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View Full Version : Holocene selection in Europe for variants associated with General Cognitive Ability



Tomenable
23-02-17, 12:43
http://i.imgur.com/l3pfZ7E.png

http://www.biorxiv.org/content/early/2017/02/20/109678

http://www.biorxiv.org/content/biorxiv/early/2017/02/20/109678.full.pdf

Abstract:

Human populations living in Eurasia during the Holocene experienced significant evolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA). Population expansion and replacement has also been proposed as an important source of GCA gene-frequency change during this time period. To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4,557 to 1,208 years of age) with a sample of 503 modern European genomes, using three different cognitive polygenic scores. Significant differences favouring the modern genomes were found for all three polygenic scores (Odds Ratio=0.92, p=0.037; 0.81, p=0.001 and 0.81, p=0.02). Furthermore, a significant increase in positive allele count over 3,249 years was found using a sample of 66 ancient genomes (r=0.217, p one-tailed=0.04). These observations are consistent with the expectation that GCA rose during the Holocene.

Comments from Eurogenes:

http://eurogenes.blogspot.fr/2017/02/were-probably-smarter-than-our-bronze.html

Angela
23-02-17, 16:19
From the paper itself:

"GCA as it was characterized by major transitions among human populations,especially in Eurasia, away from a hunter-gatherer mode of subsistence, towards asedentary agriculture-based one and beyond that to urbanization (1, 11). This boughtwith it many evolutionarily novel problems, such as having to cope with increasedpopulation densities and new forms of warfare (1, 11). Innovations that played amajor role in facilitating this transition would have included the domestication of cultivars and animals, the development of novel tools for raising the productivity ofland (such as the plough), and the development of novel weapons of war (11).Cultural innovations such as monotheism, monarchy, aristocracy, feudalism andcurrency-based economics arose in response to the need for coping with thehierarchical power distribution characteristic of large, static populations (11). Thosepopulations that were successful in using innovations to solve novel problems wouldfurthermore have had an advantage in warfare, allowing them to replace lesssuccessful populations. Population growth would have increased the chances of rare GCA enhancing mutations arising, which would have favoured the aggregate fitnessof those populations permitting them to expand to the greatest extent (1, 11). Thuspositive culture-gene co-evolutionary feedback might have rapidly increased GCA(11)."

"Ex oriente lux" redux? :) Not only with agriculture and early metallurgy going west into Europe directly, but later with herding and metallurgy again across the Caucasus.

If true, I think the climate, flora, and fauna in the Near East would have led, in the Holocene, to increased population levels, which increases the chances for novel mutations of all kinds, beneficial as well as neutral and detrimental. Then it would become a loop.

For the record, I think there are a lot more snps which affect cognitive functioning.

bicicleur
23-02-17, 16:37
Innovations that played amajor role in facilitating this transition would have included the domestication of cultivars and animals, the development of novel tools for raising the productivity ofland (such as the plough), and the development of novel weapons of war (11)

we are talking about an evolution that took 5000 years from domestication (12 ka) to the plough (7 ka)

if so, then genetic evolution went relatively slow compared to the speed e.g. lactose tolerance spread, which started less than 5000 years ago, or the spread of pale skin which would have started even later and was finished some 2-3000 years ago

Furthermore, if it is all about genes being selected in the process, how did haplogroup I2 re-emerge in Europe 2000 years after the arrival of the first farmers?
How come these EHG could adapt so fast and spread all over Europe and toward the Altai Mountains?
They must have had an added value which the farmers didn't have. I think they were able to avoid or survive the boom-bust cycles in farming which were fatal to the farmers themselves. Maybe it is an instinct the farmers had lost during the process.

By the way, I think modern humans have not yet adapted to modern day life, and that will still take a very long time

davef
23-02-17, 16:51
By the way, I think modern humans have not yet adapted to modern day life, and that will still take a very long time

I totally agree with that! We aren't meant to work 40 hrs a week. Coffee is popular for a good reason.

