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Angela
30-01-14, 22:00
Two new papers discuss the genetic legacy of the Neanderthals.

This is the link to the Reichs lab paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html

It's not open access, but the tables and supplementary information are available at the links below.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html#extended-data

http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf (http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf)

This is a link to the Vernot et al paper, which is also restricted access:
http://www.sciencemag.org/content/early/2014/01/28/science.1245938

The link for the supplementary information can be found below.
http://www.sciencemag.org/content/suppl/2014/01/28/science.1245938.DC1/Vernot.SM.pdf

Dienekes discusses them here:http://www.dienekes.blogspot.com/2014/01/neandertal-admixture-in-modern-humans.html

http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html (http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html)

My take away from my first go round with the material is that while there were some benefits to the admixture with Neanderthals, there was an undoubted cost both to the people of the time and to us, their descendents: male infertility, type 2 diabetes, Crohn's disease, lupus, rheumatoid arthritis and other auto-immune disorders, biliary cirrhosis and even smoking behavior, although I doubt they were smoking at the time. (this last might have to do with addictive behavior perhaps?)

In addition, there's a discussion of some language issues which we have been selecting against since then. I have to read that section again...it might mean that Neanderthals did indeed have some problems with communication.

Ed. Long term clinical depression is also listed as one of the diseases resulting from the admixture.

RobScotland
31-01-14, 10:05
Excellent post... I had missed this.

The write up in Nature seems to take the glass half empty stance. What about the positives? The biggie is that the resulting offspring of Neanderthal/Homo-Sapien surely expressed an almost insane amount of hybrid vigor.

After all, the resulting mixture was able to conquer the world genetically speaking (excluding Africa). Not too shabby in my opinion.


There definitely had to be some positive benefits. It would seem to me that neanderthal derived people were able to interact with the world in a much more pragmatic and creative way, hence greater accomplishments.

Sile
31-01-14, 10:18
some comments from knowledgeable people about the paper.

They did not fit onto the Y-DNA and mtDNA trees of present-day humans. They are not our ancestors. They belong on a different branch of the hominid tree.

23andMe is still using a test for supposed "Neanderthal" DNA based on the paper by Green et al., A Draft Sequence of the Neanderthal Genome, Science (2010), which over-estimated Neanderthal input into the modern gene-pool.

There was a bit of a clue in my post that I doubt whether it is accurate at all.

This "new" estimate is based entirely on the shockingly skewed 1000 Genomes Project. In other words, the "new" Neanderthal calculation does not take into account any human living between the Netherlands and China, nor any human living in the Balkans or the Middle East. Why didn't a peer reviewer point this out?
I continue to marvel at the naivete of scientists who imagine that the 1000 Genomes Project fairly represents the entire world's population and write their conclusions on that basis.

a few comments..........i did not find one positive one

seems like it will be a dud paper

bicicleur
31-01-14, 10:26
Excellent post... I had missed this.

The write up in Nature seems to take the glass half empty stance. What about the positives? The biggie is that the resulting offspring of Neanderthal/Homo-Sapien surely expressed an almost insane amount of hybrid vigor.

After all, the resulting mixture was able to conquer the world genetically speaking (excluding Africa). Not too shabby in my opinion.

I see a battlefield, on the frontline between Neanderthal and haplo CF
2 sons of CF, C and F escape from the battlefield
They'll come back later, with much more vigor, driving Neanderthal further and further, till extinct

Maciamo
31-01-14, 10:49
My take away from my first go round with the material is that while there were some benefits to the admixture with Neanderthals, there was an undoubted cost both to the people of the time and to us, their descendents: male infertility, type 2 diabetes, Crohn's disease, lupus, rheumatoid arthritis and other auto-immune disorders, biliary cirrhosis and even smoking behavior, although I doubt they were smoking at the time. (this last might have to do with addictive behavior perhaps?)

I don't understand how Sankararaman et al. could only come up with the explanation of male infertility for hybrid Neanderthal-Sapiens. I seriously doubt that it is the case because there are plenty of other examples of successful cross-breeding between subspecies more genetically distant than Homo Sapiens and Neanderthal. I have mentioned before (http://www.eupedia.com/forum/threads/27036-How-to-define-a-species) that wolves, coyotes, foxes, dogs and dingos can interbreed just fine even though their common ancestor lived over several millions years ago. How could Homo Sapiens and Neanderthals have any cross-breeding fertility issue after having evolved separately for only 600,000 years ? There would have been more issues with Denisovans then, who branched off much earlier.

The most likely explanations are:

1) The blending between the two groups happened violently, with Homo Sapiens men killing Neanderthal men and raping Neanderthal women or forcing them into assimilation within their tribe.

2) Homo Sapiens Y chromosomes produced more or better quality sperm, and supplanted Neanderthalian Y chromosomes in the long term.

3) Homo Sapiens men were better looking or possessed other desirable qualities not found among Neanderthal men, which prompted some Neanderthal women to have sex with Homo Sapiens men, but not the reverse.

When we see how fast European Y-DNA has changed in the last 10,000 years, with the near extinction of Mesolithic haplogroups like C-V20 or some I2a1 subclades, I really don't see how the extinction of Neanderthal Y-DNA after 40,000 years of blending with Homo Sapiens should necessarily require cross-breeding infertility in male offspring. That's just an easy explanation from an unimaginative person with no consideration for the study of prehistoric human behaviours, nor statistical probabilities of lineages going extinct over time through natural selection due to sexual competition.

