The genetic history of Ice Age Europe

12000 BC R1b1 in Villabruna.

Didn't I say that R1b v88 in 5500 BC Iberia with EEF aDNA is unlikely from the Steppes and probably came from a region that was close to the homeland of EEF and they catched it up there? For instance Mesopotamia Kurdistan or the Iranian Plateau? :)

As I said in the past by Neolithic era R1 lineages have been already widespred throughout Eurasia. Mark my words we will find R1b l23 that predates Bronze Age in West Asia.


And than according to this paper WHG is a pre Neolithic Anatolian component lived next to EHG and many other components and replaced Paleolithic Europeans roughly 14000 BC.
http://phys.org/news/2016-05-genetic-
analysis-ice-age-europeans.html

I hate to say it ( actually not :p) But didn't I say that the "WHG" in Neolithic farmers is not a back migration of mesolithic Europeans into Anatolia.
I said that this WHG is ancient in the region since it is also found in the Levant and even Arabia and probably represents a pre Neolithic Near Eastern component.

WHG = pre Neolithic Anatolian, EF= Neolithic Near Eastern, CHG = mesolithic_neolithic Iranian Plateau/Caucasus.
 
It seems, that:

That Italian with R1b carried no basal Eurasian ancestry:

(quote from Anthrogenica discussion):



So how did they conclude, that he came from the Near East?

Simple, Satsurbilas non basal Eurasian ancestry is what it share with Villabruna what indiciates that Basal Eurasian is a third component (probably from Arabia?) that contributed to the formation of CHG and EEF AFTER WHG already expanded towards Europe.

Means proto "UHG-ANE" or let us call it gravettian component mixed with some degree of Basal Eurasian what became EEF and CHG.
 
R1b was IMO native to the Near East and there were numerous successive emigrations of R1b from that area.

Villabruna represents one of the earliest migrations of R1b from the Near East to South Europe. Later other waves came. R1b migrated both to the Steppe (Z2103 was "intrusive" in Yamna - perhaps came from south of the Caucasus with Maykop?). Z2103 was not the majority of Yamna males - but they brought the "magic" of metallurgy, and became "shamans" / "chieftains". That's why we see them overrepresented in kurgans.

R1b-L51 in my opinion expanded directly from the Middle East to Western Europe, bringing Copper Age to Iberia (ATP3).

I really don't understand why you (or the authors of the paper) would think that the R1b in Villabruna came from the Middle East. R1b was found in Mesolithic Russia and R* in Palaeolithic Siberia. It's not a typically Middle Eastern lineage, although some tribes did end up there in the early Neolithic. The U5b2 isn't Middle Eastern either.

I admit that I didn't have time to check all the supplementary data. Is there any sign that the Villabruna R1b had Middle Eastern (CHG or ENF) rather than Palaeolithic European (WHG, EHG) or Ancient North Asian (ANE) admixture?
 
I really don't understand why you (or the authors of the paper) would think that the R1b in Villabruna came from the Middle East. R1b was found in Mesolithic Russia and R* in Palaeolithic Siberia. It's not a typically Middle Eastern lineage, although some tribes did end up there in the early Neolithic. The U5b2 isn't Middle Eastern either.

I admit that I didn't have time to check all the supplementary data. Is there any sign that the Villabruna R1b had Middle Eastern (CHG or ENF) rather than Palaeolithic European (WHG, EHG) or Ancient North Asian (ANE) admixture?

the oldest clades of both R1a and R1b today are found in NW Iran
they may have been the inhabitants of Hoti and Belt caves 14 ka

Villabruna had Asian admixture, even east Asian
 
R1b was IMO native to the Near East and there were numerous successive emigrations of R1b from that area.

Villabruna represents one of the earliest migrations of R1b from the Near East to South Europe. Later other waves came. R1b migrated both to the Steppe (Z2103 was "intrusive" in Yamna - perhaps came from south of the Caucasus with Maykop?). Z2103 was not the majority of Yamna males - but they brought the "magic" of metallurgy, and became "shamans" / "chieftains". That's why we see them overrepresented in kurgans.

