Monday, April 16, 2018

Replies



Reconstruction of a Mesolithic camp (Wikicommons, David Hawgood). Hunter-gatherers often slept in temporary shelters and were generally more exposed to the cold.



My last post generated many intelligent comments on Twitter. Here are my replies to each of them:


Alissa Mittnik - Department of Archaeogenetics, Max Planck Institute for the Science of Human History

That's why most of the aDNA studies you cite do not rely on those but use several 100Ks of polymorphic loci on the autosomes that are not functionally relevant, but whose variable frequencies across populations reflect their different histories of isolation and admixture.

Haplogroup U was once considered to be functionally irrelevant. Even if a gene seems to be noncoding "junk," it can still regulate what other genes do. The Drosophila genome has shown the functional value of noncoding genes:

There is now a wealth of evidence that some of the most important regions of the genome are found outside those that encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective constraint, particularly in Drosophila. Recent work has suggested that these regions may also have been subject to the action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive evolution. [...] Here, we examine patterns of evolution at several classes of noncoding DNA in D. simulans and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of polymorphism and divergence and a skew in the frequency spectrum toward rare variants. (Haddrill et al. 2008)

According to a recent study, most of the human genome has some kind of function, even the noncoding regions. "These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions" (The ENCODE Project Consortium 2012).

It is a myth to believe that noncoding DNA is mostly “junk.” In fact, human evolutionary change has largely occurred in that kind of DNA, apparently as a means to alter the development of complex structures like the brain:

[...] a systematic search for human-specific deletions compared with other primate genomes identified 510 such deletions in humans that fall almost exclusively in noncoding regions.

[…] Another evolutionary approach has been to focus on genomic loci that are well conserved throughout vertebrate evolution but are strikingly different in humans; these regions have been named "human accelerated regions (HARs)" [...]. So far, ~2,700 HARs have been identified, again most of them in noncoding regions: at least ~250 of these HARs seem to function as developmental enhancers in the brain. (Bae et al. 2015)

The same authors note that it is easier to determine the function of coding DNA; hence, the widespread perception that noncoding DNA serves no purpose:

It is relatively easy to detect and understand the functional consequences of changes in protein-coding sequences, compared to noncoding mutations. Mutations in a coding sequence often cause more severe phenotypes than mutations in a regulatory element associated with the same coding sequence. (Bae et al. 2015)


Alissa Mittnik

Turning around the hg U argument, one could make the case that the environmental conditions that farmers of Anatolian ancestry faced in northern Europe led to selective pressures which increased "hunter-gathererlike" functional variants (maybe introgressed) in their population. Which might lead us to underestimate the proportion of Anatolian farmer admixture.

By "environmental conditions" you seem to be referring only to the natural environment. There is also the cultural environment.

Recent human evolution has been primarily in response to the cultural environment. This may be seen in the hundred-fold acceleration of genetic change 10,000 years ago, when our ancestors began to shift from hunting and gathering to farming (Cochran and Harpending 2010; Hawks et al. 2007). By that time, humans had already spread from the tropics to the arctic. They were now adapting to new cultural environments of their own making, and not simply to existing natural environments.

Adaptation to farming was physiological, behavioral, and mental. I mentioned energy balance. Less energy was needed for body heat because sleeping environments were warmer, as were daytime environments in general. A farmer could choose the best time of day to go out into the fields. A hunter had much less choice. He could give up chasing his prey, and go home empty-handed, or he could continue chasing it hither and thither until he finally got it.

There were also mental adaptations, with some capacities being reduced. A hunter had to memorize huge quantities of spatiotemporal data for several purposes: tracking prey over time and space; predicting where they might go; charting the best path to get there; and remembering how to go home. Getting lost could be fatal, since a hunter could not always live off the land, especially in winter. This is why meat was stored in caches, whose locations likewise had to be remembered. All of that memory storage became obsolete when early Europeans became farmers. As the need for spatiotemporal memory decreased between the Mesolithic and the Neolithic, there was a corresponding reduction in cranial size (Henneberg 1988).

The Mesolithic-Neolithic transition led to reduction in other mental demands. There was less need to recognize odors (Majid and Kruspe 2018) and less need for monotony avoidance and sensation seeking (Zuckerman 2008). Meanwhile, there was a greater need to process reciprocal obligations with a larger number of people while interacting less, on average, with each person.

In sum, it is no trivial matter to go from hunting and gathering to farming. These are two very different ways of life with different demands on the mind and body. Much readjustment is needed to make the transition from one to the other.

