The genetic history of Ice Age Europe

[Silesian]

http://wizzyschool.com/images/early%20man/human%20fossil%20sites.gif

http://s24.postimg.org/tbvhtfpcl/R1a_vs_R1b.png

R1a and R1b split around 22,000YBP that does not leave a lot of time considering the distance between the samples. A parsimonious explanation will be needed.
R1b M-73[R-M478-formed 13500 ybp, TMRCA 7300 ybp] is on the Steppe and R1b-V88 R-M18[formed 17200 ybp, TMRCA 10200 ybp] is already confirmed find in Cagliari, Sardinia.

http://www.ancestraljourneys.org/palaeolithicdna.shtml
Sergey M. is placing the Villabruna 14k+/-ybp sample with additional snp's at L754+[ R1b1a on current ISOGG tree] At or near R1b base.
https://www.yfull.com/tree/R1b/

P224, M734, P285, P227, P294, P242, P238, P245, M173, P286, P236, M306, L278. [Derived for additional SNPs L754/PF6269/YSC0000022+, A702/Z8137+, CTS4244/PF6257/YSC0001279/V2997+, CTS7585+, C41/M12190/SK2062/V1501/Z8135/Y108+, L1345/PF6266/YSC0000224+, L761/PF6258/YSC0000266+, L774/PF6245/YSC0000277+, PF6263+, PF6271+ which make it R1b1a on current ISOGG tree]

I really can't see any R1b coming from the Near East. That is probably why no samples where found in Anatolia. Also the R1b Z2103+ samples are practically buried on top or beside the R1b-m73 on the Steppe. Non of the Steppe samples came back R1b-L584+; that is significant because that is what you would expect if it came from the lower Caucasus or Iran. Also Armenian are of hand about 80% R1b-L584 if I remember correctly. It looks like all the action including maybe the R1a split was within a certain region or band. Lets see what more samples show.
Eurogenes.
http://eurogenes.blogspot.ca/
It is hard to imagine all this started from the tiny blue star at the far left of this plot.

 

[Angela]

lol, maybe it is related to your U2 . No seriously it is possible. A large number of our Mesolithic mtDNA U5s have found close modern matches on FTDNA, so anything is possible. However, just as it's near impossible for a modern person to find a close mtDNA match from another random modern person with the same haplogroup, it's near impossible for an ancient person to find a close modern match from a random modern person with the same haplogroup.

I know it's a long shot, but I'd like to take a look. Did I ever tell you how once when sitting with a 94 year old female relative I was trying to explain to her that I was interested in figuring out when we arrived in our mountains and valleys? She pointed all around her and said, "We've always been here." Probably not, but it was a nice moment.

I know how tough mtDna can be. My closest match (other than family) is a "colonial American" with maternal ancestry from England or northern Ireland, and we split about 2000 years ago. I tell him some Roman brought his wife along with him to England, and their descendants are there to this day. That, or the timing is off and a Crusader taking the Via Francigena met an Italian girl and brought her home with him. Or then again, maybe it's "Celtic" and moved both south and northwest*. Take your pick, I guess.

Anyway, if the data is available somewhere I'd appreciate it if you'd let me know.

 

[LeBrok]

The paper also had some things to say about the decline in Neanderthal ancestry, and Dienekes opined upon it.

"Using one statistic, we estimate a decline from 4.3–5.7% from a time shortly after introgression to 1.1–2.2% in Eurasians today (Fig. 2). This is remarkable because it shows that most of the Neandertal ancestry of the earliest AMH in Europe was gone by the Mesolithic. It really seems that Neandertal genes were bred out of the gene pool over time. Will this trend continue into the future? Perhaps only minute traces of Neandertal DNA will remain in humans in 10,000 more years. Some of Neandertal DNA may yet prove to be neutral or beneficial, so at the limit the percentage may be more than zero. Nonetheless, the historical trend does suggest that modern humans inherited mostly genetic garbage from Neandertals and evolution is more than halfway through the process of getting rid of it.

Very biased on his part. He still can't get used to the idea of Neanderthal in us, lol. "Get rid of the garbage".

As a corollary, there may have been other episodes of archaic admixture that are no longer detectable. Perhaps our modern human lineage has repeatedly admixed with other species, but traces of those admixtures are long gone by the action of natural selection. The reason for our relative homogeneity as a species may not be that we avoided intermixing with others, but that, sadly, most others had not much that was beneficial to offer to our ancestors."

http://dienekes.blogspot.com/2016/05/neandertal-ancestry-going-going-gone.html
.

