Part 2: 8,000 years of Natural Selection in Europe.

Speaking of the Ydna in Anatolia: Anatolia_Neolithic: Y haplogroup: 7 G2a, 1 G, 2 H2, 1 H, 1 I, 1 I2c, 1 J2a, 1 C1a2
G2a: 7
G: 1
H2: 2
H1: 1
I: 1
I2c: 1
C1a2: 1
J2a:1

Whoa, that's significantly earlier than I expected any I2c outside of Europe. The supplemental data table doesn't seem to give any SNPs that tested negative though, so tough to say if this is a branch of I2c is an extinct branch that wandered away, or actually ancestral to a modern I2c branch, or what. It's even tougher to say anything about the "I" sample without knowing what tested negative. I'm very interested in that information if anybody can find it.
 
What, no I2a? Here goes my Anatalian LGM hypothesis, lol. It is unbelievable, the variety of hapogroups. All presumably belonging to WHG of Anatolia before mixing with farmers.
 
Hobby groups will always explain you the facts in their own preffered way.

Sintashta EEF seems 15% more than among Corded Ware. Which brings the schoolers of the paper to the conclusion that we aren't dealing here with an Eastward migration of Corded Ware groups, but a group which is ancestral to Corded Ware as well Sintashta. And it seems like Andronovo indeed was absorbing Yamna (Teal and EHG ) like ancestry in Central Asia which brings me to the conclusion that something Yamna like was living there.

I think it's pretty clear what the scholars (a veritable smorgasbord of nationalities and ethnic groups, by the way) are saying, and it's not the same as what's been on the internet:

"After the Poltavka period, population change occurred in Samara: the Late Bronze Age Srubnaya have ~17%Anatolian Neolithicor EEF ancestry (Extended Data Fig. 2). Previous work documented that such ancestry appeared east of the Urals beginning at least by the time of the Sintashta culture, and suggested that it reflected an eastward migration from the Corded Ware peoples of central Europe5. However, the fact that the Srubnaya also harbored such ancestry indicates that the Anatolian Neolithic or EEF ancestry could have come into the steppe from a more eastern source. Further evidence that migrations originating as far west as central Europe may not have had an important impact on the Late Bronze Age steppecomes from the fact that the Srubnaya possess exclusively (n=6) R1a Y-94 chromosomes (Extended Data Table 1), and four of them
(and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians12, very rare in present-day Europeans, and absent in all ancient central Europeans studied to date."


They seem to be pointing at admixture with EEF which came from Cucuteni Tripolyte and then moved across the forest steppe, although they're being cautious, perhaps so as not to ruffle a fellow colleague's feathers, i.e. Allentoft, but perhaps also to protect future papers. These guys are already in the process of analyzing, or know the results of other analyses of ancient people in the Balkans.

https://books.google.com/books?id=n...&q=David Anthony on Cucuteni Tripolye&f=false

I haven't thought through the situation in the east so I can't comment on that yet.
 
What, no I2a? Here goes my Anatalian LGM hypothesis, lol. It is unbelievable, the variety of hapogroups. All presumably belonging to WHG of Anatolia before mixing with farmers.

I don't think we yet know who "invented" farming, and whether the various hunter-gatherers had already mixed by that time. A related question is how far south did these I and C lineages penetrate?

I suppose it also depends on how you define "farming". I don't think it's just reaping and then storing wild grain. As to whether replanting wild seeds to have the plants closer to hand constitutes farming is one of those questions that archaeologists obsess over. :)

I can see attaching the three I and C y lineages to WHG like populations, but what about H?
 
this is only a very small part of Anatolia, from 2 sites nearby in NW Anatolia

R1b I would expect further east, maybe south of Caucasus , so no R1b-V88 here
E-V13, I'm getting more and more convinced the proposed TMRCA time of 4300 years is +/- correct
biggest surprise to me was to find I2c, which uptill now hasn't been found in the neolithic
all others were in early European neolithic
except H1, but I don't find it in the list (I have H) ; is it a typo or did you find some suplementary info?

Sorry, Bicicleur, that was a typo. It's plain H. I'll edit my original post.

I should know better than to stay up late at a "The Walking Dead" watch party and have more than my usual one drink. It would be nice to be twenty-something again for at least the physical stamina! :)

Ed. Oh, what are your thoughts about that I2c?
 
I don't think we yet know who "invented" farming, and whether the various hunter-gatherers had already mixed by that time. A related question is how far south did these I and C lineages penetrate?

