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Greekscholar
09-22-2019, 09:46 PM
So, after a couple of months of posting a little, and reading a lot, I want to try my hand at some modeling. I want to thank everyone who participates in modeling and discussions of models, and a special thanks to Agamemnon and Michalis, as this model is based mostly on their previous examples.

Tools used: VahaduoJS 19.08, Global_25_PCA_pop_averages_scaled, my own scaled G25 coordinates

Purpose: Continuum populations look very similar on many PCAs, including early Eurogene calculators like K15. The purpose of this model is to give the software specific choices of possible ancestry (like Slav vs. Celt, or Levant vs. North Africa) to find the differences between these populations. Fit does matter, but since there are many target populations, the "average fit" for the matrix was what I am looking at during the first run. This model is not specific to any one of these populations. Again, I am trying to look at the continuum populations as a whole.

Source Samples - I tried to use Metal Age samples, Bronze Age if possible. As you will see I didn't entirely succeed at this, I will try to explain why.

GRC_Mycenaean and Iberia_Northeast_Empuries2 - Following the examples of Aga and Michalis, I used two ancient Greek samples to try and capture the early Greek diversity on both sides of the Aegean Sea. Trying to use only one of the two drastically decreases fit, so both are being use. Also considered: Anatolia_Isparta_EBA. This samples worked well too, but fit was slightly better for Empuries_2

CZE_Early_Slav - Seemingly the standard model choice for the Slavic Migrations.

ARM_LBA - Following Aga again on this one. This sample only appears in small percents, but greatly helps fit. I assume it accounts for any extra Caucasus like ancestry.

ITA_Collegno_MA - I wanted something metal age out of Italy that was unlikely to have too much Continuum-like ancestry. In this model, it is offered as a "choice" to CZE_Early_Slav to account for Steepe like ancestry. Also considered: Any of the Bell Beaker populations. In the end, I went with this one because it is specific to Italy.

Levant_Canaanite_MBA - I found picking the right Levant population difficult. In the end, this one seems to overlap the Greek samples less than Levant_LBN_Roman in this model, so it was chosen. Also considered: Levant_LBN_Roman - this produced nearly identical fits. I thought of adding both, but I feared the "overfit" if this sample eats into to the Greek and other Levant samples.

Canary_Islands_Guanche - After reading other conversations, I thought a North African population was needed for both fit and historical purposes. I hope this is an ancient sample.....pretty sure it is, but I could be wrong. Also considered: EGY_Late_Period and EGY_Hellenistic - These were really fun to use, and created good fits, but in the end didn't seem like realistic options based on history. The Egyptian samples cut into the Levant amounts by alot and the Sicilian and Jewish target populations all ended up with 10-21%, which I didn't think was as accurate as the 3-8% range the Canary Island sample produced.

Target Samples -

Greeks - Cypriot, Greek_Crete, GreekScholar_scaled, - Not much choice here. I picked the two Greek populations from the islands, and included myself as a third sample. My ancestry is from the NE_Aegean islands, mostly Fourni.
Italians - Italian_Abruzzo, East_Sicily, West_Sicily - I picked Abruzzo as the counter to Cypriot, more or less the 'western' and 'eastern' ends of the Continuum populations. I went with both Sicily samples because they are frequent conversation topics here, and I have experience charting them on the K15 PCA.
Jewish- Ashkenazi_Jew, Italian_Jew, Romaniote_Jew - Ashkenazi is another much talked about population, lots of models produced and discussed. I thought picking Italian and Greek Jews would be interesting as well since you can compare them both to the Ashkenazi sample, and their gentile neighbors in Italy and Greece.

So, this is my first model, and I am sure I messed lots of stuff up. Please give me any feedback you have about any of it, the sources, the purpose, the targets, etc. I can also use these same source populations for other target populations as well. Just let me know what you want to see ��

Conclusions: Well, I don't want to form any until I get some feedback on the model. I would say the ITA_Collengo_MA vs. CZE_Early_Slave results are interesting.

https://imgur.com/RpMyAdb.jpg

Greekscholar
09-23-2019, 02:44 AM
Whoops. I think ITA_Collegno_MA is "Middle Ages" not "Metal Age." I swapped it out for Bell_Beaker_ITA. Fit improves, but Greek sources crash hard for non-Greek target populations, seemingly replaced by ARM_LBA. This is probably wrong, isn't it?


https://imgur.com/I0bYQsy.jpg

Sikeliot
09-23-2019, 03:07 AM
It is interesting how even though all of these populations roughly plot together, when you break down their components they are really quite different.

You are significantly more Slavic than the Cretan sample. I think this is because North Aegean islanders may have received more migration from the mainland than what you see in Crete. Therefore I would imagine a northern mainland Greek sample would have Slavic approaching 40%, because they should be more Slavic than the islands. But even still, the Slavic input is one of the factors differentiating even Crete from the South Italians. The other being an Italic-like component captured by the Collegno sample that is not present in Crete.

