February 13, 2015

Why do East Asians have more Neandertal ancestry than Europeans?

This is quite the paradox, because even though Neandertals are now known to have existed all the way to the Altai, they were still overall a West Eurasian-distributed species. As far as I can tell, three explanations have been proposed: (1) East Asians have at least one extra Neandertal admixture event on top of what all Eurasians share, (2) West Eurasians have at least one admixture event that reduces their Neandertal ancestry relative to what all Eurasians share, (3) Neither of them have any such events, but natural selection has acted to reduce Neandertal alleles more in Europeans than East Asians.

I don't really have an opinion on this highly technical subject, but a couple of papers in AJHG make the case for (1 or 2) and 2, and against (3).

AJHG doi:10.1016/j.ajhg.2015.01.006

Complex History of Admixture between Modern Humans and Neandertals

Benjamin Vernot, Joshua M. Akey

Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians. We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected, suggesting that differences in selection cannot explain the differences in Neandertal ancestry. We show that two additional demographic models, involving either a second pulse of Neandertal gene flow into the ancestors of East Asians or a dilution of Neandertal lineages in Europeans by admixture with an unknown ancestral population, are consistent with the data. Thus, the history of admixture between modern humans and Neandertals is most likely more complex than previously thought.

Link

AJHG doi:10.1016/j.ajhg.2014.12.029

Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations

Bernard Y. Kim, Kirk E. Lohmueller

It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data.

Link

60 comments:

andrew said...

I suspect something like this:

(1) A common Near Eastern admixture not long after Out of Africa.
(2) A separate subsequent parallel admixture of a proto-West Eurasian population and a proto-East Eurasian population during the Upper Paleolithic.
(3) Dilution of West Eurasians, but not East Eurasians, with further migration from the Near East after the LGM, that does not occur in East Eurasia.

One key data point in this analysis is the high Neanderthal admixture of Otzi the Iceman who is himself a hybrid individual.

Alexandros HoMegas said...

It true that jews also have a high rate of neaderthal genes?

terryt said...

"We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected"

Makes complete sense to me. After all we have a raised level of Denisova genetics in Australia/New Guinea which would appear at first glance to have originated in or near the Altai region. That would have to be part of a first pulse, but would negate to a large extent an original southern route to SE Asia. However it seems obvious to me that F-derived Y-DNA did move east through South Asia and so that leaves Y-DNA C as candidate for any northern movement.

Alashire said...

https://www.youtube.com/watch?v=z3hS-dXhJpM
+
https://www.youtube.com/watch?v=GyVkvhTZBfA
=
https://www.youtube.com/watch?v=lCmKwGuFnCI

watchem and weep!

Grognard said...

Single admixture idea has always been hilarious and eyeballing the raw data from IBDs a long time ago looked nothing like what I would expect for that, which seemed to show continuous admixture over a very long time.

There's still many big assumptions here, such as assuming that selected areas will always be the same which is NOT the case. We can only reasonably detect what is selected for in modern times, and that may actually be the reverse of what was previously selected for.

Europeans have the most variation in many ways but are highly, highly homogenous for a very large number of 'modern' genes. This in fact is EXACTLY what you should expect to see after a large number of genes become fixed in the population.

The other option that can make this happen is for an amazing founder effect to take place that fixes all these hair and skin and unknown genes in the population, but when we look at ancient eurasian DNA we can see this seemingly did NOT happen because these populations are much different than modern europeans.

It's a giant assumption to say ANY of these genes come from any particular source since we don't have ancient DNA for them. IE if this all came from a giant founder effect from out of africa then we would see this ALL OVER but we don't.

So there is either still some GIANT population hiding in eurasia UNTIL SURPRISINGLY RECENT TIMES (also hiding our r1b y-dna?) which later DRAMATICALLY expanded or option 3 is the correct one, or else things are way more complicated than anyone has suggested so far.

Since we don't really have any 'modern' DNA yet from either europe or africa which was around BEFORE neanderthals (and possibly such a thing does not even really exist, genetics is not like mixing oat cakes) we can't really say what happened yet and probably won't be able to reject the wrong hypothesis until we get a lot more ancient DNA in the 80k+ range from eurasia and africa.

Grognard said...

Also, to answer the original question is pretty obvious. East asia is shielded from intrusion from the west. So whatever option is correct in how eurasians came to be like they are, you expect the same result for east asians.

aniasi said...

Has any study been done to compare this to South Asian, Southeast Asian or Austalasian populations? That might provide a better clue as to what admixture events, or lack of them, led to the higher distribution in East Asia.

Mike Thomas said...

# 2 & 3

Grey said...

Or Europeans have more but it's a different kind (or kinds).

Alashire said...

https://www.youtube.com/watch?v=HDHy_WtRrgA
and here is one who might be still a male line of highland cattle, but mixed with ages of bison.

oh boy what if he is y line/ breed of highland .
I don't know if does India have other hairy cattle golden colors . but I will still guess this one is highland and Goar and been there since before Alaska was Hawaii because there is no way in hell they went by way of bering straits.


even more hilarious is to think just how Close
Both the Tamahu and the Mengewi/ Menes / Mn are near to these very same areas as these same bison.... showing a connections which spans ages before some horrid event which pushed "Beringa " where it sits now . what for sure did not happen was that our Bison did not get there by way of Beringa and where it sits now. we for sure know that our bison and highland cattle did not come from a frozen place there not without human care like highland cattle need today in sub zero areas !!

Alashire said...

http://www.ancientworlds.net/aw/Post/1130537

do those cattle/ Bison look familiar ?

Mn = Menes = Namer =
Mengewi

the world has always been a freeway until the bronze age collapse/ the events which are memorialized on the Pictish Rhyniestones and also Serpent mound.
when Alaska was by Hawaii

donaldwaggoner32 said...