I wonder if we compare modern human genome with homo sapiens of 100,000 years ago, how many genes are the same? We might have got rid of their "garbage" too.

 

[holderlin]

http://eurogenes.blogspot.be/2016/05/the-genetic-history-of-ice-age-europe.html

Abstract: Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

abstract : http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17993.html
figures and tables : http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature17993_ft.html
supplementary info : http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature17993-s1.pdf

Dank thread, awesome. Thanks for this. I've been obsessively raging about the lack of cool new papers, dreaming of Harrapan and Maykop analyses, but this, this may even be better.

Will begin reading now.

 

[LeBrok]

I also think there's a problem with this theory that the R1b1 in Villabruna is similar to R1b1 that existed south of the Caucasus and moved north into the steppe from there. The Villabruna R1b1 has no Basal Eurasian, while whatever went into the steppe from the Caucasus did have it. Plus, the Villabruna R1b1 is WHG. The authors of this paper maintain that the roughly 68% non Basal Eurasian in the CHG people was related to ANE, not to WHG. For the CHG like ancestry to move into the steppe from the south Caucasus with R1b1 people would mean that we'd have to have CHG like-ANE like R1b1 in the Caucasus, and WHG like R1b1 in Europe. It may instead be the case that R1b1 was a "Southern European"* hunter-gatherer who roamed the whole range from Italy to the border of Ukraine. The R1b1 found in Yamnaya is one branch that went east. There may be a different branch of R1b1 that is descended from Villabruna.

Some of the answers are going to have to wait for older samples from various places in the Balkans, Eastern Europe and the Middle East, although if we find it in Anatolia, I still don't see how we'd know the direction of gene flow.

Good points. After all R1b wasn't found among acquired HG Y DNA by early farmers in Anatolia or Hungary. Either it was a rare mix into WHG, or lost tribe who wandered in Italy and died there, or perhaps contamination?

 

[berun]

Again a case to doubt about R1b = IE, of unexpected date even. But the interesting fact here is who is not: R1a, the guy that expanded so much quick as IE...

 

[Sile]

So is the Veneto R1b1 a east asian or near east person?

I also think this is not Italian refugium but more likely a Adriatic Refugium ( Italo-Danubian ) . The north Adriatic area was far more important as a passage from the East into Italy before the area flooded .

 

[bicicleur 2]

the Villabruna cluster were forest dwellers
this is a vegetation map of Europe during the youngest dryas

 

[Fire Haired14]

So is the Veneto R1b1 a east asian or near east person?

No he was WHG. WHG is slightly closer to East Asia and Middle East than other pre-Neo Europeans.

 

[Sile]

No he was WHG. WHG is slightly closer to East Asia and Middle East than other pre-Neo Europeans.

Middle-East?
Iran, Anatolia and South-Caucasus are not middle-east ...............the levant is near east ................where in middle east ? Arabian peninsula?

Middle east is noted as just SW-Asian .............South Asian is India

Please explainetrified:

 

[Silesian]

......But if Z2103 is not from BMAC then it has to be directly from the southern parts of the Caspian Sea, not far from Azerbaijan province of Iran....

There is a difference in distribution between R1b-L584+ and for example R1b-9219+, both in same time frame.
R1b-9219+ 4300YBP+/-



R1b-L584+ 4700+/-YBP

 

[Angela]

Very biased on his part. He still can't get used to the idea of Neanderthal in us, lol. "Get rid of the garbage".

I wonder if we compare modern human genome with homo sapiens of 100,000 years ago, how many genes are the same? We might have got rid of their "garbage" too.

That's exactly what he's saying isn't? Also, whether you call it "garbage" or not, there's total consensus that natural selection is purging it from the human genome; if it were beneficial that wouldn't be happening.

 

[Silesian]

the Villabruna cluster were forest dwellers
this is a vegetation map of Europe during the youngest dryas

View attachment 7711

Now we know about WHG(Loschbour-Villabruna R1b- 14k+/-ybp Italian cluster)
Pretty pan-European from East to West.

http://eurogenes.blogspot.ca/2015/02/massive-migration-from-steppe-is-source.html

 

[Angela]

This is what the media is reporting, but is this actually what Reich is saying in those interviews? The part about "WHG" definitely coming from Turkey isn't found in the paper.
http://www.archaeology.org/news/4426-160502-europe-population-changes

"CAMBRIDGE, MASSACHUSETTS—BBC News reports that a new genetic study of the remains of 51 Europeans between 45,000 and 7,000 years old has been led by David Reich at Harvard Medical School. The results suggests that beginning 37,00 years ago, all Europeans came from a single founding population that developed deep branches in different parts of Europe. At the end of the last Ice Age some 19,000 years ago, people thought to have come from Spain spread northward. Then some 14,000 years ago, populations from Turkey and Greece spread westward into Europe and replaced the first group. “We see multiple, huge movements of people displacing previous ones,” said Reich. The analysis also suggests that Ice Age Europeans had dark complexions and brown eyes until about 14,000 years ago, when blue eyes began to spread across the population. Pale skin began to appear after 7,000 years ago. Earlier populations also had more Neanderthal DNA than present-day people, which is consistent with the idea that it may have had harmful effects on modern humans and was lost over time through natural selection."

