April 02, 2014

Neandertals gave Europeans lipid catabolism genes

Ann Gibbons explains in Did Europeans Get Fat From Neandertals?:
In the latest study, published online today in Nature Communications, Khaitovich and his international team analyzed the distribution of Neandertal gene variants in the genomes of 11 populations from Africa, Asia, and Europe.  
They found that Europeans inherited three times as many genes involved in lipid catabolism, the breakdown of fats to release energy, from Neandertals as did Asians. (As expected, Africans did not carry any of these Neandertal variants.) The difference in the number of Neandertal genes involved with lipid processing was “huge,” Khaitovich says. The study also offers another example of the lingering genetic legacy left in some people today by the extinct Neandertals. 
... 
The team found that Europeans had differences in the concentration of various fatty acids in the brain that were not found in Asians or chimpanzees, which suggests they had evolved recently. The Europeans also showed differences in the function of enzymes that are known to be involved with the metabolism of fat in the brain.
Now the team is trying to figure out what the fatty acids do in the brain and how differences in their concentration might affect function. “We think it’s a very strong effect with very profound physiological changes,” Khaitovich says. “Otherwise, we wouldn’t see it in the brain tissue.” 
The article itself is open access.

Nature Communications 5, Article number: 3584 doi:10.1038/ncomms4584

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans

Ekaterina E. Khrameeva et al.

Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.

Link

21 comments:

Grey said...

I wonder if there is a connection here with health effects related to the switch from animal fats to vegetable oils in diet?

Grey said...

Also, sounds like a cold adaptation?

barakobama said...

Did they ignore what has been discovered about the genetic origins of Europeans? The theory that Europeans are full blooded descendants of the first people to settle there was proven incorrect along time ago.

What do they mean by Asian? east Asian, south Asian, west Asian, central Asian? The relationship between differnt people in Asia to Europeans varies. They are using out of date ways to classify modern people.

Grey said...

@barak

"The theory that Europeans are full blooded descendants of the first people to settle there was proven incorrect along time ago."

They don't have to be.

1) If the people who lived in west Europe, east Europe and Siberia all picked up the same alleles then any reshuffling of the deck east to west would result in the same alleles being present.

2) Even if the shuffling was south to north if those alleles were particularly adaptive in the north then they could be selected for after admixture through selection in place.

(Say half the genes of population A are better versions than those of population B and vice versa. If the two populations mix then over time there would be pressure to select for the better A genes and the better B genes e.g. farmers would get the HG genes that were better and HGs would get the farmer genes that were better.)

In might even be the case that those neanderthal genes entered modern human DNA somewhere else entirely and were selected against elsewhere and only spread in the north because they were particularly useful in north.

German Dziebel said...

Amerindians were not sampled, so the whole study is a wash.

Rajarshi Banerjee said...

The map leaves a huge swath of crucial territory between between western europe north africa and japan unsampled. Including where where hybridization first occurred.

Matt said...

Thousand genomes, doesn't check the South Asian ones for some reason. Logical?

Hamar Fox said...

barakobama,

What do they mean by Asian? east Asian, south Asian, west Asian, central Asian? The relationship between differnt people in Asia to Europeans varies. They are using out of date ways to classify modern people.

Asian in this context means East Asian, specifically NE Chinese, SE Chinese, and the Japanese. I don't really see a problem in grouping together related populations in this way, especially when dealing with archaic admixture, since the recent Vernot and Akey paper found low intra-regional differences in Neanderthal ancestry, but significant inter-regional differences. The trait discussed in this current paper is fairly consistent with that general pattern.

Did they ignore what has been discovered about the genetic origins of Europeans? The theory that Europeans are full blooded descendants of the first people to settle there was proven incorrect along time ago.

While a wider range of samples is always a good thing, the similarity of relatively-more-HG and relatively-more-farmer Europeans to one another in Neanderthal ancestry seems to suggest that the HG/farmer distinction isn't particularly important in the W. Eurasian distribution of Neanderthal genes.

Likewise, the three East Asian populations also certainly differ from one another ancestrally, but not in terms of Neanderthal ancestry. This could mean many things: maybe the current archaic genetic baseline in modern humans was reached before the ancestors of all populations within a region (i.e. Europe or East Asia) split from one another. Or it could mean that deselection of archaic material was so specific that it continued after their ancestors split, but reached the same endpoint in each population of a region, meither for environmental or genetic reasons (for example that Europeans lacked their own version of a gene that Neanderthals had, while perhaps East Asians had their own gene for this already, so the gene may have been similarly, but independently, selected by the ancestors of each modern European population).

Grey,

Also, sounds like a cold adaptation?

Could be. We know that early W. Eurasian-like populations were in Siberia during the last ice age, and the ancestors of East Asians seem to have been somewhere further south during this time (based on the fact that populations that meet usually mix, and MA-1 had no East Asian admixture).