Plains Indians have the most Neanderrhal DNA which fits with their physical features (recessed zygomata, long and broad spear-like noses, large facial and mandible size, brow ridges).

http://anthropogenesis.kinshipstudies.org/2012/03/american-indians-neanderthals-and-denisovans-pca-views/

Levalloisio-Mousterian lithics are now confirmed in the southeastern USA:

http://www.academia.edu/3412562/Capps_A_Levallois-like_Prepared_Core_Technology_in_the_Southeastern_United_States

German Dziebel's out of America theory is another legitimate hypothesis, as is Multiregionalism, as the Neanderthal DNA in both Amerindians, Asians and many Europeans is simply way too high to be the result of ancient admixture. Most people have the yDNA equivalent of a Neanderthal great great great grandfather, and we haven't even extracted aDNA from a Neanderthal yet.

dwaggonerstr said...

Alexandros Homegas:

No, Jews and middle easterners have even less Neanderthal DNA than European according to Dziebel.

Arvid Eriksson said...

There is also another possible explanation:

That the African reference used to measure degree of Neanderthal admixture in non African populations is ill suited for this purpose. It has already been fairly well established that gene flow back into Africa explains the bulk of variation between populations within Africa. The gene flow back into Africa from East Asia is probably smaller than that of West Asia and Europe which is why East Asians are more different from Africans than West Asians and Europeans.

arch said...

Number 4 - the Only real plausible and likely explanation ..

What is wrongly being termed Neandertal DNA is actually stable Archaic DNA in certain regions, and its common to all modern and extinct human populations except for S.S. Africans who descend from a slightly earlier branch.

The big problem that all the Neandertal hysterics have faced and not conceded as they fanatically tried to make cases for Red Hair and Blue Eyes being 'Neandertal' contributions specific to EUROPEANS,
was once it was shown that Europeans are not in any way the most genetically similar to archaic genetic regions also found in Neandertals.

The reason that this was a huge problem was that they were at that time still attempting to ALSO defend claims that Europeans had Neandertal ancestry from much later and more recent cross breeding with Euro populations of Neandertals.

They had to run from these earlier claims, with NO public retractions or staged mea culpa's, because its not Europeans or folks with Red Hair and Blue eyes who possess most of the archaic similarity with Neandertals.

In the end, its going to come out to a case that is not politically correct, and its a showcase for why science breaks down once it hits a wall known as political correctness.

S.S. Africans are more distantly related to other modern humans that are some genomic regions within a extinct species of Neandertal, and that is the reality.

That is also something that no scientist wants to publish, mention, discuss or research because while its the only plausible reality, its also a career killer. SO we get any explanation except the most obvious, and a latice-work of interlocking theories that are in many cases completely collapsed, seeking to force through a prefabricated case that is already in ruins.

Tobus said...

@Alashire:when Alaska was by Hawaii

That's about 300 million years ago... cattle don't appear until about 10 million years ago, and bison not until 2 million. Your timing is out, by several orders of magnitude.

Beringia is not "a frozen place", it's a steppe/tundra that remains ice-free during the ice ages and thus becomes a refuge. In these times the sea levels also drop so that it becomes a land bridge that connects Siberia and Alaska, and this is why so many species have crossed it. Plants and animals can survive there while all around is uninhabitable, and then expand outwards again when it warms up. Scientists estimate modern humans may have survived in Beringia for up to 10,000 years before expanding into America.

until the bronze age collapse/ the events which are memorialized on the Pictish Rhyniestones and also Serpent mound.

I sure hope you're not talking Noah's Ark nonsense again.

terryt said...

Alashire, I don't know what you are on but Highland cattle, bison and gaur are similar only in the fact that they are all cattle. The outline of their evolution and expansion has been well covered and I advise you look it up. Cattle first originated near India and the ancestors of water buffalo and gaur moved eastward, yaks evolved from northward moving populations as did bison basically. In Europe and Africa the cattle became aurochs which survive today in the form of domestic European and African cattle.

" what for sure did not happen was that our Bison did not get there by way of Beringa and where it sits now".

It is 'for sure' that bison entered America via Beringia although European and American bison have reasonably distinct mt-DNA.

"when Alaska was by Hawaii"

Hawaii has never been anywhere near Alaska. In fact many Hawaiian islands have only been in existence for some ten million years, by which time Alaska was well and truly where it is now.

Marcel F. Williams said...

That's because there's only been one major out of Africa event (~2.1 MYA) and the common ancestor of Neanderthals, Europeans, and Asians were part of that event.

Gene flow from out of Sub-Saharan Africa into Europe via the Arabian Peninsula during subsequent interglacial periods, however, has made Europeans genetically more similar to sub-Saharan Africans.

Marcel

andrew said...

"After all we have a raised level of Denisova genetics in Australia/New Guinea which would appear at first glance to have originated in or near the Altai region. That would have to be part of a first pulse, but would negate to a large extent an original southern route to SE Asia."

I think it is far more likely that the Altai population was a relict of a population that was originally found in mainland Asia, than the other way around. Existing Denisovan DNA in human surely had its source in an Indonesian population, not a northern route one.

"Has any study been done to compare this to South Asian, Southeast Asian or Austalasian populations? That might provide a better clue as to what admixture events, or lack of them, led to the higher distribution in East Asia."

John Hawks has blogged about the fact that the Neanderthal genes in East Asians (especially the low frequency ones) do not overlap heavily with the Neanderthal genes in Europeans. There is more overlap of high frequency genes. This tends to suggest secondary admixture in both populations.

"German Dziebel's out of America theory is another legitimate hypothesis, as is Multiregionalism, as the Neanderthal DNA in both Amerindians, Asians and many Europeans is simply way too high to be the result of ancient admixture. Most people have the yDNA equivalent of a Neanderthal great great great grandfather, and we haven't even extracted aDNA from a Neanderthal yet."

