Makin a map of EEF, WHG and ANE admixtures in Europe. Please post your data.

[Angela]

ANE is present in all of Western and South Asia. It is more of an Indo_European or Proto_Caucasic signature. An evidence for this is that ANE reaches it's higest frequency among Iranic and Caucasic groups of Western Asia.

ANE reaches levels of 25% in North Caucasus.

ANE is present in small quantities in far northeastern European hunter gatherers much earlier than the possible formation of any IE groups in the Pontic Caspian steppe. Isn't it possible that likewise there was some gene flow from ANE people into some areas of the Near East and South Asia before the later movement into these areas of Indo-European speaking peoples?

[Fire Haired14]

I'm expecting samples from Samara to be >90% ANE when they come from around 6,000 years ago. Mixing with farmers would bring it down to 75-50% around 4,000 years ago. In these proportions they've entered Europe as IE. Will see soon.

There is no way they were 90% ANE. How do you explain nearly 50% WHG ancestry in Ireland when the Neolithic farmers of western Europe had only around 20-25%? Obviously the native Neolithic people of western Europe can not explain the high amounts of WHG ancestry that exist in northwest Europe. My guess is that they had more WHG ancestry than ANE.

[LeBrok]

There is no way they were 90% ANE. How do you explain nearly 50%

Before IE invasion there was only WHG and EEF admixtures in Ireland. For most northerly European countries, where farming came late, the ratio was close to 50/50. For south Europeans the admixtures were overwhelmingly EEF.

WHG ancestry in Ireland when the Neolithic farmers of western Europe had only around 20-25%? Obviously the native Neolithic people of western Europe can not explain the high amounts of WHG ancestry that exist in northwest Europe.

There was more WHG in NW Europe. In Neolithic it might not have been mixed evenly through population yet, with still some enclaves of pure WHG roaming around. Farming came late there and had few collapses letting Hunter-Gatherers recover and mix with farmers later.

My guess is that they had more WHG ancestry than ANE.

Impossible, although they had some (minority). Otherwise you can't explain about 12% level of ANE in Southern Europe and almost nothing WHG. I think IE came with ration 1 to 4, one IE to 4 locals. Assuming that they were roughly 50/50 EEF/ANE, coming from Yamna culture. Indo Iranians from farther east could have been much higher on ANE scale.

[Pax Augusta]

The latest Academic [Lazaridis] figures from April 2014;
p.111: http://biorxiv.org/content/biorxiv/s...4/001552-3.pdf

Is Lazaridis a geneticist?

[Fire Haired14]

Lebrok at this point we can only speculate. Greeks score 4% WHG on Laz's test but that actually means they have over 20% aka more than Stuttgart, and also much of their ANE ancestry is from southwest Asian not Indo European admixture. We have autosomal DNA from Swedish(northern) farmers and yes they had more hunter gatherer ancestry than southern ones but much less than modern northwest Europeans and around as much as Basque.

[Angela]

Is Lazaridis a geneticist?

He is a Post-Doctoral Fellow at David Reich's Genetics Lab at Harvard University.

[John Doe]

Lebrok at this point we can only speculate. Greeks score 4% WHG on Laz's test but that actually means they have over 20% aka more than Stuttgart, and also much of their ANE ancestry is from southwest Asian not Indo European admixture. We have autosomal DNA from Swedish(northern) farmers and yes they had more hunter gatherer ancestry than southern ones but much less than modern northwest Europeans and around as much as Basque.

How much do AJs score? I know it's very low but it is above noise level.

[Pax Augusta]

He is a Post-Doctoral Fellow at David Reich's Genetics Lab at Harvard University.

Thanks, I knew, but I asked if he was a geneticist.

According to this, He has a PhD on "Information and Computer Science"
If it's true, He is not geneticist, even if he is a Post-Doctoral Fellow at David Reich's Genetics Lab at Harvard University

http://contactbee.com/en/contact/view/5000459


Education/degrees

University of California, Irvine - Ph.D. , Information and Computer Science

University of California, Irvine - Master of Science (M.S.) , Information and Computer Science

National Technical University of Athens - Diploma in Engineering , Electrical and Computer Engineering

[sparkey]

Thanks, I knew, but I asked if he was a geneticist.