Angela
23-02-17, 17:10
we are talking about an evolution that took 5000 years from domestication (12 ka) to the plough (7 ka)

if so, then genetic evolution went relatively slow compared to the speed e.g. lactose tolerance spread, which started less than 5000 years ago, or the spread of pale skin which would have started even later and was finished some 2-3000 years ago

Furthermore, if it is all about genes being selected in the process, how did haplogroup I2 re-emerge in Europe 2000 years after the arrival of the first farmers?
How come these EHG could adapt so fast and spread all over Europe and toward the Altai Mountains?
They must have had an added value which the farmers didn't have. I think they were able to avoid or survive the boom-bust cycles in farming which were fatal to the farmers themselves. Maybe it is an instinct the farmers had lost during the process.

By the way, I think modern humans have not yet adapted to modern day life, and that will still take a very long time

Did I miss something? What "pure" EHG or WHG for that matter spread into Europe and Asia? It didn't happen. The "Indo-Europeans" all had either Caucasus or Med or both. Their herding, their metallurgy, it all came from the Near East. You're too smart not to know that, Bicicleur.

I do think the domestication of the horse (unless done initially by herders from the Caucasus), the "marriage" of cart and oxen and then horse is down to them, and perhaps a particularly war like nature, much like that of the other warlike, pastoral, herding people, the Semitic tribes. Both spread a lot of yDna around. To each their own, but the glamorization of warrior culture is not something I find congenial, to be personal for a moment.

Fwiw, my comment was rather tongue in cheek, as my emoji should have indicated. It was also a question. I'm not sure I totally buy into this idea.

As for the length of time from "farming" to the plow, that's only one indication of progress. What about the painstaking work of cultivar and animal breeding. These things take time. Also, one invention builds upon another. As time passes, the speed increases. Look at the speed in innovation from the Industrial Age to today. You're also way too smart not to know that.

LeBrok
23-02-17, 17:26
Did I miss something? What "pure" EHG or WHG for that matter spread into Europe and Asia? It didn't happen. The "Indo-Europeans" all had either Caucasus or Med or both. Their herding, their metallurgy, it all came from the Near East. You're too smart not to know that, Bicicleur.

I do think the domestication of the horse (unless done initially by herders from the Caucasus), the "marriage" of cart and oxen and then horse is down to them, and perhaps a particularly war like nature, much like that of the other warlike, pastoral, herding people, the Semitic tribes. Both spread a lot of yDna around. If you want to point to that with pride because you have slightly more WHG/EHG than "southern" ancestry, be my guest.

Fwiw, my comment was rather tongue in cheek, as my emoji should have indicated. It was also a question. I'm not sure I totally buy into this idea.

As for the length of time from "farming" to the plow, that's only one indication of progress. What about the painstaking work of cultivar and animal breeding. These things take time. Also, one invention builds upon another. As time passes, the speed increases. Look at the speed in innovation from the Industrial Age to today. You're also smart enough to know that.
I agree. It is a positive feedback loop in action. More people equals more invention, better knowledge retention, faster progress, more food production, more people, more invention, etc, etc This could have been easier to see if the progress was constant linear or constant logarithmic, but instead it was interrupted many times by population collapses due to bad spells of climate.
More about this here:
http://www.eupedia.com/forum/threads/29135-Civilization-is-a-function-of-population-density?p=418811#post418811

bicicleur
23-02-17, 18:00
Did I miss something? What "pure" EHG or WHG for that matter spread into Europe and Asia? It didn't happen. The "Indo-Europeans" all had either Caucasus or Med or both. Their herding, their metallurgy, it all came from the Near East. You're too smart not to know that, Bicicleur.

I do think the domestication of the horse (unless done initially by herders from the Caucasus), the "marriage" of cart and oxen and then horse is down to them, and perhaps a particularly war like nature, much like that of the other warlike, pastoral, herding people, the Semitic tribes. Both spread a lot of yDna around. To each their own, but the glamorization of warrior culture is not something I find congenial, to be personal for a moment.

Fwiw, my comment was rather tongue in cheek, as my emoji should have indicated. It was also a question. I'm not sure I totally buy into this idea.