Razib Khan is also on the WHG from the Near East bandwagon:
http://www.unz.com/gnxp/the-last-glacial-maximum-dictated-europes-genetic-history/#comments

If that's the case, as I pointed out early in the thread, there's a Basal Eurasian problem. Villabruna doesn't have any Basal Eurasian. Did WHG leave the Near East before it arrived? CHG is 13,300 before present, yes? It already had about 32% Basal Eurasian according to this paper. How could Villabruna, dated 14,000 YBP have avoided it? Isn't that cutting it a little close?

Also, where did it come from? I know Dienekes was always going on about a refugium in Arabia, but I don't know how likely that is, and, as I said, when did it arrive? Wouldn't the Natufians have already had it? Also, if it came from there it would have traveled south to north.

 

[Silesian]

Razib Khan is also on the WHG from the Near East bandwagon:
http://www.unz.com/gnxp/the-last-glacial-maximum-dictated-europes-genetic-history/#comments

If that's the case, as I pointed out early in the thread, there's a Basal Eurasian problem. Villabruna doesn't have any Basal Eurasian. Did WHG leave the Near East before it arrived? CHG is 13,300 before present, yes? It already had about 32% Basal Eurasian according to this paper. How could Villabruna, dated 14,000 YBP have avoided it? Isn't that cutting it a little close?..........

http://blogs.discovermagazine.com/gnxp/2011/01/the-assyrians-and-jews-3000-years-of-common-history/
LOLOL this was another gem LOLOLOL peer reviewed, no?

On a serious note, here is the latest, by David, not bad pretty good.
Clearly R-R1a and R1b cluster forming with Villabruna[14+/-k], Steppe R1a and R1b[7.5+/-k], and Malta1 R*[24k+/-]
http://eurogenes.blogspot.ca/

 

[LeBrok]

That's exactly what he's saying isn't? Also, whether you call it "garbage" or not, there's total consensus that natural selection is purging it from the human genome; if it were beneficial that wouldn't be happening.

I think it was all beneficial, it just that a better option comes with time. Like updating of OS. Our original HSS genome has been replaced with new mutations, new alleles. Does that mean that original one was harmful? No, just better mutations came along.

 

[LeBrok]

If that's the case, as I pointed out early in the thread, there's a Basal Eurasian problem. Villabruna doesn't have any Basal Eurasian. Did WHG leave the Near East before it arrived? CHG is 13,300 before present, yes? It already had about 32% Basal Eurasian according to this paper. How could Villabruna, dated 14,000 YBP have avoided it? Isn't that cutting it a little close?

Also, where did it come from? I know Dienekes was always going on about a refugium in Arabia, but I don't know how likely that is, and, as I said, when did it arrive? Wouldn't the Natufians have already had it? Also, if it came from there it would have traveled south to north.

Anatolia and South Balkans fit the best.

 

[bicicleur 2]

This is what the media is reporting, but is this actually what Reich is saying in those interviews? The part about "WHG" definitely coming from Turkey isn't found in the paper.
http://www.archaeology.org/news/4426-160502-europe-population-changes

"CAMBRIDGE, MASSACHUSETTS—BBC News reports that a new genetic study of the remains of 51 Europeans between 45,000 and 7,000 years old has been led by David Reich at Harvard Medical School. The results suggests that beginning 37,00 years ago, all Europeans came from a single founding population that developed deep branches in different parts of Europe. At the end of the last Ice Age some 19,000 years ago, people thought to have come from Spain spread northward. Then some 14,000 years ago, populations from Turkey and Greece spread westward into Europe and replaced the first group. “We see multiple, huge movements of people displacing previous ones,” said Reich. The analysis also suggests that Ice Age Europeans had dark complexions and brown eyes until about 14,000 years ago, when blue eyes began to spread across the population. Pale skin began to appear after 7,000 years ago. Earlier populations also had more Neanderthal DNA than present-day people, which is consistent with the idea that it may have had harmful effects on modern humans and was lost over time through natural selection."