No. Neither of those theories is in the least legitimate and are overwhelmingly ruled out by available evidence. The percentage reflects that admixture percentage at the time that the genes reached fixation in a hybrid modern human-Neanderthal population which was predominantly modern human in origin.

Tobus said...

@dwaggonerstr:Plains Indians have the most Neanderrhal DNA

Not according to recent research, Han Chinese seem to have the most Neanderthal DNA (eg Table 16.3 of the recent Ust'-Ishim paper)

German Dziebel's out of America theory is another legitimate hypothesis,

Modern genetics would disagree with you - look up a Y-DNA phylogeny, we most definitely came from Africa. German is a professional marketer and can certainly make his theory sound workable, but it falls apart under closer inspection.

terryt said...

"Most people have the yDNA equivalent of a Neanderthal great great great grandfather, and we haven't even extracted aDNA from a Neanderthal yet".

That is actually wrong on both counts. No surviving humans carry any Neanderthal Y-DNA (nor mt-DNA). And Neanderthal a-DNA has been extracted and it is this that applies to your comment, 'equivalent of a Neanderthal great great great grandfather'. Or great great great grandfather (actually just great-great grandparent). No way to tell which.

Mark Moore (Moderator) said...

There was an article in the daily mail on this which claimed the data pointed against what one might consider the most parsimonious explanation, that further gene flow from Africa "watered down" the Neanderthal DNA in Europeans, but not Africans.

One idea that was alluded to in the article, but I have not seen here, is that there was an intermediate population which passed on the Neanderthal like-DNA, not the Neanderthal's themselves.

I have one more theory for you to consider. There were two early Eurasian human populations. The biggest one interbred with a population of something (Neanderthals or N-like in the Near East. The second population did not, either on the on the Y-Chromosome side or not at all. That second population mixed with Europeans but not East Asians. The Neanderthal genes were "watered down" but not with SS African DNA gene flow, but rather flow from a subset of their own population that re-integrated with the European half of the rest of it.

German Dziebel said...

@donaldwaggoner32 re: @Tobus

"German is a professional marketer and can certainly make his theory sound workable, but it falls apart under closer inspection."

Tobus is a nameless, jobless cryptocreationist who manipulates scientific data to trace biblical migrations around the globe from a Garden of Eden in Africa. German is a professional anthropologist whose out-of-America theory is the only one that explains the totality of interdisciplinary evidence in the most explicit, simple but provocative manner.

:)

dwaggonerstr said...

Tobus and TerryT, you are wrong. Neanderthal DNA in modern humans isn't found on the mitochondrial line, cuz that contribution, even if we assume Out of Africa is correct, came from a Neandethal male, not a female.

The YDNA clearly shows that Adam is a Neanderthal, and all Eurasians are thus Neanderthals. This will be revised in the near future as Out of Neanderthal denialists scramble to cover for their broken theory.

Amerindians have the most Neanderthal DNA which fits with their physical features. Don't get me wrong, Han ChInese are high, but not as high as Cheyenne-Arapaho-Piegan.

http://anthropogenesis.kinshipstudies.org/2012/03/american-indians-neanderthals-and-denisovans-pca-views/



http://th02.deviantart.net/fs70/PRE/i/2014/093/3/1/portrait_of_chief_wolf_robe_by_madfork-d7cxc56.jpg

Grognard said...

@andrew - out of africa is obliterated by finding neanderthal dna in people today at all.

It is the height of foolishness to think that finding A00 in africa (13/15 were actualy found in france) means that's where it came from. If we applied the same silly idea to r1b then r1b also originated in africa.

OOA has an admitted political origin, and the facts get blown to bits more and more every day. There's not one shred of archaeology that ever showed any out of africa migration of any kind, but numerous showing the opposite.

Paabo is in sweden which is the most bolshevized place in europe that is chock full of anti-white propaganda. He doesn't seem to give a damn about any facts he comes up with, and completely ignores them. He also predicted they would find zero neanderthal DNA in people today.

Reich is from harvard which has many of the same issues and also isn't a serious science center. He still maintains that yamanaya is the center of r1b origins even though that's been completely falsified by genetics. That has made me realize this is all lame propaganda, and it seems more and more that svante paabo is of the same bent.

Even with the 37k year old DNA in europe showing an ancient person who was very similar to people today, 90% of the articles I online found ways to spin it saying basically the opposite somehow.

terryt said...

dwaggonerstr, you've got it wrong. Neither Tobus nor I claimed survival of either mt-DNA or Y-DNA from the Neanderthals. It was donaldwaggoner32 who made the original totally incorrect comment.

"cuz that contribution, even if we assume Out of Africa is correct, came from a Neandethal male, not a female".

We have no way of knowing whether the surviving Neanderthal a-DNA in modern humans came from Neanderthal males or females.

"The YDNA clearly shows that Adam is a Neanderthal"

That is a very surprising conclusion you have come to there. On what grounds do you claim it to be the case? The root of modern human Y-DNA is placed reasonably convincingly in Africa, a continent where Neanderthals were completely absent.

"It is the height of foolishness to think that finding A00 in africa (13/15 were actualy found in france) means that's where it came from".

When the individuals in France with the mutation come from the western region of sub-Saharan Africa it does rather argue in favour of an Africa origin for the haplogroup.

"If we applied the same silly idea to r1b then r1b also originated in Africa".

That argument in itself is a silly idea. R1b is much more widespread than just in Africa. Consequently no-one would even begin to consider an African origin for the haplogroup.

"He also predicted they would find zero neanderthal DNA in people today".

And I predicted nearly ten years ago that we would. Does that make me an expert?

"Tobus is a nameless, jobless cryptocreationist who manipulates scientific data to trace biblical migrations around the globe from a Garden of Eden in Africa".