According to this, He has a PhD on "Information and Computer Science"
If it's true, He is not geneticist, even if he is a Post-Doctoral Fellow at David Reich's Genetics Lab at Harvard University

http://contactbee.com/en/contact/view/5000459


Education/degrees

University of California, Irvine - Ph.D. , Information and Computer Science

University of California, Irvine - Master of Science (M.S.) , Information and Computer Science

National Technical University of Athens - Diploma in Engineering , Electrical and Computer Engineering

Lazaridis often co-authors with Nick Patterson, who is usually described as a "computational biologist" rather than a geneticist, and the same may apply to Lazaridis. Lazaridis also often co-authors with David Reich, who is in fact a geneticist, in the strictest sense of the term.

[Angela]

Thanks, I knew, but I asked if he was a geneticist.

According to this, He has a PhD on "Information and Computer Science"
If it's true, He is not geneticist, even if he is a Post-Doctoral Fellow at David Reich's Genetics Lab at Harvard University

http://contactbee.com/en/contact/view/5000459


Education/degrees

University of California, Irvine - Ph.D. , Information and Computer Science

University of California, Irvine - Master of Science (M.S.) , Information and Computer Science

National Technical University of Athens - Diploma in Engineering , Electrical and Computer Engineering

I'm afraid I don't get your point. The study of population genetics is heavily dependent on such disciplines. It is not only or even primarily focused on the changes in the cells. Population genetics is, in fact, a new discipline. Regardless, the paper to which you refer was prepared by the Reich Lab at Harvard Medical School under the direction of David Reich (who is a geneticist proper), with Lazaridis as the lead author. The paper also lists as contributing authors a whole host of renowned population geneticists.

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
doi: http://dx.doi.org/10.1101/001552

[Angela]

How much do AJs score? I know it's very low but it is above noise level.

As has been posted, the academic results upon which all these analyses are based (Lazaridis et al from the Reich Lab at Harvard), show that AJ's can be fitted with no WHG at all. In other words, they can be seen solely as a combination of EEF and ANE.

The only claim that AJ's have even a very minority slice of WHG comes from a calculator produced by a blogger, and its results are in contradiction to the Lazaridis et al results, have very wide margins of error, and produce some bizarre results for some European groups.

[Angela]

Sparkey said it more succinctly. :)

[Fire Haired14]

Angela, Stuttgart absorbs WHg ancestry, a sample has to have more than her(probably over 20%) to score any WHG. If AJs have admixed with any Europeans at all they have some WHG ancestry, same goes for other non-European people.

[John Doe]

As has been posted, the academic results upon which all these analyses are based (Lazaridis et al from the Reich Lab at Harvard), show that AJ's can be fitted with no WHG at all. In other words, they can be seen solely as a combination of EEF and ANE.

The only claim that AJ's have even a very minority slice of WHG comes from a calculator produced by a blogger, and its results are in contradiction to the Lazaridis et al results, have very wide margins of error, and produce some bizarre results for some European groups.

Alright, got it, thanks.

[John Doe]

Angela, Stuttgart absorbs WHg ancestry, a sample has to have more than her(probably over 20%) to score any WHG. If AJs have admixed with any Europeans at all they have some WHG ancestry, same goes for other non-European people.

Not true, Sicilians, Maltese, Greek islanders and Cypriots don't have any WHG ancestry and they're considered Europeans, AJs may have admixed with Greek Islander like populations who in the first place are overwhelmingly EEF.

[John Doe]

As has been posted, the academic results upon which all these analyses are based (Lazaridis et al from the Reich Lab at Harvard), show that AJ's can be fitted with no WHG at all. In other words, they can be seen solely as a combination of EEF and ANE.

The only claim that AJ's have even a very minority slice of WHG comes from a calculator produced by a blogger, and its results are in contradiction to the Lazaridis et al results, have very wide margins of error, and produce some bizarre results for some European groups.

Do you have a link for the study, the link you posted above says nothing of AJs.

[Angela]

Angela, Stuttgart absorbs WHg ancestry, a sample has to have more than her(probably over 20%) to score any WHG. If AJs have admixed with any Europeans at all they have some WHG ancestry, same goes for other non-European people.

Angela, Stuttgart absorbs WHg ancestry, a sample has to have more than her(probably over 20%) to score any WHG. If AJs have admixed with any Europeans at all they have some WHG ancestry, same goes for other non-European people.