I suppose it also depends on how you define "farming". I don't think it's just reaping and then storing wild grain. As to whether replanting wild seeds to have the plants closer to hand constitutes farming is one of those questions that archaeologists obsess over. :)

I can see attaching the three I and C y lineages to WHG like populations, but what about H?

IMO H, which is very old (TMRCA 45000 years) is paleolithic India where microliths were invented.
H2 (I guess the H is also H2) must have come west and survived LGM in either the southern Levant or on the bottom of the Persian Gulf.
 
I don't think we yet know who "invented" farming, and whether the various hunter-gatherers had already mixed by that time. A related question is how far south did these I and C lineages penetrate?

I suppose it also depends on how you define "farming". I don't think it's just reaping and then storing wild grain. As to whether replanting wild seeds to have the plants closer to hand constitutes farming is one of those questions that archaeologists obsess over. :)

I can see attaching the three I and C y lineages to WHG like populations, but what about H?

there seem to have been 2 different incipient farming cultures :

the Natufians, based on cereals

SE Anatolia, based on nuts, pulses and domesticates - 12000 yo Hallan Cemi didn't have cereals
http://www.persee.fr/doc/paleo_0153-9345_1998_num_24_1_4667
IMO it's these people that build Göbekli Tepe temple
https://en.wikipedia.org/wiki/Göbekli_Tepe

we need 12000 yo DNA to check ;)
 
Look, who actually defended the ydna J is not EEF but a EEF+Teal merging idea based on the fact that it is close cousin of I? ME

BUT the point is that J is Obviously connected to farming /Herding cultures why is it so hard to understand. All other J samples are in Teal and EEF context. But than we have one Keralian J who has no autosomal sign of anything farmer like. That brings us back to our (Angela and me) initial theory, that this and as well some of the R1b in Samara H&G could be founder effect and through mixing with local WHG groups the Teal could have been so deluded until it autosomally disappeared.

So if there is J without any sign of farming genes in Karelian, there is R1b in Neolithic Iberian without any sign of EHG admixture. Why shouldn't it be possible that the autosomal DNA got deluted in both groups?

What you say is possible. However how do you know Teal people gave J to Mesolithic Karelia if Teal ancestry is so diluted it's impossible to detract? You're assuming it is teal with no evidence. My opinion is that R1b1 and J are very old so Neolithic Anatolians and Mesolithic Russians belonged to both lineages but neither appear to be partly descended from each other. So, J in Karelia isn't prove they had Near Eastern ancestry and isn't evidence R1b1 has a Near Eastern origin.
 
What you say is possible. However how do you know Teal people gave J to Mesolithic Karelia if Teal ancestry is so diluted it's impossible to detract? You're assuming it is teal with no evidence. My opinion is that R1b1 and J are very old so Neolithic Anatolians and Mesolithic Russians belonged to both lineages but neither appear to be partly descended from each other. So, J in Karelia isn't prove they had Near Eastern ancestry and isn't evidence R1b1 has a Near Eastern origin.
Oh really? And where was that hg. J from? It didn't came out of the blue and has to come from somewhere. And that somewhere is West Asia, where also R1a and R1b are from.
 
I don't think we yet know who "invented" farming, and whether the various hunter-gatherers had already mixed by that time. A related question is how far south did these I and C lineages penetrate?

I suppose it also depends on how you define "farming". I don't think it's just reaping and then storing wild grain. As to whether replanting wild seeds to have the plants closer to hand constitutes farming is one of those questions that archaeologists obsess over. :)

I can see attaching the three I and C y lineages to WHG like populations, but what about H?
Right, we still don't know haplogroups of first farmers (Natufians) or surrounding them HGs. What took me be surprise is the plethora of haplogroups. If it comes to HG haplogroups we had quite uniformity in Europe, SHG were I2a, Samara all R1b, farther north R1a, only in the south we could see some mixing of C and I. Either farmers started with already highly mixed base or picked variety from bordering HGs, the fact is that by end of Mesolithic the Near East was already highly diverse in Y chromosomes.
Or maybe I'm ahead of myself once again, because the variety of haplogroups could be just ENF doing. Near East Neolithic was in full swing for at least 2 thousand years , as the PPN, Pre Potery Neolithic, since 8,000 BC, 2ky before they came to West Anatolia
220px-Map_of_fertile_crescent.svg.png

https://en.wikipedia.org/wiki/Pre-Pottery_Neolithic

During PPN they had spread from Egypt to Mesopotamia to South Anatolia. 2,000 years is a long time to interact with all the HGs around introducing their Y DNA throughout farmer community. H could have been from Mesopotamia, J2 from Assyria, G2a Natufians. I and C1 native to Anatolia.
 
