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?
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.
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
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https://books.google.ca/books?id=mfANqS-SnwgC&printsec=frontcover&hl=fr#v=onepage&q&f=false 
13 comments:
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".
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.
"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.
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.
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.
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).
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.
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.
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.
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).
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.
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?
I think you're dwelling on Skoglund's old model too much. A lot has been discovered since 2012. I don't recall seeing any direct models of modern Euros using Anatolia Neolithic in any recent DNA papers, likely because the focus is on the ancient samples and PCA/admixture graphs already say enough, but I've seen dstats and qpadm with NW Euros and NE Euros within a 10-15 point margin.
Btw, you can absolutely pick a Latvian out of a Dutch crowd.
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