Maciamo
31-01-14, 11:14
I see a battlefield, on the frontline between Neanderthal and haplo CF
2 sons of CF, C and F escape from the battlefield
They'll come back later, with much more vigor, driving Neanderthal further and further, till extinct

It is almost certain that hybrids drove pure Neanderthals to extinction. The question is: how often did interbreeding take place ? The first series of interbreeding happened in the Middle East some 100,000 to 60,000 years ago. So the first Homo Sapiens to reach Europe were almost certainly already hybrids, although perhaps only 5-10% Neanderthalian since their physical traits were much closer to African Homo Sapiens.

The most recent sign of admixture between Homo Sapiens and relatively pure Neanderthals was found in southern Spain (Gibraltar actually) 28,000 years ago. So we can know for sure that Homo Sapiens interbred with Neanderthals many times, starting in Southwest Asia at least 60,000 years ago and ending with the disappearance of pure Neanderthals in Western Europe 28,000 years ago.

What happened between those periods ? Did these slightly hybridised Early Cro-Magnons (probably Y-haplogroup C or F) regularly interbreed with Neanderthal ? Perhaps they did, but most of them were replaced by subsequent waves of Homo Sapiens (hg F or I). A lot of things can happen in tens of thousands of years. Some hybridisation might have produced more successful mixes than others, leading to population booms by one kind of hybrid to the detriment of others. There could have been dozens of successive population replacements in various parts of Europe, some inhabited by pure or relatively pure Neanderthals, others by very hybridised people, and other still by slightly hybridised Homo Sapiens.

Periods of cooling of the climate over the millennia would have reinforced the selection of the better adaptive among them. Add to this a regular flow of Homo Sapiens from the Middle East, and probably also some direct migrations from West Africa via the Gibraltar Strait, given the presence of Y-haplogroup A1a in modern Nordic people and sub-Saharan admixture among most Mesolithic samples tested to date (La Brana, Motala).

The whole picture could be extremely complex. It would be interesting to know how much Neanderthal admixture the La Brana, Loschbour and Motala samples had. It was probably more than modern Europeans. But some of the most important hybridisations might have taken place in Central Asia during the Upper Paleolithic, rather than in Europe. That would explain why Y-haplogroup K became so successful as to eventually replace 80% of all male lineages in Eurasia. Surely Central Asian Neanderthals were different from European ones (and many regional variations existed within Europe), and the former could have carried unique mutations that led to a much better global adaptation in general. After all, the descendants of Central Asian hybrids did not "just" recolonise all Eurasia, but also colonise for the first time the American continent and Polynesia. There was definitely something special in their genes that European and Middle Eastern hybrids didn't have 30,000 years ago.

When you consider all this, it becomes clear that comparing the DNA of European Neanderthals with that of modern Europeans is not the way to go. It's Central Asian Neanderthals that may have contributed most of our modern genes, followed by Middle Eastern ones, then only European ones.

bicicleur
31-01-14, 11:25
I don't understand how Sankararaman et al. could only come up with the explanation of male infertility for hybrid Neanderthal-Sapiens. I seriously doubt that it is the case because there are plenty of other examples of successful cross-breeding between subspecies more genetically distant than Homo Sapiens and Neanderthal. I have mentioned before (http://www.eupedia.com/forum/threads/27036-How-to-define-a-species) that wolves, coyotes, foxes, dogs and dingos can interbreed just fine even though their common ancestor lived over several millions years ago. How could Homo Sapiens and Neanderthals have any cross-breeding fertility issue after having evolved separately for only 600,000 years ? There would have been more issues with Denisovans then, who branched off much earlier.

The most likely explanations are:

1) The blending between the two groups happened violently, with Homo Sapiens men killing Neanderthal men and raping Neanderthal women or forcing them into assimilation within their tribe.

2) Homo Sapiens Y chromosomes produced more or better quality sperm, and supplanted Neanderthalian Y chromosomes in the long term.

3) Homo Sapiens men were better looking or possessed other desirable qualities not found among Neanderthal men, which prompted some Neanderthal women to have sex with Homo Sapiens men, but not the reverse.

When we see how fast European Y-DNA has changed in the last 10,000 years, with the near extinction of Mesolithic haplogroups like C-V20 or some I2a1 subclades, I really don't see how the extinction of Neanderthal Y-DNA after 40,000 years of blending with Homo Sapiens should necessarily require cross-breeding infertility in male offspring. That's just an easy explanation from an unimaginative person with no consideration for the study of prehistoric human behaviours, nor statistical probabilities of lineages going extinct over time through natural selection due to sexual competition.

I agree, I don't think there was any romance nor love between homo sapiens and Neanderthal, only rape.
I think it was the other way around. When homo sapiens first met Neanderthal, Neanderthal was in a stronger position and Neanderthal men raped sapiens women.
Has there any homo sapiens DNA been found back inside Neanderthal DNA?

bicicleur
31-01-14, 11:36
It is almost certain that hybrids drove pure Neanderthals to extinction. The question is: how often did interbreeding take place ? The first series of interbreeding happened in the Middle East some 100,000 to 60,000 years ago. So the first Homo Sapiens to reach Europe were almost certainly already hybrids, although perhaps only 5-10% Neanderthalian since their physical traits were much closer to African Homo Sapiens.

The most recent sign of admixture between Homo Sapiens and relatively pure Neanderthals was found in southern Spain (Gibraltar actually) 28,000 years ago. So we can know for sure that Homo Sapiens interbred with Neanderthals many times, starting in Southwest Asia at least 60,000 years ago and ending with the disappearance of pure Neanderthals in Western Europe 28,000 years ago.

