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Sunday, March 29, 2015

European foragers were almost wiped out by the ice age


I think what this article is really saying is that the effective population size of Europeans might have dropped to as little as 30 after the LGM peak. If so, that's pretty close to a genetic precipice for most animals. In any case, it looks like there are more hunter-gatherer genomes on the way, including from Denmark and Switzerland, courtesy of Ron Pinhasi's team, which brought us the ancient Hungarian genomes last year (see here).

‘As an archaeologist and anthropologist, I was quite shocked to see how limited, how small the population numbers were. You know, shockingly small,’ said Prof. Pinhasi, based at University College Dublin, Ireland.

‘I think that what happened, it’s on a catastrophic level of demography for a long time in human evolution,’ he said.

The impacts of this are significant for understanding the origins of many Europeans today, as it is forcing researchers to reconsider models of human expansion and colonisation of the continent, as well as our genetic ancestry.

By analysing the genomes of human remains, the researchers are able to gather demographic data and clues to potential population sizes.

Prof. Pinhasi’s team has found that the genomes sequenced from hunter-gatherers from Hungary and Switzerland between 14 000 to 7500 years ago are very close to specimens from Denmark or Sweden from the same period.

These findings suggest that genetic diversity between inhabitants of most of western and central Europe after the ice age was very limited, indicating a major demographic bottleneck triggered by human isolation and extinction during the ice age.

‘We’re starting to be able to reconstruct the actual dynamics of migrations and colonisation of the continent by modern humans and that’s never been done before the genomic era,’ explained Prof. Pinhasi.

He believes that early humans crossed the continent in small groups that were cut off while the ice was at its peak, then successively dispersed and regrouped over thousands of years, with dwindling northern populations invigorated by humans arriving from the south, where the climate was better.

Source: Francesca Jenner, Ice-age Europeans roamed in small bands of fewer than 30, on brink of extinction, 26 March 2015, Horizon Magazine

117 comments:

Krefter said...

I guess this confirms WHG was in Switzerland 14,000 years ago.

Chad Rohlfsen said...

Prof. Pinhasi’s team has found that the genomes sequenced from hunter-gatherers from Hungary and Switzerland between 14 000 to 7 500 years ago are very close to specimens from Denmark or Sweden from the same period.

I guess that means EHG was a late arrival in Scandinavia and not present in all hunters. I still think archaeology backs this fact. I think that the Motala people were not the norm, but something of a new arrival.

Colin Welling said...

I think what this article is really saying is that the effective population size of Europeans might have dropped to as little as 30 after the LGM peak.

They are saying that the effective population size of the european bands, who would repopulate europe after the LGM, were as low as 30. In other words, the population of europe was never as low as 30, only that a stable, reclusive, population could be as low as 30. Previously it was thought that a stable population required a breeding pool of about 500. Keep in mind that even though it only takes two people to reproduce it takes a much larger number to keep on reproducing over the generations as a healthy population.

In some cases, small bands of potentially as few as 20 to 30 people could have been moving over very large areas, over the whole of Europe as a single territory, according to Professor Ron Pinhasi, principal investigator on the EU-funded ADNABIOARC project.

This demographic model is based on new evidence that suggests populations were much smaller than is generally thought to be a stable size for healthy reproduction, usually around 500 people. Such small groupings may have led to reduced fitness and even extinctions.

Davidski said...

It appears as if EHG groups penetrated Scandinavia, probably from the north, during the Mesolithic, and mixed with the WHG groups that were already there.

Colin Welling said...

my goodness. when are they going to sample south east europe during the same period of time. Its the biggest question mark in my mind.

Davidski said...

Colin,

"In some cases, small bands of potentially as few as 20 to 30 people could have been moving over very large areas, over the whole of Europe as a single territory, according to Professor Ron Pinhasi, principal investigator on the EU-funded ADNABIOARC project."

This suggests to me that at this time the effective population size was less than 30 for all of Europe. Right?

Chad Rohlfsen said...

I think with ice cover in the Baltic, it may have been by boat and foot, from the east, for the most part. Scandinavia was pretty homogenous, all the way up north. Any big influx from the north should be noticeable in the Saami, but they're fairly similar in ANE to their neighbors.

Chad Rohlfsen said...

Maybe 30+ bands of 20-30 people.

Chad Rohlfsen said...

As a near minimum?

Davidski said...

They can't estimate the number of bands and how many people were in each band from genomics data.

Pinhasi must be talking about effective population size, because that's really all they can estimate, and the figure of 30 or so would be "shockingly small" for a whole continent like Europe.

Chad Rohlfsen said...

Taking into account the number of sites and remains across a certain space and time, they could possibly take a guess.

Chad Rohlfsen said...

We can see some structure between 7-8kya. It might be fairly obvious at 14.

Fanty said...

An effective population size of 30 would definately lead to fixation of uniparental markers in a handfull of generations, no matter if it startet with 30 different ones.

Krefter said...

Wouldn't it make sense that Mesolithic Euros who descended from a Southwestern refuge all spoke a related language?

Grey said...

whg / ehg

https://ipadmusiced.files.wordpress.com/2013/11/globe3t.gif

five bowls created by the physical geography imo with mountains, swamps, jungles etc as the borders
- oceania
- east asia
- india spilling over into central asia
- african border zone
- hyperborean triangle: baltic to siberia to himalayas to baltic

with WHG being african border zone and EHG hyperborean

Maju said...

Once again, extending what is seen in Central Europe to "all Europe" is a crass error.

Read please (or at least browse the maps and tables): http://www.evolhum.cnrs.fr/bocquet/jas2005.pdf

After the LGM Central Europe as place of habitation shrank to a small pocket in Moravia. Whether the population was 30 (effective pop.) or something between 270-4500 (actual pop. estimated from artifact use) matters less: what is clear is that Central Europe was brutally bottlenecked by the event.

But, on the other hand, SW Europe thrived. The estimated population of SW Europe more than doubled in the LGM and multiplied x12 after the LGM. So let's not jump to hyped "pop" conclusions before considering the whole picture, which, as usual, is much larger than just Central Europe.

Shaikorth said...

"Any big influx from the north should be noticeable in the Saami, but they're fairly similar in ANE to their neighbors. "

This should be fairly easy to test with currently available tools. Run qpAdm with Early Neolithic, WHG, Karelian EHG and Han for Norwegians, Lithuanians, Kargopol Russians and Saami_WGA, maybe include English for comparison.

Chad Rohlfsen said...

You've got to find extreme Dstats, then get a model through qpWave first. It's not quite so easy.

Mike Thomas said...

@ Colin

"my goodness. when are they going to sample south east europe during the same period of time. Its the biggest question mark in my mind."

They have. the BEAN project has sampled 100s of sites from the Mesolithic Danube Gorge

@ DAVIDSKI

"It appears as if EHG groups penetrated Scandinavia, probably from the north, during the Mesolithic, and mixed with the WHG groups that were already there"

I think there were also new "WHG-type' arrivals in N and NW Europe.

Quite possibly, this included Hg I* and derivatives.

I think C was the true Palaeolithic marker, which nearly vanished.

Shaikorth said...

The qpWave readme says it's meant to be run as a precursor to qpAdm runs but perhaps not necessary in this case. Some of the 15 outgroups of Haak et al. should work as right pops no problem and there's no substitutes for EEF+HG's.

Chad Rohlfsen said...

Shaikorth,

Right now, everything that is

Han
Karelia
MN

is failing. Same with Nganasan, instead of Han. I'll keep trying.

Chad Rohlfsen said...

It all comes back as rank 3. Still working.

Shaikorth said...

Try EN, WHG, Karelia, Han. That shouldn't fail in qpAdm since M. Myllyla apparently has succeeded with similar fits.