And German is a cryptocreationist who manipulates scientific data to trace biblical migrations around the globe from a Garden of Eden in America. Mind you, I see he has procured a few disciples.

Tobus said...

@dwaggonerstr:
The YDNA clearly shows that Adam is a Neanderthal

What makes you think this? AFAIK no Neaderthal Y-DNA haplogroups have been found in any modern humans.

Amerindians have the most Neanderthal DNA...

The data German used in that post is a PCA from 2012 that also implies Europeans have more Neanderthal than East Asians. This is contradicted by a number of more recent studies using more robust methods like D-stats and shared drift. It sounds like you've already made your mind up and no amount of evidence is going to change it, but if you are genuinely interested in having a rational discussion I suggest you read some recent papers, like the ones Dienekes mentions in his blog post, and the Ust'Ishim paper I referred to above.

... which fits with their physical features

At less than 3% Neadnerthal amixture I'd be surprised if there were any effect on phenotype at all.


@German:
Tobus is a nameless, jobless cryptocreationist who manipulates scientific data to trace biblical migrations

Wrong, wrong and wrong... but hey, don't let the truth get in the way of good marketing campaign. :)

#Grognard:
It is the height of foolishness to think that finding A00 in africa ... means that's where it came from.

But it would be even more foolish to then assume that it's where it *doesn't* come from.

..(13/15 were actualy found in france)..

That can't be right - the original paper has 11 samples all from Cameroon. I can only find reliable references to a single "French" sample, apparently an immigrant with sub-Saharan ancestry.

dwaggonerstr said...

@Tobus

"At less than 3% Neadnerthal amixture I'd be surprised if there were any effect on phenotype at all."

At less than one half of one percent of the entire genome, I would not expect the Y-chromosome to make the difference between being born a male or a female.

But it do. And they is.

"What makes you think this? AFAIK no Neaderthal Y-DNA haplogroups have been found in any modern humans."

Altai Neanderthals: Haplogroup R.

Git sum.

German Dziebel said...

@Tobus

"The data German used in that post is a PCA from 2012 that also implies Europeans have more Neanderthal than East Asians. This is contradicted by a number of more recent studies using more robust methods like D-stats and shared drift. "

In Prufer et al., which is 2014, in Table 13.1. in (http://www.nature.com/nature/journal/v505/n7481/extref/nature12886-s1.pdf) Amerindians are again closer to the Altai Neandertal than East Asians.

Yes, some most recent studies showed that Han is closer to Neandertals than Karitiana. This may change as more populations get screened. But considering that East Asians absorbed gene flow from North America some 12,000 years ago, while Karitiana may not have (or had it less), East Asians may end up being more Neandertal-like than Karitiana. It's still very premature to be definitive about these recent D-stats.

But in the meantime such a strict parameter as the length of Neandertal segments shows that Amerindians have them longer than East Asians, while the latter are longer than those of Europeans. (http://anthropogenesis.kinshipstudies.org/2014/10/ancient-ust-ishim-dna-as-seen-from-the-americas/).

"What makes you think this? AFAIK no Neaderthal Y-DNA haplogroups have been found in any modern humans."

Neither did mtDNA haplogroups. Even Cann et al. 1987 wrote that they didn't find any divergent lineages outside of Africa, hence there was no gene flow from Eurasian hominins into modern humans. Isn't it something? We supposedly mated with Neadertals but neither human men nor human women show prove of that. On the other hand, African-specific Y-DNAs A, B and A00 (and their mtDNA counterparts) could have easily introgressed from local African hominins in support of my inference of admixture with African archaics in Africa. They fit the original requirement of great divergence from (now) Eurasian Y-DNAs and mtDNAs perfectly well. Then what does all this whole-genome evidence for affinity with Neadertals mean? If not admixture, then common descent.

"Wrong, wrong and wrong... but hey, don't let the truth get in the way of good marketing campaign. :)"

So, please announce yourself to the group: your full legal name and your job, if you have them. And then we'll see who's wrong. As for good marketing, out-of-Africa is definitely a marketing campaign that uses all possible channels (including the TV just like any consumer packaged goods brand) to perpetuate itself. Breeding confused cryptocreationists such as yourself and TerryT. Out-of-America compared to it is pure science.

@TerryT

"And German is a cryptocreationist who manipulates scientific data to trace biblical migrations around the globe from a Garden of Eden in America. Mind you, I see he has procured a few disciples."

I didn't coin the words 'mtDNA Eve' and 'Y-DNA Adam' - people like you did. How's that Gospel-reading hour working for you, Terry? And BTW, let me repeat one scientific fact for you: "German is a professional anthropologist whose out-of-America theory is the only one that explains the totality of interdisciplinary evidence in the most explicit, simple but provocative manner."

terryt said...

"Altai Neanderthals: Haplogroup R".

Any reference for that? If a Neanderthal-looking individual carries Y-DNA R it is a hybrid with modern humans.

"At less than one half of one percent of the entire genome, I would not expect the Y-chromosome to make the difference between being born a male or a female."

Different genes. I think you need to brush up on your genetics. The presence of a Y-chromosome defines an individual as male.

"Amerindians are again closer to the Altai Neandertal than East Asians".

Yes, because as everyone keeps trying to tell you Amerindians are a mix of Central Eurasian and ancient East Asian. Therefore it makes complete sense that Amerindians are closer to the Altai Neandertal than they are to East Asians.

"How's that Gospel-reading hour working for you, Terry?"

I have no idea what you're talking about. I presume it's rubbish as usual.

Tobus said...

@dwaggonstr:
Altai Neanderthals: Haplogroup R.

Altai Neanderthal sample: female.... "Git sum" indeed.

On your original point, even your noble leader German agrees: "East Asians may end up being more Neandertal-like than Karitiana".


@German:
...your full legal name and your job, if you have them. And then we'll see who's wrong.