What happened between those periods ? Did these slightly hybridised Early Cro-Magnons (probably Y-haplogroup C or F) regularly interbreed with Neanderthal ? Perhaps they did, but most of them were replaced by subsequent waves of Homo Sapiens (hg F or I). A lot of things can happen in tens of thousands of years. Some hybridisation might have produced more successful mixes than others, leading to population booms by one kind of hybrid to the detriment of others. There could have been dozens of successive population replacements in various parts of Europe, some inhabited by pure or relatively pure Neanderthals, others by very hybridised people, and other still by slightly hybridised Homo Sapiens.

Periods of cooling of the climate over the millennia would have reinforced the selection of the better adaptive among them. Add to this a regular flow of Homo Sapiens from the Middle East, and probably also some direct migrations from West Africa via the Gibraltar Strait, given the presence of Y-haplogroup A1a in modern Nordic people and sub-Saharan admixture among most Mesolithic samples tested to date (La Brana, Motala).

The whole picture could be extremely complex. It would be interesting to know how much Neanderthal admixture the La Brana, Loschbour and Motala samples had. It was probably more than modern Europeans. But some of the most important hybridisations might have taken place in Central Asia during the Upper Paleolithic, rather than in Europe. That would explain why Y-haplogroup K became so successful as to eventually replace 80% of all male lineages in Eurasia. Surely Central Asian Neanderthals were different from European ones (and many regional variations existed within Europe), and the former could have carried unique mutations that led to a much better global adaptation in general. After all, the descendants of Central Asian hybrids did not "just" recolonise all Eurasia, but also colonise for the first time the American continent and Polynesia. There was definitely something special in their genes that European and Middle Eastern hybrids didn't have 30,000 years ago.

When you consider all this, it becomes clear that comparing the DNA of European Neanderthals with that of modern Europeans is not the way to go. It's Central Asian Neanderthals that may have contributed most of our modern genes, followed by Middle Eastern ones, then only European ones.

homo sapiens and Neanderthal have lived together in Europe for a verly long time
there were at least 2 aurignacian invasions in Europe, and 1 gravettian
first aurignacian was some 45.000 years ago
but even before aurignacian, there were homo sapiens with technology very similar to neanderthal technology : 'Emiran' in the Levant, 50000 years ago and 'Bohunician' in Moravia, Europe 48000 years ago
it is for archologists very dificult to distinct these pré-Aurignacian homo sapiens from Neanderthal

Maciamo
31-01-14, 11:52
I agree, I don't think there was any romance nor love between homo sapiens and Neanderthal, only rape.
I think it was the other way around. When homo sapiens first met Neanderthal, Neanderthal was in a stronger position and Neanderthal men raped sapiens women.
Has there any homo sapiens DNA been found back inside Neanderthal DNA?

It could have happened both ways, of course. But, although Neanderthals were physically stronger, it is hard to deny that Homo Sapiens were technologically superior, hence their success in replacing Neanderthals. With better weapons or a more organised team play, Homo Sapiens men could have killed Neanderthal men in battle regardless of the difference in physical strength. Anyway it is 100% certain that Homo Sapiens men interbred with Neanderthal women since modern Eurasian have some Neanderthal genes on the X chromosome.

I am confident that Neanderthal men also raped Homo Sapiens women, but either this was much less frequent, or Neanderthal Y-DNA wasn't competitive in the long term, because we haven't found any Neanderthal Y-DNA yet, even in Mesolithic European samples.

Maciamo
31-01-14, 11:53
homo sapiens and Neanderthal have lived together in Europe for a verly long time
there were at least 2 aurignacian invasions in Europe, and 1 gravettian
first aurignacian was some 45.000 years ago
but even before aurignacian, there were homo sapiens with technology very similar to neanderthal technology : 'Emiran' in the Levant, 50000 years ago and 'Bohunician' in Moravia, Europe 48000 years ago
it is for archologists very dificult to distinct these pré-Aurignacian homo sapiens from Neanderthal

A sure sign of heavy hybridisation among pre-Aurignacian populations.

I am even wondering if some Homo Sapiens didn't enter Europe much earlier that suspected, perhaps 60,000 years ago or even as much as 100,000 years ago. This might have been a mere trickle, a few tribes wandering out of Southwest Asia into Europe, and quickly hybridising with far more numerous Neanderthals. The result would have been an early introgression of Homo Sapiens genes among Neanderthal populations, rather than the other way round. Overall there might have anything between 1% and 10% of Homo Sapiens admixture in Europe during this period. There are two reasons why I believe this might have happened:

1) If Homo Sapiens or Sapiens-Neanderthal hybrids were living in Southwest Asia back then, what prevented them from migrating to Europe ? If there was no major obstacle to their progression, then some of them surely ended up in Europe. The time frame is 100,000 to 45,000 years before present. Can anybody seriously consider that in 50,000 years no Homo Sapiens tried to migrate from the Near East to Europe, while during that periods they colonised most of Asia and reached Australia ? By the sheet force of logic, it is almost certain that Homo Sapiens entered Europe before 45,000 years ago. What archeological remains show is that only from 45,000 years ago relatively pure Homo Sapiens managed to advance through Europe in large number enough to keep their physical appearance, even if some hybridisation took place.

