The Genetic Legacy of the Neanderthals

[Greying Wanderer]

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

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

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]

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 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 indig?ne of the amazonienne forest.

 

[Angela]

"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]

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]

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]

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 computer 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]

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]

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]

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]

Interesting lecture about Neanderthals:

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

 

[Yetos]

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]

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.