GEDMatch HarappaWorld Gedmatch, post and compare your admixtures to ancient and contemporary.

Interesting that the Mycenaeans plot so differently here (and on other amateur calcs) compared to the Lazaridis PCA. Also of note is how much more southerly they are compared to Sicilians and south Italians here, whereas in the Lazaridis plot they're very close. Any reason for such contrast?

PCAs aren't calibrated at cardinal points. They are not made to see who is more north or who is more south, which is irrelevant. A PCA, a statistical procedure, is based on components. These components influence the position of the various samples in a PCA, and the samples in turn affect each other, and every calculator is different from the other. Lazaridis uses more sophisticated tools, while ancient samples on gedmatch are often of low quality or of variable quality. Always check how many SNPs are used in the calculator's evaluation. Ancient samples less and less than any modern sample. Anyway Mycenaeans are not much more southerly compared to Sicilians and south Italians in this PCA, Mycenaeans are simply more Neolithic-shifted (Greece-Neolithic or Sardinian-shifted), and the position of the Sardinians, which are a genetically isolated population, still varies greatly from admixture calculator to admixture calculator.


@Pratt,
I read somewhere that only one of the Mycenaean samples is of really good quality. Do you happen to know which one it was?


Likely I9041? Based on gedmatch SNPs all the Mycenaeans seem to be of lower quality than Minoans. But I could be wrong.


Pratt, i was also surprised at the variation. The only two Mycenaeans that group tightly are great friends with the South Italians. As for the one far to the left near the neolithic groups...why is it plotting so far out? I'm beginning to question whether he/she's an actual mycenaean and not just a foreign visitor. I know they are mostly Anatolian, but that one plots too far from the rest.

Were the Mycenaens this diverse?

You mean Mycenaean I9010? Because it has greater percentage of Mediterranean/EEF.

I would be dishonest if I tell you I know the reason. In forums there are already too many users who have the answers, often wrong, and never ask the right questions.

Trying to find a common sense answer it may be that the ancient samples, already from the start lower in quality than the modern ones, in the process of converting to gedmatch uploadable formats, may lose even more quality. On gedmatch all these samples tend to have very few components, and this could distort their position in a PCA as well. Especially with the oldest samples, many SNPs had not yet formed, and on gedmatch all these samples have less SNPs evaluated than modern samples.

Another common sense explanation it may be that the ancient samples are different because they have always been so: southern Europe has already been inhabited and the process of assimilation of new migrants (Yamnaya-like or Caucasian-like or whatever) has never been homogeneous, because that is how it happens also in real life. Someone blends with newcomers first and more than others. Others, on the other hand, mingle less, but then, culturally, are assimilated by the dominant culture imposed by new migrants. For a whole picture we need more ancient samples.
 
Lets use average Mycenaean. The last, far right numbers.

PCA with the average Mycenaean.

PCA_Minoans_and_Mycenaeans_average.jpg



Can we add Natufian. I have a feeling that Minoans are on a cline exactly between Greek Neolithic and Natufians. If it is true, it would mean that Minoans had nothing to do with Anatolian Chalcolithic/BA, but could be a product of Natufian Neolithic 1/3 and mixed with Later Greek Neolithic 2/3. Though 2/3 Anatolian EN and 1/3 Jordan Neolithic fits the bill too. Anyway, they really look like a mixture of EN populations.

Have you Natufian results?

Is there a lot of work to flip the first PCA left-right, so the samples will agree geographically with typical PCA charts that we are used to? Will be less confusing for inexperienced peole.

I can try, but I think it's not possible with the kind of software I'm using.
 
Have you Natufian results?

M041601 Merged
Natufian
Run time 6.39
S-Indian -
Baloch -
Caucasian 13.98
NE-Euro -
SE-Asian -
Siberian -
NE-Asian -
Papuan 0.68
American -
Beringian -
Mediterranean 27.39
SW-Asian 53.62
San -
E-African 4.33
Pygmy -
W-African -

And Levant Neolithic

M115616I0867
Levant Neolithic
Run time9.93
S-Indian-
Baloch-
Caucasian25.97
NE-Euro-
SE-Asian0.07
Siberian-
NE-Asian0.06
Papuan-
American-
Beringian-
Mediterranean32.53
SW-Asian39.86
San-
E-African1.52
Pygmy-
W-African-

I can try, but I think it's not possible with the kind of software I'm using.
How about flipping values (negative/positive) on just Component 1 axis? By the way, what kind of software is this?
 
PCA with the average Mycenaean.