2) There is undeniable skeletal evidence that Neanderthals evolved and became less robust and closer to Homo Sapiens over time, starting at least 100,000 years ago. Besides, Mediterranean Neanderthals were the ones that became less robust than their northern counterparts, and if hybridisation with Homo Sapiens had taken place, it would have been in southern Europe first.

bicicleur
31-01-14, 13:05
It could have happened both ways, of course. But, although Neanderthals were physically stronger, it is hard to deny that Homo Sapiens were technologically superior, hence their success in replacing Neanderthals. With better weapons or a more organised team play, Homo Sapiens men could have killed Neanderthal men in battle regardless of the difference in physical strength. Anyway it is 100% certain that Homo Sapiens men interbred with Neanderthal women since modern Eurasian have some Neanderthal genes on the X chromosome.

I am confident that Neanderthal men also raped Homo Sapiens women, but either this was much less frequent, or Neanderthal Y-DNA wasn't competitive in the long term, because we haven't found any Neanderthal Y-DNA yet, even in Mesolithic European samples.

I am not a geneticist, but is the presence of Neanderthal genes in the X chromosone solid proof of male Homo Sapiens injection in the Neanderthal DNA ?
Y-DNA is the pure paternal line, and mtDNA the pure maternal line. So isn't all other chromosomes, including X chromosomes affected by both the paternal and the maternal side?

As for homo sapiens technology, I doubt that first homo sapiens that entered Eurasia were very technological advanced. After all they were fugitives, probably driven away by homo sapiens in Africa who were more technological advanced than them.
I think homo sapiens in Eurasia lost their first confrontation with Neanderthal but survived and develloped better technology after that and came back to confront Neanderthal again.

bicicleur
31-01-14, 13:07
A sure sign of heavy hybridisation among pre-Aurignacian populations.

I am even wondering if some Homo Sapiens didn't enter Europe much earlier that suspected, perhaps 60,000 years ago or even as much as 100,000 years ago. This might have been a mere trickle, a few tribes wandering out of Southwest Asia into Europe, and quickly hybridising with far more numerous Neanderthals. The result would have been an early introgression of Homo Sapiens genes among Neanderthal populations, rather than the other way round. Overall there might have anything between 1% and 10% of Homo Sapiens admixture in Europe during this period. There are two reasons why I believe this might have happened:

1) If Homo Sapiens or Sapiens-Neanderthal hybrids were living in Southwest Asia back then, what prevented them from migrating to Europe ? If there was no major obstacle to their progression, then some of them surely ended up in Europe. The time frame is 100,000 to 45,000 years before present. Can anybody seriously consider that in 50,000 years no Homo Sapiens tried to migrate from the Near East to Europe, while during that periods they colonised most of Asia and reached Australia ? By the sheet force of logic, it is almost certain that Homo Sapiens entered Europe before 45,000 years ago. What archeological remains show is that only from 45,000 years ago relatively pure Homo Sapiens managed to advance through Europe in large number enough to keep their physical appearance, even if some hybridisation took place.

2) There is undeniable skeletal evidence that Neanderthals evolved and became less robust and closer to Homo Sapiens over time, starting at least 100,000 years ago. Besides, Mediterranean Neanderthals were the ones that became less robust than their northern counterparts, and if hybridisation with Homo Sapiens had taken place, it would have been in southern Europe first.

I meant, it was hard for archeologists to distinguish Neanderthal technology from early pré-Aurignacian homo sapiens technology, but indeed many skeletons looked like hybrid too.

Maciamo
31-01-14, 14:07
I am not a geneticist, but is the presence of Neanderthal genes in the X chromosone solid proof of male Homo Sapiens injection in the Neanderthal DNA ?
Y-DNA is the pure paternal line, and mtDNA the pure maternal line. So isn't all other chromosomes, including X chromosomes affected by both the paternal and the maternal side?

Yes, you are right. X chromosomes could have been passed by Neanderthal fathers through daughters. But since no Neanderthal Y-DNA survives, at one point hybrids had to have exclusively Homo Sapiens fathers. But Neanderthal Y-DNA could have survived among Cro-Magnons for a long time, perhaps until the Gravettian or Solutrean. I just wanted to explain why I disagree with Sankararaman et al.'s statement that male hybrids would have been infertile. Since interbreeding was apparently quite common for a very long period (tens of thousands of year), and that Neanderthal populations show progressive signs of "Sapienisation", it is unthinkable that hybrid infertility was a constant issue.


As for homo sapiens technology, I doubt that first homo sapiens that entered Eurasia were very technological advanced. After all they were fugitives, probably driven away by homo sapiens in Africa who were more technological advanced than them.
I think homo sapiens in Eurasia lost their first confrontation with Neanderthal but survived and develloped better technology after that and came back to confront Neanderthal again.

Perhaps we should see the Sapiens-Neanderthal hybridisation as an extremely protracted process, in which a constant flow of Homo Sapiens from Africa and the Middle East progressively diluted Neanderthal DNA from 100,000 years ago until Homo Sapiens DNA became predominant and Neanderthal traits got so diluted that they seem to disappear from the archaeological record roughly 28,000 years ago. It doesn't really matter who raped who, and who was technologically superior. The time frame is so huge that such questions become moot. What matters is the result: Neanderthal genes became progressively diluted until they only formed a small part of the genomes of the human beings in Europe.

Angela
31-01-14, 14:17
some comments from knowledgeable people about the paper.

They did not fit onto the Y-DNA and mtDNA trees of present-day humans. They are not our ancestors. They belong on a different branch of the hominid tree.

