problem is that none of these except perhaps C and perhaps IJ have left significant traces as ancient trees for today. So, my "bet" is on these.

"How plausible is it that these Neanderthal-enriched Europeans had their genomes subsequently diluted back proto-Eurasian levels by new OOA migrants?"

Inigo,

Not plausible, at all. There is no record of ooA after ~60,000 ya (and only a slight one after ~130,000 - 105,000 ya, to boot) until the spread of Afro-Asiatic languages in fairly recent times, and for the most part, this is restricted to North Africa and (the extreme) SW Asia with some recent admixture in the Mediterranean and other European coastal cities, during historic times.

It is much more likely that multiple waves of AMHs, with a fairly constant 2-4% Neanderthal admixture, arrived via several corridors between then and the present. The most noteworthy are the Gravettian, the post LGM expansion, the Neolithic, the "Mesolithic revenge" period (medium to late Neolithic), and then the Copper Age/ Chalcolithic, the Bronze Age, and the Iron Age.


arch,

Why are you so afraid that Europeans actually have Neanderthal DNA, when the majority of your genome is archaic (i.e., it is the same as Chimpanzees to about 95%)? The Max Planck Institutes are Germany's best research centers - comparable to Stanford, Berkeley, Harvard, MIT, etc. Why indulge in conspiracy theories, when in reality all of the world-wide anthropology, genetics, and archaeology has been closing in on the same results for decades?

Grognard said...
This comment has been removed by the author.
arch said...

"@arch I wonder, what would be the value of proving Neanderthal introgression in non-Africans for any "politically correct purpose"? How is the alternative un-PC?"

My guess.. and I fully concede its my guess.. is that German industry is mega-funding Planck in a way that is 'kid in a candy store' to those within its ranks receiving Das Bounty, however there is to me clearly a reluctance to delve into the 'meat and potato' potential of ancient or historically modern genetics, my guess is because of the Eugenics legacy dating back to the 19th century.. I think this does not affect Planck alone, and its my opinion that this is why we get nonsense about wild boar genetics and ancient bear DNA, and any remote human population that does not relate to European or old world historical populations which could be accused of fostering racism or nationalism. The German industrial powerhouse is a formidable source of near bottomless funding, but I suspect it may quite likely be more willing to fund certain venues of inquiry that are not controversial.

While Germany is in no way alone in its involvement in historical Eugenics and genetic precursor 'fields of study' that are today either discredited (skull measuring to detect future criminals, trying to prove someone of some group to be inherently better than others etc..) or considered suspect/nationalist, its probably a lot more sensitive to a fresher communal legacy and awareness due to NatSoc ideology, and I think its probably scared that its 'bad for business' to be seen as incrementally moving toward something perceived as 'eugenics'.
'Cavemen' are not Eugenics because it offends no one living, and alleging that primitive Neandertal gave modern Europeans their Blue eyes or fair hair is actually 'counter-eugenics' to the point that you might get a award from someone for this brave and collapsed pronouncement at this point in history. (I do not think Planck was involved in the Neandertal phenotype mutation hysteria, however I point this case out as only ONE example of how badly this particular field of study was abused in my opinion)

I think this could also play a role in why a Scando-Estonian, a non German, was selected to head these efforts, since it places a non-German decision maker between German industrial funding of Planck's DNA sciences effort, and the content of its efforts.

To have ANY legit study that is not being subconsciously or deliberately SHEPARD-ED to a certain conclusion, I think you need to do two things -
1/ concede prominantly that this archaic material common across primates, extinct human populations and modern humans in some cases is in SOME MEASURE inherited material from a common ancestral inheritance.
2/ explain HOW you separate ancestral component from the material attributed to sexual ingress across extinct and modern human populations.

While even I have no doubt of any sort that at some point some Neandertals / Anatomically modern humans biologically could impregnated one another, I do not think that any of them would survive into modern humans in any sort of scale, and I DO NOT think this is remotely the best interpretation of data when we already know that some of this material statistically virtually has to be common (asexual) ancestry from common ancestors.

I also think that ONE modern human legacy genome would exist SOMEWHERE on planet earth, more likely in at least ONE reservoir human population, that contained a Hg derived from the Neandertal legacy Hg. While you can correctly point out that some ancient Hg or Ht are present in ancient A.M.-human remains but absent in modern human populations, SOME ancestral Hg from Y-Chromosomal Adam still exist and we carry it. Its not credible to me that they had any substantial ingress, yet not one single legacy sub-HG is carried by one maternal line in eastern Siberia or Central Mongolia, or some lone example SOMEWHERE.

arch said...