Right, we still don't know haplogroups of first farmers (Natufians) or surrounding them HGs. What took me be surprise is the plethora of haplogroups. If it comes to HG haplogroups we had quite uniformity in Europe, SHG were I2a, Samara all R1b, farther north R1a, only in the south we could see some mixing of C and I. Either farmers started with already highly mixed base or picked variety from bordering HGs, the fact is that by end of Mesolithic the Near East was already highly diverse in Y chromosomes.
Or maybe I'm ahead of myself once again, because the variety of haplogroups could be just ENF doing. Near East Neolithic was in full swing for at least 2 thousand years , as the PPN, Pre Potery Neolithic, since 8,000 BC, 2ky before they came to West Anatolia
220px-Map_of_fertile_crescent.svg.png

https://en.wikipedia.org/wiki/Pre-Pottery_Neolithic

During PPN they had spread from Egypt to Mesopotamia to South Anatolia. 2,000 years is a long time to interact with all the HGs around introducing their Y DNA throughout farmer community. H could have been from Mesopotamia, J2 from Assyria, G2a Natufians. I and C1 native to Anatolia.

I think the PPN went a bit further north into Anatolia than this graphic shows, and this includes southeast Anatolia. Also, as Bicicleur pointed out, there were different kinds of "farming", cereals-Natufians (but some scholars say also or perhaps even earlier in the foothills further inland with a perhaps different population ), and pulses, nuts etc. slightly north, but generally I agree.

It's quite different, the mix of yDna, compared to Mesolithic Europe. The archaeology supports it, I think. These people were fortunate. Their environment was rich with plants, animals, had a good, moderate climate, and adequate water during most periods. The population grew pretty rapidly even before they actually domesticated the animals and plants.

These larger populations came into contact with each other, and they wound up exchanging seeds, animals, technology, etc., for a few thousand years before a bunch of them set off for Europe. I think the genetics got really mixed as well, although perhaps Egypt was a bit apart. I think the farmers were pretty mixed by the time they got there. The mixing population that went into East Africans was still closest to "Sardinians" and Stuttgart, after all.

Large populations and contact with other cultures bring their challenges but they certainly have their advantages as well; more chance for beneficial mutations to arise and spread, and more chance for advances in technology to do the same thing. Hybrid vigour and all that. :)
 
Oh really? And where was that hg. J from? It didn't came out of the blue and has to come from somewhere. And that somewhere is West Asia, where also R1a and R1b are from.

MA1 had R* and lived in Siberia 24,000 years ago. EHG is MA1's closest relative and had lots of R1a1 and R1b1. Native Americans are their next closest and Amerindians have Y DNA Q1a as did some EHG. There's a clear correlation. R1a1 and R1b1 could be from West Asia. Anything is possible. R1a1 and R1b1 may be from North Asia and came to Russia and mixed with WHG types(who had hg J and I?) there. What matters is where R1b-L23 and R1a-M417 are from because 90%+ of R1a and R1b today belongs to those lineages.
 
MA1 had R* and lived in Siberia 24,000 years ago. EHG is MA1's closest relative and had lots of R1a1 and R1b1. Native Americans are their next closest and Amerindians have Y DNA Q1a as did some EHG. There's a clear correlation. R1a1 and R1b1 could be from West Asia. Anything is possible. R1a1 and R1b1 may be from North Asia and came to Russia and mixed with WHG types(who had hg J and I?) there. What matters is where R1b-L23 and R1a-M417 are from because 90%+ of R1a and R1b today belongs to those lineages.

my guess - Q survived the LGM in Siberia, but not R who survived after moving further south near the Hindu Kush and after that R1 tribes moved west toward NW Iran, only after the youngest dryas some R1 tribes crossed the Caucasus to enter the steppe
this J was an individual they picked up south of the Caucasus, just like R1b-V88 learned about cattle herding from J

there is a 2014 study by Underhill claiming origin of R1a in NW Iran
http://www.eupedia.com/forum/threads/29701-New-R1a-Paper-by-Underhill-et-al-(2014