All right. For the sake of argument, let’s assume that genetic change has been primarily in response to the natural environment. As Anatolian farmers advanced farther into northern Europe, they adapted to a colder climate by allocating more energy to body heat. To this end, they acquired functional variants like haplogroup U, perhaps through introgression. Natural selection then raised their incidence of haplogroup U to higher and higher levels.

But … that's … not … what … happened. Haplogroup U went into decline after farming came and is now rare in northern Europeans. So this is not even a "just so" story. This is an "ain't so" story. In reality, farmers could control their living conditions by building warmer homes, by spending more time indoors, and by planning when they went outdoors. Hunter-gatherers had less control, often having to stay out in the worst weather.


Alissa Mittnik

You also say WHG is a genetic dead end, which is definitely not true, WHG is one of the distinct ancestral source populations for modern Europeans. In fact, East Baltic HGs are genetically WHGs.

Brace et al. (2018) argue that early British farmers had about a 10% residue from native hunter-gatherers. Of course, those farmers also had admixture from WHGs on the continent. So the total residue is higher, all the more so without the genetic change that is wrongly attributed to admixture. So I stand corrected: WHGs did make a contribution to the present-day gene pool.

My basic point is that farmers replaced hunter-gatherers much more in western Europe than in northern Europe. In western Europe, hunter-gatherers had very low population densities, being small bands of nomads. In northern Europe, especially around the North Sea and the Baltic, they were able to achieve much higher population densities by exploiting marine resources. Consequently, those hunter-fisher-gatherers suffered less population replacement because they were too numerous to replace.

I disagree with your second point. East Baltic HGs seem to be closest to Scandinavian HGs. They show the same phenotype of fair skin and a variety of hair and eye colors. WHGs had a different phenotype: dark skin, dark hair, and blue eyes.


Iosif Lazaridis - Department of Genetics, Harvard Medical School

"Lazaridis et al. (2014) estimated Anatolian farmer admixture in East Baltic peoples at 30%."

There were no Anatolian farmers known at the time, so I doubt we estimated Anatolian farmer admixture; also model did not account for Yamnaya ancestry (also unsampled at the time). In Haak, Lazaridis et al. (2015) we estimate 17.4% LBK_EN ancestry in Lithuanians. Given that LBK_EN is ~10% WHG, this translates to ~15% Anatolian ancestry which seems about right.

So East Baltic peoples have ~15% Anatolian ancestry. That figure is considerably lower than the estimate of 52% for northwest Europeans (Skoglund et al. 2012). Such a difference in ancestry would surely produce a visible difference in the way people look.

Does it? Can you identify a Latvian in a room full of Dutch people? Let’s put aside the mathematical models, and their unstated assumptions. Does such a difference in ancestry seem plausible?


Razib Khan - www.razib.com (geneticist and science writer)

didn't read your whole piece in detail. 2 comments 1) u overread from SNP data on pig[mentation]. gen background matters for blondism in KITLG. my 2 sons r heterozygote (like 25% of Scandinavians) have brown hair. 2) ppl in the reich lab don't think SHG contributed ancestors to later ppl

Variation in hair color is determined mainly by alleles at MC1R, and these were the alleles that Günter et al. (2018) measured in their study of ancient DNA from Scandinavian hunter-gatherers. An SNP close to KITLG (rs12821256) plays a measurable but secondary role in hair color variation (Sulem et al. 2007). Using this and other loci would provide a finer-grained simulation of hair color in early Scandinavians, but the overall picture is already clear.

I'm sure the folks at David Reich's lab exclude natural selection from their mathematical models. When I was a university student I learned the normative view that culture has greatly reduced the importance of natural selection in our species. Instead of adapting genetically to our environment, we adapt culturally. In reality, culture has accelerated human evolution by creating human-made environments, each of which requires its own set of adaptations (Cochran and Harpending 2010; Hawks et al. 2007). Instead of adapting only to climate, wildlife, and vegetation, we have had to adapt to diet, clothing, shelter, way of life, social organization, sedentary versus nomadic living, religious strictures, and so on.

That is a very different view of things, and my impression is that most academics are still working with the old view.


Allium

Narva was a technically in the SHG group and it contributed ~10% to Corded Ware. About decreasing U, it can be both to the introduction of new mtDNA from both Anatolia and the Steppe, but also normal selection against it due to its heat/atp balance.

