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View Full Version : Central and South Italian K15 results



Blanco
20-03-18, 19:20
From Tuscany, Central Italy (HGDP sample) Kit Number: Z481041



#
Population
Percent


1
Atlantic
26.49


2
East_Med
24.34


3
West_Med
22.66


4
North_Sea
15.58


5
West_Asian
6.88


6
Baltic
2.34


7
Red_Sea
1.71



Single Population Sharing:



#
Population (source)
Distance


1
Tuscan
9.02


2
North_Italian
9.47


3
West_Sicilian
11.6


4
Spanish_Andalucia
12.77


5
Spanish_Murcia
13.04


6
Italian_Abruzzo
13.57


7
Spanish_Extremadura
13.58


8
Spanish_Valencia
13.88


9
Portuguese
14.5


10
Spanish_Castilla_La_Mancha
14.88


11
Spanish_Cataluna
15.12


12
Spanish_Castilla_Y_Leon
15.21


13
Spanish_Aragon
16.05


14
South_Italian
16.18


15
East_Sicilian
16.24


16
Spanish_Galicia
16.25


17
Greek
16.57


18
Central_Greek
16.62


19
Greek_Thessaly
17.28


20
Spanish_Cantabria
17.4



Mixed Mode Population Sharing:



#

Primary Population (source)
Secondary Population (source)
Distance


1

53.5%
Spanish_Aragon
+
46.5%
Italian_Jewish
@
6.18


2

58.9%
Italian_Jewish
+
41.1%
French_Basque
@
6.18


3

70.5%
Spanish_Aragon
+
29.5%
Lebanese_Druze
@
6.19


4

57.9%
Spanish_Valencia
+
42.1%
Italian_Jewish
@
6.27


5

55.1%
Spanish_Aragon
+
44.9%
Algerian_Jewish
@
6.46


6

59.5%
Spanish_Valencia
+
40.5%
Algerian_Jewish
@
6.53


7

76.3%
Spanish_Andalucia
+
23.7%
Lebanese_Druze
@
6.53


8

70.4%
Spanish_Aragon
+
29.6%
Lebanese_Christian
@
6.55


9

65%
Spanish_Aragon
+
35%
Cyprian
@
6.58


10

74.3%
Spanish_Valencia
+
25.7%
Lebanese_Druze
@
6.58


11

60.7%
Spanish_Andalucia
+
39.3%
Italian_Jewish
@
6.6


12

50.2%
Spanish_Aragon
+
49.8%
South_Italian
@
6.67


13

74.1%
Spanish_Valencia
+
25.9%
Lebanese_Christian
@
6.69


14

56%
Spanish_Castilla_La_Mancha
+
44%
Italian_Jewish
@
6.75


15

69.1%
Spanish_Valencia
+
30.9%
Cyprian
@
6.77


16

57.6%
Algerian_Jewish
+
42.4%
French_Basque
@
6.88


17

72.8%
Spanish_Castilla_La_Mancha
+
27.2%
Lebanese_Druze
@
6.88


18

54.9%
Spanish_Valencia
+
45.1%
South_Italian
@
6.89


19

62.4%
Spanish_Andalucia
+
37.6%
Algerian_Jewish
@
6.91


20

60.9%
West_Sicilian
+
39.1%
Spanish_Aragon
@
6.92






From Catanzaro, South Italy: Kit Number: A552689



#
Population
Percent


1
East_Med
33.78


2
Atlantic
15.33


3
West_Med
15.19


4
West_Asian
15.1


5
Baltic
7.49


6
Red_Sea
6.86


7
North_Sea
5.09


8
Southeast_Asian
0.89


9
Northeast_African
0.25


10
Eastern_Euro
0.01



Single Population Sharing:



#
Population (source)
Distance


1
South_Italian
5.98


2
Sephardic_Jewish
6.01


3
Italian_Jewish
7.31


4
Algerian_Jewish
7.9


5
East_Sicilian
8.01


6
Central_Greek
8.37


7
Tunisian_Jewish
9.08


8
West_Sicilian
9.81


9
Ashkenazi
9.86


10
Italian_Abruzzo
10.15


11
Cyprian
10.99


12
Greek
12.54


13
Libyan_Jewish
13.38


14
Lebanese_Muslim
14.45


15
Greek_Thessaly
14.66


16
Tuscan
15.69


17
Syrian
15.89


18
Samaritan
17.24


19
Turkish
17.88


20
Lebanese_Christian
18.53



Mixed Mode Population Sharing:



#

Primary Population (source)
Secondary Population (source)
Distance


1

83.5%
South_Italian
+
16.5%
Lebanese_Druze
@
4.66


2

89.8%
South_Italian
+
10.2%
Yemenite_Jewish
@
4.68


3

67.9%
South_Italian
+
32.1%
Tunisian_Jewish
@
4.72


4

83.4%
South_Italian
+
16.6%
Palestinian
@
4.74


5

50.4%
South_Italian
+
49.6%
Sephardic_Jewish
@
4.77


6

74.8%
Cyprian
+
25.2%
Spanish_Valencia
@
4.8


7

83.6%
South_Italian
+
16.4%
Lebanese_Christian
@
4.85


8

80.7%
Cyprian
+
19.3%
French_Basque
@
4.85


9

82.7%
South_Italian
+
17.3%
Samaritan
@
4.87


10

77.3%
Cyprian
+
22.7%
Southwest_French
@
4.9


11

53.6%
West_Sicilian
+
46.4%
Cyprian
@
4.91


12

77.1%
Sephardic_Jewish
+
22.9%
Greek
@
4.93


13

75.1%
Cyprian
+
24.9%
Spanish_Castilla_Y_Leon
@
4.94


14

76.5%
Cyprian
+
23.5%
Spanish_Aragon
@
4.95


15

80.2%
South_Italian
+
19.8%
Lebanese_Muslim
@
4.96


16

74.8%
South_Italian
+
25.2%
Cyprian
@
4.99


17

74%
Cyprian
+
26%
Spanish_Andalucia
@
5.03


18

91.1%
South_Italian
+
8.9%
Saudi
@
5.06


19

67.3%
Sephardic_Jewish
+
32.7%
Central_Greek
@
5.07


20

85%
South_Italian
+
15%
Jordanian
@
5.07

Angela
20-03-18, 20:17
Well, goodness, if that really is a Tuscan sample from HGDP, then this really is a really TERRIBLE calculator. A genetic distance of over 9? When you're dealing with moderns, if the distance isn't at least 4 or 5 forget it.

This must be as bad as Polako's "J" calculator where everybody has huge percentages of "Jewish" ancestry. :)

Like I said, some amateurs, especially those from eastern Europe, have Jews on the brain.

davef
20-03-18, 20:57
Right, Angela, and it's weird that Ashkenazi are scoring 26 percent ashkenazi on that, there's some weird sorcery behind that thing we may never figure out. Normal calculators with an ashkenazi component give 100 percent or perhaps a bit less of that to ashkenazi users.

Angela
20-03-18, 21:50
Right, Angela, and it's weird that Ashkenazi are scoring 26 percent ashkenazi on that, there's some weird sorcery behind that thing we may never figure out. Normal calculators with an ashkenazi component give 100 percent or perhaps a bit less of that to ashkenazi users.

If it's giving real Ashkenazi Jews 26%, then it's crap and should be taken off gedmatch.

Blanco
20-03-18, 21:58
Eurogenes calculators are one of the best because of the high SNP numbers.160-180k SNP is good for a Gedmatch calculator. Harappaworld is also good and better for Mediterranean and Near Eastern populations because Eurogenes was specified for people of Predominately European ancestry.

PuntDNAL works well for the Calabrese because it's made for Mediterranean populations: It's great to see how they remained pure from Indo-European, Slavic invasions unlike the Northern parts of Mainland Greece that's why they get closer to even Cyprus than most parts of Mainland Greece even. :smile: East Med brotherhood:grin:



#
Population
Percent


1
SW_Europe
37.96


2
West_Asia
27.15


3
SW_Asia
18.14


4
NE_Europe
13.4


5
SE_Asia
2.19


6
East_Africa
0.92


7
Oceania
0.17


8
South_Africa
0.07



Single Population Sharing:



#
Population (source)
Distance


1
Sephardic_Jew
3.88


2
Italian_Sicilian
4.49


3
Ashkenazy_Jew
4.72


4
Italian_Abruzzo
9.55


5
Cypriot
9.63


6
Greek_Central
9.72


7
Turkish
13.08


8
Lebanese_Christian
14.82


9
Turkish_Kayseri
14.94


10
Syrian
15.02


11
Greek_Thessaly
15.07


12
Lebanese_Druze
15.45


13
Albanian
15.76


14
Lebanese_Muslim
16.41


15
Turkish_Aydin
16.87


16
Kosovar
16.92


17
Jordanian
16.95


18
Italian_Tuscan
17.14


19
Palestinian
19.72


20
Armenian
20.08



Mixed Mode Population Sharing:



#

Primary Population (source)
Secondary Population (source)
Distance


1

69.4%
Ashkenazy_Jew
+
30.6%
Cypriot
@
2.29


2

71.3%
Italian_Sicilian
+
28.7%
Cypriot
@
2.45


3

79.6%
Italian_Sicilian
+
20.4%
Lebanese_Christian
@
2.49


4

83.9%
Ashkenazy_Jew
+
16.1%
Samaritan_Jew
@
2.56


5

80.6%
Italian_Sicilian
+
19.4%
Lebanese_Druze
@
2.58


6

78.7%
Ashkenazy_Jew
+
21.3%
Lebanese_Christian
@
2.6


7

85%
Italian_Sicilian
+
15%
Samaritan_Jew
@
2.62


8

81.8%
Italian_Sicilian
+
18.2%
Lebanese_Muslim
@
2.66


9

85%
Italian_Sicilian
+
15%
Assyrian
@
2.74


10

79.9%
Ashkenazy_Jew
+
20.1%
Lebanese_Druze
@
2.77


11

50.2%
Italian_Abruzzo
+
49.8%
Cypriot
@
2.78


12

80.8%
Italian_Sicilian
+
19.2%
Syrian
@
2.79


13

81.1%
Ashkenazy_Jew
+
18.9%
Lebanese_Muslim
@
2.85


14

71.6%
Lebanese_Christian
+
28.4%
French_Basque
@
2.86


15

85.2%
Italian_Sicilian
+
14.8%
Armenian
@
2.87


16

70.7%
Lebanese_Druze
+
29.3%
French_Basque
@
2.87


17

64.8%
Cypriot
+
35.2%
Italian_Tuscan
@
2.89


18

75.6%
Cypriot
+
24.4%
Spaniard
@
2.9


19

79.9%
Ashkenazy_Jew
+
20.1%
Syrian
@
2.92


20

89.4%
Sephardic_Jew
+
10.6%
Balkar
@
2.99

Angela
20-03-18, 22:38
If your algorithm is lousy, and your clusters are wrong it doesn't matter how many snps you use. The proof is in the pudding as we say. His calculators can't recognize a Tuscan accurately, or Jews, so they're crap for at least Italians and Jews.

Is this a joke? A calculator is good for Calabrians which doesn't have a southern Italian reference sample? Are you aware that if there's no Southern Italian or Calabrian reference sample, it can't come up in the prediction? Therefore we can't know if it captures Calabrians adequately or not? Get it?

I feel like Alice after she fell down the rabbit hole. :)

Could you telegraph that you're a t-roll any more clearly? You know I'm half quasi-Tuscan, and my husband is half Calabrian and so you present calculators that show we're both high in "Jewish" ancestry?

So what? Is that supposed to hurt my feelings? (That would be absolutely fine with both me and my husband if it were true, btw.) Go away and find something productive to do with your time other than t-rolling Italians you idiotic racist.

Keep going and you'll start getting infractions for posting provocative, disruptive material.