A perfect example of how you just make shit up to suit your purposes German. Are you seriously proposing that you know if I have a full legal name and a job better than I do? You sir, are an idiot.

the length of Neandertal segments shows that Amerindians have them longer than East Asians

Amerindian heterozygosity is lower than East Asian, suggesting a smaller effective population. 2,000 people interbreeding will result in more recombination than 1,000 people interbreeding... think about it.

dwaggonerstr said...

TerryT, you are the one who needs to brush up on genetics. The Y-chromosome is less fhan one half of one percent of the human genome. If you are born with one, you are male. If you are born without one, you are female.

All genes are therefore not created equal. Some genes are more powerful than others, and produce great differences from individual to individual, even when they make up a tiny amount of the overall genome.

The Neanderthal DNA within us is certainly a lot and definitely explains then differences between Africans and non-Africans. It's percentage is not an indicator of interbreeding between two species. It is the stable, founding base population of Eurasians. We are all Neanderthals.

I suspect that your nagging fear of Neanderthal DNA in modern humans, as well as your enthusiasm for OoA stems from a deep seated fear that you yourself are somehow deficient of this magnificent lineage, for whatever reason, thus making you a deviant.

The sex of the the Altai Neaneerthal has no bearing whateoever on the haplogroup identified; any insinuiation to the contrary is a wazte product of a juenile and dyseducated mind.

And one last comment for TerryT: Native Americans have ancestry from west Eurasians (upper paleolithic Europeans) not "central Asians". The lineage is traced back to SIBERIA via Ma'lta, but has nothing to do with modern central or east Asians (Mongoloids), who did not exist in the Paleolithic.

No matter how uncomfortable it makss you feel, we are Neanderthals, we are not the same, and we do not have a single origin.

German Dziebel said...

@Tobus

"Are you seriously proposing that you know if I have a full legal name and a job better than I do?"

You just need to prove it. Just like your other fantasies. But you can't even make your own identity explicit. Instead, you spread lies about my own, although I don't even hide it. That's how you get a name for yourself - Tobus Nameless Liar.

"You sir, are an idiot."

A scientist moves from words to facts. A pseudoscientist from words to insults. Get a job!

"Amerindian heterozygosity is lower than East Asian, suggesting a smaller effective population. 2,000 people interbreeding will result in more recombination than 1,000 people interbreeding... think about it."

More creationist pseudoscience (with every more and more recent bottleneck genetic proximity to an ancient sister species increases). Nothing to think about.

@terryT

"I have no idea what you're talking about."

That's the sad part.

"Yes, because as everyone keeps trying to tell you Amerindians are a mix of Central Eurasian and ancient East Asian. Therefore it makes complete sense that Amerindians are closer to the Altai Neandertal than they are to East Asians. "

And Amerindians are even closer to Altai Neandertals than Europeans, so your ideas get falsified over and over again. It's hilarious how you're trying to explain Neandertal affinities of Amerindians by referencing a hypothetical admixture between East Asians and Europeans, while the other cryptocreationist, Tobus Namesless Liar, explains it by invoking the logical opposite - a bottleneck that Amerindians supposedly went through after they split from East Asians.

Tobus said...

@dwaggonerstr:
The Y-chromosome is less fhan one half of one percent..
All genes are therefore not created equal.


The Y-chromosome is not a gene, it's a chromosome. You are comparing a structural difference in a specific fraction of the genome to a quantitative difference spread over the whole thing. White Americans with less than 3% African DNA don't (typically) show evidence of the African phenotype, I highly doubt that the typical Amerindian phenotype is the result of any extra Neanderthal DNA (which, in terms of difference to other Eurasians, is far less than 1%).

The sex of the the Altai Neaneerthal has no bearing whateoever on the haplogroup identified

Females _DON'T HAVE_ Y-chromosomes. If someone told you the Y-DNA haplogroup of the Altai Neanderthal is R, they were pulling your leg... she doesn't _have_ any Y-DNA.

@German:
You just need to prove it.

No I don't, I live it everyday. But just like with your Out Of America theory you'd rather believe your own imagination than the empirical observations of somebody with experience in the area. Good luck with that.

you spread lies about my own

What lie did I spread about you? Are you saying you're *not* a professional marketer?

A scientist moves from words to facts

Actually a good scientist moves from facts (observation) to words (model). You should try it one day.

Get a job!

I would... but I'VE ALREADY GOT ONE!! Too bad, so sad.

More creationist pseudoscience

No worries German, entry-level genetics is obviously over your head and experience tells me you wouldn't change your mind anyway - let's just agree to disagree.

terryt said...

"No matter how uncomfortable it makss you feel, we are Neanderthals, we are not the same, and we do not have a single origin".

Correct. We do not have a single origin. We are the product of a very complex interplay of various human groups going right back to when Homo erectus first formed.

"The Y-chromosome is less fhan one half of one percent of the human genome"

You really are displaying your ignorance here. The Y-Chromosome is a whole chromosome. That is why it is called 'Y-Chromosome'. Humans have 23 pairs of chromosomes which means the Y-Chromosome makes up one forty-sixth of the male human genome, roughly 2%. Besides which it is precisely the presence of a Y-chromosome that determines the formation of a male.

"It is the stable, founding base population of Eurasians. We are all Neanderthals".

No. We all (non-Africans anyway) share a partly Neanderthal ancestry.

"I suspect that your nagging fear of Neanderthal DNA in modern humans, as well as your enthusiasm for OoA stems from a deep seated fear that you yourself are somehow deficient of this magnificent lineage, for whatever reason, thus making you a deviant".

Why would it make any difference to me whether I had Neanderthal ancestry or not?

"The sex of the the Altai Neaneerthal has no bearing whateoever on the haplogroup identified"

If it wasn't a male it wouldn't have a Y-chromosome for a start!

