February 4, 2014

What were Neanderthal genes good for?

Many years ago, Gregory Cochran began pushing the idea that modern humans have some small percentage of Neanderthal inheritance, and that humanity as it exists today acquired by interbreeding with Neanderthals certain useful gene variants that had been evolving separately in cold Europe. Both predictions appear to be true, and now studies are looking at which fitness-enhancing gene versions were picked up wholesale from Neanderthals.

At West Hunter, Cochran reviews some new data:
Exactly which kinds of Neanderthal alleles would give advantage was less obvious.  I suspected that Neanderthals would be resistant to local pathogens, and that such genetic defenses could easily pay off in modern humans moving into Eurasia.  It looks as if some of that happened – there is a good chance that some common HLA alleles in Eurasians originated in Neanderthals, and some Neanderthal variants involved with defense against viruses have become common. 
I thought that anatomically modern humans might have picked up alleles that dealt better with the big swings in day length characteristic of northern latitudes.  In an earlier talk, Sakararaman  mentioned a common Neanderthal version of the CLOCK gene in Europeans, but that doesn’t show up in the paper, so maybe that turned out to be a mistake. 
It looks as if both Europeans and East Asians have picked up Neanderthal versions of  several keratin filament genes, involved in hair and skin formation. Not fixed, but pretty common.  This might have something to do with the non-kinky hair found in most Eurasians. 
Some of these common Neanderthal alleles may have some effect on the central nervous system, but as usual, we have such a poor understanding of gene function that it’s hard to tell. A Neanderthal variant of TANC1 is common in Europeans, and that gene is thought to regulate dendritic spines and excitatory synapses.  Looking at the broader question, an unusual number of selected Neanderthal alleles were found that are associated with major depression. So maybe those alleles affected mood regulation. Perhaps depression is part of a strategy for dealing with long winters. 
There are gene deserts in which you find very few Neanderthal alleles, presumably because those alleles didn’t work well in modern humans. There is a dearth of testes-associated gene,  not too surprising because they evolve particularly rapidly and are therefore more likely than average to be incompatible with a sister group that diverged some time ago.  The area around FOXP2 is such a desert:  Neanderthals were perhaps worse at speech, or any rate different in some way that didn’t mesh. 
There are some signs of reproductive incompatibility with modern humans, but obviously not enough to prevent adaptive introgression. David Reich suggests that Neanderthals were “at the very edge of being biologically incompatible”.  I doubt that, for two reasons.  First, the known cases of species intersterility in primates all took longer to develop. Bonobos and chimps manage, and they’ve been separated something like 800,000 years. In addition, there is evidence that African hunter-gatherers (Bushmen and Pygmies)  picked up some genetic material from an unknown archaic group, one that split off considerably earlier than Neanderthals, something like 900,000 years. ...
In our book, we suggested that the big bang of the Upper Paleolithic,  the dramatic increase in cultural complexity seen in Europe some 40,000 years ago, might have been triggered, at least in part, by an influx of adaptive Neanderthal alleles. Right now, from the evidence in these papers, I’m not seeing a strong case for that. Of course we only understand what half these genes are doing,  so the fat lady hasn’t finished singing, but  we may well be wrong.  Of course that dramatic increase in cultural complexity did happen, and for that matter, it is still true that average IQ scores are quite low in sub-Saharan Africa and its diaspora.  But IQ scores are also low in populations such as Australian Aborigines that have about the same amount of Neanderthal admixture as other people outside of Africa – so at minimum the story is  more complicated.
     

26 comments:

Anonymous said...

Is this another example of how the epigenes affect the action of genes? And isn't the epigenome determined more by environmental influences? Maybe cold, harsh climates forced different genetic behavior (work, problem solving, etc.) not necessary in warm, fertile regions, affecting mental processing and ability.

JayMan said...

@Anonymous:

You might not like what Cochran would tell you for even mentioning epigenetics.

gcochran said...

This 'anonymous' guy is all over the map. Sometimes he makes good sense, other times (like here) he seems to be a pluperfect idiot.



Anonymous said...

Maybe the depression gene served to encourage self-murder, providing the tribe with disease-free meat for cannibalism during the lean months.

JayMan said...

@gcochran:

I know, this "Anonymous" dude is a total box of chocolates...

Why can't he consistently be the coconut cream, dang it?

Anonymous said...

Google "low hanging fruit", "why", "were Neanderthals human" and "real-life Sheldon Cooper" {{(not/Motl)}}. Hilarity may result.

slumber_j said...

"What are they bad for," is another interesting way of looking at this--hinted-at in the possible genetic predisposition to depression. Being so disposed may have been good in some way in northern climes in the olden days, but maybe not so good now.

What about alcoholism? Maybe there wasn't enough opportunity to get high off fermented fruit in Europe for such a propensity to matter, so that squeaked through somehow?