But it's hard to understand why relatively-more-neolithic Europeans have as much (and more, in the case of the IBS sample) of this trait as relatively-more-HG Europeans if it's purely a cold adaptation.

MOCKBA said...

How did Ann Gibbons come up with such a title? The paper circumvented the "who's fat" questions by complicated normalization withing the three ancestry groups of brain tissue samples. The only question they asked was, which subgroup of the 14 tissue specimens has more internal diversity in its fatty acid makeup. (Either due to greater internal genetic diversity or due to a greater lifestyle diversity within the European-American subgroup)

BTW the African-ancestry brain tissue specimens were actually African American rather than Sub-Saharan, so one would expect a sizable Neanderthal admixture there too. Of course with so few fat tissue samples, the "greater biochemical diversity" conclusion might be a fluke too?

Ryan said...

"But it's hard to understand why relatively-more-neolithic Europeans have as much (and more, in the case of the IBS sample) of this trait as relatively-more-HG Europeans if it's purely a cold adaptation."

It would make sense if it's a dietary adaptation though. Mesolithic hunters ate relatively more fish than Neolithic farmers did they not?

If (and it's a BIG if) East Eurasians followed a more coastal (or even just wetter) migration route, it would make sense that these traits would have conferred less of an advantage in East Eurasian than West Eurasia, wouldn't it? I wish there was a South Asian sample in the study to compare to.

CarolAST said...

When I have been able to look up research on the function of specific genes mentioned in this kind of study, I have found that there has been very, very little research, and the function of those genes is largely unknown. Also, it sometimes turns out to be different than originally thought. So I wouldn't put any weight on these findings for that reason.

Alexandros HoMegas said...

Its true that jews have more neanderthal DNA than gentiles?

CarolAST said...

I wish they'd say something about the human leukocyte antigen (HLA) system. At least there are some islands of knowledge in the sea of ignorance.

Texas Arcane said...

Other hominids nothing more than animals that can walk erect and grunt a few syllables. Only Neanderthals were human. The rest were only simulacra made in the shape of people. They squatted in the mud with a place for sleeping and a fire and no sign of families or organised burial or any abstract reasoning.

Sorry everybody else, reality is tough but that's what the evidence says.

Annie Mouse said...

Not true Texas.

H erectus made necklaces with Tasmanian tigers teeth and a lot of the very early Australian settlement evidence is likely to be erectus. That potentially includes art. Probably a lot of the very early stuff in asia also.

terryt said...

"Its true that jews have more neanderthal DNA than gentiles?"

No. Most non-Africans have about the same amount.

Hamar Fox said...

Estimates of Neanderthal ancestry in ancient West Eurasian specimens (European and Siberian hunter-gathers and European farmers) are now available in the updated supplement to the Lazardis 2013 paper, SI 6:

http://biorxiv.org/content/biorxiv/suppl/2014/04/05/001552.DC4/001552-3.pdf

As I guessed above would be the case, there's no essential difference between the mesolithic and neolithic populations.

I'm not sure the figures can be directly compared with Sankararaman et al.'s recent estimates of Neanderthal ancestry in modern populations, since different methods of estimation may have been employed. Lazaridis et al. seem to compare the ancient levels to a ~2% average in moderns, from which the ancient populations don't diverge (with the exception of both the Skoglund farmer and the Skoglund HG).

terryt said...

"H erectus made necklaces with Tasmanian tigers teeth and a lot of the very early Australian settlement evidence is likely to be erectus".

Not many would claim the early Australians as erectus. 'Modern' haplogroups have been found in them apart from a possible pre-sapiens mt-DNA in one of the Lake Mungo individuals.

Annie Mouse said...

Some sites are just too old to reasonably be Sapiens IMO.

Australian archaeology is such a mess, nothing can be retested, the Mungo site is deteriorating, and even if something new is found chances are we wont be allowed to look at it anyway.

terryt said...

"Some sites are just too old to reasonably be Sapiens IMO".

As far as I'm aware no site is undisputably older than around 50,000 years. Certainly nothing in Tasmania approaches even that date.

"Australian archaeology is such a mess, nothing can be retested, the Mungo site is deteriorating, and even if something new is found chances are we wont be allowed to look at it anyway".

Have you seen the paper on the non-modern Mungo haplogroup? That individual was the only one that didn't have a modern haplogroup although the paper is from before the full phylogeny was constructed. What I found surprising was the lack of a distinction between the Kow Swamp and the Lake Mungo specimens:

http://www.pnas.org/content/98/2/537.full

German Dziebel said...

A potentially higher concentration of Neandertal "fat" genes in Amerindians over Asians (and European) is suggested at http://patagoniamonsters.blogspot.com/2014/04/neanderthals-fat-and-peopling-of-america.html