Razib Khan is also on the WHG from the Near East bandwagon:
http://www.unz.com/gnxp/the-last-glacial-maximum-dictated-europes-genetic-history/#comments

If that's the case, as I pointed out early in the thread, there's a Basal Eurasian problem. Villabruna doesn't have any Basal Eurasian. Did WHG leave the Near East before it arrived? CHG is 13,300 before present, yes? It already had about 32% Basal Eurasian according to this paper. How could Villabruna, dated 14,000 YBP have avoided it? Isn't that cutting it a little close?

Also, where did it come from? I know Dienekes was always going on about a refugium in Arabia, but I don't know how likely that is, and, as I said, when did it arrive? Wouldn't the Natufians have already had it? Also, if it came from there it would have traveled south to north.

this paper suggests gravettian spread during LGM from middle Danube (Vestonice?) to refuges in the Balkans and Anatolia : http://maajournal.com/Issues/2004/Vol-1/Full1.pdf

apart from the single R1b all Villabruna are I or C1a, same as Vestonice and El Miron
could this gravettian in SW Anatolia, in the Antalya area (Karain B and Öküzini Caves) be the source of Villabruna?
it was one of the areas that was forested soon after LGM

the paper also says the Gravettian in SW Anatolia was geographically seperated from the Kebaran/Natufian, the presumed source of farming

 

[Fire Haired14]

@Everyone,

The media reporting all of Europe being repopulated after 14,000 years ago from people originating in the Near East are a result of their unfamiliarity with the subject. We don't have enough ancient DNA to say this is correct or not. The El Miron cluster, which genomes from Spain and Germany dating 19,000-15,000 years old belong to, is very closely related to WHG. It's not WHG, but very related. So, WHG wasn't a complete forigner to Europe who then repopulated it after 14,000 years ago.

Furthermore in terms of mtDNA/Y DNA, there's plenty of evidence WHG originated deep in Europe. We see mtDNA U5b and Y DNA I in the El Miron cluster 19,000-15,000 years ago, and we see mtDNA pre-U5 and pre-I and C1a2 in the Vestonice cluster 30,000 years ago. The relation between the Middle East(especially EEF and modern Middle East) to WHG could be because the Middle East and Europe was one big breeding ground. Treating them as two completely distinct worlds is stupid. It's one continuous piece of land. We shouldn't assume affinity between Europe and the Middle East means there was migration from the Middle East to Europe. Why can't it be migration from Europe to the Middle East?

I find it very likely that 30,000-40,000 years ago the same "West Eurasian" family which populated Europe was also in the Middle East. "West Eurasian" had distant relatives(ANE) living deep in Northern Asia and maybe even in America, so it's in no way unlikely they were living as far east as India.

 

[Angela]

this paper suggests gravettian spread during LGM from middle Danube to refuges in the Balkans and Anatolia : http://maajournal.com/Issues/2004/Vol-1/Full1.pdf

apart from the single R1b all Villabruna are I or C1a
could this gravettian in SW Anatolia, in the Antalya area (Karain B and Öküzini Caves) be the source of Villabruna?
it was one of the areas that was forested soon after LGM

My reading of the paper and supplement indicates that Gravettian and Villabruna are distinct. In fact, they seem to be saying that Gravettian people left almost no autosomal trace in modern Europeans. That doesn't mean modern Europeans don't carry some of their mtDna, for example, but that's a different issue. You can carry a uniparental line associated with X autosomal group and not be similar to them autosomally at all. (The usual R1b Chadian example comes to mind.)

However, I went and checked the chronology. This WHG "out of the Near East" scenario is possible if the WHG like people were already in Europe by or before 20,000 YBP*, and the Basal Eurasian arrived in most of the Near East after that. Of course, the results could also be explained by some WHG moving into the northern Near East after the LGM.

So, that's why in the paper, at least, the authors aren't definitely choosing one scenario over another. The answers will only come with ancient dna from the pre-Neolithic Near East.

*Logically, of course, these distinctions are meaningless imo. Anatolia and Europe were one land mass in this era, so to call one Europe and one the Near East doesn't make much sense to me. These particular hunter-gatherers could have roamed from Italy to Anatolia and west into the Balkans.

Given that we're dealing with the Reich Lab, it's possible that they have already analyzed some really old Anatolian samples and we know they've been working on Iberian Bell Beaker for quite some time, so perhaps, although they don't want to tip their hand until they've totally worked all this out, they may be leaning more one way than the other.

Just when I start to lose interest in this whole field, they just pull me back in.