For clarity to those who haven't read my previous posts... West Sicily is Trapani, East Sicily is Ragusa, both being academic samples. Neither sample, nor the Abruzzese, come up with any significant Slavic signal.

Trapani is probably the least Hellenized part of South Italy, and second to Malta is the area with the next highest North African. It's interesting that both Sicilian samples have roughly equal Levantine, but the West sample has higher North African, which suggests to me that these migrations likely did not happen at the same time.. and if you add up Levant + North African, it'll almost always come out highest in western Sicily.

Cyprus is, far and away, more Levantine than any of the other Continuum samples which is why they are transitional. You can say that Sicilians, Cretans, Western Jews still plot as "European" even if on the edge of that cluster but Cypriots are transition.

On the note of why the West Sicily sample is so different, see this from the Crete study. All of the Sicilian samples -- Palermo, Ragusa, Catania, Agrigento -- plot right with Crete while the Trapanese deviate, and I believe this is because they are significantly less ancient Aegean.

This is a direct quote from the study's Supplementary Information that I think is consistent with what you found.


PCA plot for Cretans and Sicily. There is an overlap between most of the Sicilians with the Cretan samples. With the exception of two samples from Trapani, the Sicilians seem to be in the same cluster as the Cretans.

https://i.imgur.com/KBe1o3m.png




Whoops. I think ITA_Collegno_MA is "Middle Ages" not "Metal Age." I swapped it out for Bell_Beaker_ITA. Fit improves, but Greek sources crash hard for non-Greek target populations, seemingly replaced by ARM_LBA. This is probably wrong, isn't it?


https://imgur.com/I0bYQsy.jpg


Ok now you are getting what I did -- Trapani as a mixture of Levantine, Berber, Italic, and North European with almost no Greek. But you still need Greek for the other two south Italian samples.

And you also found Ashkenazim not to have much Greek-like admixture, and to be more Italic. This is what I found too!

Censored
09-23-2019, 03:18 AM
Some of the components are already quite similar to one another, that allows some populations to cluster next to one another despite getting drastically different amounts of one component or another.

Greekscholar
09-23-2019, 03:26 AM
Thanks for the analysis. I think you hit on the big point this model shows, Jewish people and Italians both show at least some North African and some version of Bell Beaker-like Steppe ancestry. The Greek samples do not, they have Slavic and Levantine instead. I will duplicate the source populations and some some new target populations, including Mainland Greece tomorrow. I had Mainland Greece in my pilot runs, but I tried to keep this first role out to 9 targets.....which is already a lot to digest.

Anybody have any guess on why the Bell Beaker inclusion pushed some of much of the Mycenaean amount towards Armenia? The fit may be closer, but I am not sure that model is a reflection of history.

Sikeliot
09-23-2019, 03:26 AM
Out of curiosity can you show me what it looks like when you include both Egypt and Levant but exclude Guanche?

Sikeliot
09-23-2019, 03:29 AM
Thanks for the analysis. I think you hit on the big point this model shows, Jewish people and Italians both show at least some North African and some version of Bell Beaker-like Steppe ancestry. The Greek samples do not, they have Slavic and Levantine instead. I will duplicate the source populations and some some new target populations, including Mainland Greece tomorrow. I had Mainland Greece in my pilot runs, but I tried to keep this first role out to 9 targets.....which is already a lot to digest.

Anybody have any guess on why the Bell Beaker inclusion pushed some of much of the Mycenaean amount towards Armenia? The fit may be closer, but I am not sure that model is a reflection of history.

All of the Continuum populations show Levantine admixture (I think this will fall sharply for mainland Greeks), the difference seems to be Slavic versus Italic, and the lack of North African in the Greeks.

The inclusion of Bell Beaker has the sharpest impact on the Trapanese and Ashkenazim, who end up losing their Mycenaean in favor of Armenian/Caucasian, which I noticed the exact same thing when I tried modeling them. This suggests to me that both groups have very little Greek ancestry, but did acquire Anatolian or Caucasian admixture from a different migration -- maybe Elymians for Trapani, and the migration of Jews into Anatolia for Ashkenazim.

Greekscholar
09-23-2019, 03:33 AM
Some of the components are already quite similar to one another, that allows some populations to cluster next to one another despite getting drastically different amounts of one component or another.

Yes, some of that is on purpose to try and force the software to make a choice (Slav vs. Bell Beaker?) (Levant vs. North Africa?) The two ancient Greek samples are an attempt to "capture" as much ancient Greek ancestry as possible, so I am adding both together rather than viewing the results as one or the other. Including both really reduces distance though.......probably the dreaded "overfit" I read so much about. :)

Any suggestions on how to improve the model? This is my first one.

Greekscholar
09-23-2019, 03:35 AM
Out of curiosity can you show me what it looks like when you include both Egypt and Levant but exclude Guanche?