R1b-L51 in my opinion expanded directly from the Middle East to Western Europe, bringing Copper Age to Iberia (ATP3).


I tried to explain this so many times but nice to see that it holds water now.

Only the facts that we found R1b v88 in Neolithic Iberia with EEF ancestry 5500 BC proves the point that it could not have come via the Steppes and must have been from a region nearby to the homeland of early farmers, like Kurdistan, Mesopotamia or the Iranian Plateau thats what I have been preaching for so long.
 
I tried to explain this so many times but nice to see that it holds water now.

Only the facts that we found R1b v88 in Neolithic Iberia with EEF ancestry 5500 BC proves the point that it could not have come via the Steppes and must have been from a region nearby to the homeland of early farmers, like Kurdistan, Mesopotamia or the Iranian Plateau thats what I have been preaching for so long.

Els Trocs were herders 7.5 ka amidst native HG tribes, R1b-V88 might as well have come through North-Africa
R1b-V88 probably never got on the Pontic steppe, R1b-M269 and R1b-M73 did though
 
it is what the paper says
do you have other info?

Not quite, he has them swapped. Pavlov1 is the I/pre-I, Vestonice16 is the C1a2.
 
There's no special connection with West Asia and the WHG R1b guy from Italy. He had as much connection to West Asia as anyother WHG. He lived far away from West Asia. His results don't suggest any special connection between West Asia and R1b. We don't have enough ancients samples to say there's a connection or not, but none of them yet say there is.
 
There's no special connection with West Asia and the WHG R1b guy from Italy. He had as much connection to West Asia as anyother WHG. He lived far away from West Asia. His results don't suggest any special connection between West Asia and R1b. We don't have enough ancients samples to say there's a connection or not, but none of them yet say there is.

There is a reason why the study obviously mentions that this Villabruna individuals had connections to the Near East in comparison to other paleolithic samples. So they must know something they haven't yet presented. And they even give a hint with saying that WHG itself differs from other components found their prior which indicates that WHG came from the Near East earlier than EEF. And this explains the WHG like ancestry in EEF.
 
I've added mtDNA/Y DNA results to my spreadsheet with the list of samples. I also labelled each according to the cluster they were assigned using F3-stats.

New Paleo European Genomes

The ~30,000 year old Italian and Central European samples form a cluster. They're closer to WHG than Kostinki and 30,000 ear old Belgium are. Their Y DNA is C1a and IJKH(inlu. confirmed I). Their mtDNA is U2*, pre-U5*, U8*, U2'3'4'7'8'9*, and M. Looks like a good canidate for the ancestor of WHG.

Fire-Haired, wasn't there an mtDna "H" in central Europe in a Gravettian context?

It's not in your charts.

Of course, mtDna "H" could still have greatly diversified and expanded in that later warm period.

At least one of the Spanish samples that was labeled mtDna "H" definitely isn't, though. The methodology used in those old papers definitely left a lot to be desired.
 
the oldest clades of both R1a and R1b today are found in NW Iran
they may have been the inhabitants of Hoti and Belt caves 14 ka

Villabruna had Asian admixture, even east Asian

The oldest subclades of R1a and R1b are found in Iran because there is so little data from Central Asia. But anyway it doesn't contract my theory that R1b originated near and spread early around the Caspian Sea.

If Villabruna has East Asian admixture it is clearly a sign that it came from Siberia via Eastern Europe, not from the Middle East.
 
There is a reason why the study obviously mentions that this Villabruna individuals had connections to the Near East in comparison to other paleolithic samples. So they must know something they haven't yet presented. And they even give a hint with saying that WHG itself differs from other components found their prior which indicates that WHG came from the Near East earlier than EEF. And this explains the WHG like ancestry in EEF.

WHG's relation to the Near East could also be because of EuropeanWHG admixture in West Asia. All we know is that there was gene flow between West Asia(inclu. Caucasus/CHG) and Europe after 30,000 years ago.
 