23andMe is still using a test for supposed "Neanderthal" DNA based on the paper by Green et al., A Draft Sequence of the Neanderthal Genome, Science (2010), which over-estimated Neanderthal input into the modern gene-pool.

There was a bit of a clue in my post that I doubt whether it is accurate at all.

This "new" estimate is based entirely on the shockingly skewed 1000 Genomes Project. In other words, the "new" Neanderthal calculation does not take into account any human living between the Netherlands and China, nor any human living in the Balkans or the Middle East. Why didn't a peer reviewer point this out?
I continue to marvel at the naivete of scientists who imagine that the 1000 Genomes Project fairly represents the entire world's population and write their conclusions on that basis.

a few comments..........i did not find one positive one

seems like it will be a dud paper

Really? I read the same blog...as another poster there has pointed out, the same person complains every time the 1000 genomes project is used, and the reason is that it doesn't include any Polish genomes, as if that would make a difference when comparing Neanderthal genomes to modern genomes.

Also, what the poster was referring to as "inaccurate" were the estimates of Neanderthal ancestry based on a 2010 paper. That was the paper which 23andme has been using, and which has inflated values for the amount of Neanderthal genetic material present in modern humans.

This is going to be a very high impact set of papers.

bicicleur
31-01-14, 15:03
[QUOTE
Perhaps we should see the Sapiens-Neanderthal hybridisation as an extremely protracted process, in which a constant flow of Homo Sapiens from Africa and the Middle East progressively diluted Neanderthal DNA from 100,000 years ago until Homo Sapiens DNA became predominant and Neanderthal traits got so diluted that they seem to disappear from the archaeological record roughly 28,000 years ago. It doesn't really matter who raped who, and who was technologically superior. The time frame is so huge that such questions become moot. What matters is the result: Neanderthal genes became progressively diluted until they only formed a small part of the genomes of the human beings in Europe.[/QUOTE]

Maybe. But it seems homo sapiens expanded into south- and southeast-Asia first, before coming to Europe and Siberia.
I think the reason was not only climate, but also Neanderthal.
Neanderthal appeared in Europe some 300000 years ago, but 80000 years ago they started expanding : to the Levant, to the Zagros Mountains, to the Caspian Sea area, to Central Asia and even to southern Siberia. In the process they may have chased Denisovan further east. (in central Asia there were allready humans 200000 years ago but I would rather suspect Denisova than Neanderthal).
The expansion seams to have been finally blocked by homo sapiens who after that forced Neanderthal into retreat.
There may have been hybrid species in between both. There are indeed skelettons suggesting that.

bicicleur
31-01-14, 16:18
So you're saying the Central Asian Neanderthal was the golden child of all Neanderthal. Kind of like the blue-eyed, blonde haired savage brute "stud of the Steppes"? Has a familiar ring to it.

Hmmm, sometimes I feel like I'm an extra in the movie Groundhog Day.

I do feel like we're making progress though, Maciamo. I like how we are posturing to claim a bigger, better chunk of Neanderthal rather than hiding or even disowning his contributions.

And don't worry, I agree with the vast majority of your postulations on this thread.

But remember, my Neanderthal trumps your Neanderthal. :)

P.S. If some of the University studies break the way I think they might, my Neanderthal and your Neanderthal may in fact be the same guy-- or at least shared a zip code. But now we are in a virtual black sea of mystery, only time will tell.

There were several branches of Neanderthal.
Do any of the papers specify from wich Neanderthal branch(es) DNA was inserted into homo sapiens?
Do you expect some paper will reveal the zip code?

Sile
31-01-14, 19:31
Really? I read the same blog...as another poster there has pointed out, the same person complains every time the 1000 genomes project is used, and the reason is that it doesn't include any Polish genomes, as if that would make a difference when comparing Neanderthal genomes to modern genomes.

Also, what the poster was referring to as "inaccurate" were the estimates of Neanderthal ancestry based on a 2010 paper. That was the paper which 23andme has been using, and which has inflated values for the amount of Neanderthal genetic material present in modern humans.

This is going to be a very high impact set of papers.

Mr Greens 2010 paper?

testing 5 samples by mr Reich seems very few to determine anything

Sile
31-01-14, 19:37
Yes, you are right. X chromosomes could have been passed by Neanderthal fathers through daughters. But since no Neanderthal Y-DNA survives, at one point hybrids had to have exclusively Homo Sapiens fathers. But Neanderthal Y-DNA could have survived among Cro-Magnons for a long time, perhaps until the Gravettian or Solutrean. I just wanted to explain why I disagree with Sankararaman et al.'s statement that male hybrids would have been infertile. Since interbreeding was apparently quite common for a very long period (tens of thousands of year), and that Neanderthal populations show progressive signs of "Sapienisation", it is unthinkable that hybrid infertility was a constant issue.



Perhaps we should see the Sapiens-Neanderthal hybridisation as an extremely protracted process, in which a constant flow of Homo Sapiens from Africa and the Middle East progressively diluted Neanderthal DNA from 100,000 years ago until Homo Sapiens DNA became predominant and Neanderthal traits got so diluted that they seem to disappear from the archaeological record roughly 28,000 years ago. It doesn't really matter who raped who, and who was technologically superior. The time frame is so huge that such questions become moot. What matters is the result: Neanderthal genes became progressively diluted until they only formed a small part of the genomes of the human beings in Europe.