PCA_Minoans_and_Mycenaeans_average.jpg





Have you Natufian results?



I can try, but I think it's not possible with the kind of software I'm using.

he is a natufian

Kit Num: M632231
Threshold of components set to 1.000
Threshold of method set to 0.25%
Personal data has been read. 20 approximations mode.
Gedmatch.Com
HarappaWorld 4-Ancestors Oracle
This program is based on 4-Ancestors Oracle Version 0.96 by Alexandr Burnashev.
Questions about results should be sent to him at: [email protected]
Original concept proposed by Sergey Kozlov.
Many thanks to Alexandr for helping us get this web version developed.

23 April 2013 - Oracle reference population percentages revised.

Admix Results (sorted):

# Population Percent
1 SW-Asian 34.60
2 Mediterranean 34.48
3 Caucasian 27.79
4 NE-Euro 2.52
 
he is a natufian

Kit Num: M632231
Threshold of components set to 1.000
Threshold of method set to 0.25%
Personal data has been read. 20 approximations mode.
Gedmatch.Com
HarappaWorld 4-Ancestors Oracle
This program is based on 4-Ancestors Oracle Version 0.96 by Alexandr Burnashev.
Questions about results should be sent to him at: [email protected]
Original concept proposed by Sergey Kozlov.
Many thanks to Alexandr for helping us get this web version developed.

23 April 2013 - Oracle reference population percentages revised.

Admix Results (sorted):

# Population Percent
1 SW-Asian 34.60
2 Mediterranean 34.48
3 Caucasian 27.79
4 NE-Euro 2.52
He is Levant/Jordan Neolithic, not real Natufian from Israel or Palestine area. Also this sample is 2,000 years younger than Natufian Culture. But thanks for helping. :)
 
He is Levant/Jordan Neolithic, not real Natufian from Israel or Palestine area. Also this sample is 2,000 years younger than Natufian Culture. But thanks for helping. :)
what age are you looking for ................the age of this sample is 9573 ± 39ybp which equals 1950AD missus 9573 gives ..........
granted , it is stated/assumed he was from north-east anatolia
 
I added Mycenaean, the averaged sample and matadwarf.
Mat fits in Peloponnese and Greece mainland in general very well. Mycenaean is closest to Greek East Islander but is missing a bit of Steppe and even more Levant component SW Asian. It also has way more Med left from Neolithic farmers.

Greeks# of samplesS-IndianBalochCaucasianNE-EuroSE-AsianSiberianNE-AsianPapuanAmericanBeringianMediterraneanSW-AsianSanE-AfricanPygmyW-African
Greece, mainland150831250000002690000
Greece, Macedonia50831250000002590000
Greece, Peloponnese50931240000002690000
matadworf108292500000127100000
Other mainland50730260000002690000
Greece, Ionian209341800000026120000
MycenaeansAverage0239130000003690000
Greek, Islands, East1309381500000023140000
Greek, island and mainland average08342000000024110000
Cyprus411044610000020170000
 
Last edited:
Here is matadwarf among other Peloponnese samples:

Greece, PeloponnesePopulationS-IndianBalochCaucasianNE-EuroSE-AsianSiberianNE-AsianPapuanAmericanBeringianMediterraneanSW-AsianSanE-AfricanPygmyW-African
1Peloponnese 0.06 8.61 34.61 19.84 0.87 0.28 0.48 0.29 24.07 10.59 0.28
2Peloponnese 8.46 27.25 24.97 - 0.93 0.21 0.40 28.67 9.10
3Peloponnese 7.60 32.93 24.56 0.15 0.78 0.49 25.20 8.03 0.27
4Peloponnese 9.62 28.79 25.05 1.31 0.17 0.36 23.63 11.02
5Peloponnese 9.12 30.48 24.60 0.36 26.44 8.60 0.16 0.25
6matadworf 7.62 29.17 25.27 0.13 0.84 27.28 9.65 0.05
Greece, Peloponnese60931240000002690000
 
Peleponese number 1 seems more islander like. Didn't get as much slavic or steppe admixture i suppose.
 
Thanks for the comparison. BTW three grandparents are from Messinia, one from the Arcadian/Laconian border NE of Sparta (city).
 
Peleponese number 1 seems more islander like. Didn't get as much slavic or steppe admixture i suppose.
Yes people move around and one can spot outlier everywhere, but surprisingly Greece mainland is very uniform, together with Tosk Albanians. Modern greek movements from Turkey or islands or elsewhere didn't register much of effect, or the effect could have been evenly distributed.
 