If you want to investigate the question fully (and as a side benefit, also to inoculate against the reactionary argument that you're only seeing what you want to see), that might be another way to think about the question.

Titus Didius Tacitus said...

If you think Danny Vendramini's Neanderthal predation (NP) theory is right, and I do, the main value of Neanderthal genes, if you had enough of them, might have been not being eaten first by Neanderthals. (And the main cost of Neanderthal genes, if you had too many of them, might have been being killed by humans when they had been sufficiently selected for a propensity for successful warfare and started to push back.)

Due to the population bottleneck imposed by Neanderthal predation, a lot of Neanderthal genetic influence could then have persisted as "founder effect" with no specific survival value needed. If you're down to fifty or so humans that are going to have any genetic say in the future and they are all carrying some Neanderthal genes (just because Neanderthals liked to rape humans as well as liking to eat them - which would make sense, as Neanderthals were cannibals) then there's going to be long term genetic influence even if your Neanderthal genes don't do much for you but give you straight hair, a nasty temper and a tendency to depression.

Sam said...

What do all these Neaderthal gene discoveries do to Rushton's theory?

Anonymous said...

Red hair, grey/green eyes, freckled pale skin and vitamin D6.

Bottledwater said...

Why do people keep obsessing about a measly couple percent Neanderthal genes? Even if we do carry their genes, what difference does it make? the amount is trivial. For all practical purposes the total replacement hypothesis is correct. It's like finding out you're 2% black. Or black finding out he's 2% white. It has no impact on your appearance, IQ, or behavior.

Bottledwater said...

What do all these Neaderthal gene discoveries do to Rushton's theory?

Nothing. The Out of Africa hypothesis still stands, and the minuscule amount of Neanderthal admixtures is inconsequential. Even if neanderthals contributed useful traits, if they were so useful in eurasia they would have evolved independently regardless.

Anonymous said...

"It has no impact on your appearance, IQ, or behavior."

Then again maybe it has an impact on all three.

.

"if they were so useful in eurasia they would have evolved independently regardless"

Yep. Without Neanderthals we'd be evolving those traits in about 260,000 years time and you'd be typing on a stone laptop in a cave.

No wifi for yoooo.

Bottledwater said...

In addition, there is evidence that African hunter-gatherers (Bushmen and Pygmies)  picked up some genetic material from an unknown archaic group, one that split off considerably earlier than Neanderthals, something like 900,000 years. ..

Could this explain why bushmen and pygmies have IQ's 13 points lower than other Negroids?

And what explains why native Americans have IQ's 13 points lower than other Mongoloids? Sasquatch genes?

Native American legend has it that such breeding took place and the childen were accepted as human by the tribe, though considered a little slow.

Titus Didius Tacitus said...

Another reason to care about Neanderthal genes is that it's not necessarily just the same few percent for everybody (except black Africans). "Only a few percent" of the global population (bar Africans) could be more than a few percent of specifically Neanderthal genes for some extended families.

The difference is likely to be "under the hood" and reflected in health, intelligence and behavior rather than primarily visible, assuming severe negative selection for overtly non-human traits.

President Obama shows how this could work. Any benefits he gains from his partly white genetics are "under the hood". On the surface he is admirably African, and so he doesn't suffer any of the negative consequences of being (partly) white.

None of this necessarily does anything to Rushton. But it's interesting.

sunbeam said...

I read that site regularly.

It's usually interesting, though I have no way to evaluate the basis of anything Cochran claims.

I mean if I were going to make the effort to learn something new at my age, I think I would go whole hog for Electrodynamics. It's got cool math, graphs, the whole shebang.

Not the deep end of the knowledge pool these days, but still fun. And it looks cool, darn it.

Genetics... just nasty. Too messy. No easy way to go from first principles, and make a beautiful model of how the universe works.

And the math. Ugh. Probability. Statistics. I can see why you have to stoop to this, but unless you go down to the level of electrons and particles, it's just nasty. This kind of math... it's like the syphilitic bastard child of real, beautiful math.

Anyway, despite the rambling I gather from that site (assuming I didn't get something wrong):

1) Prior to the trek of Cro Magnons out of Africa, there was admixture between the nascent human population in Africa 500,000 to 700,000 years ago and some other primeval population of proto-humans (not Neanderthals or Denisovans, something else). Additionally I don't think the "humans" in our direct lineage were even Cro Magnon at that point.

2) There was admixture in the middle east between modern (Cro Magnon) humans and Neanderthals, and probably in Europe as well.

3) There was the Denisovan admixture in Asia.

Kind of real curious about 1), I haven't heard that anywhere else.

Also I've been curious for a while about how the Toba explosion and the genetic bottleneck theory would have affected other populations that were around then, besides modern humans. Not sure if the Denisovans were still around, but what effect did it have on Neanderthals? They would have been as affected by it as Cro Magnons surely.