As for the length of time from "farming" to the plow, that's only one indication of progress. What about the painstaking work of cultivar and animal breeding. These things take time. Also, one invention builds upon another. As time passes, the speed increases. Look at the speed in innovation from the Industrial Age to today. You're also way too smart not to know that.

it was I-DNA and mtDNA U which reemerged in Europe, I didn't say replace
same for EHG, I said spread, not replaced, you added the word 'pure'
Yamna has no EEF, nor Natufian, the only SW Asian component is CHG, I estimate some 15 %

in Europe there was a clear resurgence of the WHG component after the first wave of farmers
the data is scarce, but it looks that that allready happened in megalithic Europe (Iberia and France) and later also in TRB
and out of the Pontic steppe and the northern European forests spread people with an EHG component
both WHG and EHG were lacking completly in meso- and neolithical SW Asia acording to the data we have so far

on the level of Y-DNA it is even a step further, because in the expansion out of the Pontic steppe and the northern European forests it looks like practically no SW Asian clades were part of it

my point is that if those EHG hadn't developped any genes for farming they were quick to adapt and they were creative to domesticate horses which proved more beneficial on the steppe than cattle or any other domesticates

as I pointed out in another thread I suspect that R1b-V88 and R2 were present in the Zagros mountains when through selective hunting techniques the domestication of goats developped 12-13 ka

maybe the R1a/R1b tribes - not R1b-V88 nor R2 - did the same in the Pontic steppe with horses
it may tell something about skills of the R-tribe related to hunting and understanding animal behaviour,
although I admit, I'm speculating quite a lot now

for the plough and draught animals, the first evidence we have is in TRB, I think it is very likely that it was invented in Vinca culture, which I suspect to be EEF, but no data availble on that either. I wouldn't be surprised if there was a good deal of WHG admixture, as in Vinca there was also fishing and hunting, which LBK people didn't do. LBK people relied completely on farming and domesticates. It may be the reason why they busted. Vinca had a much more diversified economy.

before the invention of the wheel there were oxens pulling sledges
the oxens where there before the wheel and the cart
I still think Cucuteni-Tripolye might be a good candidate for this invention

LeBrok
23-02-17, 18:35
it was I-DNA and mtDNA U which reemerged in Europe, I didn't say replace
same for EHG, I said spread, not replaced, you added the word 'pure'
Yamna has no EEF, nor Natufian, the only SW Asian component is CHG, I estimate some 15 %


My best model for Yamnaya. 27% Iranian Neolithic, 68% EHG, 5% WHG.




0.27


0.68


0.05




Real Yamnaya



M967114 I1290

M737081


M325047
KO1, I-L68
Model Yamnaya

M828815
Rise552


Iranian Neolithic
10 kya

Kvalinsk HG (I0122+I0124+I0433)
Hungarian, Tiszaszőlős-Domaháza
7.7 kya




Ulan iV, Yamnaya
4.5 kya


Run time
7.91

Run time
8.15

Run time
9.43

Run time


Run time
9.08


S-Indian
6.13

S-Indian
0

S-Indian
0

S-Indian
1.66

S-Indian
0


Baloch
62.71

Baloch
20.2

Baloch
0

Baloch
30.67

Baloch
33.24


Caucasian
24.97

Caucasian
0

Caucasian
0

Caucasian
6.74

Caucasian
6.58


NE-Euro
0

NE-Euro
71.08

NE-Euro
80.37

NE-Euro
52.35

NE-Euro
56.02


SE-Asian
0

SE-Asian
0

SE-Asian
0

SE-Asian
-

SE-Asian
0


Siberian
0

Siberian
0

Siberian
0

Siberian
-

Siberian
0


NE-Asian
0

NE-Asian
0

NE-Asian
0

NE-Asian
-

NE-Asian
0


Papuan
0.35

Papuan
0

Papuan
0.53

Papuan
0.12

Papuan
0


American
0

American
6.89

American
0

American
4.69

American
2.46


Beringian
0

Beringian
1.7

Beringian
0

Beringian
1.16

Beringian
0.75


Mediterranean
0

Mediterranean
0

Mediterranean
18.59

Mediterranean
0.93

Mediterranean
0


SW-Asian
3.88

SW-Asian
0

SW-Asian
0

SW-Asian
1.05

SW-Asian
0


San
0.18

San
0

San
0

San
0.05

San
0


E-African
0

E-African
0

E-African
0

E-African
-

E-African
0


Pygmy
0

Pygmy
0

Pygmy
0

Pygmy
-

Pygmy
0


W-African
1.78

W-African
0.13

W-African
0.5

W-African
0.59

W-African
0.95

Angela
23-02-17, 19:18
My best model for Yamnaya. 27% Iranian Neolithic, 68% EHG, 5% WHG.