Thanks for the comparison. BTW three grandparents are from Messinia, one from the Arcadian/Laconian border NE of Sparta (city).
You are welcome. I added location to your name in my database.
 
Harappaworld does not seem to be able to distinguish Minoans from Levant_N and Natufian_merged. Yet, they are not exactly the same. Interesting then how the Bronze Age of the Levant is different from the Neolithic era and more like the modern Levant.




GRK5hMm.jpg
 
My results here:

# Population Percent
1 NE-Euro 44.54
2 Mediterranean 24.98
3 Caucasian 17.06
4 Baloch 7.05
5 SW-Asian 3.93
6 NE-Asian 1.53
 
My results here:

# Population Percent
1 NE-Euro 44.54
2 Mediterranean 24.98
3 Caucasian 17.06
4 Baloch 7.05
5 SW-Asian 3.93
6 NE-Asian 1.53

Thanks for sharing.

How many ethnic groups do you belong?

Ethnic group Bosniak, Serb, Croat, Czech, German
 
Harappaworld does not seem to be able to distinguish Minoans from Levant_N and Natufian_merged. Yet, they are not exactly the same. Interesting then how the Bronze Age of the Levant is different from the Neolithic era and more like the modern Levant.

I think you flipped them on both axes, can you flip them only on component 2 axis. If imposible, leave them the way they were.




They are so different they should not plot that close. Could you check the numbers again please.

M041601 MergedAverage
NatufianGreeceMinoan
Run time 6.39Total run time 11.63
S-Indian -S-Indian -
Baloch -Baloch -
Caucasian 13.98Caucasian 47.12
NE-Euro -NE-Euro 1.33
SE-Asian -SE-Asian -
Siberian -Siberian -
NE-Asian -NE-Asian -
Papuan 0.68Papuan -
American -American -
Beringian -Beringian -
Mediterranean 27.39Mediterranean 38.91
SW-Asian 53.62SW-Asian 12.66
San -San -
E-African 4.33E-African -
Pygmy -Pygmy -
W-African -W-African -
 
Thanks for sharing.

How many ethnic groups do you belong?

Ethnic group Bosniak, Serb, Croat, Czech, German

No problem.

My dad was fully Bosniak, as far as I know, so 50% there. My mom is more mixed, primarily Croat (Bosnian and Croatian) and Serb (Bosnian and Serbian) in different proportions, and more distantly my great-great grandfather was Bavarian German, and another one was most likely Czech or Polish (we haven't been able to confirm either way 100%).
 
No problem.

My dad was fully Bosniak, as far as I know, so 50% there. My mom is more mixed, primarily Croat (Bosnian and Croatian) and Serb (Bosnian and Serbian) in different proportions, and more distantly my great-great grandfather was Bavarian German, and another one was most likely Czech or Polish (we haven't been able to confirm either way 100%).
You are almost indistinguishable from Chroats. Your 1.53% of NE Asian is peculiar though. Usually in Balkans it is found in sub 1%. Could be Turkish in origin, Bulgar or Hun. I have it too, but in Poland it is more likely of Tatar and Mongolian origin.

Europeans# of samplesS-IndianBalochCaucasianNE-EuroSE-AsianSiberianNE-AsianPapuanAmericanBeringianMediterraneanSW-AsianSanE-AfricanPygmyW-African
Saami4130591183124500003
Finland6143710610011130000
Latvia5177650100001900000
Lithuania5187620001012010000
RussiaHarappa1413640300111300000
BelorussiaHarappa1510641100001610000
UkraineHarappa1612580100001720000
PolandLeBrok1710571100002210000
Czechy3199520000102620000
Slovenia30715500100002430000
Croatia80717450100002440000
Bosnian Boss 0717450020002540000
Bosnia20921410100102350000
Serbia10820400100102740000
Austria20715431000003040000
Hungary30915470100102520000
Romania50823351100002560000
Bulgaria50925340000002470000
Macedoniaselectivememri0625350100012570000
Albania170628290000002780000
Albania, Tosk70730250000002790000
Greece, Mainland50730260000002690000
Greece, Ionian209341800000026120000
Greek, Islands, East1309381500000023140000
Crete508391500100021140000
Cyprus411044610000020170000
Europeans# of samplesS-IndianBalochCaucasianNE-EuroSE-AsianSiberianNE-AsianPapuanAmericanBeringianMediterraneanSW-AsianSanE-AfricanPygmyW-African
Ashkenazi1107331600000025150100
Sephardi, Tunisia61733800000024220301
Turkey411544110430011190000
Armenia712052300000010130000
Georgia6021587010000560000
Lebanon701145200000015240100
Samaritans30745000000015310200
PalestineHarappa1739100000012310502
IranHarappa4274051211015130000
 
Thanks! Not to worry, I wasn't taking it literally. Is d stats just some glorified oracle that bases it's predictions on results from a gedmatch calculator?