I also find interesting the report I saw on that site that the original hunter/gatherer people had dark skin (and blue eyes, at least the individual from Spain). Apparently lighter skin comes from the Middle East and early farmers.

Always heard pale skin and red hair were associated with Neanderthals. Maybe, maybe not, since pale skin at least came way after the Neanderthal admixtures in the middle east.

And exactly what is white skin useful for? If it is not Vitamin D, what? I know when you talk about an ugly field of knowledge like genetics it is tricky, and a combination of genes.

But what does it do? Ramzan Kadyrov has white skin, but he sure doesn't seem very gracilized.

ben tillman said...

Why do people keep obsessing about a measly couple percent Neanderthal genes? Even if we do carry their genes, what difference does it make? the amount is trivial. For all practical purposes the total replacement hypothesis is correct. It's like finding out you're 2% black. Or black finding out he's 2% white. It has no impact on your appearance, IQ, or behavior.

You have no basis for your assertions.

Anonymous said...

This 'anonymous' guy is all over the map.

Yes, I am very diverse. That is my strength. I am also thick-skinned, a Neanderthal trait no doubt.

Anonymous said...

After Aborigines were isolated in Australia, rapid evolution continued to occur in Europe and Asia - which may explain the IQ differential. Wonder what the variables/ factors that prolonged evolutionary changes there.

Bottledwater said...

After Aborigines were isolated in Australia, rapid evolution continued to occur in Europe and Asia - which may explain the IQ differential. Wonder what the variables/ factors that prolonged evolutionary changes there.

Probably agriculture which increased population size which increased the odds of novel mutations. According to Richard Lynn, small population size explains why bushmen, pygmies and australoids score lower than other blacks, and also why native Americans and arctic people score lower than other Mongoloids.

Meanwhile climate explains why non-white caucasoids (i.e. Arabs, South Asians) score lower than whites.

So two variables pretty much explain all ethnic variation in IQ: climate and population size.

The only thing they can't explain is the high Ashkenazi IQ. We need entire new theories just to explain this one group. Could this be where Neanderthal genes play a role?

james wilson said...

Out of Africa is a theory, and a very Leaky theory, repeated even here without contest. Like a weed it will grow roots in the best or thinnest soil.

The remarkable and continuous flow of discovery informs us best when we can see past our assumptions and follow trails where ever they may lead.

If Africa marked the beginnings of homo sapien, Africans would have the fewest alleles. Those emigrants leaving Africa, acquiring many new characteristics that would eventually distinguish them, would have the most. The reverse is true.

As has been said in threads, 2% Neanderthal dna in non-Negroid humans is interesting but not likely to be significant. It would be fascinating to understand how it got into Australian Aborigines.

Anonymous said...

"And exactly what is white skin useful for? If it is not Vitamin D, what?"

Iodine and Vitamin D help brain development in children.

So you need 1) a mechanism to generate Iodine and vitamin D in a nursing mother and 2) a mechanism to transmit that vitamin D and iodine to the baby.

.

"And what explains why native Americans have IQ's 13 points lower than other Mongoloids? Sasquatch genes?"

If EDAR is the East Asian version of mechanism (2) then Native Americans may have got that but not the part that provides mechanism (1).

Anonymous said...

"If Africa marked the beginnings of homo sapien, Africans would have the fewest alleles."

Doesn't follow.

The number of alleles will be a function of the amount of random mutation plus the strength of selection pressure. Populations who have most **recently** experienced strong selection to adapt to a newer environment should have fewer because the selection pressure will have been stronger more recently.

(There's also the possibility / likelihood that climate may effect the mutation rate.)

Bottledwater said...

Iodine and Vitamin D help brain development in children.

Could that be an environmental explanation for the black-white IQ gap in the U.S. White skin is needed to get brain essential vitamin D in a northern country like America, so blacks raised in America lack the nutrition to develop their genetic cognitive potential because their dark skin is shielding it out?

Anonymous said...

@Bottledwater
"Could that be an environmental explanation for the black-white IQ gap"

Part of it possibly

http://blogs.discovermagazine.com/crux/2013/07/23/how-adding-iodine-to-salt-boosted-americans-iq/#.UvLVUGJ_uSo

"Nationwide, that averages out to a 3.5-point rise in IQ because of iodization"

lots of others from google e.g.

http://ajcn.nutrition.org/content/83/1/108.long

Anonymous said...

I have an additional idea. Neanderthal genes are not evenly distributed among modern humans. Native Americans have the most,followed by Asians and then whites. So what characteristic do those three groups display, in that order of prominence, and which is lacking in black Africans?

The answer, it seems to me, is the willingness to do unglamorous, grind work.

Everyone who has hired Latino work crews will tell you that they work circles around black crews and don't complain. Asians are also much respected for their work ethic, and they edge out whites by a bit in that regard. But the gap between whites and blacks is immense.

Neanderthals were not clever but everything we know about them tells us that they were prodigious workers. And I think some of that lives on.