As I said, as per Lazaridis et al, AJ's can be fitted as a solely EEF /ANE population.

Whatever proportion of ancient WHG is present within EEF (Stuttgart) is not relevant, in my opinion. (and not settled)

From the Lazaridis et al results, the AJ population doesn't have any more WHG than that which is buried in EEF, and than would be expected in a pre-Islamic migrations and pre-African slavery Levantine/East Mediterranean population.

If you choose to find the "calculator" results more accurate than those of the academic paper, that's of course another matter, and your prerogative.

[John Doe]

As I said, as per Lazaridis et al, AJ's can be fitted as a solely EEF /ANE population.

Whatever proportion of ancient WHG is present within EEF (Stuttgart) is not relevant, in my opinion. (and not settled)

From the Lazaridis et al results, the AJ population doesn't have any more WHG than that which is buried in EEF, and than would be expected in a pre-Islamic migrations and pre-African slavery Levantine/East Mediterranean population.

If you choose to find the "calculator" results more accurate than those of the academic paper, that's of course another matter, and your prerogative.

Do Sicilians, South Italians, Maltese, Greeks, Greek islanders and Cypriots get any WHG?

[Angela]

Do you have a link for the study, the link you posted above says nothing of AJs.

From the link which I provided, you can access the 193 page pdf file. This is the direct link.
http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf

If you go to page 40, you'll find Extended Data Table 3, which lists the EEF/WHG/ANE proportions for all of the populations which they tested. The AJ show up as 0 WHG. So do the Maltese and the Sicilians. The Greek Islanders were not tested, and you would have to make inferences, or use the Near East calculator, which seems pretty good.

I would happily reproduce the table here for easier reference, but I can't seem to post tables other than to save them to my computer and then post, and I've reached my maximum for attachments.

Ed. maybe someone who hasn't used up their attachment space can do it.

Southern Italians were also not tested. Greeks have .058 WHG. However, from what I can gather, this was a northern mainland Greek population. I would speculate that this might derive from the early medieval period "Slavic" migrations.

[John Doe]

From the link which I provided, you can access the 193 page pdf file. This is the direct link.
http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf

If you go to page 40, you'll find Extended Data Table 3, which lists the EEF/WHG/ANE proportions for all of the populations which they tested. The AJ show up as 0 WHG. So do the Maltese and the Sicilians. The Greek Islanders were not tested, and you would have to make inferences, or use the Near East calculator, which seems pretty good.

I would happily reproduce the table here for easier reference, but I can't seem to post tables other than to save them to my computer and then post, and I've reached my maximum for attachments.

Ed. maybe someone who hasn't used up their attachment space can do it.

Alright thanks, I suspected Maltese and Sicilians would end up as 0 as well, the study basically says that there are 2 types of European populations that are different, the first (Sicilians, Maltese and AJs) have a lot more EEF ancestry, 0 WHG ancestry probably due to a larger amount of Near Eastern ancestry through the EEF ancestry, which is also the reason said populations plot in the gap between European and Near Eastern populations. The second group are Finns, Mordovians and Russians from northeastern Europe who seem to be drawn to East Asians probably due to Siberian admixture. On the Near East calculator I show up as 84% Near Eastern and 16% ANE. I got a long reading in front of me, but it'll be worth it. :)

[John Doe]

So according to Extended Data Figure 4 AJs, Maltese and Sicilians are plotted in the gap between Near Eastern and European populations (Cypriots are further down, closer to Lebanese).


P.S Greeks get around 6% WHG, so only AJs, Maltese and Sicilians get 0% WHG.

Is the calculator for Southeast Europeans/West Asians as accurate as the results produced by the study at hand?

[Pax Augusta]

I'm afraid I don't get your point. The study of population genetics is heavily dependent on such disciplines. It is not only focused on the changes in the cells. Regardless, the paper to which you refer was prepared by the Reich lab at Harvard Medical School under the direction of David Reich, with Lazaridis as the lead author.

My point? Facts from primary sources.

The whole thing makes him a geneticist? I don't deny he could have an important skill on genetics, but he's always a computer scientist probably specialized on databases. "Iosif Lazaridis could indeed be the person hidden behind the pseudonym Dienekes Pontikos", Maciamo said. If it is true, what is the reason for his anonymity?