Those predictions you see on anthrogenica are mostly nMonte based on Global 10. nMonte is a R script that runs a Monte Carlo simulation, it does not analyze the genome, it's Statistics and Probability. nMonte is extremely malleable but its results are also very manipulable.

https://en.wikipedia.org/wiki/Monte_Carlo_method

You can play a lot with
nMonte.

I’ve used Mycenaean average as a fixed population reference, and from time to time I added a single modern ethnicity. 3 for Eastern Europe (Bulgaria, Romania, Poland), 3 for Western Europe (French_East, England_Kent, Irish), 1 for Northern Europe (Swedish). All the averages are from Global 10.

These are the results for Greeks, Italian_Tuscan, Italian_Bergamo, and Italian_South. Greeks (Greek average) on Global 10 and Basal 7 are Northern Greeks from Greek Macedonia.

Unfortunately there aren't other Greek samples (neither mainlanders nor islanders) on Gobal 10 except the current sample from Thessaloniki.


Eastern Europe


A) Mycenaean + Bulgarian


1- Greek:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Bulgarian
0.01895134 0.01912255


[1] "distance%=0.2851 / distance=0.002851"

Greek

Mycenaean 50.2
Bulgarian 49.8


2- Italian_Tuscan:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Bulgarian Mycenaean
0.01752737 0.02128371

[1]"distance%=0.4699 / distance=0.004699"


Italian_Tuscan

Bulgarian 55.1
Mycenaean 44.9


3- Italian_Bergamo:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Bulgarian Mycenaean
0.01275418 0.03002748


[1] "distance%=0.903 / distance=0.00903"


Italian_Bergamo

Bulgarian 76.0
Mycenaean 23.9


4-Italian_South:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Bulgarian
0.01165325 0.03379267


[1] "distance%=1.0296 / distance=0.010296"


Italian_South

Mycenaean 85.5
Bulgarian 14.5


5 - Italian_CentralSicilian:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Bulgarian

[1] "distance%=0.8053 / distance=0.008053"

Italian_CentralSicilian

Mycenaean 84.5
Bulgarian 15.4



B) Mycenaean + Romanian


1- Greek:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Romanian Mycenaean
0.01888201 0.01895134

[1] "distance%=0.2883 / distance=0.002883"

Greek

Romanian 50.1
Mycenaean 49.9



2- Italian_Tuscan:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Romanian Mycenaean
0.01682399 0.02128371

[1] "distance%=0.3651 / distance=0.003651"


Italian_Tuscan

Romanian 56.1
Mycenaean 43.9


3- Italian_Bergamo:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Romanian Mycenaean
0.01198668 0.03002748

[1] "distance%=0.8391 / distance=0.008391"

Italian_Bergamo

Romanian 77.1
Mycenaean 22.9


4- Italian_South:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Romanian
0.01165325 0.03310893


[1] "distance%=1.0077 / distance=0.010077"

Italian_South

Mycenaean 84.3
Romanian 15.7


5- Italian_CentralSicilian:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Romanian
0.009930509 0.032354286


[1] "distance%=0.79 / distance=0.0079"

Italian_CentralSicilian

Mycenaean 83.9
Romanian 16.1



C) Mycenaean + Polish


1- Greek:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Polish
0.01895134 0.04971803


1] "distance%=0.5474 / distance=0.005474"

Greek

Mycenaean 73.2
Polish 26.9


2- Italian_Tuscan:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Polish
0.02128371 0.04745861


[1] "distance%=0.5853 / distance=0.005853"


Italian_Tuscan

Mycenaean 69.7
Polish 30.3



3- Italian_Bergamo:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Polish
0.03002748 0.03876120


[1] "distance%=0.6419 / distance=0.006419"


Italian_Bergamo

Mycenaean 56.6
Polish 43.4


4- Italian_South:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Polish
0.01165325 0.06411999


[1] "distance%=1.0808 / distance=0.010808"


Italian_South

Mycenaean 93.55
Polish 6.45


5- Italian_CentralSicilian:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Polish
0.009930509 0.063157290