0.27


0.68


0.05




Real Yamnaya



M967114 I1290

M737081


M325047
KO1, I-L68
Model Yamnaya

M828815
Rise552


Iranian Neolithic
10 kya

Kvalinsk HG (I0122+I0124+I0433)
Hungarian, Tiszaszőlős-Domaháza
7.7 kya




Ulan iV, Yamnaya
4.5 kya


Run time
7.91

Run time
8.15

Run time
9.43

Run time


Run time
9.08


S-Indian
6.13

S-Indian
0

S-Indian
0

S-Indian
1.66

S-Indian
0


Baloch
62.71

Baloch
20.2

Baloch
0

Baloch
30.67

Baloch
33.24


Caucasian
24.97

Caucasian
0

Caucasian
0

Caucasian
6.74

Caucasian
6.58


NE-Euro
0

NE-Euro
71.08

NE-Euro
80.37

NE-Euro
52.35

NE-Euro
56.02


SE-Asian
0

SE-Asian
0

SE-Asian
0

SE-Asian
-

SE-Asian
0


Siberian
0

Siberian
0

Siberian
0

Siberian
-

Siberian
0


NE-Asian
0

NE-Asian
0

NE-Asian
0

NE-Asian
-

NE-Asian
0


Papuan
0.35

Papuan
0

Papuan
0.53

Papuan
0.12

Papuan
0


American
0

American
6.89

American
0

American
4.69

American
2.46


Beringian
0

Beringian
1.7

Beringian
0

Beringian
1.16

Beringian
0.75


Mediterranean
0

Mediterranean
0

Mediterranean
18.59

Mediterranean
0.93

Mediterranean
0


SW-Asian
3.88

SW-Asian
0

SW-Asian
0

SW-Asian
1.05

SW-Asian
0


San
0.18

San
0

San
0

San
0.05

San
0


E-African
0

E-African
0

E-African
0

E-African
-

E-African
0


Pygmy
0

Pygmy
0

Pygmy
0

Pygmy
-

Pygmy
0


W-African
1.78

W-African
0.13

W-African
0.5

W-African
0.59

W-African
0.95




There u go, more than enough to transfer some higher cognitive function genes.:)

To be clear, I don't know if I buy this analysis, but if it's true the conclusion is inescapable that these mutations and the developments to which they led took place in the Near East. It is what it is whatever the levels of development there now.

Please ,enough with the tortured logic about ydna I people in Europe. A lot of them were totally EEF and the rest had a big chunk of it.

I like your last statement Le Brok. So true. Now is the best time to live and hopefully it will get better for more people in the future.

Angela
23-02-17, 20:27
If it happened this way it also happened in China; they're the most "Neolithic" farmer people in the world. Large population sizes matter.

bicicleur
23-02-17, 21:26
My best model for Yamnaya. 27% Iranian Neolithic, 68% EHG, 5% WHG.

yes I said CHG, not Iranian neolithic

and to be more precise, it is a CHG-like component in a K=14 admixture, so I was not acurate, hence 'I estimate some 15 %'

EHG is R1, in Iran Neolithic there is also some R2 and I guess some R1b-V88 too
so EHG and Iran Neolithic may have some parts in common, even without making conatct, which would not be the case for CHG

anyway, these models give good indications, but I don't think one should pinpoint on exact percentages as this depends on the choice of the ancestral components

bicicleur
23-02-17, 21:34
There u go, more than enough to transfer some higher cognitive function genes.:)

To be clear, I don't know if I buy this analysis, but if it's true the conclusion is inescapable that these mutations and the developments to which they led took place in the Near East. It is what it is whatever the levels of development there now.