Nganasan and all Siberians/Native Americans probably drain ANE/EHG in fits so Han are preferable.

Chad Rohlfsen said...

You can only have 4 pops on the left, including the target pop. Two have to be combined. I keep getting rank 3, either way, any kind of mix that I make. I'm still trying.

Shaikorth said...

qpAdm should allow four-way mixes. Otherwise how would one get, for instance, these results:

http://terheninenmaa.blogspot.com/2015/03/estimating-ancient-genes-among-present_24.html

Chad Rohlfsen said...

I'd like to see the ranks and what exactly he's running. If he has rank 3, it's no good. I'll try.

Chad Rohlfsen said...

Can you get his left and right pops?

Roy King said...

Interesting interview. My expertise is in the Greek/Mediterranean and it is clear that the population of the Greece from the LGM until the Holocene was very, very small. During the Holocene a new group of immigrant hunter/forager/fishers move in and fished tuna/tunny in the Mediterraean. Just like EHG is different from WHG, there will be (I suggest) a Southern HG population arriving in the Mediterranean. A hint of this (which Davidski knows about since he commented on it on Dienekes a couple of years ago) was an aDNA presnetation of mtDNA of Msolithic and Neolithic Greece where both Mesolithic and Neolithic samples from Greece had low Fst with LBK farmers but were highly differentiated from WHG.

Shaikorth said...

We only see the left pops from the results he's posted in his blog, for instance http://www.elisanet.fi/mauri_my/tiedostot/qpadm3.xlsx

So no idea about right groups. Something from the World15 list is as far as I can guess.

Chad Rohlfsen said...

Those pops make a mess, all across the board. I need the exact samples for the Neolithic and East Asian, plus the right pops, in order. I just used the LBK, and Han, for East Asian. It's no good.

Nick told me to use four in the left, so that's what I try and stick to.

Shaikorth said...

Only the number of right pops is recommended to be kept small in the manual though. It's prolly worth it to e-mail Nick about M.M's results since they seem to match Haak figure S9.26 quite well and in many cases chisq etc are very good.

M. Myllylä said...

It is very likely that before farming the livelihood and game was much more relevant than compass points. So the population growth could have been bigger near Scandinavuian than in Central Europe if there was enough big game and fish on seasides. On the other hand when the climate allowed farming in Central Europe it gave a huge advantage there compared to the north, but only after that time.

Chad Rohlfsen said...

M. Myllyla,

I've also posted this at your blog;

How did you set up your L and R pops? I am curious about how they look in qpWave and qpAdm. Thanks!

Krefter said...

@Coline,
"my goodness. when are they going to sample south east europe during the same period of time. Its the biggest question mark in my mind."

Exactly.

Grey said...

If multiple depigmentation genes developed in different places in a northern interior triangle then maybe one of the others that had already spread in the west duplicated the selection-critical part of EDAR?

(whatever that is/was)

Cine Braille said...

Some day we shall be able to prove that a similar kind of climate-related bottleneck was behind Neanderthal extinction. I find this article inspiring in that way too.

Matt said...

This is interesting to me:

(Pinhasi) believes that early humans crossed the continent in small groups that were cut off while the ice was at its peak, then successively dispersed and regrouped over thousands of years, with dwindling northern populations invigorated by humans arriving from the south, where the climate was better.

However, he doesn’t think there was necessarily regular contact between these groups. In fact, one impact of the research, he believes, is that we’ll start to find more evidence of ‘lineages’ or ancestors that never made it into the modern gene pool because they died out.

‘You see a real reduction in population numbers and diversity, so you see the few lineages that probably split or separated before the ice age, and then stayed isolated during the ice age,’ he said. ‘Some time after the ice age, they kind of re-emerge, or disperse, and get together, as we see new contributions to European lineages from Asia and in particular the Near East.’


So these populations are very similar in many ways, yet also he seems to be saying that he thinks that they are very structured during the LGM as well, and then less structure after the LGM, as these groups combine to form "WHG".

@Roy King: Just like EHG is different from WHG, there will be (I suggest) a Southern HG population arriving in the Mediterranean. A hint of this (which Davidski knows about since he commented on it on Dienekes a couple of years ago) was an aDNA presentation of mtDNA of Msolithic and Neolithic Greece where both Mesolithic and Neolithic samples from Greece had low Fst with LBK farmers but were highly differentiated from WHG.

That doesn't seem surprising. Do we have any knowledge of Italy by comparison? It may still within the realm of possibility that Mesolithic Greek and maybe Italians were LBK like, and Spain where we have the La Brana sample is the "odd man out" in Southern Europe in having a WHG like Mesolithic population.

Mike Thomas said...

I think that Balkan hunter gatherers ("BHG") will be mixed
1) some WHG like
2) some "proto-Sardino-Cypriate"
3) some perhaps even tending to EHG (due to admixture from Ukrainian refugium)

Chad Rohlfsen said...

I'm also wondering why EDAR was selected among SHG, but not WHG, when both are pretty much equally related to the Han.

Yoruba LaBrana1 Han Papuan -0.0192 -5.003
Yoruba Loschbour Han Papuan -0.0196 -5.127
Yoruba HungaryGamba_HG Han Papuan -0.0227 -5.643
Yoruba Motala_HG Han Papuan -0.0209 -7.280
Yoruba Karelia_HG Han Papuan -0.0341 -8.993

Matt,

I too believe that the structure is going to be blatantly obvious, just post LGM. That should make it easier to figure out what is different about our three WHG. The evidence is there, but I don't have a modern reference that shows me where it's at. Just little hints.

Krefter said...

Chad,

We don't have enough SHG, WHG, etc. samples to say confidently either had more or less EDAR or anything else.

Chad Rohlfsen said...

Modern distribution leans that way, but we'll see.

Chad Rohlfsen said...

A note from Nick..

A technical request. qpWave has a parameter maxrank with default 4. If you have more than 4 pops
in the left list you need to code maxrank: 10 (say) in the parameter file.

Krefter said...

Incase anyone's interested.

http://www.anthrogenica.com/showthread.php?4234-Member-s-Hirisplex-results&p=76975#post76975

Davidski said...

I just exchanged a couple of e-mails with someone from the Rise project.

Question: I'm hearing rumors that lots of Stone and Bronze Age genomes have now been sequenced as part of the project, and that a paper is about to be published in Nature. Is this true? If so, how long do we have to wait?

Answer: I don't know but hopefully not too long.

Nirjhar007 said...

Great to Hear.

Chad Rohlfsen said...

Some stuff for you guys to ponder...

Yoruba LaBrana1 Karitiana Dai -0.0238 -5.834 14812 15533 334084
Yoruba Loschbour Karitiana Dai -0.0301 -7.765 15508 16471 351075
Yoruba HungaryGamba_HG Karitiana Dai -0.0285 -6.911 10772 11403 243623
Yoruba Motala_HG Karitiana Dai -0.0462 -16.056 15104 16567 346177
Yoruba Karelia_HG Karitiana Dai -0.0725 -18.552 14645 16936 341554
Yoruba MA1 Karitiana Dai -0.0773 -17.684 10792 12599 253297
Yoruba LaBrana1 Karelia_HG Dai -0.1095 -19.954 14424 17972 323706
Yoruba Loschbour Karelia_HG Dai -0.1184 -21.655 14973 18995 338485
Yoruba HungaryGamba_HG Karelia_HG Dai -0.1223 -20.638 10356 13241 235365
Yoruba Motala_HG Karelia_HG Dai -0.1565 -38.902 14399 19744 337671
Yoruba MA1 Karelia_HG Dai -0.1092 -17.986 11026 13730 245167
Yoruba LaBrana1 MA1 Dai -0.0601 -9.981 11138 12562 239972
Yoruba Loschbour MA1 Dai -0.0618 -10.549 11664 13200 251027
Yoruba HungaryGamba_HG MA1 Dai -0.0640 -9.747 8088 9194 174887
Yoruba Motala_HG MA1 Dai -0.0900 -20.815 11263 13491 248302
Yoruba Karelia_HG MA1 Dai -0.1090 -18.448 11031 13730 245167

Tobus said...