David Reich is a geneticist, that's sure. But I don't remember him as an expert of ancient and modern-day Eurasian populations. It will be my problem, no doubt. Anyway, what's your source on this? "the paper to which you refer was prepared by the Reich lab at Harvard Medical School under the direction of David Reich". The full version paper? Reich is just accredited as co-senior author, I don't find any official Harvard participation.

If the paper was really prepared by the Reich lab at Harvard Medical School under the direction of David Reich, why is the paper available on biorxiv.org only? biorxiv.org is "a free online archive and distribution service for unpublished preprints in the life sciences". Can you explain me this? Have some scientific publisher accepted this paper? I don't see any evidence of this.

The paper also lists as contributing authors a whole host of renowned population geneticists.

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick, Peter H. Sudmant, Joshua G. Schraiber, Sergi Castellano, Karola Kirsanow, Christos Economou, Ruth Bollongino, Qiaomei Fu, Kirsten Bos, Susanne Nordenfelt, Cesare de Filippo, Kay Prüfer, Susanna Sawyer, Cosimo Posth, Wolfgang Haak, Fredrik Hallgren, Elin Fornander, George Ayodo, Hamza A. Babiker, Elena Balanovska, Oleg Balanovsky, Haim Ben-Ami, Judit Bene, Fouad Berrada, Francesca Brisighelli, George B.J. Busby, Francesco Cali, Mikhail Churnosov, David E.C. Cole, Larissa Damba, Dominique Delsate, George van Driem, Stanislav Dryomov, Sardana A. Fedorova, Michael Francken, Irene Gallego Romero, Marina Gubina, Jean-Michel Guinet, Michael Hammer, Brenna Henn, Tor Helvig, Ugur Hodoglugil, Aashish R. Jha, Rick Kittles, Elza Khusnutdinova, Toomas Kivisild, Vaidutis Kučinskas, Rita Khusainova, Alena Kushniarevich, Leila Laredj, Sergey Litvinov, Robert W. Mahley, Béla Melegh, Ene Metspalu, Joanna Mountain, Thomas Nyambo, Ludmila Osipova, Jüri Parik, Fedor Platonov, Olga L. Posukh, Valentino Romano, Igor Rudan, Ruslan Ruizbakiev, Hovhannes Sahakyan, Antonio Salas, Elena B. Starikovskaya, Ayele Tarekegn, Draga Toncheva, Shahlo Turdikulova, Ingrida Uktveryte, Olga Utevska, Mikhail Voevoda, Joachim Wahl, Pierre Zalloua, Levon Yepiskoposyan, Tatijana Zemunik, Alan Cooper, Cristian Capelli, Mark G. Thomas, Sarah A. Tishkoff, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, David Comas, Rem Sukernik, Mait Metspalu, Matthias Meyer, Evan E. Eichler, Joachim Burger, Montgomery Slatkin, Svante Pääbo, Janet Kelso, David Reich, Johannes Krause
doi: http://dx.doi.org/10.1101/001552

Have these contributing authors really worked with Lazaridis? Or Lazaridis have just used their studies?

Here a previous work of Lazaridis:

Fault Tolerant Evaluation of Continuous Selection Queries over Sensor Data

Iosif Lazaridis Department of Computer Science, University of California, Irvine, CA, USA
Qi Han Department of Math and Computer Sciences, Colorado School of Mines, Golden, CO, USA
Sharad Mehrotra Department of Computer Science, University of California, Irvine, CA, USA
Nalini Venkatasubramanian Department of Computer Science, University of California, Irvine, CA, USA

Published in:
Journal International Journal of Distributed Sensor Networks archive
Volume 5 Issue 4, July 2009
Pages 338-360
Taylor & Francis, Inc. Bristol, PA, USA

http://dl.acm.org/citation.cfm?id=1572676

[AgnusDei]

This is the Middle Eastern version of the spreadsheet courtesy of poster MfA

MfA's spreadsheet :

Near East 89.622
ANE 10.378

[John Doe]

This is the Middle Eastern version of the spreadsheet courtesy of poster MfA

I got 84% Near East and 16% ANE.

[AgnusDei]

I got 84% Near East and 16% ANE.

Nice,to see other member's results !
Thanks for sharing !