"Native Americans have ancestry from west Eurasians (upper paleolithic Europeans) not 'central Asians'.

No. West Eurasians, ancient Central Eurasians and Native Americans all share a level of a common gene pool.

terryt said...

"It's hilarious how you're trying to explain Neandertal affinities of Amerindians by referencing a hypothetical admixture between East Asians and Europeans, while the other cryptocreationist, Tobus Namesless Liar, explains it by invoking the logical opposite - a bottleneck that Amerindians supposedly went through after they split from East Asians".

I think Tobus and I agree in large part. The bottleneck Tobus refers to occurred after the admixture event I refer to. Simple.

"That's the sad part".

Well, please explain so we simple folk can begin to grasp the immensity of your mind.

Tobus said...

@Terry: I think Tobus and I agree in large part.

Yes we do.

You are discussing genetic affinity while I'm discussing tract lengths... German seems to think they are one and the same thing. Poor, confused German.

German Dziebel said...

@Tobus

"What lie did I spread about you? Are you saying you're *not* a professional marketer?"

I'm a professional anthropologist with two doctorates and two peer-reviewed books out. I don't have a marketing degree and I have never had a job with a marketing title. You ARE a liar, Tobus Nameless Liar.

No I don't, I live it everyday. "I would... but I'VE ALREADY GOT ONE!! Too bad, so sad." Prove it, Tobus, Nameless Liar!

"entry-level genetics is obviously over your head and experience tells me you wouldn't change your mind anyway"

My critique of the current genetic consensus and my alternative to it is well beyond your entry-level genetics ceiling. You can't even figure out the realities of modern life and you're trying to solve human origins.

@TerryT

"I think Tobus and I agree in large part. The bottleneck Tobus refers to occurred after the admixture event I refer to. Simple."

Simply wrong. You are postulating two radically different demographic scenarios with opposite genetic effects on a population to explain one phenomenon: the greater genetic proximity of Amerindians to Neandertals compared to Europeans and East Asians.

German Dziebel said...

@Tobus

"You are discussing genetic affinity while I'm discussing tract lengths... German seems to think they are one and the same thing. Poor, confused German."

I'm happy you agree with cryptocreationist Terry Toohill. "Tract lengths" is evidence for genetic affinity between humans and Neandertals. And it's using those lengths that geneticists calculate the timing of that admixture event. The longer the tracts the closer to the admixture event. Amerindians are the closest to Neandertals among all modern humans. the trick here is that they can't be closer to them "in time" (unlike Ust-Ishim). They can only be closer to them in common descent. Their low effective population size and isolation made this "conservation" possible. This is consistent with the pattern of homozygosity whereby Amerindians are closer to Neandertals than other modern humans. Neandertals were also shown to have blood type O, which is most frequent in the Americas. And it's just a short list of genomic data consistent with the tract lengths situation.

Tobus said...

@German:
I'm a professional anthropologist

Funny, "Head of Digital Strategy and Brand Planning" at a "top healthcare advertising agency" doesn't sound much like anthropology to me.... sounds like marketing. :)

I have never had a job with a marketing title

I don't see "anthropologist" in your title either, yet you still frame yourself a professional anthropologist.. does that make you a liar?

The longer the tracts the closer to the admixture event

"Closer" in terms of the number of recombination events since the admixture. If there's an a priori reason to expect less recombination (eg smaller effective population size) then "closer" in tract length won't necessarily translate to "closer" in genome-wide affinity or any other measurement.

..the trick here..

The "trick" here is contradicted by direct measurements of genetic affinity... you just "tricked" yourself into believing something that isn't true.

This is consistent with the pattern of homozygosity whereby Amerindians are closer to Neandertals than other modern humans

You know, I very nearly included "What's the bet he brings up heterozygosity again and confuses himself even more!" at the end of my last post. Poor confused German!

terryt said...

"You are postulating two radically different demographic scenarios with opposite genetic effects on a population to explain one phenomenon"

As Tobus just pointed out we are using different data to come to the same conclusion. If you can't see that then I agree with Tobus once mere when he says, 'entry-level genetics is obviously over your head'.

"cryptocreationist Terry Toohill"

I still have no idea what you mean by 'cryptocreationist'. Please explain.

German Dziebel said...

@Tobus

"f there's an a priori reason to expect less recombination (eg smaller effective population size) then "closer" in tract length won't necessarily translate to "closer" in genome-wide affinity or any other measurement."

There's an apriori reason to consider most of writing nonsense.

":The "trick" here is contradicted by direct measurements of genetic affinity..."

It is direct measurement of genetic affinity. And it's supported by all other direct measurements. Karitiana are closer to Neandertals than Europeans by tract lengths and by D-stats. East Asians showed up a bit higher in the latter but this means nothing considering that East Asians are heavily admixed with Northern Amerindians, and for the latter we don't have Neandertal affinity data at all.

"You know, I very nearly included "What's the bet he brings up heterozygosity again and confuses himself even more!" at the end of my last post"

It's good you didn't. Maybe scientific reasoning is finally sinking in.

"I don't see "anthropologist" in your title either, yet you still frame yourself a professional anthropologist.. does that make you a liar"

Poor Tobus Nameless Liar! You are web crawling through Linkedin but not deep enough. Keep digging and scrolling. An anthropologist becomes professional when he gets a doctorate in the field. Then he gets a job. You are obviously not one of us.

Tobus said...

@German:East Asians showed up a bit higher in the latter but this means nothing

It means everything if we're discussing the statement that Amerindians "have the most Neanderrhal (sic) DNA", because it proves that statement is false.

Then he gets a job.

... as a professional marketer! :)






German Dziebel said...

@Tobus

"Then he gets a job.

... as a professional marketer! :)"

No, Tobus Nameless Liar. As an applied anthropologist. Keep surfing Linkedin.