Since its stated that N man cannot breed with modern woman.............but modern Man can breed with N woman, then this is one reason N died out. The N man ran out of females.
The only % of N in any of us is via females.

I doubt very much that any lab can accurately measure the N in any modern person to any degree of accuracy.

Tabaccus Maximus
01-02-14, 23:38
When you consider all this, it becomes clear that comparing the DNA of European Neanderthals with that of modern Europeans is not the way to go. It's Central Asian Neanderthals that may have contributed most of our modern genes, followed by Middle Eastern ones, then only European ones.

Excellent point. By the time Sapiens began populating Europe, they were already numerically much greater and already admixed. The population of Europe appears to have been largely replaced several times over anyway just during its Sapien occupation. So European Neanderthals don't seem the best comparision as you've said.

Also agree with questioning the theory on male sterility. The most likely reason for the absence of Neanderthal uniparental markers is just the fact that statistically its unlikely that they would have continued from that time frame anyway. Then add selection and population dynamics.

Sile
02-02-14, 04:22
Initial paper , stated neaderthal
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0076182;jsessi onid=325557460E434F28E2A49440CC278F75

8 months later, the paper above was 5000 years out.........its 15th century human bones
http://www.sciencedirect.com/science/article/pii/S004724841300239X

what more can we say!

Greying Wanderer
02-02-14, 05:52
Two new papers discuss the genetic legacy of the Neanderthals.

This is the link to the Reichs lab paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html

It's not open access, but the tables and supplementary information are available at the links below.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12961.html#extended-data

http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf (http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf)

This is a link to the Vernot et al paper, which is also restricted access:
http://www.sciencemag.org/content/early/2014/01/28/science.1245938

The link for the supplementary information can be found below.
http://www.sciencemag.org/content/suppl/2014/01/28/science.1245938.DC1/Vernot.SM.pdf

Dienekes discusses them here:http://www.dienekes.blogspot.com/2014/01/neandertal-admixture-in-modern-humans.html

http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html (http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html)

My take away from my first go round with the material is that while there were some benefits to the admixture with Neanderthals, there was an undoubted cost both to the people of the time and to us, their descendents: male infertility, type 2 diabetes, Crohn's disease, lupus, rheumatoid arthritis and other auto-immune disorders, biliary cirrhosis and even smoking behavior, although I doubt they were smoking at the time. (this last might have to do with addictive behavior perhaps?)

In addition, there's a discussion of some language issues which we have been selecting against since then. I have to read that section again...it might mean that Neanderthals did indeed have some problems with communication.

"while there were some benefits to the admixture with Neanderthals, there was an undoubted cost"

Given the list of costs the benefit from certain specific Neanderthal traits must have been very high.

This is not surprising if Neanderthals had spent 100s of generations adapting to northern latitudes and the traits relating to that were the ones that were kept by AMH.

martiko
02-02-14, 13:12
I don't understand how Sankararaman et al. could only come up with the explanation of male infertility for hybrid Neanderthal-Sapiens. I seriously doubt that it is the case because there are plenty of other examples of successful cross-breeding between subspecies more genetically distant than Homo Sapiens and Neanderthal. I have mentioned before (http://www.eupedia.com/forum/threads/27036-How-to-define-a-species) that wolves, coyotes, foxes, dogs and dingos can interbreed just fine even though their common ancestor lived over several millions years ago. How could Homo Sapiens and Neanderthals have any cross-breeding fertility issue after having evolved separately for only 600,000 years ? There would have been more issues with Denisovans then, who branched off much earlier.

The most likely explanations are:

1) The blending between the two groups happened violently, with Homo Sapiens men killing Neanderthal men and raping Neanderthal women or forcing them into assimilation within their tribe.

2) Homo Sapiens Y chromosomes produced more or better quality sperm, and supplanted Neanderthalian Y chromosomes in the long term.

3) Homo Sapiens men were better looking or possessed other desirable qualities not found among Neanderthal men, which prompted some Neanderthal women to have sex with Homo Sapiens men, but not the reverse.

When we see how fast European Y-DNA has changed in the last 10,000 years, with the near extinction of Mesolithic haplogroups like C-V20 or some I2a1 subclades, I really don't see how the extinction of Neanderthal Y-DNA after 40,000 years of blending with Homo Sapiens should necessarily require cross-breeding infertility in male offspring. That's just an easy explanation from an unimaginative person with no consideration for the study of prehistoric human behaviours, nor statistical probabilities of lineages going extinct over time through natural selection due to sexual competition.

The experience of the America showed us the terrible impact of the provision of new food such sweetens it and alcohol and it with maldie news and the whole conjugant with new technology in domains of agriculture more particularly, it is notably translated nowadays for the indigne of the amazonienne forest.

Angela
02-02-14, 18:39
"while there were some benefits to the admixture with Neanderthals, there was an undoubted cost"

Given the list of costs the benefit from certain specific Neanderthal traits must have been very high.

This is not surprising if Neanderthals had spent 100s of generations adapting to northern latitudes and the traits relating to that were the ones that were kept by AMH.

Well, that's the thing...it doesn't seem that the benefit was high at all.

I'm still not done going through the supplements, and maybe I missed something, but the only things I saw mentioned were some changes to the skeletal structure, and thickened skin, nails, hair etc., (caused by increased keratin levels) and the latter seems to have had more effect in East Asians than West Asians. The function of the BNCA gene is unknown.

I was actually pretty amazed at how different they were...David Reich has said that when the encounters happened, the two groups were "at the edge of biological incompatibility". That explains the fertility problems that the hybrids experienced.