Chad,

Those results seem pretty much as expected to me... is there something particular you think is worth pondering over?

Chad Rohlfsen said...

Just that I think we have a cline here, rather than WHG being something completely distinct and unadmixed. Whether or not it's pre-LGM is the only thing unanswered.

Tobus said...

I think you have to be very careful interpreting D-stats across pops - particularly when there is different coverage between the samples. There's an extra 15,000 SNPs looked at between the LB and Loschbour vs Karitiana runs, and almost 100,000 extra between LB and Hungary. It would only take a small difference in affinity in these missing/extra sites to change the result by the amounts we're seeing here - there's less than 1000 SNPs between the ABAB and ABBA counts in the Karitiana runs for example. It *could* be something real, but it could also just be like getting 501 heads out of 1,000 coin tosses and then getting 499 when using a different coin - ie. within the bounds of chance and not enough samples to say there's a definite pattern.

I ran some complementary stats:
Loschbour LaBrana1 Karitiana Yoruba 0.0033 0.608 13367 13280 331055
HungaryGamba_HG LaBrana1 Karitiana Yoruba 0.0005 0.081 9755 9745 230628
HungaryGamba_HG Loschbour Karitiana Yoruba -0.0015 -0.271 9753 9783 241456
Loschbour LaBrana1 Dai Yoruba -0.0044 -1.002 13115 13231 331055
HungaryGamba_HG LaBrana1 Dai Yoruba -0.006 -1.215 9568 9685 230628
HungaryGamba_HG Loschbour Dai Yoruba -0.0009 -0.196 9651 9668 241456

While none of these are significant*, the LaBrana sample is marginally more Dai-like and less Karitiana-like sites than the others, which would explain the variance in the stats you ran.

*Significance here is the sum of standard errors on the jackknife run. In my understanding this is basically saying how "clumped" together the differences are - if there is genuine genetic affinity then there should be blocks of the genome (ie "ancestry segments") that show more difference than others. If it's just chance then the "difference" will be spread randomly (and thus pretty evenly) throughout the genome.

Alberto said...

I guess that a cline is normal, since there were no natural borders between east and west Europe. But what we don't know exactly is where the HGs with ANE started.

Poland? Lithuania? Belarus?

And in the south: Romania? Ukraine? Russia?

Without ancient DNA we can't know, but it might still be interesting to know which populations received more admixture from EHG and which from WHG. Like:

Karelia_HG Motala_HG Polish Yoruba
Motala_HG Loschbour Polish Yoruba

With different European populations (Ukrainian, Romanian, Bulgarian, Greek, Hungarian, Belarusian, Lithuanian...)

Chad Rohlfsen said...

The significance is higher when you compare Motala to LaBrana and Loschbour.

LaBrana Loschbour Motala_HG Yoruba

There you'll see like -7.2 on the Zscore. There is structure.

Krefter said...

More info on the Bronze age Poles from Hrubieszow, Poland.

http://www.muzeum-hrubieszow.com.pl/index.php?cat=rogalin

They belonged to the "strzyżowski culture". They tested Y-STRs and his son or cousin or whatever was buried with them.

Krefter said...

19,000YBP Spaniard has mtDNA H, according to jeanL!!!

http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News&p=77357&viewfull=1#post77357

Krefter said...

Check out this quote from the abstract of a new paper.

Link: http://www.sciencedirect.com/science/article/pii/S1040618215000580

"Ancient DNA studies in European human remains indicated a genetic discontinuity between the hunter–gatherers and later populations. *However, some of the mtDNA lineages found in the Cantabrian fringe in Paleolithic–Mesolithic times persist in present-day populations.*"

Chad Rohlfsen said...

I see H3, T2, and K as well. Are these legit?

Chad Rohlfsen said...

If that's true, I think the SW refugia may not be so important to overall hunter ancestry, circa 8kya.

Krefter said...

Chad, they tested samples dating from the Upper Palaeolithic to almost the Middle Ages. I don't know what date they all come from yet.

Chad, do you think H being absent in Mesolithic Central-North Europe might have something to do with La Brana-1's uniqueness?

Chad Rohlfsen said...

Okay. Give the paper a gander. Let me know what you see.

There is something unique about LaBrana. He is closest to Loschbour, and the furthest from Motala. He may have a little North African hunter. Africans, especially Somalis, favor him in several runs. I'm still working on it.

Btw, I'll be posting modern euro and ancient Zscores in the next couple hours.

Matt said...

The quoted text on that linked forum says:

The mitochondrial variability from the hunter–gatherer individuals from the five Cantabrian fringe sites was assorted into four different mitochondrial haplotypes [the same haplotype was found in El Mirón (MR) and La Pasiega (PS) sites and three different haplotypes in each of the following sites: Erralla (ERR), La Chora (CH) and Aizpea (AIZ)] (Table 1). These haplotypes correspond to two haplogroups (haplogroups U and H) (frequency values of 40% and 60% respectively). The hunter–gatherer groups from Europe analyzed until now showed the highest frequency values for haplogroup U (mostly U5) (>50%) than any other population. The hunter–gatherers from the Northern of the Iberian Peninsula also showed a high frequency value for haplogroup U but they differentiated from the other European groups by a relatively high frequency for haplogroup H.

KO1 has mtdna R, Loschbour U, La Brana U, ancient Swedes other U, I think.

Could be that SHG is U and "WHG" U and H? It's not so improbable to find 2 U out of 3 if it has like a 60% frequency... IDK the mtdna record as well as you guys though.

Grey said...

my guess

three bowls:

1) WHG in the african border zone (including europe's coastal hinterland)

2) ASE out of India

3) hyperboreans in the northern interior triangle

then

WHG + hyperboreans -> SHG (in western contact zone)

ASE + hyperboreans = population X (in central contact zone)

population X + more hyperboreans = EHG (in northern contact zone)

jeanlohizun said...

If anybody wants a copy of the paper email me at: jeanlohizun at Hotmail dot com and I'll send you a copy of it.

Krefter said...

All the Mesolithic Spanish have U5b, and all their Upper Palaeolithic samples have H. Makes me wonder if WHG came out of Italy or the Balkans in the LGM and were newcomers in Iberia.

Mike Thomas said...

Chad , Alberto

Wasn't La Brana Hg C ?
Either way, given that he is all the way in Spain , he must retain a more basal (however we might call it) signature going back to the earliest colonisation of Europe ; which was subsequently overridden during the post -glacial recolonisation in other parts of Europe (ie central- North)

Mike Thomas said...

Krefter

From arcaheological view ; the two unequivocal refugia in LGM were Franco -Cantabria and ukraine .

People also often discuss italy ; the balkans and Central Europe.:
Indeed an epigravettian persisted in Central Europe ; from Moravia to the Carpathian basin and northern balkans well into the LGM. But this was not continuously occupied until the end of LGM; but was abandoned c. 17kya (more due to the incipient aridity than 'coldness" per se; that is all of the above mentioned areas apart from northern balkans, which does shows evidence of continuous stratigraphy (danube gorge area- lepinski vir, etc).

Italy is a bit controversial . Whilst italian archaeologists suggest it was a refuge; there are few sites; and certainly less so than the eastern Alps region . Maybe much of it was in cave sites in the Adriatic land bridge between Dalmatia and italy, now under water (?)

Chad Rohlfsen said...