but your guesses are as good as mine
 
Right, we still don't know haplogroups of first farmers (Natufians) or surrounding them HGs. What took me be surprise is the plethora of haplogroups. If it comes to HG haplogroups we had quite uniformity in Europe, SHG were I2a, Samara all R1b, farther north R1a, only in the south we could see some mixing of C and I. Either farmers started with already highly mixed base or picked variety from bordering HGs, the fact is that by end of Mesolithic the Near East was already highly diverse in Y chromosomes.
Or maybe I'm ahead of myself once again, because the variety of haplogroups could be just ENF doing. Near East Neolithic was in full swing for at least 2 thousand years , as the PPN, Pre Potery Neolithic, since 8,000 BC, 2ky before they came to West Anatolia
220px-Map_of_fertile_crescent.svg.png

https://en.wikipedia.org/wiki/Pre-Pottery_Neolithic

During PPN they had spread from Egypt to Mesopotamia to South Anatolia. 2,000 years is a long time to interact with all the HGs around introducing their Y DNA throughout farmer community. H could have been from Mesopotamia, J2 from Assyria, G2a Natufians. I and C1 native to Anatolia.

no farmers entered Egypt or Africa before the 8.2 ka climate event

but the variety of haplogroups in SW Asia was much bigger than what showed up in this study dealing with NW Anatolia
the haplogroups that entered Africa 8.2 ka were totaly different of those that entered Europe (R1b-V88 and T)
 
MA1 had R* and lived in Siberia 24,000 years ago. EHG is MA1's closest relative and had lots of R1a1 and R1b1. Native Americans are their next closest and Amerindians have Y DNA Q1a as did some EHG. There's a clear correlation. R1a1 and R1b1 could be from West Asia. Anything is possible. R1a1 and R1b1 may be from North Asia and came to Russia and mixed with WHG types(who had hg J and I?) there. What matters is where R1b-L23 and R1a-M417 are from because 90%+ of R1a and R1b today belongs to those lineages.
You are talking about R*. EHG could be close to MA1 because MA1 was found in that area/region. SO it would be very obvious that it would be close to that area.

Also, later on R* evolved into R1* and R2*. South Central Asia is the home where R2* is very frequent. This means that R* migrated further south into SouthCentral Asia. This is a fact. From there on it migrated into West Asia through the Iranian Plateau. In West Asia R1* evolved into R1b and R1a. And together with J, R1a migrated into the north. You don't have to be a genius to understand this.

Hg. J is native to West Asia. There is J in Northern Europe. You can't deny that J came originally from West Asia and migrated into Europe. So for me this means that R1a* also was native to West Asia and migrted into Europe.


R1b-L23 was full Gedrosia component. R1b-L23 was native to the Iranian Plateau and migrated into the Steppes. The same can be said with R1a-M417...
 
my guess - Q survived the LGM in Siberia, but not R who survived after moving further south near the Hindu Kush and after that R1 tribes moved west toward NW Iran, only after the youngest dryas some R1 tribes crossed the Caucasus to enter the steppe
this J was an individual they picked up south of the Caucasus, just like R1b-V88 learned about cattle herding from J

there is a 2014 study by Underhill claiming origin of R1a in NW Iran
http://www.eupedia.com/forum/threads/29701-New-R1a-Paper-by-Underhill-et-al-(2014

but your guesses are as good as mine
Exactly, this is how it is. Think only about the hg. R2*. It's more southern than northern...
 
Exactly, this is how it is. Think only about the hg. R2*. It's more southern than northern...

yes, R2 TMRCA estimated is 10.200 years, probably somewhere in northern Pakistan, 1000 years before arrival of agriculture in Mehrgarh

but IMO PIE was somewhere on the steppe, 5th mill BC R1b1a1a-M478* (TMRCA 7300 years), R1b1a2-M269 (TMRCA 6400 years) and R1a1a-M417 (TMRCA 5500 years)*

* PS see Ray Banks Tree https://docs.google.com/document/d/1Ev4PSiPdCqiY5ZiCGZD96cks-cXchF2saTfKjNDG21o/edit

R1b1a1 P297/PF6398 (18656508 G->C)
• • • •R1b1a1a M73 (21888874..21888874 ins->del 2 base pairs)
• • • • R1b1a1a1 M478 (23444054 T->C)
• • • •R1b1a1b M269 (22739367 T->C)

 
Interesting new paper, although from what I have read so far it confirms everything we already suspected. As I had predicted many years ago, Sintashta evolved from Corded-Ware-related R1a population from north-west Russia, but obviously from a separate branch of R1a than the one that advanced to Poland, Germany and Scandinavia, since Central and South Asians descended from Sintashta are all R1a-Z93. That could easily be inferred from modern data.