If the incidence of haplogroup U decreased partly because of Anatolian admixture, we should see a steeper decline when farming was first introduced and a gentler decline thereafter (as a result of natural selection). Instead, we see a steady decline throughout the Neolithic and post-Neolithic.


Hernan Cortes

did the corresponding hunter gatherer Y chromosome decrease at same rate?

As far as I know (and I'm willing to stand corrected), the decrease in the incidence of haplogroup U was the single largest genetic change associated with the transition from hunting and gathering to farming. I'm using the word "associated" liberally because this change continued long past the actual transition.


References

Bae, B-I., D. Jayaraman, and C.A. Walsh. (2015). Genetic changes shaping the human brain, Developmental Cell 32(4): 423-434.
https://www.sciencedirect.com/science/article/pii/S1534580715000787

Brace, S., Y. Diekmann, T.J. Booth, Z. Faltyskova, N. Rohland, S. Mallick, et al. (2018). Population replacement in early Neolithic Britain, BioRxiv, February 18. http://dx.doi.org/10.1101/267443  

Cochran, G. and H. Harpending. (2010). The 10,000 Year Explosion: How Civilization Accelerated Human Evolution, New York: Basic Books.

Günther, T., H. Malmström, E.M. Svensson, A. Omrak, F. Sánchez-Quinto, G.M. Kilinç, et al. (2018). Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol 16(1): e2003703. https://doi.org/10.1371/journal.pbio.2003703     

Haddrill, P.R., D. Bachtrog, and P. Andolfatto. (2008). Positive and Negative Selection on Noncoding DNA in Drosophila simulans, Molecular Biology and Evolution 25(9): 1825-1834
https://academic.oup.com/mbe/article/25/9/1825/1296531  

Hawks, J., E.T. Wang, G.M. Cochran, H.C. Harpending, and R.K. Moyzis. (2007). Recent acceleration of human adaptive evolution, Proceedings of the National Academy of Science USA 104:20753-20758.
https://www.researchgate.net/profile/Henry_Harpending/publication/5761823_Recent_Acceleration_of_Human_Adaptive_Evolution/links/0c9605240c4bb57b55000000.pdf   
Henneberg, M. (1988). Decrease of human skull size in the Holocene, Human Biology 60(3): 395-405.
http://www.jstor.org/stable/41464021  

Lazaridis, I., N. Patterson, A. Mittnik, G. Renaud, S. Mallick, K. Kirsanow, et al. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans, Nature 513(7518): 409-413
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/    

Majid, A., and N. Kruspe. (2018). Hunter-gatherer olfaction is special, Current Biology 28(3): R108-R110.
https://www.sciencedirect.com/science/article/pii/S0960982217316160   

Skoglund, P., H. Malmström, M. Raghavan, J. Storå, P. Hall,  E. Willerslev, M.T. Gilbert, A. Götherström, and M. Jakobsson. (2012). Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe, Science 336:466-469.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.469.9827&rep=rep1&type=pdf  

Sulem, P., D.F. Gudbjartsson, S.N. Stacey, A. Helgason, T. Rafnar, K.P. Magnusson, et al. (2007). Genetic determinants of hair, eye and skin pigmentation in Europeans, Nature Genetics 39(12): 1443-1452.
https://s3.amazonaws.com/academia.edu.documents/44886961/ng.2007.13.pdf?AWSAccessKeyId=AKIAIWOWYYGZ2Y53UL3A&Expires=1523646396&Signature=kZsjpuNLQW7xj4mL5RltXbQ5TV0%3D&response-content-disposition=inline%3B%20filename%3DGenetic_determinants_of_hair_eye_and_ski.pdf  

The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome, Nature 489: 57-74
https://www.nature.com/articles/nature11247   

Zuckerman, M. (2008). "Genetics of Sensation Seeking," (pp. 193- 210) in J. Benjamin, R.P. Ebstein, and R.H. Belmaker (eds) Molecular Genetics and the Human Personality, Washington D.D.: American Psychiatric Publishing Inc.
https://books.google.ca/books?id=mfANqS-SnwgC&printsec=frontcover&hl=fr#v=onepage&q&f=false  


12 comments:

Anonymous said...

WHEN applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome".

The Gunther paper says "We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations".

Luke Lea said...

One simple way to think about gene expression, at least the way I do it, is to imagine all the different shapes you can construct out of lego blocks, which way outstrips the number of shapes of the blocks themselves.

Anonymous said...

"Such a difference in ancestry would surely produce a visible difference in the way people look. Does it?"

