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Tomenable
28-03-19, 14:03
From this study: https://www.biorxiv.org/content/biorxiv/early/2018/09/20/422295.full.pdf

I uploaded this prehistoric man to GEDmatch:

Sample: ZBC IPB001.B/C0101
AHG (Anatolian Hunter-Gatherer)
Age: 13,642-13,073 cal BCE
Haplogroup Y-DNA: C1a2
Haplogroup mtDNA: K2b

GEDmatch Genesis kit number - DY9790520

Eurogenes K15:

Admix Results (sorted):

# Population Percent
1 West_Med 46.28
2 East_Med 24.06
3 Atlantic 18.82
4 North_Sea 5.07
5 Red_Sea 4.92
6 Baltic 0.86

Single Population Sharing:

# Population (source) Distance
1 Sardinian 6.95
2 North_Italian 27.3
3 Tuscan 27.31
4 West_Sicilian 28.11
5 Spanish_Andalucia 28.13
6 Algerian_Jewish 28.9
7 South_Italian 29.57
8 Spanish_Extremadura 29.74
9 Italian_Jewish 29.8
10 Spanish_Valencia 30.09
11 East_Sicilian 30.2
12 Spanish_Castilla_La_Mancha 30.25
13 Portuguese 30.26
14 Spanish_Murcia 30.28
15 Moroccan 30.53
16 Mozabite_Berber 30.53
17 Spanish_Aragon 30.56
18 Spanish_Cantabria 30.88
19 Central_Greek 30.88
20 Greek 30.94

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 90.4% Sardinian + 9.6% Yemenite_Jewish @ 4.07
2 91.1% Sardinian + 8.9% Saudi @ 4.69
3 88.9% Sardinian + 11.1% Samaritan @ 4.74
4 89.7% Sardinian + 10.3% Lebanese_Christian @ 4.84
5 89.8% Sardinian + 10.2% Palestinian @ 4.86
6 90.3% Sardinian + 9.7% Lebanese_Druze @ 4.9
7 87.4% Sardinian + 12.6% Libyan_Jewish @ 5.02
8 90.1% Sardinian + 9.9% Egyptian @ 5.11
9 90.4% Sardinian + 9.6% Jordanian @ 5.17
10 90.5% Sardinian + 9.5% Bedouin @ 5.18
11 87.9% Sardinian + 12.1% Tunisian_Jewish @ 5.24
12 86.4% Sardinian + 13.6% Algerian_Jewish @ 5.31
13 89% Sardinian + 11% Cyprian @ 5.33
14 91.8% Sardinian + 8.2% Kurdish_Jewish @ 5.44
15 90.7% Sardinian + 9.3% Syrian @ 5.44
16 87.3% Sardinian + 12.7% Italian_Jewish @ 5.48
17 90.8% Sardinian + 9.2% Lebanese_Muslim @ 5.51
18 88% Sardinian + 12% Sephardic_Jewish @ 5.54
19 92.2% Sardinian + 7.8% Iranian_Jewish @ 5.57
20 89% Sardinian + 11% Tunisian @ 5.79

K36 Similarity Map:

https://i.imgur.com/iHhwsqd.png

He is from Pinarbaşı but I'm not sure which one (probably the one in in Konya Province?):

https://en.wikipedia.org/wiki/P%C4%B1narba%C5%9F%C4%B1

Angela
28-03-19, 15:26
What have I been saying all along about the fact that the earliest farmers of Anatolia (here, even the preceeding hunter-gatherers who were virtually the same people) would probably show "Levantine" or even Saudi in these calculators and so one needn't go looking for all or even mostly relatively "modern" admixture????

That was obvious way back when Otzi and Gok were analyzed, who were very similar to Sardinians. Both the North African and the SW Asian are higher than in modern North Italians and Tuscans.

https://i.imgur.com/Gvl1wUh.png

Nik
28-03-19, 18:04
How are they closest to Sardinians but on the K36 similarity map Sardinia has just 37 while Lazio/Latium has 63. Pardon my ignorance.