"It means everything if we're discussing the statement that Amerindians "have the most Neanderrhal (sic) DNA", because it proves that statement is false."

It's not false at all. It represents a sum total of all published results to date. There are still gaps, to be true, but this is normal at this stage of research. The fact that East Asians showed up as being more Neandertal than Karitiana by some measures (in one recent study contradicted by a host of others), only means that Northern Amerindians who contributed genes to East Asia 12-10,000 years ago must have preserved a different set of Neandertal-like alleles than Karitiana. This is consistent with an opinion of many that East Asians absorbed two waves of Neandertal-like admixture. But it's obvious that East Asians couldn't have got it from Neandertals themselves because in this case Europeans would have experienced a second and potentially third wave of Neandertal gene flow, too. And South Amerindians would have had as much Nenadertal heritage as East Asians. But since both situations are unobserved, an excess of Neandertal genes in East Asians compared to Europeans and South Amerindians must have been mediated by another population. Northern Amerindians fit the bill perfectly as we know that East Asians are closer to Northern Amerindians then to Southern Amerindians genomically.

Tobus said...

@German:
As an applied anthropologist

You're kind of proving my point German, describing Head of Digital Strategy and Brand Planning at an advertising agency as "an applied anthropologist" is genius marketing spin!... You should really get a job in marketing - oh wait, you ALREADY HAVE ONE!!

East Asians showed up as being more Neandertal than Karitiana by some measures ... only means that Northern Amerindians who contributed genes to East Asia

More marketing gold! Accept the data that proves you wrong but then twist it so it seems like it's actually supporting your idea! You should really get a job in marketing - oh wait....

German Dziebel said...

@Tobus

"Accept the data that proves you wrong but then twist it so it seems like it's actually supporting your idea! "

The data is still being collected. And no it hasn't proven me wrong. Out of Africa and into the Americas at 12,000 years, on the other hand, has been proven wrong every year now.

" describing Head of Digital Strategy and Brand Planning at an advertising agency as "an applied anthropologist" is genius marketing spin!"

You are just an ignorant fool. Why are we discussing this? You need a job, Tobus Nameless Liar?

Tobus said...

@German:
And no it hasn't proven me wrong

Really? The premise you are defending is "Amerindians have the most Neanderthal DNA". The data says Han Chinese have the most Neanderthal DNA. By any logical methodology that premise is proven wrong.

Why are we discussing this?

Because you accused me of lying when I said you were a "professional marketer". I'm happy to stop discussing it when you offer your personal public apology.

German Dziebel said...

@Tobus

"Really? The premise you are defending is "Amerindians have the most Neanderthal DNA". The data says Han Chinese have the most Neanderthal DNA. By any logical methodology that premise is proven wrong."

No, it hasn't. The "premise" is an outcome of multiple lines of evidence. We'll see more in the future. D-stats can easily be explained as product of Holocene migration out of North America to East Asia.

"Because you accused me of lying when I said you were a "professional marketer". I'm happy to stop discussing it when you offer your personal public apology."

You are a liar. It's a proven fact. I'm not a professional marketer. You are also an ignorant liar. So here you go, Tobus Nameless Ignorant Liar. It's only getting worse for you.

Tobus said...

@German:
The "premise" is an outcome of multiple lines of evidence

One line of empirical evidence directly contradicts that outcome so it cannot be correct, whatever the other lines might make you think.

German Dziebel said...

@Tobus

"One line of empirical evidence directly contradicts that outcome so it cannot be correct, whatever the other lines might make you think."

It does not contradict it at all. There's a good explanation for the data piece you brought up. We just need more evidence.

German Dziebel said...

@Tobus

X chromosome furnishes good example of a locus in which Northern Amerindians have higher frequencies of Neandertal-like alleles than Southern Amerindians. http://anthropogenesis.kinshipstudies.org/2012/03/american-indians-neanderthals-and-denisovans-pca-views/.

Tobus said...

@German:
There's a good explanation for the data

Whatever the explanation, this piece of data says that Han Chinese have more Neanderthal DNA than Amerindians, agreed?

X chromosome furnishes good example...

I'm sure it does.

Grognard said...

@Tobus - but they did have red hair gene, and some had light eye genes. Claiming that these genes are totally separate from modern people's is plain ridiculous, especially when molecular clock nonsense is taken seriously.


@andrew

"No. Neither of those theories is in the least legitimate and are overwhelmingly ruled out by available evidence. The percentage reflects that admixture percentage at the time that the genes reached fixation in a hybrid modern human-Neanderthal population which was predominantly modern human in origin."

I'd say rather that OOA is ruled out because the molecular clock crap is utter nonsense and due to finding neanderthal and denisovan and other LOCALIZED archaic DNA completely rules this out as a credible theory, only political correctness allows it to pathetically shamble along. Not to mention never finding modern human migration out of africa in archaeology or ancient DNA in africa, what a joke. OOA is possible, not falsified, it's just got very little to support it though you have towonder how camels came to saudi arabia from america and why megafauna died there first and not africa where large predators STILL survive. Of course if you don't look for it you will never find it, and archaeology is famous for discouraging people from exploring the 'wrong' hypothesis.

Tobus said...

@Grognard:
but they did have red hair gene, and some had light eye genes

What does this have to do with what I'm saying?

Claiming that these genes are totally separate from modern people's is plain ridiculous

No, it's plain science. The SNPs suspected of causing these traits in Neanderthals have never been found in any modern human. They are in similar locations, which is why the phenotypic inference exists, but to date, none of them are the same.

especially when molecular clock nonsense is taken seriously.

Any random event can be measured and an average interval calculated - a bit like when scientists say there are X lightning strikes per minute. Given a big enough sample size this will be a consistent average and one could make a reasonably accurate estimation of time simply by counting lightning strikes. The same applies to the mutation rate, it's not "nonsense", it's just an estimation from empirical measurement. How accurate an estimation is yet to be determined.