Blanco
20-03-18, 23:11
If your algorithm is lousy, and your clusters are wrong it doesn't matter how many snps you use. The proof is in the pudding as we say. His calculators can't recognize a Tuscan accurately, or Jews, so they're crap for at least Italians and Jews. It's true. However most users who tested Eurogenes K13-K15 got accurate results for the most part. Altough Eurogenes calulators were created for people of North-Central European ancestry, therefore it will be less accurate for Mediterranean populations. Still Eurogenes is better than Gedrosia, MDLP calculators. I do agree with you that Polako is often biased and Nordicist in many terms, given his Skadi past. I don't symphatize with him, but neither with the Nordicist ideas which try to throw any connections between Italians and Eastern Mediterranean population under the bus.
Could you telegraph that you're a t-roll any more clearly? You know I'm half quasi-Tuscan, and my husband is half Calabrian and so you present calculators that show we're both high in "Jewish" ancestry? I don't know you nor your heritage, and I don't know why it has anything to do with this topics. I just posted these results because I'm interested of it.:cool-v: I never claimed that Italians have Jewish ancestry I just said once in my post that due to shared Neolithic Mediterranean ancestry these populations can get similar results. There are no genetic Jews, but due to close intermarriages and with this being said most Ashkenazi Jews are closely related given by the bottleneck effect they're genetically a district, yet similar populations to those who carry high Anatolian Neolithic, Armenian EBA, Barchin Neolithic and other ancestral links high in Basal Eurasian with moderately to high Villaburra related ancestry.
So what? Is that supposed to hurt my feelings? (That would be absolutely fine with both me and my husband if it were true, btw.) Go away and find something productive to do with your time other than t-rolling Italians you idiotic racist. Italians are great people and in fact I think they're the most admired and envied people in the Western heisphere. I have friends from Italy and they're absolutely chill and good hard working people. Am I racist? how I can't be racist against my own akin, I just don't support the Eurocentric point of view which considers the Mesolithic-Paleothic rich Indo European populations more desirable than the Basal-Neolithic rich populations who brought farming and created the European civillizations. By the way the term Europe is also from the Near East via by Phoenicians. :smile:

AdeoF
21-03-18, 00:02
K15 is not that accurate it says that my first is Portuguese from the Single Population Sharing. Yeah by looking at it it's not very good it needs to be removed also it's not accurate for both northern Italians and Jews.

Pratt
21-03-18, 02:43
In the PCA the Tuscan kit goes close to the Spaniards, while Catanzaro is south of Southern Italian samples. Unusual results or bad calculator?

https://i.imgur.com/pk6W5zM.jpg

Angela
21-03-18, 14:11
Pratt;535908]In the PCA the Tuscan kit goes close to the Spaniards, while Catanzaro is south of Southern Italian samples. Unusual results or bad calculator?

What do you mean by unusual results? Do you mean unrepresentative samples?

Is the Catanzaro sample the one that Lazaridis said behaved strangely and might be an extremely drifted?

The HGDP samples are the ones chosen by Cavalli-Sforza aren't they?

Something is definitely wrong, however.

https://i.imgur.com/pk6W5zM.jpg[/QUOTE]

davef
21-03-18, 14:47
quadrant 1 is Celtic Germanic land, q2 is Iberian Sardinian north Italy land, q3 is East Med land, q4 is Slavic land

q5 is candy land

Blanco
21-03-18, 15:24
From Nicotera, Calabria: T227284



#
Population
Percent


1
East_Med
30.19


2
West_Asian
17.14


3
West_Med
16.4


4
Atlantic
15.66


5
Red_Sea
6.75


6
North_Sea
6.56


7
Baltic
3.78


8
Northeast_African
1.49


9
Eastern_Euro
1.44


10
South_Asian
0.59



Single Population Sharing:



#
Population (source)
Distance


1
South_Italian
4.1


2
East_Sicilian
5.58


3
Sephardic_Jewish
5.69


4
Central_Greek
6.33


5
Italian_Jewish
6.67


6
Italian_Abruzzo
7.25


7
West_Sicilian
7.71


8
Algerian_Jewish
8.13


9
Ashkenazi
8.32


10
Tunisian_Jewish
9.91


11
Greek
11.71


12
Cyprian
12.14


13
Tuscan
13.41


14
Libyan_Jewish
13.5


15
Greek_Thessaly
13.52


16
Lebanese_Muslim
15.09


17
Syrian
16.32


18
Turkish
16.36


19
Samaritan
18.89


20
Bulgarian
19.51



Mixed Mode Population Sharing:



#

Primary Population (source)
Secondary Population (source)
Distance


1

70.5%
Cyprian
+
29.5%
Spanish_Castilla_La_Mancha
@
2.89


2

63.7%
Lebanese_Muslim
+
36.3%
Spanish_Andalucia
@
2.91


3

75.4%
West_Sicilian
+
24.6%
Georgian_Jewish
@
2.91


4

76.9%
Cyprian
+
23.1%
French_Basque
@
2.99


5

74.2%
West_Sicilian
+
25.8%
Assyrian
@
3


6

64.2%
Italian_Abruzzo
+
35.8%
Cyprian
@
3.11


7

72.7%
Lebanese_Muslim
+
27.3%
French_Basque
@
3.14


8

68.8%
Cyprian
+
31.2%
Spanish_Andalucia
@
3.15


9

72%
Cyprian
+
28%
Spanish_Aragon
@
3.16


10

64.8%
South_Italian
+
35.2%
Sephardic_Jewish
@
3.2


11

54.3%
Kurdish_Jewish
+
45.7%
Spanish_Andalucia
@
3.21


12

58.1%
Sephardic_Jewish
+
41.9%
Italian_Abruzzo
@
3.21


13

67.1%
Lebanese_Muslim
+
32.9%
Spanish_Aragon
@
3.22


14

70.2%
Cyprian
+
29.8%
Spanish_Valencia
@
3.22


15

76.1%
West_Sicilian
+
23.9%
Armenian
@
3.22


16

70.4%
Cyprian
+
29.6%
Spanish_Castilla_Y_Leon
@
3.24


17

59.2%
Italian_Abruzzo
+
40.8%
Tunisian_Jewish
@
3.31


18

65.2%
Lebanese_Muslim
+
34.8%
Spanish_Valencia
@
3.32


19

75.8%
West_Sicilian
+
24.2%
Kurdish_Jewish
@
3.35


20

72.5%
Cyprian
+
27.5%
Spanish_Cantabria
@
3.37





From Carfizzi, Calabria



#
Population
Percent


1
East_Med
29.99


2
West_Med
18.27


3
Atlantic
12.61


4
North_Sea
11.65


5
West_Asian
9.27


6
Baltic
6.3


7
Red_Sea
4.98


8
Eastern_Euro
4.97


9
Northeast_African
1.15


10
Siberian
0.81



Single Population Sharing:



#
Population (source)
Distance


1
East_Sicilian
6.27


2
West_Sicilian
6.46


3
Ashkenazi
6.65


4
Central_Greek
6.7


5
South_Italian
7.08


6
Italian_Jewish
7.85


7
Italian_Abruzzo
8.06


8
Greek_Thessaly
8.87


9
Greek
9.15


10
Algerian_Jewish
9.18


11
Sephardic_Jewish
10.01


12
Tuscan
10.65


13
Tunisian_Jewish
13.46


14
Libyan_Jewish
13.61


15
Bulgarian
16.28


16
Cyprian
16.46


17
North_Italian
16.49


18
Romanian
18.18


19
Lebanese_Muslim
20.22


20
Serbian
20.61



Mixed Mode Population Sharing:



#

Primary Population (source)
Secondary Population (source)
Distance


1

83.3%
Italian_Jewish
+
16.7%
Ukrainian
@
3.69


2

51%
Greek_Thessaly
+
49%
Algerian_Jewish
@
3.75


3

53.8%
Italian_Jewish
+
46.2%
Greek_Thessaly
@
3.75


4

80.1%
Italian_Jewish
+
19.9%
Hungarian
@
3.82


5

74.8%
Italian_Jewish
+
25.2%
Serbian
@
3.86


6

79.3%
Italian_Jewish
+
20.7%
Moldavian
@
3.89


7

83.2%
Italian_Jewish
+
16.8%
Ukrainian_Lviv
@
3.9


8

85.9%
Italian_Jewish
+
14.1%
Estonian
@
3.91


9

83.5%
Italian_Jewish
+
16.5%
South_Polish
@
3.91


10

76.9%
Algerian_Jewish
+
23.1%
Hungarian
@
3.94


11

80.6%
Italian_Jewish
+
19.4%
Croatian
@
3.94


12

84.5%
Italian_Jewish
+
15.5%
Polish
@
3.95


13

85.3%
Italian_Jewish
+
14.7%
East_Finnish
@
4.02


14

71%
Algerian_Jewish
+
29%
Serbian
@
4.04


15

85.1%
Italian_Jewish
+
14.9%
Finnish
@
4.05


16

85.4%
Italian_Jewish
+
14.6%
Kargopol_Russian
@
4.1


17

85%
Italian_Jewish
+
15%
Southwest_Finnish
@
4.11


18

82.3%
Italian_Jewish
+
17.7%
East_German
@
4.12


19

85.5%
Italian_Jewish
+
14.5%
Estonian_Polish
@
4.13


20

82.5%
Algerian_Jewish
+
17.5%
North_Swedish
@
4.15




Both results on Eurogenes K15 PCA plot:

https://i.imgur.com/EZv4ppm.png

Angela
21-03-18, 15:48
Is this why my husband is so smart? You people traffic in stereotypes, so has that occurred to you? I'm sure you'd say that's why he's so successful in business too, yes? :)

My God, people, get a life.

Pratt
23-03-18, 01:31
What do you mean by unusual results? Do you mean unrepresentative samples?

Is the Catanzaro sample the one that Lazaridis said behaved strangely and might be an extremely drifted?

The HGDP samples are the ones chosen by Cavalli-Sforza aren't they?

Something is definitely wrong, however.

I meant that it shouldn't be there in a PCA, in that position. The PCA is better than the Oracle, the latter is more deceptive. The Oracle for the individual Tuscan HGDP chooses all Spaniards as the first population (and the Spaniards in a PCA are in a secluded position, certainly not at the center of a PCA) and even the Oracle chooses a super-isolated population like the Basques, so then the Oracle is forced to choose a second population much more to the south-east. Oracle in this way demonstrates all its frailty by failing to choose a more adequate population. And perhaps this is also due to the spreadsheet of the K15 not specifically to the software or to weird results. From the looks of it the individual Tuscan HGDP looks like a Sardinian-shifted North Italian, or even a Sardinian-shifted Tuscan.

Catanzaro is not an academic sample, according to Gedmatch she is a person from Decollatura, Catanzaro, Calabria, while HGDP are Stanford University's samples as I know.

To understand something more I did another Eurogenes K15 PCA with all the HGDP academic samples in it, both Bergamo and Tuscan HGDP, including the one posted above. And with some surprise, not only 5 individuals Tuscan HGDP have a shift towards Sardinia, but also 5 individuals of Bergamo HGDP have this shift, with all very high atlantic and north sea that is instead lowered, exactly like HGDP posted by OP, so it's a common problem that both these samples have. While the rest of HGDP samples plot where are supposed to be, with a more balanced ratio between north sea and atlantic.

I did a further test. I added to the PCA 10 people from Lombardy and 10 people from Tuscany, non academic samples, and none of these individuals shifts in this way and they all seem to plot correctly.

You're right. There is something definitely wrong. It could be something wrong with raw data of some of the HGDP samples. I suppose something went wrong in the process of converting from the academic format to a format suitable for uploading to gedmatch, probably low-coverage data. Or who knows, maybe it's something wrong with this calculator. We should see how the same samples behave in the other calculators.


https://i.imgur.com/Fsc5VV0.jpg

Angela
23-03-18, 01:57
I don't get why 5 Tuscan and 5 Bergamo academic samples would behave so strangely on a PCA. If something went wrong during the transfer to gedmatch wouldn't all the samples have been effected? Why only a portion of them?

I wonder if some of the samples uploaded to gedmatch are the actual HGDP samples? Is there any way to check?

As you say, it's either that, or the calculator is even more flawed than I suspected, or both.

As to Oracle, it's not that it's wrong, imo, it's that people don't know how to interpret it, or they choose to interpret it incorrectly for their own reasons. As you say, the algorithm tells you the "direction" perhaps, of where the gene flow is coming from. It's not saying that exact population was part of an admixture event that resulted in the subject population.

I was explaining this to people on 23andme six years ago, the same people, some of them, btw, some in the context of English results where they'd get a French percentage, for example, and think that meant actual French admixture in their family tree. . Either they're just remarkably stupid, or they just pretend not to understand.

Pratt
23-03-18, 02:18
I don't get why 5 Tuscan and 5 Bergamo academic samples would behave so strangely on a PCA. If something went wrong during the transfer to gedmatch wouldn't all the samples have been effected? Why only a portion of them?