Please ,enough with the tortured logic about ydna I people in Europe. A lot of them were totally EEF and the rest had a big chunk of it.

I like your last statement Le Brok. So true. Now is the best time to live and hopefully it will get better for more people in the future.

sorry to bother you about haplo I again Angela,

I noticed there is a difference.
Barcin, Starcevo, LBK, cardium ware have some I but no European mtDNA U (U2, U4, U5, U8a, U8c).
These I are not European in origin, they are Anatolian in origin.

The WHG European I are in the company of European mtDNA U.
Of course later European and Anatolian I mixed and it gets realy complicated.

bicicleur
23-02-17, 21:39
There u go, more than enough to transfer some higher cognitive function genes.:)


yes there is some autosomal inherited
but it would be a coincidence that this means they kept all the cognitive genes while dispensing of all the Y DNA
it is possible though ..

bicicleur
23-02-17, 22:04
I don't understand the conclusions of the paper.
As far as I can understand, the GCA improved since the holocene.
But what is the correlation with agriculture?
The GCA did improve not only when agriculture was introduced but also in bronze and iron age.
Furthermore it seems to me the authors even don't know which were farmer DNA and which not :

' Consistent with this, as a possible result of the Neolithicrevolution and during the Bronze Age in Europe, three Y-chromosomal haplogroupspeer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.bioRxiv preprint first posted online Feb. 21, 2017; doi: http://dx.doi.org/10.1101/109678. The copyright holder for this preprint (which was not 12(R1a, R1b, I1), which are associated with farming or pastoralist cultures, came tomostly replace the formerly dominant hunter-gatherer lineages (associatedpredominantly with haplogroups G2a and I2) (32).'

Or maybe I just don't understand the paper.
Please tell me.

Angela
23-02-17, 22:22
sorry to bother you about haplo I again Angela,

I noticed there is a difference.
Barcin, Starcevo, LBK, cardium ware have some I but no European mtDNA U (U2, U4, U5, U8a, U8c).
These I are not European in origin, they are Anatolian in origin.

The WHG European I are in the company of European mtDNA U.
Of course later European and Anatolian I mixed and it gets realy complicated.

I'm going to assume that was sincere, so I'll say you never "bother" me. :) I look for your posts. Your intelligence and knowledge of many of the subjects we discuss here is obvious, as is your civility. That doesn't mean I always agree with you, of course, perhaps not in this case, although I agree with this post completely. I certainly wouldn't personally take any autosomal analysis done by Genetiker seriously.

By the way, although I carry mtDna U2e, I still think it might have been a loser in the evolutionary game.I try really hard to just follow the data wherever it leads in as logical a way as possible. We may very well find that mtDna "H", or at least some clades of it, carry an evolutionary advantage. Perhaps with U2e it has to do with some extreme cold weather adaptations that carry some negative baggage, whereas with "H", we already know it may confer some benefits in terms of fighting infections.


yes there is some autosomal inherited
but it would be a coincidence that this means they kept all the cognitive genes while dispensing of all the Y DNA
it is possible though ..


I don't think it's a coincidence at all. I think that's how evolution works. Organisms that possess beneficial mutations for a certain environment survive to pass on those mutations. There's no bigger advantage that brains, even in primitive times, and they're beneficial in any environment, more so even than braun, and especially so if mixed with braun, at least in more primitive times.

I don't remember now, but the mutations that provided high altitude adaptation in Tibetans, did they occur in the same yDna people as form the majority there now? Well, that might be the case, right, it's certainly isolated enough for that to be true.

In Europe, prior yDna lines are not totally gone. In the steppe we don't see anything but R1. However, isn't that the mantra of so many armchair population geneticists, i.e. that "CHG", which shared about 80% of its genes with Iran Neolithic, yes, was all female mediated? Who knows, maybe some R1 sojourned long enough in and south of the Caucasus to pick up some of those genes.

I don't know, and, as I've said repeatedly, I'm not sold on this idea. There are probably hundreds of genes that affect cognitive functioning. This may not be the whole story.

Now, I'm going to clean up and start dinner. A guest is coming. Back tomorrow.