Ygorcs
28-03-19, 19:06
From this study: https://www.biorxiv.org/content/biorxiv/early/2018/09/20/422295.full.pdf

I uploaded this prehistoric man to GEDmatch:

Sample: ZBC IPB001.B/C0101
AHG (Anatolian Hunter-Gatherer)
Age: 13,642-13,073 cal BCE
Haplogroup Y-DNA: C1a2
Haplogroup mtDNA: K2b

GEDmatch Genesis kit number - DY9790520

Eurogenes K15:

Admix Results (sorted):

# Population Percent
1 West_Med 46.28
2 East_Med 24.06
3 Atlantic 18.82
4 North_Sea 5.07
5 Red_Sea 4.92
6 Baltic 0.86

Single Population Sharing:

# Population (source) Distance
1 Sardinian 6.95
2 North_Italian 27.3
3 Tuscan 27.31
4 West_Sicilian 28.11
5 Spanish_Andalucia 28.13
6 Algerian_Jewish 28.9
7 South_Italian 29.57
8 Spanish_Extremadura 29.74
9 Italian_Jewish 29.8
10 Spanish_Valencia 30.09
11 East_Sicilian 30.2
12 Spanish_Castilla_La_Mancha 30.25
13 Portuguese 30.26
14 Spanish_Murcia 30.28
15 Moroccan 30.53
16 Mozabite_Berber 30.53
17 Spanish_Aragon 30.56
18 Spanish_Cantabria 30.88
19 Central_Greek 30.88
20 Greek 30.94

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 90.4% Sardinian + 9.6% Yemenite_Jewish @ 4.07
2 91.1% Sardinian + 8.9% Saudi @ 4.69
3 88.9% Sardinian + 11.1% Samaritan @ 4.74
4 89.7% Sardinian + 10.3% Lebanese_Christian @ 4.84
5 89.8% Sardinian + 10.2% Palestinian @ 4.86
6 90.3% Sardinian + 9.7% Lebanese_Druze @ 4.9
7 87.4% Sardinian + 12.6% Libyan_Jewish @ 5.02
8 90.1% Sardinian + 9.9% Egyptian @ 5.11
9 90.4% Sardinian + 9.6% Jordanian @ 5.17
10 90.5% Sardinian + 9.5% Bedouin @ 5.18
11 87.9% Sardinian + 12.1% Tunisian_Jewish @ 5.24
12 86.4% Sardinian + 13.6% Algerian_Jewish @ 5.31
13 89% Sardinian + 11% Cyprian @ 5.33
14 91.8% Sardinian + 8.2% Kurdish_Jewish @ 5.44
15 90.7% Sardinian + 9.3% Syrian @ 5.44
16 87.3% Sardinian + 12.7% Italian_Jewish @ 5.48
17 90.8% Sardinian + 9.2% Lebanese_Muslim @ 5.51
18 88% Sardinian + 12% Sephardic_Jewish @ 5.54
19 92.2% Sardinian + 7.8% Iranian_Jewish @ 5.57
20 89% Sardinian + 11% Tunisian @ 5.79

K36 Similarity Map:

https://i.imgur.com/iHhwsqd.png

He is from Pinarbaşı but I'm not sure which one (probably the one in in Konya Province?):

https://en.wikipedia.org/wiki/P%C4%B1narba%C5%9F%C4%B1

How intriguing that in the K36 Similarity Map he is quite closer to Corsican and Central Italian samples than to the Sardinian samples, which are the closest fit according to Eurogenes K15. What could explain that? Does this Anatolian HG have more European HG (WHG) than the average ANF that eventually colonized Europe? What about the 9.6% Yemenite Jewish deemed necessary as a complement to Sardinian, which suggests, I think, some higher affiniy with Levant_Neo (and also possibly Iranian_Neo) influences?

Angela
28-03-19, 19:31
How are they closest to Sardinians but on the K36 similarity map Sardinia has just 37 while Lazio/Latium has 63. Pardon my ignorance.

@Nik,
Tuscan is only one point lower, at 62, and the highest of all is Corsica with 64, Corsica with its Tuscan like dialect and its history of Tuscan like inheritance. Plus, the very southern part of Toscana is quite like Northern Lazio.

Sardinia is so drifted I don't know why it would be used at all; it's bound to throw things off.

As for why there are differences between the different Eurogenes products, the one to be asked is him. I'm no big fan of any of them.

Plus, calculators based on modern populations are always going to give results that are very hard to interpret, which I've been saying for years, for all anyone seems to listen. That's why I pointed out that "Levantine" percentages are not always going to be very precise.

For what it's worth, however, it's long been known that the most EEF is usually found in Central and Northern Italy; certainly not in the Near East.

Carlos
28-03-19, 21:28
I have heard that in 2 million modern samples there are 20 modern Europeans with the C dnaY. Of the 20, four would be from Spain.

Regio X
28-03-19, 21:59
How are they closest to Sardinians but on the K36 similarity map Sardinia has just 37 while Lazio/Latium has 63. Pardon my ignorance.