Okay, the run with Karelia, Loschbour / Motala, Loschbour, was very uninformative. Loschbour carries the day, expecially up North. It really seems to be more about who had more WHG during the MN. I'm going to go about this another way. It'll be a little bit.

Chad Rohlfsen said...

The only interesting thing is that Greeks really don't prefer Loschbour over the Karelians much, nor do they pick Loschbour over Motala, by anything worth mentioning. I think this suggests the Greeks do have Steppe ancestry, which the Haak et al. (2015) paper suggested.

batman said...

Grey is getting close.

Please note that the old maps of "Ice-age Scandinavia" are grossly wrong. The all-extending "Scandianvian Ice Sheet" (SIS) never existed as hypothesized in the 1960-ties and thus depicted ever since - as one big ice-sheet encompassing both Fenno-Scandia as ell as the Baltic ocean, simultaniously.

Today there are a lot of geological tests and archeobotanic finds contradicting that hypo, proviung that the reality was quite different than 'anticipated'. Based on facts the new picture of the maximum glaciation of Scandinavia - some minimum 20.000 years ago - were more like todays Greenland, with 90% of the shores ice-free, far north of the arctic circle. The reason seem to have been the Gulfstream, that constantly kept theese waters above freezing-level. Then add that a soutern limb of the Gulfstream could reach through the English channel and into the Baltic Ocean too, below todays southern border of Denmark.

Moreover it starts looking like the Finnish Bay have been connected to the White Sea all the way up to LGM and Older Dryas - making Fenno-Scandia an island.

Thus we may explain an enormous but still limited inland ice-sheet across this 'sub-continent' - similar to the mentioned Greenland.

Today it's clear that there existed a number of ice-free areas during the a number of micro-organisms it's by now clear that also moss, grass, lingonberries, birch, pine, spruce, beavers, reindeers, elks, lynx and bears did survive both the Last Glacial Maximum - as well as Dryas - within the realms of the Fenno-Scandian penninsula.

http://sciencenordic.com/trees-survived-ice-age-scandinavia

http://sciencenordic.com/spruce-and-pine-survived-last-ice-age-norway

During the middle as well as the upper paleolithic period there where people roaming the shores of the Western Baltics, as their genetic cousins would populate Spain, France, England and Germany - as well as the Baltics, Finland, Volga, Ural and Siberia, Bactria, Kaukasus, Anatolia, Greece and Balkan - until the onset of the LGM, when they all started to disappear.

After the serious cold of LGM and Older Dryas the last men and mammoths starts to disappear - first in the east, then in the west. With the sudden and terminal cold-dip of Younger Dryas, ignited by the Laacher Zee volcano eruption in NW Germany - the deepest cold on record, Yonger Dryas started 12.900 yrs ago, leaving also the occidental part of the continent deserted by larger mammals.

As far as we know from present archaeology there were very few, small communities of people - as well as mammoths - left in Eurasia when Older Dryas came to an end. They are all found around between the Baltics and England.

Chad Rohlfsen said...

Stats galore, on some farmers. Check it out...

http://www.anthrogenica.com/showthread.php?4050-Statistical-Analysis-of-Ancient-Genomes-using-qpAdm-Dstats-and-F3/page2

Chad Rohlfsen said...

Analysis of Modern Euros
EN vs Yamnaya
MN vs Yamnaya

http://www.anthrogenica.com/showthread.php?4050-Statistical-Analysis-of-Ancient-Genomes-using-qpAdm-Dstats-and-F3/page2

batman said...

The climate crisis hitting the northern hemisphere during the last part of ice-time is rather well documented. A general overview of the period between 25.000 and 12.000 years BP explains rather well why the northern population got isolated adn close to extinction:
http://www.accuracyingenesis.com/Holocene_extinction.html#The_Pleistocene_or_Ice_Age_extinction_event

AFAIK our archaeologists have found only ONE line that surely made it through the Younger Dryas (YD). This timeline is by now documented from the islands of Denmark and Scania, at the time of YD surrounded by atlantic water.

Here the northern branch of the Mousterien/Gravettian - often called 'Hamburg-culture' would survive half way into the YD:

http://da.wikipedia.org/wiki/Brommekultur#

Three centuries later the climate started to improve - and by 12.000 the old Hamburg/Federmesser-culture starts to re-appear, in both the eastern and western Baltics - as well as in the more southern part of the continent:
http://en.wikipedia.org/wiki/Ahrensburg_culture

About 11.500 calibrated years ago they had brougth their boats and sledges, dogs and deers, grinders and pots, spinners and weavers, fishing-nets and hunting-weapons, art and symbolism all the way to the North cape - as well as to Finland, Russia, Ukraine, Anatolia, Balkans and SW Europe. Crete and Sardinia included.

https://www.academia.edu/4345390/A_14_000-year-old_amber_elk_and_the_origins_of_northern_European_art

Since then a lot have happened and much have changed - especially in the south. In the cold north things were substantially more cool and stable. During the arctic winters and the short, hectic seasons of hunting, gathering and harvesting the neighbour you have is the neighbour you need.

Thus todays geneticians may find these Fenno-Scandians and north Russians to be the closest to the orignal - i.e. the SMALL number of arctic people that had developed in an isolated REFUGIA, where they had adapted to the darkness by loosing melanin and countering the cold and work-consuming conditions by consuming animal fat and meat, grounded seeds and diaries.

http://sciencenordic.com/scandinavians-are-earliest-europeans

Chad Rohlfsen said...

West Asia is up. I may attack that a couple more directions.

http://www.anthrogenica.com/showthread.php?4050-Statistical-Analysis-of-Ancient-Genomes-using-qpAdm-Dstats-and-F3/page3

Maju said...

The data we have now for European Paleolithic and Epipaleolithic seems to be that:

→ 100% U in Central-North Europe
→ around 50-50 U/H in the Cantabrian region
→ 11% H in Epipaleolithic Karelia

Plus (untested for any sort of confirming marker):
→ R*-CRS (possible H* or H1) in Britain, Portugal, Andalusia and Arif (North Morocco)
→ Likely H17'27 in Sunghir
→ R*-other (can also be H) in Portugal, Andalusia, North Morocco and the Italian Alps

My interpretation of the data (which lacks info for the most important pre-Neolithic area: France) is that there was a cline of decreasing U and increasing H from Central Europe to Southern Iberia. Portugal, Andalusia and Arif (across the strait but culturally related at Solutrean-Oranian level) seem to have the highest frequencies of H but the data is so far unconfirmed by proper c.r. or RFPLs testing (although Chandler et al. seem to have used HVS-II in Portugal, what adds to certainty).

There was surely another pocket of Paleolithic H in Russia and maybe also Britain and/or Italy. In brief: it's possible that there was H everywhere in the subcontinent... except in Central-North Europe, which has been recently claimed (with good archaeological reason) to have suffered a dramatic bottleneck in the LGM.

Case solved: test France, test Iberia, test Morocco, test Britain.

Krefter said...

Maju,

K01, a WHG person from Hungary, had R3.

There has been mtDNA testing on Pre-Neolithic remains in France. I know of one sample and it is R-CRS(HV1), and H negative.

https://docs.google.com/document/d/1aj1zus574tUY-oy7A2SVKcNn8Pvaxz8dIiQEVQSxnzk/edit
(It's ID is Téviec 1)

"except in Central-North Europe, which has been recently claimed (with good archaeological reason) to have suffered a dramatic bottleneck in the LGM. "

The U in Central-North European hunter gatherers is pretty diverse. U5b1, U5b2(U5b2b, U5b2a2), U5a2a, U5a2c3, U5a2d, U5a1, U2e, U4, U*. There's U5b1, U5a2a, U5b2a2 and U5a2c3 dating back over 10,000 years.