The author of the other paper, Joshua Akey, made a statement to the effect that we have spent the thousands of years since the encounters purging the Neanderthal sequences from our genome. That's quite a statement.

Oh, I omitted one of the listed diseases...depression. I'll edit my post to include it.

It's interesting that most of the diseases mentioned are auto-immune disorders. Perhaps someone more knowledgeable than I am could comment on why those kinds of disorders, in particular, would result from the admixture.

Also, I find it interesting that both depression and addictive behavior are mentioned, given the linkage we see today between those two disorders. I have to check if they looked for the genes sometimes postulated as being connected to alcoholism.

The most disastrous result, however, from an evolutionary point of view, at least to me, would seem to be the language disorders associated with this admixture. It's only through communication that technology is shared, and the advances in civilization were only made possible by sophisticated means of communication leading ultimately to writing systems. How long were those developments delayed while we waited for some of these sequences to be purged? And have they even all been purged? Could it be this admixture is related to all the language development issues we see in children today, including dyslexia?

LeBrok
02-02-14, 20:42
Well, that's the thing...it doesn't seem that the benefit was high at all.

I'm still not done going through the supplements, and maybe I missed something, but the only things I saw mentioned were some changes to the skeletal structure, and thickened skin, nails, hair etc., (caused by increased keratin levels) and the latter seems to have had more effect in East Asians than West Asians. The function of the BNCA gene is unknown.

I was actually pretty amazed at how different they were...David Reich has said that when the encounters happened, the two groups were "at the edge of biological incompatibility". That explains the fertility problems that the hybrids experienced.

The author of the other paper made a statement to the effect that we have spent the thousands of years since the encounters purging the Neanderthal sequences from our genome. That's quite a statement.

Oh, I omitted one of the listed diseases...depression. I'll edit my post to include it.

It's interesting that most of the diseases mentioned are auto-immune disorders. Perhaps someone more knowledgeable than I am could comment on why those kinds of disorders, in particular, would result from the admixture.

Also, I find it interesting that both depression and addictive behavior are mentioned, given the linkage we see today between those two disorders. I have to check if they looked for the genes sometimes postulated as being connected to alcoholism.

The most disastrous result, however, from an evolutionary point of view, at least to me, would seem to be the language disorders associated with this admixture. It's only through communication that technology is shared, and the advances in civilization were only made possible by sophisticated means of communication leading ultimately to writing systems. How long were those developments delayed while we waited for some of these sequences to be purged? And have they even all been purged? Could it be this admixture is related to all the language development issues we see in children today, including dyslexia?

Sometimes when research is fresh it is easy to jump to misleading conclusions, or researchers often want to dramatize their papers in order to have bigger audience and make the study more interesting.
I might sound anticlimactic here saying that to our knowledge mixed descendants of Sapiens and Neanderthals did indeed start civilisation in Near East, Asia and Europe. I realise, that it is hardly a proof that Neanderthal admixture was needed to run civilization, but at least we know that it wasn't much of a hindrance, or their autoimmune diseases very crippling.
I agree though, that it is very likely that many combinations of S and N genes could have given rise to new afflictions or even life ending outcomes. However positive effects must have outnumbered negative, or some positives, like lighter skin, had to be essential for spreading out of Africa, that we see N admixture in all out of Africa people.
The small percentage of surviving N admixture in us points to the fact how little of N was actually needed to prosper out of Africa, and outcompete other hominids. It also might give us a clue that the rest of N admixture might have been crippling enough to be "weeded out" eventually. On other hand, low N admixture could have been caused by many consecutive migrations from Africa ever lowering N genes to the point of leaving bare-essential of N in us at 2-3%.
In future we should be able to draw better conclusions ones we know how fast Neanderthal admixture was falling down through the times. If the drop was very quick it would point to crippling combinations of S&N genes and rapid "weeding out" process. If it was long and steady it would point to waves of "fresh" african DNA flow.

Angela
02-02-14, 21:57
Sometimes when research is fresh it is easy to jump to misleading conclusions, or researchers often want to dramatize their papers in order to have bigger audience and make the study more interesting.
I might sound anticlimactic here saying that to our knowledge mixed descendants of Sapiens and Neanderthals did indeed start civilisation in Near East, Asia and Europe. I realise, that it is hardly a proof that Neanderthal admixture was needed to run civilization, but at least we know that it wasn't much of a hindrance, or their autoimmune diseases very crippling.
I agree though, that it is very likely that many combinations of S and N genes could have given rise to new afflictions or even life ending outcomes. However positive effects must have outnumbered negative, or some positives, like lighter skin, had to be essential for spreading out of Africa, that we see N admixture in all out of Africa people.
The small percentage of surviving N admixture in us points to the fact how little of N was actually needed to prosper out of Africa, and outcompete other hominids. It also might give us a clue that the rest of N admixture might have been crippling enough to be "weeded out" eventually. On other hand, low N admixture could have been caused by many consecutive migrations from Africa ever lowering N genes to the point of leaving bare-essential of N in us at 2-3%.
In future we should be able to draw better conclusions ones we know how fast Neanderthal admixture was falling down through the times. If the drop was very quick it would point to crippling combinations of S&N genes and rapid "weeding out" process. If it was long and steady it would point to waves of "fresh" african DNA flow.

Very interesting points, Le Brock. I certainly agree that we have to wait for the dust to settle and more papers to be done before we come to any firm conclusions. That supplemental data was pretty convincing, though.