Grognard said...

"Any random event can be measured and an average interval calculated - a bit like when scientists say there are X lightning strikes per minute. Given a big enough sample size this will be a consistent average and one could make a reasonably accurate estimation of time simply by counting lightning strikes. The same applies to the mutation rate, it's not "nonsense", it's just an estimation from empirical measurement. How accurate an estimation is yet to be determined."

Only if you take a giant assumption there's no such thing as natural selection and that rates of change are constant. Which are assumptions that are completely invalid. That is why these age estimates have been proven wrong by a factor of ten times or more in nonhuman DNA.

"No, it's plain science. The SNPs suspected of causing these traits in Neanderthals have never been found in any modern human. They are in similar locations, which is why the phenotypic inference exists, but to date, none of them are the same."

That means nothing. Why is it OK to make an imaginary trail back along mtdna lines but now along other lines?

The reason your logic fails is that there's no other source found for these genes either. Supposedly these light hair and eye genes are very recent. Yet already something similar existed. It's much more logical that these evolved from neanderthal, or come from a common ancient source. Claiming they evolved separately is just some pathetic ethnocentric nonsense.

terryt said...

"Only if you take a giant assumption there's no such thing as natural selection and that rates of change are constant"

I agree that there is no real reason to assume rates of change are constant. Replacement of parent haplogroups by offspring ones would be an almost random event.

"there's no other source found for these genes either. Supposedly these light hair and eye genes are very recent. Yet already something similar existed".

They could be recent as they exist now but are presumably derived from something at least similar to the surviving examples.

Tobus said...

@Grognard:
Only if you take a giant assumption there's no such thing as natural selection and that rates of change are constant

The only assumption is that random events will tend to a mean over time. Since they are based on empirical measurements, any effects of selection and/or variation in the rate of change are already included in the calculations.

Why is it OK to make an imaginary trail back along mtdna lines but now along other lines?

Because these "imaginary" trails in mtDNA are following by identical mutations - they are an actual physical reality, not just a vague association of similarity.

The reason your logic fails is that there's no other source found for these genes either

De novo mutations - the ultimate source of all SNPs.

It's much more logical that these evolved from neanderthal, or come from a common ancient source

Yes it's logical, and that's why scientists are looking there in the first place. But to date, they've found nothing. Until something concrete turns up, the best bet is that cause of similar phenotype is similar environment, not common genetics.

Claiming they evolved separately is just some pathetic ethnocentric nonsense.

"Pathetic ethnocentric nonsense" that is based on fact. Neanderthals simply don't have the same depigmentation mutations that modern Europeans have... at least none of the Neanderthals that we've got DNA from anyway.

Grognard said...

Altai neanderthal did have a y-chromosome.

Grognard said...

"The only assumption is that random events will tend to a mean over time"

RANDOM events is a huge assumption. Get a couple math and science degrees and you won't make such a silly statement.

"The reason your logic fails is that there's no other source found for these genes either

De novo mutations - the ultimate source of all SNPs."

Which supports my case, not yours.

""Pathetic ethnocentric nonsense" that is based on fact. Neanderthals simply don't have the same depigmentation mutations that modern Europeans have... at least none of the Neanderthals that we've got DNA from anyway."

There's no facts here, just fairy tales. There's no way to tell which genes come from neanderthals and which don't. Having several obvious sources of grenes, says that the single source hypothesis is wrong. It's completely falsified.

Not only do we have severl ancient sources of modern genes outside of africa but NONE that are IN africa. What a joke.

Not to mention how out of africa and "consensus" seem to be mentioned together at all times. Consensus is the opposite of science.

OOA has no evidence for it, and has been falsified.

Falsofying multiregional type evolution or simply "evolution" would be next to impossible. You could only do it by showing ancient DNA in africa that is 100% 'modern', and existed there before eurasia. Which is something that won't ever happen, especially when even the archaeology doesn't exist in africa in the first place.

The archaeology for people moving out of africa would be a million times easier to find, and would have been found by now but it hasn't. In spite of the fact almost all the attention of archaeologists goes to africa and barely any goes to china and india, still we have more from those places than africa, for anyone who is willing to be remotely honest with themselves.


The brain size at concurrent times is always much larger outside africa than in africa. Archaeological evidence shows tons of migrations into africa, none coming out. The first cave art in 55k years old in europe. Cave art only came to africa 8-10k years ago, starting in the NE. All the big animals became extinct outside africa. There's tons of ape fossils in asia but none in africa.

Nothing ever came out of africa, and potential populations in jungle environments of SSA are too low for anything to have ever come out of africa, or for any sort of civilization to ever occur. Africa is a dead end, and not the origin of a single thing until modern times.


Tobus said...

@Grognard:
Altai neanderthal did have a y-chromosome.

The first sentence of The complete genome sequence of a Neanderthal from the Altai Mountains: "We present a high-quality genome sequence of a Neanderthal woman from Siberia".

The original data did include a small number of reads that mapped to the Y-chromosome (altogether representing only about 0.5% of the total Y-chromosome), which were attributed to contamination. In any case, no Y haplogroup could be determined.

RANDOM events is a huge assumption.

Are you saying DNA mutations *don't* happen randomly? Let me guess, God has a timetable?

Which supports my case, not yours.

And how is that? The SLC24A5 mutation most likely arose from a de novo mutation, not archaic introgression.

There's no facts here, just fairy tales. There's no way to tell which genes come from neanderthals and which don't.

An allele with a post-Neanderthal coalescence and no known occurrence in any Neanderthal genome is almost certainly not from Neanderthals. One that predates Neanderthal extinction and does appear in Neanderthal genomes almost certainly is.

OOA has no evidence for it, and has been falsified.

So who needs a couple of Maths and Science degrees?