We autosomal testing on an Upper Palaeolithic Iberian. Were they WHG, part WHG, or something differnt? It's hard to imagine Loschbour was descended of H-rich LGM people from Spain. Could his ancestors be from somewhere else, like Italy?

Tobus said...

@Chad:The significance is higher when you compare Motala to LaBrana and Loschbour.

Finally got time to look at this and yes, and also with HungaryHG... I get:
LaBrana1 Loschbour Motala_HG Yoruba -0.0351 -6.707 13173 14133 324978
LaBrana1 HungaryGamba_HG Motala_HG Yoruba -0.0289 -5.225 9663 10237 226662
Loschbour HungaryGamba_HG Motala_HG Yoruba 0.0066 1.339 10031 9899 236347

... La Brana is definitely different in this respect. It could be "central WHG" admixture into SHG:

Karelia_HG Loschbour Motala_HG Yoruba -0.0285 -5.639 15369 16270 334629
Samara_HG Loschbour Motala_HG Yoruba -0.0345 -6.421 9256 9917 203114
Karelia_HG LaBrana1 Motala_HG Yoruba 0.0045 0.832 15234 15098 320677
Samara_HG LaBrana1 Motala_HG Yoruba -0.0037 -0.671 9161 9230 195698
... SHG is closer to Loschbour than to EHG but not closer to LaBrana, and:

LaBrana1 Loschbour Samara_HG Yoruba -0.0054 -0.704 7991 8078 195253
LaBrana1 Loschbour Karelia_HG Yoruba -0.0087 -1.238 13184 13416 320734
... there is no extra EHG in Loshbour.

There also seems to be a small amount of Samara-specific admixture with HungaryHG:

Loschbour HungaryGamba_HG Karelia_HG Yoruba -0.0012 -0.159 9687 9710 233238
LaBrana1 HungaryGamba_HG Karelia_HG Yoruba -0.0087 -1.143 9629 9799 223756
.... no significant Karelia in all 3 WHG's, but:

Loschbour HungaryGamba_HG Samara_HG Yoruba -0.0174 -2.21 5819 6025 142264
LaBrana1 HungaryGamba_HG Samara_HG Yoruba -0.0231 -2.674 5854 6130 137150
.... borderline significant Samara/Hungary affinity not in the other two WHGs.

It seems like you are right, and there's not a clean WHG/SHG/EHG split.

Matt said...

The Meso HG stats are pretty interesting - it looks like La Brana HG (Iberian_HG?) is further from other HG than Loschbour / HungaryGambaHG without being closer to any "world" outgroups.

Implication for modern populations is world outgroup based modeling wouldn't be able to distinguish between Loschbour / HungaryGambaHG admixture into Europeans vs La Brana type admixture into modern Europeans...

Essentially seems like a method like qpAdm couldn't distinguish between "WestCentralHG" admixture vs La Brana HG admixture, unless the right populations included EHG / SHG (... which might mess things up).

Despite this being the case those different types of admixture would have a slight effect on modern relatedness to ancient samples (and any moderns who bear "true" LaBrana vs Loschbour / HungaryGambaHG admixture).

It would be a pretty slight effect though - the West HGs are pretty close, I think.

Alberto said...

@Chad

"Okay, the run with Karelia, Loschbour / Motala, Loschbour, was very uninformative. Loschbour carries the day, expecially up North"

I expected 2 possible scenarios. One less realistic driven just by ANE levels, in which most pop would prefer Motala except SW Euros who would prefer Loschbour. And a second more realistic one where most pops would prefer Loschbour, except maybe some Baltic preferring Motala and maybe Finns and Russians preferring karelia.

What you say about Greeks is interesting, but then populations North East of Greece should tend to Karelia even more: Bulgarians, Romanians and definitely Ukrainians. Unless Greeks remained half Steppe while the other pops received more migrations from Loschbour-rich populations (if Slavs really prefer Loschbour). Could that mean that the pre-Slavic Balkans were the most Yamnaya area? Strange, but who knows...

Alberto said...

@Mike

"Wasn't La Brana Hg C ?
Either way, given that he is all the way in Spain , he must retain a more basal (however we might call it) signature going back to the earliest colonisation of Europe ; which was subsequently overridden during the post -glacial recolonisation in other parts of Europe (ie central- North)"

Yes, possibly. But the difference with Loschbour is small enough to think that both populations mixed in the Franco-Cantabrian refuge to a great degree. They really belong to the same population with just subtle differences that could come from the pre-admixed populations, but also could just have happened after they separated, and in this case, the haplogroup wouldn't necessarily be they key differentiator. We'd need to find an I haplogroup HG from Spain to know if he's closer to LaBrana or to Loschbour.

Maju said...

@Krefter: If you read the original thesis (→ http://thesesups.ups-tlse.fr/1392/1/2011TOU30177.pdf), you will notice that the Téviec sample is possibly Neolithic:

Datation C14 : entre 5640/5090 – 4450/4250 B.C., Mésolithique tardif jusqu’au néolithique moyen

On the contrary Linatzeta is clearly Epipaleolithic and so far the oldest H sequence known the Basque Country (there are older ones in nearby Cantabria though).

Lacan also found H(xH1,H3) in Franchthi Cave (borderline Neolithic or transitional Meso-Neolithic of Southern Greece) but described Téviec as "undetermined", while considered Rendina and Les Cannes as "mix" ("melange", hence useless for analysis, I understand).

My English language synthesis: http://forwhattheywereweare.blogspot.com/2012/06/mtdna-h-found-in-epipaleolithic-basques.html

If Téviec is indeed HV1, as you suggest, then it could explain the arrival of this lineage to Britain (only region in West Europe where it has some prevalence). I would attribute it to Neolithic rather than Paleolithic though. However it can't be discarded that it's a rare Paleolithic lineage with a late localized founder effect, as other HV(xH) has also been detected in Paleolithic Italy, suggesting that probably European Paleolithic H originally arrived with some "cousins", which left some scattered legacy. The most notable is maybe HV0: this lineage has yet to be detected in Paleolithic samples but its presence in North Africa, paralleling that of H, clearly of Iberian origin and surely Iberomaurusian (=Oranian, of Gravetto-Solutrean Iberian roots) does suggest it is of that age (on the other hand K is surely Neolithic and also has some presence in North Africa, so maybe not after all).

In any case we are still awaiting for clearly Paleolithic sequences from the French demarcation. And I would rather look in Dordogne and Aquitaine than in Brittany and the Southeast.

Mike Thomas said...

Alberto ; you might be right . Im speculating, but I think the evidence for Labschour and Motala points to East- Central Europe / northern balkans rather than iberia .

Mike Thomas said...

Alberto

"Could that mean that the pre-Slavic Balkans were the most Yamnaya area? Strange, but who knows."

I highly doubt it
We already know that from the BA Hungary sample and Iron Age thracian samples - which were Italian like . .
If it wasn't for Justinian and heraclius , the balkans would still be very "farmer" like

Alberto said...

@Mike

Yes, difficult to say. Motala is probably a mix of Loschbour and some EHG-type. That's why it's closer to Loschbour than to La-Brana. But what it's clear is that at some point La-Brana-C-type and Loschbour-I-type must have mixed to become very similar. Whether it was pre-LGM or during LGM is hard to say.

Re: Greeks, I also doubt they were very Yamnaya like. Maybe they show little preference for Loschbour vs. Karelia just because the Mesolithic HG from the Balkans already had similar affinity with WHG and EHG. Or any other possibility.

Also Chad's results showing almost all of Europe preferring Loschbour might be because Ukraine didn't have Karelian-like EHG, but rather WHG like in Hungary. In this case, Western Yamnaya people could have taken all of their ANE from the Caucasus-like population and not from EHG.

Still many possible combinations to be certain about just one of them.

Mike Thomas said...