Fire-Haired, wasn't there an mtDna "H" in central Europe in a Gravettian context?

It's not in your charts.

Of course, mtDna "H" could still have greatly diversified and expanded in that later warm period.

At least one of the Spanish samples that was labeled mtDna "H" definitely isn't, though. The methodology used in those old papers definitely left a lot to be desired.

Like with older papers, the H7a1 result for a Gravettian sample is probably contamination. One part of the paper labels her as U and another labels her as H7a1. Considering the 90%+ U frequency in pre-Neolithic Europeans, for now I'm trusting the U result. Also, that same sample was fully sequenced in that recent mtDNA paper and came out U5*.
 
R1b was found in Mesolithic Russia and R* in Palaeolithic Siberia.

I think that you refer SVP44 of Lebyazhinka IV site, but if you look at this Russian site, it was neolitic "Middle Volga Culture" (VI-V millenia), so it's not a sure HG

http://www.povolzie.archeologia.ru/14.htm
 
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.

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 don't see how the statement exactly flows from statistics that don't refer to the levels in the Mesolithic, but I get the point.

Ed. I take it back. :) I see from the supplement that the levels were indeed down to that by the Mesolithic.
 
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asgjb6.png


Previous studies assumed that Kostenki14 was the oldest European man with Basal Eurasian ancestry, who survived the Ice Age, but Fu et al. (2016) put it more accurately. Kostenki14 was likely to be a mixed-race individual between populations related to East Asians (hg C) and the ancestors of Europeans (hg U2). This new study also found that some of the Villabruna Cluster individuals such as Loschbour and LaBrana1 are closely associated with Han Chinese but not all Villabruna individuals have an affinity with East Asians. The ancestors of Loschbour and LaBrana1 in the Villabruna Cluster may have interbred with ancient populations related to East Asians as well, which was why excess allele sharing with East Asians was detected. Moreover, the ‘Villabruna Cluster’ is composed of 15 post-Last Glacial Maximum individuals from 14,000–7,000 years ago. Of these fifteen Villabruna samples, older twelve samples belonged Haplogroup R or R1 and haplogroups R1b and R1b1 only appear in more recent three samples, which are dated around 7,000 years ago (Table S4.2. Details of Y haplogroup SNPs in Villabruna Cluster samples).

The Villabruna Cluster is represented by the largest number of individuals in this study. This allows us to study heterogeneity within this cluster (Supplementary Information section 13). First, we detect differences in the degree of allele sharing with members of the El Mirón Cluster, as revealed by significant statistics of the form D(Test1, Test2; El Mirón Cluster, Mbuti). Second, we detect an excess of allele sharing with east Asians in a subset of Villabruna Cluster individuals— beginning with an ~13,000-year-old individual from Switzerland—as revealed by significant statistics of the form D(Test1, Test2; Han, Mbuti) (Fig. 4b and Extended Data Fig. 3). For example, Han Chinese share more alleles with two Villabruna Cluster individuals (Loschbour and LaBrana1) than they do with Kostenki14, as reflected in significantly negative statistics of the form D(Kostenki14, Loschbour/LaBrana1; Han, Mbuti)4. This statistic was originally interpreted as evidence of Basal Eurasian ancestry in Kostenki14. However, because this statistic is consistent with zero when Han is replaced with Ust’-Ishim, these findings cannot be driven by Basal Eurasian ancestry, and must instead be driven by gene flow between populations related to east Asians and the ancestors of some Europeans (Supplementary Information section 8).
 