There are more NW Europeans who look like Colin Farrell, and more NE Europeans who look like Mika Hakkinen, so yes there's a visible difference.

Sean said...

I don't think there is a big enough difference. Farrell is untypical of northern Europe generally because he is dark. There was selection against dark pigmentation though (see 1st comment above). It may be there is more Anatolian farmer in the Dutch and West Europeans generally than you could tell from looking at them because Anatolian looks have been purged, even though most genes remain to divulge the actual ancestry.

Extensive farming in Estonia started through a sex-biased migration from the Steppe indicates admixture of Anatolian farmer women into the Steppe people who introduced agriculture to Estonia, and fairness may have been selected there too. That ten thousand yeas ago there were no people who were at all genetically similar to the modern Dutch does not mean that there was no population ten thousand years ago that looked quite like the modern Dutch.

Anonymous said...

Ireland is 40% dark brown haired, so Colin Farrell is not that untypical. In comparison, Finland is less than 2% dark brown haired. That's a pretty big difference.

Peter Frost said...

Anon,

I was using the Dutch as my comparison. But let's assume that the Dutch are Scandinavians (and not northwest Europeans). Scandinavians are estimated to be 31-41% Anatolian. That figure is still more than twice the estimated Anatolian admixture in East Balts. Do you see that big a difference between Scandinavians and East Balts?

In his reply on Twitter, Lazaridis said that Anatolian admixture is overestimated for northwest Europeans because no allowance is made for Yamna admixture. All of these admixture estimates are consequently very sensitive to the assumptions one makes.

Sean,

The sex bias could be a reflection of the decline in haplogroup U (which is maternally transmitted).

Anonymous said...

In the 20th century the Harvard school actually thought Neolithic Anatolians were not so dissimilar to the Dutch and Scandinavians. They might even be thought some generalised prototype, from which both 'Mediterranean' and 'Nordic' races evolved locally. They noted similarities to the Cordeds who were located not far away, but not to the Neolithic people further north in the interior of Russia or in the East Baltic.

Sean said...

Farrell is swarthy and hardly an example of the Irish average skin colour. The average Irish person is certainly no less pale-skinned than the average Finn, and if the Finns are more blonde, the the Irish are more redheaded. This is a puzzle for those who pretend they still think it is natural selection for vitamin D synthesis that is responsible for skin hair and eye colour, or there is some secret reason.

Anonymous said...

I wasn't talking about skin color. Farrell obviously tans. He's naturally light (as all Europeans are), and the light skin genes came from Anatolian farmers anyway, like the dark hair.

But it's not just pigmentation. It's skull and face shape too. NE Europeans are more East Baltic and Neo-Danubian. NW Europeans are more Nordic and Mediterranean.

Also remember that Yamnaya were half Iranian Farmer, which is similar to Anatolian Farmer. That Mediterranean ancestry created Corded Nordics that spread everywhere from Finland to Britain.

Sean said...

Read this please MONDAY, APRIL 9, 2018, Not so fast. The light eyes , skin and hair phenotype was already there in the north a very long time before agriculturists could possibly have arrived.


I think you're thinking in terms of simple admixture without selection, but the phenotypic suite of traits (including craniofacial morphology) must have originally appeared for a reason, and it certainly was not to do with agriculture or latitude. The alternative is an unknown benefit (as variously implied or suggested by Cochran and Razib) or a selection pressure for feminine looks. The north west of Europe has most feminine face shape and they have the lightest skin too. They also have the most feminine digit ratio (Denmark).

Peter Frost said...

I'm puzzled why you want to bring the British Isles into the discussion. During the Mesolithic, the people of the British Isles had dark skin, dark hair, and blue eyes. So one could expect to see some physical differences between them and East Baltic peoples. About 10% of the current British gene pool seems to be of native Mesolithic origin, and the real figure might be higher if one adjusts for genetic change due to natural selection and founder effects.

The situation was different for Mesolithic Europeans north of a line running from the Low Countries to the Black Sea. In the Mesolithic they looked pretty much as they do now. Yet some researchers have argued for high levels of Anatolian mixture north of that line. There is now some backtracking, at least for the East Baltic. But if there was little or no Anatolian admixture there, why should we expect to see high levels of admixture farther west in Scandinavia or the Netherlands? We will probably see a downward adjustment of the figures there too.

Anonymous said...

They looked much as they do now, only if you cherry pick particular phenotypic traits, that can now be traced to single genes. There might be a strong continuity in the east, meaning Russia and the Baltic, but is there in the Low Countries?