Alberto

I think the WHG samples from Mesolothic europe definitely homogenised *after* the LGM. Quite literally, during the LGM vast expanses of europe were depopulated, and the pockets which survived were literally cut off for hundreds to thousands of years

Mike Thomas said...

@ Alberto

"Also Chad's results showing almost all of Europe preferring Loschbour might be because Ukraine didn't have Karelian-like EHG"

Would you mind clarifying what you mean please ?

Tobus said...

Alberto: Motala is probably a mix of Loschbour and some EHG-type

I think so too, and the admixture happened after the La Brana and Loschbour lineages had split. I note that while Motala is closer to Loschbour than to La Brana, it is still closer to La Brana than to EHG:
Samara_HG Motala_HG LaBrana1 Yoruba -0.051 -8.176 8334 9230 195698
Karelia_HG Motala_HG LaBrana1 Yoruba -0.0489 -8.55 13691 15098 320677

Combined with the previous results this looks like SHG is a Loschbour-like WHG pop with EHG admixture.

Alberto said...

@Mike

I mean that the samples we have from EHG and from Yamnaya are from a rather remote region, around Samara (and Karelia for the EHG).

We don't know if Ukraine had those kind of HGs or if they were like the ones in Hungary, which were pure WHG. Or maybe they were something in between.

Chad said that almost all of Europe was closer to Loschbour than Motala or Karelia_HG. This could mean that the supposed mass migration from Yamnaya to Europe could have been a mix of WHG + Caucasus-like, and not EHG + Caucasus like, as the ones from Samara.

I'm just saying it's a possibility, like any other. Not that it seems the most likely to me. We need more samples to really know.

Mike Thomas said...

I see. That's what I thought you meant. I think its certainly possible.

The only piece of evidence comes from Kostenki 14, which is 37 kya. haak's supplementary discussion states that he is closer to Mesolithic WHGs than EHGs (Karelia, Samara). But, little to hang a hat on.

Im sure changes occurred during the LGM in the east, also.

Tobus said...

Most modern EU populations are closer to Loschbour than to La Brana1 - the top 5:
LaBrana1 Loschbour Lithuanian Yoruba -0.0179 -4.493 13376 13864 331055
LaBrana1 Loschbour English Yoruba -0.0175 -4.565 13320 13794 331055
LaBrana1 Loschbour Estonian Yoruba -0.0179 -4.694 13356 13843 331055
LaBrana1 Loschbour Icelandic Yoruba -0.0195 -5.156 13307 13838 331055
LaBrana1 Loschbour Belarusian Yoruba -0.0203 -5.398 13293 13844 331055

I couldn't find any modern population (I tested EU, North Africa, Middle East, Central and South Asia) that is closer to La Brana than to Loschbour. It appears that all surviving WHG is from the Loschbour lineage.

Alberto said...

@Tobus

Someone commented that there's a better quality sample from LaBrana coming. The current one is more noisy than Loschbour, so that might also have an influence in these tests. With that better sample maybe at least Spaniards might be closer to it than to Loschbour.

Not that it matters much, since La Brana being Y haplogroup C seems like a dead end, and besides LaBrana and Loschbour are as similar as 2 Mesolithic individuals separated by ~2000 km. and ~1000 years can be.

Chris Davies said...

With claims of African affinity in La Brana, which is Y DNA haplogroup C-V20 (C6?) IIRC, I would be interested to know any results from ancient DNA from North Africa. Now that Xu et al. 2014 found C-M130 in Biaka pygmies and C-M217 in Mbuti pygmies [supplementary data]. Was C once more common in Africa?

Maju said...

What a fastidious habit of mixing Y-DNA with autosomal DNA: they do not have to be related in any way!

Chris Davies said...

@ Maju - Yes, true of course. For example, the case of R1b in north Cameroon, where those populations show little to no West Asian autosomal affinity.

Maju said...

Indeed, that's an almost archetypal example. But anyhow in this case we have only 2 samples, rather separated in geography, which seem to have similar autosomal profiles (i.e. they do belong to the same population: WHG) but different Y-DNA (i.e. they represent two random picks within the Y-DNA diversity of that same population).

Lochsbour (and maybe other samples from that same Rhine-Danube area, if we extrapolate from mtDNA) happen to have similar lineages to those found in Sweden (which belong however to a different population: SHG), however that's not what we see in the other fraction of the WHG population. So we should simply conclude that WHG had at least two different sub-populations, one at the Rhine-Danube (represented by Lochsbour and, mtDNA-wise also by other samples from Suabia, etc.) and at least another one in Iberia (represented so far only by La Braña with its oddball Y-DNA lineage but mtDNA-wise notorious for its high frequencies of H). I say *at least another one* because I hypothesize (based on some archaeological evidence) that there were probably two WHG sub-populations in Iberia: one including most of the peninsula (dominated by mtDNA H) and another in the Basque Country and surely extending to much of modern France (with much higher frequencies of mtDNA U5, but also some H). The three populations would all be WHG in terms autosomal (although it's indeed possible that the Iberian one had some minor North African input, as has been suggested).

Chad Rohlfsen said...

Tobus,

All moderns prefer Loschbour, because he is closer to Motala, and eastern admixture from later events.

result: Samara_HG Motala_HG Loschbour Yoruba -0.0792 -13.824 8461 9917 203114
result: Karelia_HG Motala_HG Loschbour Yoruba -0.0758 -13.881 13977 16270 334629
result: Samara_HG Motala_HG LaBrana1 Yoruba -0.0510 -8.176 8334 9230 195698
result: Karelia_HG Motala_HG LaBrana1 Yoruba -0.0489 -8.550 13691 15098 320677
result: Samara_HG Motala_HG Loschbour LaBrana1 -0.0325 -4.021 6871 7334 193912
result: Motala_HG LaBrana1 Loschbour Yoruba -0.0513 -8.553 14133 15660 324978

Tobus said...

@Chris Davies:
With claims of African affinity in La Brana

Where do you see this? I ran Loschbour/LaBrana/X/Chimp D-stats for all African pops and all came back as even.

@Chad:
All moderns prefer Loschbour, because he is closer to Motala

Possible but I don't think so - as shown above Loschbour has no extra affinity to EHG, so it doesn't look like he's the admixed one.

Krefter said...

Assuming the Mesolithic mtDNA results in Portugal are legit. We have U5b(undefined), U5b1c2, U5b2c1, U4, H*(Not enough coverage), H1b1a-h, H6, and L3(N?) from Pre-Neolithic Iberia. H looks like the most popular haplogroup, and then typical Central-North hunter U subclades are next.

Although I still doubt all the ancient Iberian mtDNA from old studies is legit. Some results just don't make sense. Like consistent L3(N?), and extremely high frequency of R(R0+) and R(xR0).

The Neolithic Spanish results from Haak 2015 are just like what we find in Central Europe and make more sense.



Chad Rohlfsen said...

Tobus,

result: Karelia_HG MA1 Loschbour Yoruba 0.0623 8.673 11921 10524 242938
result: Karelia_HG MA1 LaBrana1 Yoruba 0.0545 7.273 11323 10152 233148
result: Dai Yamnaya Loschbour Yoruba -0.0835 -23.128 16151 19094 349736
result: Dai Yamnaya LaBrana1 Yoruba -0.0752 -19.148 15478 17994 333085
result: Yoruba Yamnaya Loschbour Chimp -0.3378 -93.441 14174 28638 349736
result: Yoruba Yamnaya LaBrana1 Chimp -0.3345 -87.309 13499 27067 333085
result: Yoruba Yamnaya Loschbour Ust_Ishim -0.1034 -24.151 15848 19505 349032
result: Yoruba Yamnaya LaBrana1 Ust_Ishim -0.0985 -22.423 15101 18401 332384

Chad Rohlfsen said...