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The Reich Lab has made the whole paper available:
http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/FuQ_nature17993.pdf

The graph is handy for figuring out these relationships:
Fu et al Ice Age Europeans graph.PNG

"Beginning around 14,000 years ago with the Villabruna Cluster, the strong affinity to GoyetQ116-1 seen in El Mirón Cluster individuals who belong to the Late Glacial Magdalenian culture becomes greatly attenuated (Supplementary Information section 10). To test if this change might reflect gene flow from populations that did not descend from the >37,000-year-old European founder population, we computed statistics of the form D(Early European, Later European; Y, Mbuti) where Y are various present-day non-Africans. If no gene flow from exogenous populations occurred, this statistic is expected to be zero. Figure 4b shows that it is consistent with zero (|Z|<3) for nearly all individuals dating to between about 37,000 and 14,000 years ago. However, beginning with the Villabruna Cluster, it becomes highly significantly negative in comparisons where the non-European population (Y) is Near Easterners (Fig. 4b; Extended Data Fig. 3; Supplementary Information section 11). This must reflect a contribution to the Villabruna Cluster from a lineage also found in present-day Near Easterners (Fig. 4b)."

So, while admixture isn't going to show this "Near Eastern" affinity, formal stats do show it. What's being lost in the renewed R1a vs R1b wars as to who is the most Indo-European of them all, is that the authors leave open two possibilities: one that the Villabruna set was in Europe as early as the "Gravettian" group, and just represents substructure in Europe, and one that they arrived in Europe somewhere around 14000 YBP from the southeast, through Greece perhaps.

If the former was true, why all this Near Eastern "affinity", unless there was some inflow that changed them slightly perhaps?

Maybe they are just being really cautious. I guess we need to stay tuned.

It doesn't seem then that Magdalenian expansions left all that large a trace; most "European hunter-gatherer" ancestry is WHG or related to the Villabruna group.

Twitter-Iosif Lazaridis (one of the co-authors)

"It seems that there was a hunter-gatherer "reset" ~14,000 years ago that left only the "Villabruna cluster" as the inheritors of Europe..."
 
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This is a link to the supplement where you can find the formal stats from which they deduce this Near Eastern affinity.
http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature17993-s1.pdf

They do not say it necessarily came from the Near East to Europe. They leave open the possibility of gene flow from Europe to western Anatolia. Much less did they say anything about R1b having been born in the Middle East and being the catalyst for bringing WHG to Europe. People are really jumping the gun with all this. Maybe they know the answer and just aren't saying, but regardless, we have to wait for the data.

"Affinities of pre-Neolithic Europeans to the Near East When neither of the two pre-Neolithic Europeans analysed in the statistic is in the Villabruna Cluster—that is, both are older than about 14,000 BP—they tend to be symmetrically related to populations outside Europe including present-day and ancient Near Easterners. However, when one lived prior to the Villabruna Cluster (e.g. Vestonice16, ElMiron, Kostenki14, KremsWA3, and GoyetQ116-1) and the other is in the Villabruna Cluster (e.g. BerryAuBac, Bichon, CuiryLesChaudardes1, Falkenstein, Hungarian.KO1, LaBrana1, Loschbour, Ranchot88, Rochedane and Villabruna), there is a distinct attraction of the Villabruna Cluster samples to Near Eastern populations (Figure 4b; Extended Data Figure 3). Table S11.1 shows the statistics when the Near Eastern population is Iraqi_Jew. There are several possible explanations for these findings. One is gene flow between relatives of Near Easterners and pre-Neolithic Europeans after ~14,000 years ago, beginning with the Villabruna Cluster. A second is population substructure in Europe. In this scenario, after post-glacial re-peopling of Europe, the balance of ancestry could have shifted toward populations that were more closely related to Near Easterners. In either case, however, major population turnovers must have occurred. The affinity of pre-Neolithic Europeans to Near Easterners beginning around 14,000 years ago is distinct from the affinity to East Asians in Mesolithic Europeans."

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.

Just on a personal note, is the full sequence for the U2 found in southern Italy 28,000 years ago somewhere in the paper or supplement? I'd like to see how mine compares.

Ed.* On reflection I don't think the refugia was in the Ukraine. It doesn't seem to have the right climate or flora and fauna at that period. It seems more likely that it spanned the area from Italy to the Balkans.
 
Just on a personal note, is the full sequence for the U2 found in southern Italy 28,000 years ago somewhere in the paper or supplement? I'd like to see how mine compares.

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.
 

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