How intriguing that in the K36 Similarity Map he is quite closer to Corsican and Central Italian samples than to the Sardinian samples, which are the closest fit according to Eurogenes K15. What could explain that? Does this Anatolian HG have more European HG (WHG) than the average ANF that eventually colonized Europe? What about the 9.6% Yemenite Jewish deemed necessary as a complement to Sardinian, which suggests, I think, some higher affiniy with Levant_Neo (and also possibly Iranian_Neo) influences?As you know, ANF were mostly AHG, with minor Iran and Levant Neo ancestries. Then, in Europe, ANF picked up some more WHG and became something else (closely related to Sardinians).

I guess the explanation is more simple than that. Firstly, they are different calculators; and K36 vs Similarity Map has a little problem, apparently. This possible problem is that the reference for West Med would be virtually Sardinian itself(?), a drifted pop, as Angela pointed out. If so, it would be the same reference for the cluster "and" for the population (in the map): West Med = Sardinian. I won't say it's not very clever because the calculator and the similarity map are different things. The last was built based on the former.
Indeed, if you access http://gen3553.pagesperso-orange.fr/ADN/similitude.htm and put 100% at K36 West Med cluster, you'll see that Sardinians get 85. ;) So almost the same. The result is that most of non-Sardinians will show up in this K36 map as very distantly related to Sardinians, because Sardinians get too much West Med (Sardinians). And we know Sardinian is not the only pop in Europe and Asia with a chunck of ANF, so it's expected that some segments of this AHG individual fits in various K36 clusters.

This problem apparently doesn't happen in K15. Perhaps its reference for West Med is different, wider, after all, it has not 35 other competing clusters. Its references could include even the Basques too, whereas in K36 there is an exclusive Basque cluster. Curiously, it seems the overlap between Basque cluster and actual Basques (in the map) doesn't equal West Med vs Sardinians, possibly also because Basques are not so drifted. Anyway, it's enough to make many non-Basques distantly related to Basques in the map.

Ygorcs
29-03-19, 00:55
As you know, ANF were mostly AHG, with minor Iran and Levant Neo ancestries. Then, in Europe, ANF picked up some more WHG and became something else (closely related to Sardinians).

I guess the explanation is more simple than that. Firstly, they are different calculators; and K36 vs Similarity Map has a little problem, apparently. This possible problem is that the reference for West Med would be virtually Sardinian itself(?), a drifted pop, as Angela pointed out. If so, it would be the same reference for the cluster "and" for the population (in the map): West Med = Sardinian. I won't say it's not very clever because the calculator and the similarity map are different things. The last was built based on the former.
Indeed, if you access http://gen3553.pagesperso-orange.fr/ADN/similitude.htm and put 100% at K36 West Med cluster, you'll see that Sardinians get 85. ;) So almost the same. The result is that most of non-Sardinians will show up in this K36 map as very distantly related to Sardinians, because Sardinians get too much West Med (Sardinians). And we know Sardinian is not the only pop in Europe and Asia with a chunck of ANF, so it's expected that some segments of this AHG individual fits in various K36 clusters.

This problem apparently doesn't happen in K15. Perhaps its reference for West Med is different, wider, after all, it has not 35 other competing clusters. Its references could include even the Basques too, whereas in K36 there is an exclusive Basque cluster. Curiously, it seems the overlap between Basque cluster and actual Basques (in the map) doesn't equal West Med vs Sardinians, possibly also because Basques are not so drifted. Anyway, it's enough to make many non-Basques distantly related to Basques in the map.

Excellent explanation, now it looks much clearer to me. Thank you very much! This matter reminded me why we should never take the results of any calculator or analysis too literally and in isolation from several others. Since the reality of the genetic history of populations is much more complex and interconnected, with lots of overlaps and the confusing effect of drift, one is bound to make incorrect conclusions if one reads these calculators as received truth, and not clues that must be taken together with other clues and then made some sense without ever forgetting things like history, geography and even basic common sense.

Angela
29-03-19, 01:51
Excellent explanation, now it looks much clearer to me. Thank you very much! This matter reminded me why we should never take the results of any calculator or analysis too literally and in isolation from several others. Since the reality of the genetic history of populations is much more complex and interconnected, with lots of overlaps and the confusing effect of drift, one is bound to make incorrect conclusions if one reads these calculators as received truth, and not clues that must be taken together with other clues and then made some sense without ever forgetting things like history, geography and even basic common sense.

Amen, Ygorcs. :)