Closer to Yamnaya too. That should help explain it.

Tobus said...

As discussed above, your comparisons are using different sized sets of SNPs (up 15,00+ extra in the Loschbour sample!) so how can you expect them to return the exact same Z-scores? Minor differences like this aren't necessarily signs of increased affinity - even with the same SNP sets there will be small differences due to random drift, within-population diversity, sample quality etc.

The following stats are direct comparisons between La Brana and Loschbour affinities and neither shows a significant preference to Yoruba, MA1, EHG, Dai or Yamnaya.

LaBrana1 Loschbour Yoruba Chimp -0.0031 -0.597 11574 11646 331055
LaBrana1 Loschbour MA1 Yoruba 0.0013 0.187 9707 9681 237767
LaBrana1 Loschbour Samara_HG Yoruba -0.0054 -0.704 7991 8078 195253
LaBrana1 Loschbour Karelia_HG Yoruba -0.0087 -1.238 13184 13416 320734
LaBrana1 Loschbour Dai Yoruba 0.0044 1.002 13231 13115 331055
LaBrana1 Loschbour Yamnaya Yoruba -0.0064 -1.501 13408 13582 330062

The increased affinity between Loschbour and Motala is thus best explained by Motala (not Loschbour!) containing both WHG and EHG gene flow... and since Motala is closer to all WHGs than to EHGs, Motala is thus best described as being WHG with EHG admixture.

Chad Rohlfsen said...

We know what Motala is. Obviously, Loschbour is closer to Motala. I'm more interested in what makes LaBrana different. There may also be some Motala in the Karelian, therefore, very minor Loschbour.

It can't just be about Loschbour mixing into Motala. Loschbour has to be different from LaBrana, or there would be no significant difference in the two against Motala. KO1 in Hungary has almost the same significant score over LaBrana, with Motala.

Chad Rohlfsen said...

KO1 also has a lower number of SNP's, like LaBrana, still the same difference in relation to Motala. Coverage doesn't seem to be the big issue here. There is something more.

Mike Thomas said...

Chad
I think you're getting at something
Must be related to the LGM separation and post -LGM remixing ; but we are still seeing deep signals of the pre LGM separation

I.e. La Brana preserved more of the franco- cantabrian refuge peoples whilst motala , Labschour and KO1 are more East - central european "epi-Gravettian" derived (?)

Chad Rohlfsen said...

Watch your outgroup too. They can change your Z score from something trivial to significant, or vice versa. They aren't related to the hunters equally. Even Africans differ in their pick. Not a huge difference, but it can affect the outcome.

result: Loschbour LaBrana1 Yamnaya Yoruba 0.0064 1.501 13582 13408 330062
result: Loschbour LaBrana1 Yamnaya Chimp 0.0087 1.459 13856 13616 330062
result: Loschbour LaBrana1 Yamnaya Mbuti 0.0079 1.711 13677 13462 330062
result: Loschbour LaBrana1 Yamnaya Dai 0.0112 2.347 12878 12592 330062
result: Loschbour LaBrana1 Yamnaya Ju_hoan_North 0.0078 1.644 13728 13515 330062
result: Loschbour LaBrana1 Yamnaya Papuan 0.0118 2.129 12982 12679 330062
result: Loschbour LaBrana1 Yamnaya Mandenka 0.0054 1.220 13553 13408 330062
result: Loschbour LaBrana1 Yamnaya BantuSA 0.0092 2.043 13641 13393 330062

Look for a pop that shows as close to zero preference as possible, for your L1 and L2, or R1 and R2. Depending on how you're setting it up. You don't want to inadvertently find close to a significant score, and have it be the outgroup that the score is reflecting. That's at least how I'm going to do Dstats from now on. Find my outgroup of non-preference first.

For example..

result: Loschbour LaBrana1 Luo Chimp 0.0047 0.884 11703 11592 331055
result: Loschbour LaBrana1 Gambian Chimp 0.0009 0.158 11619 11599 331055
result: Loschbour LaBrana1 Yoruba Chimp 0.0031 0.597 11646 11574 331055
result: Loschbour LaBrana1 Ju_hoan_North Chimp 0.0014 0.249 10503 10474 331055
result: Loschbour LaBrana1 Mandenka Chimp 0.0043 0.824 11688 11587 331055
result: Loschbour LaBrana1 BedouinB Chimp 0.0112 1.943 13670 13368 331055
result: Loschbour LaBrana1 Tunisian Chimp 0.0070 1.231 13406 13221 331055
result: Loschbour LaBrana1 BantuSA Chimp -0.0001 -0.020 11385 11387 331055
result: Loschbour LaBrana1 Mbuti Chimp 0.0014 0.262 10770 10739 331055
result: Loschbour LaBrana1 Papuan Chimp -0.0022 -0.342 13130 13189 331055
result: Loschbour LaBrana1 Dai Chimp -0.0016 -0.271 13424 13469 331055

The BantuSA look like they would be least likely to take any kind of ranking, from this vantage at least. So, personally, I'd rather go by the BantuSA score for Yamnaya.

If you'll notice, the decrease in the score with the Yoruba outgroup, is about the same as the difference below, between the Bantu and Yoruba.


Tobus said...

Chad,

Loschbour is closer to Motala. I'm more interested in what makes LaBrana different

My point is that LaBrana *isn't* very different:

LaBrana1 Motala_HG Loschbour Yoruba 0.0513 8.553 15660 14133 324978
Loschbour Motala_HG LaBrana1 Yoruba 0.0862 14.946 15660 13173 324978
- LaBrana and Loschbour are closer to each than either is to Motala. It's Motala that is "different" to the other WHGs, and in a decidedly EHG way.

KO1 also has a lower number of SNP's, like LaBrana, still the same difference in relation to Motala

Perhaps you are confusing topics. The issue with SNP count (and drift!) is when using the difference between 2 significant Z-scores to infer different affinity.

For example, you previously posted:
result: Samara_HG Motala_HG Loschbour Yoruba -0.0792 -13.824 8461 9917 203114
result: Karelia_HG Motala_HG Loschbour Yoruba -0.0758 -13.881 13977 16270 334629

The same D-stat but with KO1 gets:
result: Samara_HG Motala_HG HungaryGamba_HG Yoruba -0.0536 -7.887 6108 6800 142388
result: Karelia_HG Motala_HG HungaryGamba_HG Yoruba -0.0656 -10.809 9825 11204 232832

My point is that it would be a mistake to infer that Motala is closer to Loschbour than to KO1 from this result.



Chad Rohlfsen said...

I never said that. My point is that LaBrana is different from the other two. You need to look beyond just Motala.

Maju said...

@Krefter: "The Neolithic Spanish results from Haak 2015 are just like what we find in Central Europe and make more sense".

Sigh! They are all from the Mediterranean basin.

The point of contention is what was happening in all that large Atlantic area spanning from Portugal to Southern Sweden? We don't know yet: only Gökhem samples are somewhat informative on this matter, and probably also the already mentioned issue of two different populations relative to lactose tolerance mixing at the edges of Basque Chalcolithic. My supposition is that the Atlantic Neolithic populations were decisive in the shaping of modern Europeans, in Iberia as in Germany.

Tobus said...

Chad,

I never said that

No, but you did say it about La Brana based on his almost identical D-stat result.

My point is that LaBrana is different from the other two

All three are different from each other:
LaBrana1 Loschbour HungaryGamba_HG Yoruba -0.0578 -7.531 9125 10245 228531
LaBrana1 HungaryGamba_HG Loschbour Yoruba -0.0002 -0.031 10240 10245 228531
Loschbour HungaryGamba_HG LaBrana1 Yoruba 0.0576 7.427 10240 9125 228531

... but as I pointed out earlier, all of these differences are negligible compared to any other sample we have. There's no need or reason to look for admixture as a cause, the difference within the WHG samples can be explained by population structure and drift within a single "WHG" branch.