[1] "distance%=0.8587 / distance=0.008587"


Italian_CentralSicilian

Mycenaean 92.6
Polish 7.4


Western Europe


D) Mycenaean + French_East


1- Greek:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean French_East
0.01895134 0.02993343


[1] "distance%=0.666 / distance=0.00666"


Greek

Mycenaean 62.2
French_East 37.8


2- Italian_Tuscan:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean French_East
0.02128371 0.02748697


[1] "distance%=0.6585 / distance=0.006585"


Italian_Tuscan

Mycenaean 56.9
French_East 43.1


3- Italian_Bergamo:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
French_East Mycenaean
0.01815305 0.03002748


[1] "distance%=0.5284 / distance=0.005284"


Italian_Bergamo

French_East 63
Mycenaean 37


4-Italian_South:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean French_East
0.01165325 0.04431207


[1] "distance%=1.095 / distance=0.01095"


Italian_South

Mycenaean 91.5
French_East 8.5



5 - Italian_CentralSicilian:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean French_East
0.009930509 0.043130787


[1] "distance%=0.8752 / distance=0.008752"


Italian_CentralSicilian

Mycenaean 90
French_East 10



E) Mycenaean + England_Kent


1- Greek:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean English_Kent
0.01895134 0.03793397


[1] "distance%=0.5471 / distance=0.005471"


Greek

Mycenaean 67.4
English_Kent 32.6


2- Italian_Tuscan:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean English_Kent
0.02128371 0.03576606


[1] "distance%=0.5996 / distance=0.005996"


Italian_Tuscan

Mycenaean 63.3
English_Kent 36.7


3- Italian_Bergamo:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
English_Kent Mycenaean
0.02716300 0.03002748


[1] "distance%=0.6516 / distance=0.006516"


Italian_Bergamo

English_Kent 52.6
Mycenaean 47.4


4-Italian_South:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean English_Kent
0.01165325 0.05255509


[1] "distance%=1.0847 / distance=0.010847"


Italian_South

Mycenaean 92.35
English_Kent 7.65


5 - Italian_CentralSicilian:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean English_Kent
0.009930509 0.051521945


[1] "distance%=0.8643 / distance=0.008643"


Italian_CentralSicilian

Mycenaean 91.2
English_Kent 8.8


F)
Mycenaean + Irish


1- Greek:average[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Irish
0.01895134 0.04114518

[1] "distance%=0.4333 / distance=0.004333"


Greek

Mycenaean 68.9
Irish 31.1


2- Italian_Tuscan:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Irish
0.02128371 0.03905056


[1] "distance%=0.5137 / distance=0.005137"


Italian_Tuscan

Mycenaean 65.2
Irish 34.8


3- Italian_Bergamo:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Irish
0.03002748 0.03097496


[1] "distance%=0.7017 / distance=0.007017"


Italian_Bergamo

Mycenaean 50.8
Irish 49.2


4-Italian_South:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Irish
0.01165325 0.05559131


[1] "distance%=1.062 / distance=0.01062"


Italian_South

Mycenaean 91.9
Irish 8.1



5 - Italian_CentralSicilian:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Irish
0.009930509 0.054719330


[1] "distance%=0.8401 / distance=0.008401"


Italian_CentralSicilian

Mycenaean 91.1
Irish 8.9



Northern Europe


G) Mycenaean + Swedish


1- Greek:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Swedish
0.01895134 0.04555579


[1] "distance%=0.5702 / distance=0.005702"


Greek

Mycenaean 71.5
Swedish 28.6


2- Italian_Tuscan:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Swedish
0.02128371 0.04307875


[1] "distance%=0.554 / distance=0.00554"


Italian_Tuscan

Mycenaean 67.5
Swedish 32.5


3- Italian_Bergamo:average


[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Swedish
0.03002748 0.03426947


[1] "distance%=0.5707 / distance=0.005707"


Italian_Bergamo

Mycenaean 53.4
Swedish 46.6


4-Italian_South:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Swedish
0.01165325 0.05958714


[1] "distance%=1.0685 / distance=0.010685"


Italian_South

Mycenaean 92.65
Swedish 7.35


5 - Italian_CentralSicilian:average

[1] "1. CLOSEST SINGLE ITEM DISTANCES"
Mycenaean Swedish
0.009930509 0.058629904


[1] "distance%=0.8429 / distance=0.008429"


Italian_CentralSicilian

Mycenaean 91.7
Swedish 8.3
 
Very interesting Pratt, thanks!
 

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