Also, while I think subsequent migrations might be important in terms of the differing levels of Neanderthal admixture we see in West Eurasians today, I also think those different levels might have resulted from the number of encounters each of our three major ancestral groups, as per Lazaridis et al, had with Neanderthals. I saw a post on the Dienekes' site by an always informed poster speculating that people in the greater Middle East might have had only one such encounter, whereas others occurred in central Asia and then northern Eurasia as well. The WHGs and the ANE peoples would have had Neanderthal admixture from all three encounters. When the initial population of EEF peoples was formed, they had less of it because they had only had one encounter. Therefore, when they moved into Europe, they diluted the amount of Neanderthal in our genomes. That makes sense to me from all prior studies and from the levels of Neanderthal in the various European populations today as is shown in the paper. So, perhaps two processes are involved with the differing levels of Neanderthal ancestry.

As for the fact that the admixture must have resulted in more positives than negatives, I don't see how that follows really. The admixture happened, it wasn't planned. It could have been a totally negative event that led to catastrophic consequences. That doesn't seem to be the case. However, as I said, I couldn't find any major benefits listed in the paper. For example, if Neanderthals had pale pigmentation, they didn't pass on those specific genes to us, except for one, which has to do with pigment saturation, although who knows what its original function might have been. Many of the pigmentation alleles we possess seem to have been random albinism mutations which just happened to come in handy after the change to agriculture. Certainly, there are still hunter gatherer groups today, like the Eskimos or the Sami, who are still rather dark pigmented although their habitat is cold and snowy.

Anyway, for now these are just speculations. Perhaps we'll get some more data soon. The papers seem to be coming out fast and furiously.

LeBrok
07-02-14, 02:48
Here is a Big News.
Even though single people have up to 4% of Neanderthal genome, these are not the same N genes in all of as. Recent paper speculates that there might be as much as 20% of N DNA still floating around in modern humans.
http://www.livescience.com/42933-humans-carry-20-percent-neanderthal-genes.html



Although 20 percent might sound like a lot of mingling happened between Neanderthals and the ancestors of modern humans, it could have resulted from as few as 300 mating events, Vernot said.
The research team's computerhttp://images.intellitxt.com/ast/adTypes/icon1.png (http://www.livescience.com/42933-humans-carry-20-percent-neanderthal-genes.html#) simulations of modern-human intermingling with Neanderthals suggest about 40 percent of the Neanderthal genome may actually survive within modern human genomes. "We just identified 20 percent is all," Vernot said.
To identify the other 20 percent or so of Neanderthal genome hidden within modern humans, the scientists estimate they would need about 1,000 individuals from any given modern-human population — for instance, Europeans — to find nearly all the Neanderthal DNA present there.
However, identifying Neanderthal DNA will be challenging. "Because we're so similar to Neanderthals, there could be many, many regions that are virtually identical, with no differences that we can tell apart," Vernot said.

Maciamo
07-02-14, 13:14
Here is a Big News.
Even though single people have up to 4% of Neanderthal genome, these are not the same N genes in all of as. Recent paper speculates that there might be as much as 20% of N DNA still floating around in modern humans.
http://www.livescience.com/42933-humans-carry-20-percent-neanderthal-genes.html

Thanks for sharing. I had been wondering about the total DNA inherited from Neanderthals in the modern gene pool. Obviously it wasn't the same in all of us since Europeans and East Asians have inherited quite different genes. This confirms that Homo sapiens interbred with Neanderthals several times in prehistory, probably with different Neanderthal subspecies.

LeBrok
07-02-14, 17:47
Thanks for sharing. I had been wondering about the total DNA inherited from Neanderthals in the modern gene pool. Obviously it wasn't the same in all of us since Europeans and East Asians have inherited quite different genes. This confirms that Homo sapiens interbred with Neanderthals several times in prehistory, probably with different Neanderthal subspecies.
This actually surprised me, as I thought we only picked up the essentials and rest was weeded out. It turns that essentials were the skin colour and few immune genes but the rest of 20% floats around as a substitute for human genes. Most likely the rest have almost identical structure and functionality, therefore works as well as HS genes. There was no need to weed it out.
I knew it would be very hard to recognize some genes where they came from after 50k years and many mutations. I'm equally surprised that scientists have so much confidence in gene recognition to put bold claim like this, and Neanderthal label on it.

Aberdeen
22-04-14, 04:15
Bumping an old thread because there seems to be a new paper out concerning the differences between Neanderthals and modern humans. I can only access the abstract, which doesn't say much, at least to me, but an article about it on the Archeology News website indicates that the researchers think the reason there were so many differences between two types of humans whose DNA is so similar is because a lot of DNA is switched off in Neanderthals but active in humans. If someone can access the full paper, and can translate sciencese into English, I'd be interested in learning more about this idea.

www.sciencemag.org/content/early/2014/04/16/science.1250368

Tomenable
18-09-14, 00:37
Interesting lecture about Neanderthals:

https://www.youtube.com/watch?v=0uRCVyJ7-0c#t=403


https://www.youtube.com/watch?v=0uRCVyJ7-0c

Yetos
18-09-14, 04:24
Is it true that Neanderthl's weak point was running and jumping ability?
he was slower comparing his 'african cousin'
although double or triple muscle power?

LeBrok
18-09-14, 07:00
The weakest point was Neanderthals social skills or lack of them. Homo Sapiens were extremely good in group organization, maintaining order in big groups, technological exchange and cultural contacts over big distances.