I wonder if some of the samples uploaded to gedmatch are the actual HGDP samples? Is there any way to check?

As you say, it's either that, or the calculator is even more flawed than I suspected, or both.

The academic samples, especially in the past, are never released in a format compatible with Gedmatch, they need to be converted to a build 37 format. I think something may have gone wrong in this conversion process.

Hauteville
23-03-18, 12:30
Carfizzi is Arbereshe

Angela
23-03-18, 14:04
The academic samples, especially in the past, are never released in a format compatible with Gedmatch, they need to be converted to a build 37 format. I think something may have gone wrong in this conversion process.

I still find it a bit odd that only some of the samples were effected. Why not all?

Also, if this could happen with some of the Italian samples, it could happen with samples from other countries.

One more reason for me not to place too much confidence in gedmatch results.

davef
23-03-18, 14:17
Why didn't these conversion issues show up in other Southern European populations like the Greeks and Iberians who have a lot in common with Italians? Just curious

Pratt
23-03-18, 14:23
I still find it a bit odd that only some of the samples were effected. Why not all?

Also, if this could happen with some of the Italian samples, it could happen with samples from other countries.

One more reason for me not to place too much confidence in gedmatch results.


Of course it's odd.



Why didn't these conversion issues show up in other Southern European populations like the Greeks and Iberians who have a lot in common with Italians? Just curious


There are no Greeks and Iberians on HGDP to begin with.

Pax Augusta
23-03-18, 16:25
The HGDP samples are the ones chosen by Cavalli-Sforza aren't they?

I have no idea if these results are accurate and I don't trust so much Gedmatch, many calculators are full of bugs, but here is where the Tuscan HGDP is placed in the Tolan's tool. It does remind of the Etruscan who plotted with the Iberians.

Tuscan HGDP are from the south of Tuscany, just kidding, but not so much, its position supports a decidedly Neolithic origin of the Etruscans. :)

https://i.imgur.com/h1qipEM.jpg

Angela
23-03-18, 17:45
I have no idea if these results are accurate and I don't trust so much Gedmatch, many calculators are full of bugs, but here is where the Tuscan HGDP is placed in the Tolan's tool. It does remind of the Etruscan who plotted with the Iberians.

Tuscan HGDP are from the south of Tuscany, just kidding, but not so much, its position supports a decidedly Neolithic origin of the Etruscans. :)

https://i.imgur.com/h1qipEM.jpg

If the "Tuscan" sample here is the sample from around Firenze, odd that HGDP Tuscans from further south geographically are slightly north and west of them toward the Iberians genetically.

As to Pratt's point maybe what we're seeing with the HGDP samples is internal diversity? Is that possible?

Anyway, in this paper the authors see no difference between the HGDP and HapMap Tuscan samples, so I don't know what the heck is going on.

See:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/

Pax Augusta
24-03-18, 04:19
If the "Tuscan" sample here is the sample from around Firenze, odd that HGDP Tuscans from further south geographically are slightly north and west of them toward the Iberians genetically.

We do not know which sample was used to calculate this average, whether HGDP, TSI or the mix of both.



As to Pratt's point maybe what we're seeing with the HGDP samples is internal diversity? Is that possible?

Maybe yes.



Anyway, in this paper the authors see no difference between the HGDP and HapMap Tuscan samples, so I don't know what the heck is going on.

See:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506643/


That paper says that North Italians from Bergamo are similar to Tuscans (Bergamo HGDP samples are labeled as Italians in this paper) and it's difficult to distinguish between the two populations. And if it's difficult to distinguish between Bergamo and Tuscan samples, it would be also more difficult to distinguish between Tuscan HGDP and the Tuscan from the HapMap (TSI).



Italians are similar to Tuscans (both TSI/HapMap and Tuscans/HGDP) and it is difficult to distinguish between the two populations, with individuals showing high AMids for Italian, Sardinian and Tuscan. The third Italian population, from the isle of Sardinian, is clearly distinguishable and much more homogeneous.(...) Of the three Italian populations, the Sardinians show differences in many AMids from Italians and Tuscan, which are closer to one another. The Tuscan from the HGDP are indistinguishable from the Tuscan from the HapMap (TSI).