It's nice to have some samples from the Khvalynsk culture confirming that both R1a1 and R1b1 were already in the Volga region by 5000 BCE. I am not surprised to find both haplogroups there since it is a buffer region between the southern R1b cultures (Yamna, Maykop) and the northern R1a cultures (Corded Ware, Abashevo, Sintashta).

Likewise, I had placed the Poltavka culture as a mixture of R1a and R1b on my migrations maps, and indeed it was so. The only minor surprise was the presence of Q1a in Khvalynsk, but it isn't far from Siberia and Central Asia, so a bit of admixture with neighbours is to be expected.

The mixture of EHG and an Armenian like group began about 5200 BC, "with some individuals resembling EHG and some resembling Yamnaya". The proportion was about 74%/26%.

So Armenian-like R1b would have moved to the Pontic Steppe around 5200 BCE ? I needed confirmation on that point, but it is actually the timing I had suggested in my history of R1b. Here is what I wrote in 2009:

Maciamo said:
It is not yet entirely clear when R1b crossed over from eastern Anatolia to the Pontic-Caspian steppe. This might have happened with the appearance of the Dnieper-Donets culture (c. 5100-4300 BCE). This was the first truly Neolithic society in the Pontic-Caspian Steppe. Domesticated animals (cattle, sheep and goats) were herded throughout the steppes and funeral rituals were elaborate. Sheep wool would play an important role in Indo-European society, notably in the Celtic and Germanic (R1b branches of the Indo-Europeans) clothing traditions up to this day.
...
The first clearly Proto-Indo-European culture was Sredny Stog (4600-3900 BCE), when small kurgan burials begin to appear, with the distinctive posturing of the dead on the back with knees raised and oriented toward the northeast, which would be found in later steppe cultures as well. There is evidence of population blending from the variety of skull shapes. Towards the end of the 5th millennium, an elite starts to develop with cattle, horses and copper used as status symbols.

My migration map showed R1b crossing the Caucasus to the Pontic Steppe some time between 6000 and 5000 BCE, and my first migration map of R1b (the Flash version, which I can't paste on the forum) indicated 7000 ybp for that trans-Caucasian migration. So it is reassuring that was intuition was right on the timing as well as the geography.

old_neolithic_map.gif





What this paper and other recent papers on ancient Y-DNA have shown is that natural selection has been very active for Y-chromosomes in the last 8,000 years.

For example, what happened to the Anatolian and Balkanic Neolithic H2 ? If we look at region with very high G2a frequencies and EEF ancestry today like Sardinia, the Apennines or Georgia, there isn't any H2 anywhere. One possible explanation is that H2 Y-chromosomes were less competitive and produced less offspring, which gradually weeded it out from the population. But this seems to have happened for quite a few paternal lineages that were once common during the Mesolithic and throughout the Neolithic and even the Early Bronze Age, such as C1a2, F, I*, I2*, J*, K*, P1*, or R1*. The asterisk might as well serve as a reminder that these lineages didn't leave descendants, and therefore no further subclade is available today. Only their brothers or cousins with new mutations perpetuated those haplogroups and what became G2a3b1a, I1a, I2a1a, I2a2a, R1b1a2a1, R1a1a1a, and so on. C1a2, H2 and P1 never got the right mutations and are virtually extinct today.

In light of this, it would make a lot of sense if the tremendous success of R1a-M417 and R1b-L11 was not purely the result of superior Indo-European technology, warfare, conquest and political domination, but also of advantageous genetic mutations increasing male fertility on the one hand, but also typically male behavioral traits such as dominance, as I suggested in this thread.
 
I posted a thread: Traits that were Selected for in the last 8,000 years. Focused on the Natural Selection aspect of this paper. Something important to understand IMO is most traits are polygentic. Angela has pointed this out many times. So, each one of the SNPs that showed strong signs of selection are probably only one small part of what causes someone to have a certain trait.

It is interesting that a mutation for defensive reaction to glutine first appears in Neolithic farmers, which probably means it is a farmer-mutation because only farmers eat glutine. Selection for Lactose Tolerance, Pale skin, and reduced fat are the most significant. For most mutations they significantly rose in frequency in the last 4,000 years. A lot can happen in 4,000 years even if there's mostly genetic-continuation in some regions.
 
@Maciamo,

The circa 2500 BC R1a-Z94 guy from Poltavka culture was a genetic outlier. He was genetically just like Sintashta, Corded Ware, etc. He was either an immigrant or from an early wave R1a-Z93 people from the West into the Steppe. The Poltavka culture itself probably had 0 or little R1a-Z93 or anykind of R1a, and was almost exclusively R1b-Z2103.
 

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