"Arch
Interesting comments. Are u saying there's is a secret Neanderthal lobby? Ha ha . But in seriousness , is this PC agenda yr implying a move toward proving indiginism of modern europeans ?"

I predicted here in another thread that the sexual ingress familiars would get their clocks cleaned in their original set of theories, and the main Neandertal admix claimants did have to 'jump ship' their original theories. I suggested some would eventually begin slowly working their way back to trying to particularly link Neandertals to Europeans. The original claims some asserted tying Neadertals to the phenotypes found ONLY in Europid peoples collapsed (I do not think, as far as I am aware, Planckers specifically were responsible or related to that debacle).

Those who were promoters or sympathetic to the sexual ingress claims had a lot of people on their hands who their peers had assured that they got their red hair or blue eyes from their G.g.g-infiniti Neadertal grand-daddy/mother, so they created a last ditch theory that required sexual ingress IN EUROPE but on a micro scale IMMEDIATELY after AMH's migrated.. I THINK this was custom tailored primarily to avoid placing the point of admix in North Africa, which would have been a verdant paradise at this point in time, nearly a agrarian paradise, before the modern Bantu grazing practices destroyed and silified what is now the Sahara.

There was no reason that such admix could not be in the well watered North African or central african locale, except it basically opens them up to those who have long criticised the goals of many of the admix promoters which was trying to find a specific tie to Europeans - i WILL admit it made sense at the time, to look for such a specific link. It made sense THEN, but not given what we now know. Given that a Indigenous Borneo native or a average East Asian generally had as much or more claimed 'Neandertal' ingress as a Spaniard population living in a late stage Neandertal inhabited preserve, the simplest answer is the most likely.

I think, its always acceptable and fundable to suggest DNA evidence for a 'cave man' or extinct primitive ancestry for Europids, because no one is going to take to streets burning cars, protesting or demanding your firing. You need to explain and open for others to critique exactly how you managed to detect ancestral origin genetics from sexual ingress genetics, and what the relative proportions are.

If you are truly, TRULY asserting that ALL such material is EXCLUSIVELY sexual ingress in origin, then you need to state that in paragragh 1A, and stand up to the critique, not bury a "we cant rule out ___" clause 100 pages into the study where your backside is covered but you obfuscate the "we cant rule out" in a place where it will not be exhumed. I have not read this particular study, since, well, no one has, but I will read it to see if my "we cant rule out ______" can be found hiding like a 'Wheres Waldo' caricature.

I also dont like these 'LEAKED' Studies, because I suspect it may well be used to close up holes in the study offerings before it gets into the wild, but I already stated that this particular case may present a critique opportunity that I am eager to investigate. DOES the ancient sample share SOME material in common with ONLY other extinct Neadertal/Densiovans, that are NOT found in any modern extant human populations????

THAT would be the mark of legit case of ancient sexual ingress - on the other hand, if it does not share significant segments that are LOST in ALL MODERN HUMANS, but are in common with a immediate relative in its own time who was a complete biological Neanderthal, the material is simply a common genetic ancestral component of all populations derived from a commmon ancient ancestor, and the matter is settled - much to the dissatisfaction of the admix promoters.

Groggard said...

@Arch LOL


People don't care about dismissing skull shape as anthropologically meaningful due to eugenics (which was never a use) but so they can obscure any differences in european populations (but no other ones). This is because in much of europe the current inhabitants are relatively recent conquerors, and to undercut the deep roots some of the people DO have such as basques in spain. Not to mention to go along with the whole 'race doesn't exist' communist dogma for which physical anthropology is an inconvenient fact.

The people doing all the research are from red sweden, the most politically correct place on earth, and the planck institute and a little bit of the ivy league, which all suffer the same issues. No real ethnic german is likely to have any chance to get tenure in the first place unless he is publicly as self hating as humanly possible. That is the main reason we get many of these ridiculous studies. Or rather good data (though often looking in places that are not that interesting) followed by laughable conclusions that are little more than political diatribing.

There's an incredible bias here but it is very much the opposite of what you believe. Svante Paabo works incredibly hard to paint europeans as nonneanderthal, and expected to find zero neanderthal in europeans, which is the 'anti-racist' politically correct theory, that we all share a very recent african origin.

But I agree that it's better to say 'archaic' not neanderthal. We don't know where those genes come from, or when. OTOH we don't know where 'modern' genes come from or when either. It's not like they have been found in ancient african DNA.

http://www.scirp.org/journal/PaperInformation.aspx?paperID=19566#.VSF0suEvcWk

According to this study, while A y-dna is the oldest...caucasian y-dna simply doesn't descend from it. They have an older common ancestor at some point, not yet found.