You need to look beyond just Motala.

You seem to be trying to find a reason for the tiny difference between LaBrana and Loschbour while ignoring the much larger difference between any WHG and Motala. If Loschbour has extra Motala then he should also have extra EHG, and he doesn't. OTOH if Motala has extra Loschbour then he should also have extra WHG, which he does. Motala as WHG+EHG seems to fit all the D-stats.

Chad Rohlfsen said...

But, only Loschbour and KO1 share the Motala score. It is the same significance. I'm saying the flow is into Loschbour and KO1, and not LaBrana. How else can KO1 and Loschbour share the same affinity to Motala and different affinity to LaBrana? There are other places to look that you're missing, but I'm too tired. I'll show you more tomorrow. Check your outgroups, before you run anything.

Tobus said...

But La Brana *does* share affinity with Motala:
Samara_HG Motala_HG LaBrana1 Yoruba -0.051 -8.176 8334 9230 195698
Karelia_HG Motala_HG LaBrana1 Yoruba -0.0489 -8.55 13691 15098 320677

... this is in between the two KO1 Z-scores (-7 and -10) and less than Loschbour's (both -13 ) - where do you see the same Motala significance for Loschbour and KO1?

One possible reason for the increased Loschbour score is that WHG had "Iberian" and "Central" branches and Motala is a "Central" branch pop that received gene flow from EHG - it was already closer to Loschbour when it got it's EHG.

I've already explained why you alternative proposal of Motala gene flow into Loschbour doesn't work - Motala has increased EHG affinity, so any WHG population that received Motala admixture to the exclusion of others should have an increased affinity to EHG as well as Motala. Loschbour/KO1 don't show this, although KO1 does have a small Samara affinity over both LaBrana and Loschbour - perhaps this is why his Motala comes out the same as Loschbour but his LaBrana doesn't (he's matching part of the EHG in Motala as well as the WHG)?

I run all my stats with both Yoruba and Chimp to make sure they're in agreement - if Chimp isn't a reliable outgroup then something is very wrong.

Chad Rohlfsen said...

Your thinking is in the box. Again, think outside of the hunters. You'll see why it has to be into Loschbour. Loschbour wasn't repopulating the globe.

Chad Rohlfsen said...

Don't forget to check L1,L2, vs your out group, each run. You might be surprised how much that can change your Zscore.

Tobus said...

I'm not really sure what you're getting at Chad, the "box" is simply what the D-stats suggest. Sure, Loschbour wasn't repopulating the the globe, but Germany to Sweden...? Quite possibly.

As I just said, I always try to run D-stats with two different outgroups to highlight any cases where there's a hidden bias. I also like to run with two different subject samples where possible (eg Karelia/Samara for EHG, Karitiana/Surui for NAm, Han/Dai for EAs etc.) for the same reason. There are always small differences, which is why I find your interpretation of the marginal LaBrana/Loschbour variances a bit "out of the box".


Chad Rohlfsen said...

No, you're still in the box, looking at the same groups. I can't lead you too much here. This is important to what I'm doing here, so I can't give you everything. I'm not posting anything else here on the subject. This is the furthest I'm taking it.

result: LaBrana1 Loschbour Makrani BantuSA -0.0076 -2.078 13142 13342 331055
result: LaBrana1 Loschbour Sindhi BantuSA -0.0063 -1.712 13226 13394 331055
result: LaBrana1 Loschbour Pathan BantuSA -0.0060 -1.620 13258 13417 331055
result: LaBrana1 Loschbour Hazara BantuSA -0.0071 -1.775 13228 13416 331055
result: LaBrana1 Loschbour Tajik_Pomiri BantuSA -0.0074 -1.832 13322 13520 331055
result: LaBrana1 Loschbour Iranian BantuSA -0.0064 -1.595 13260 13432 331055
result: LaBrana1 Loschbour Yemen BantuSA -0.0042 -1.081 12992 13103 331055
result: LaBrana1 Loschbour Saudi BantuSA -0.0077 -1.853 13162 13366 331055
result: LaBrana1 Loschbour BedouinB BantuSA -0.0115 -2.857 13053 13357 331055
result: LaBrana1 Loschbour Iraqi_Jew BantuSA -0.0078 -1.826 13220 13429 331055
result: LaBrana1 Loschbour Lebanese BantuSA -0.0099 -2.421 13132 13394 331055
result: LaBrana1 Loschbour Armenian BantuSA -0.0074 -1.869 13267 13465 331055
result: LaBrana1 Loschbour Georgian BantuSA -0.0079 -1.941 13280 13493 331055
result: LaBrana1 Loschbour North_Ossetian BantuSA -0.0103 -2.567 13271 13547 331055
result: LaBrana1 Loschbour Lezgin BantuSA -0.0109 -2.709 13262 13555 331055
result: LaBrana1 Loschbour Egyptian BantuSA -0.0073 -2.062 12962 13152 331055
result: LaBrana1 Loschbour Tunisian BantuSA -0.0072 -1.964 12890 13077 331055
result: LaBrana1 Loschbour Somali BantuSA -0.0019 -0.661 12227 12273 331055
result: LaBrana1 Loschbour Yoruba BantuSA -0.0033 -1.682 11296 11370 331055
result: LaBrana1 Loschbour Luo BantuSA -0.0049 -2.119 11353 11466 331055
result: LaBrana1 Loschbour Yamnaya BantuSA -0.0092 -2.043 13393 13641 330062

Tobus said...

Maybe, but as I said, it's the D-stats that make these groups, not me. These last results seem consistent with all modern populations getting their WHG from a (slightly) more Loschbour-like than LaBrana-like WHG population. Makes sense since you'd reach Germany before Spain coming from both the Levant and the Steppe.

Good luck with whatever you are working on, is it something we'll be able to read one day?

Chad Rohlfsen said...

I hope so.

batman said...

@ Chad

What if the Mottala-modal is older than Loschbour, Karelia, Samara and La Brana?

batman said...

Nature and culture?

"Applying ancient DNA calibration, we date the Y-chromosomally most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck.

In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky.

We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males."

http://www.researchgate.net/publication/273631580_A_recent_bottleneck_of_Y_chromosome_diversity_coincides_with_a_global_change_in_culture

batman said...

Please note that the assumptions about a extensive Scandianvaian Iced-Sheet (SIS) during late Pleistocene is flawed.

As Willeslev points out in the video above the last decade have brougth us new and major break-throughs within quartary-geology, glaciology and archeo-botany, along with genetics - proving that both larger plants as well as land-animals have survived close to the shores of the North-Atlantic, on or in the immediate vicinity of the Scandianvian penninsula.

Consequently we can't (anymore) rule out the possibility of a NW refugia to be the origin of the paternal lines from y-dna F, that were able to actually survive the coldest Eurasian climate on record, namely the Dryas I and II.

That would imply that Ust-Ishim, Afonsova Gora and MA-1 represents outliers from F(KL) that died out during LGM or Dryas.

Since the discovery of epi-paleolithic settlements northernmost tier of Fenno-Scandia (North Cape) already 11.300 years ago - and a later discoveries of settlements withing the Oslo Bay (11.800+) and the Botnic Bay (11.000+) there is reason to believe that the paternal lines that pioneered and settled the northern and barren parts of pre-boreal and boreal Eurasia had a common origin - from a late-glacial refugia between the western Baltics and the English Channel, were a climatic pocket is known to have existed.

http://sverigesradio.se/sida/artikel.aspx?programid=2054&artikel=3270787

I still wonder how such a starting-point would look through the lenses, maths and models of the present knowledge of the Eurasian genome?