You bet, both Egyptian samples (Late and Hellenistic) take a big chunk out of the Levant totals, which is ultimately why I went with Guanche instead.

Sikeliot
09-23-2019, 03:39 AM
You bet, both Egyptian samples (Late and Hellenistic) take a big chunk out of the Levant totals, which is ultimately why I went with Guanche instead.

I actually believe the primary source of North African admixture into Sicily is from Egypt and Tunisia, and therefore using Egypt is probably more historically accurate for them than using Guanches. Most far NW African migration into Europe went into Iberia instead. While Sicilian Arabic/Maltese is a Maghrebi dialect, it is possible more actual migration occurred from Egypt.

I wonder if forced to choose between Egypt and Levant, if Sicilians and Jews will lose more of their Levantine to Egyptian than Greek islanders would. I genuinely believe there was very, very little North African input into Greece.

What did you think of the PCA plot from the Crete study? Do you think it explains what we see in your models at least partially?

Censored
09-23-2019, 03:48 AM
Yes, some of that is on purpose to try and force the software to make a choice (Slav vs. Bell Beaker?) (Levant vs. North Africa?) The two ancient Greek samples are an attempt to "capture" as much ancient Greek ancestry as possible, so I am adding both together rather than viewing the results as one or the other. Including both really reduces distance though.......probably the dreaded "overfit" I read so much about. :)

Any suggestions on how to improve the model? This is my first one.

No it appears to be a good model and the results are consistent with what one would expect. I was just explaining to the other user why those populations seem similar on a plot despite having different origins. Greek Mycenean and Iberia NE are similar to one another.

Greekscholar
09-23-2019, 11:17 PM
Alright. Guanche swapped out for Egypt Late Period and Egypt Hellenistic. As you will see, both cut significantly into the Levant amount.......except in the Greek samples.

https://imgur.com/1cRryz9.jpeg



https://imgur.com/hcNF48K.jpeg

Greekscholar
09-23-2019, 11:36 PM
Here are Mainland Greece, and near by populations. Fit isn't bad considering the source samples were not chosen specifically for this group. Much more Slavic, and ancient Greek populations, less Levant and ARM_LBA.

https://imgur.com/bVS3VzH.jpeg

Sikeliot
09-23-2019, 11:52 PM
Alright. Guanche swapped out for Egypt Late Period and Egypt Hellenistic. As you will see, both cut significantly into the Levant amount.......except in the Greek samples.


Makes sense. There is clearly something in Sicilians and Western Jews that is of an Arabian-like background, combined with some Berber-like admixture, which Egyptian samples would capture, and I do believe there is some Egyptian ancestry in Sicilians from the period of Arab rule although maybe not as much as these models show.

Island Greeks do not have this, and seem to have a more solidly northern "West Asian" component. The mainland Greeks do not seem to have any substantial Near Eastern that cannot be captured by ancient Aegean samples.

Adding Egyptian also cuts even further into Greek input into Trapani and Ashkenazim, and I think this is correct -- we can create "false" Mycenaean by the right mixture of components but both groups have a more "Italic + MENA" base than do East Sicilians or Aegean islanders.

Greekscholar
09-24-2019, 12:08 AM
Makes sense. There is clearly something in Sicilians and Western Jews that is of an Arabian-like background, combined with some Berber-like admixture, which Egyptian samples would capture, and I do believe there is some Egyptian ancestry in Sicilians from the period of Arab rule although maybe not as much as these models show.

Island Greeks do not have this, and seem to have a more solidly northern "West Asian" component. The mainland Greeks do not seem to have any substantial Near Eastern that cannot be captured by ancient Aegean samples.

Adding Egyptian also cuts even further into Greek input into Trapani and Ashkenazim, and I think this is correct -- we can create "false" Mycenaean by the right mixture of components but both groups have a more "Italic + MENA" base than do East Sicilians or Aegean islanders.

I do think these mainland populations benefit from having a Levant source population included though. Distance definitely increases when it is left out. Leaving the Levant out does boost those Greek source populations up to nearly 50% for Mainland Greece. I am not sure there are any Levant or Greek populations that are completely mutually exclusive from each other (although I would love to hear there are some :)

https://imgur.com/gmCdj5t.jpeg

Sikeliot
09-24-2019, 12:39 AM
I do think these mainland populations benefit from having a Levant source population included though. Distance definitely increases when it is left out. Leaving the Levant out does boost those Greek source populations up to nearly 50% for Mainland Greece. I am not sure there are any Levant or Greek populations that are completely mutually exclusive from each other (although I would love to hear there are some :)

https://imgur.com/gmCdj5t.jpeg

Mainland Greeks likely have some Levantine input, as do all Southeast Europeans, but nowhere near on the level of the Aegean islanders or Sicilians.

What I do think though is there is overlap between the Mycenaean/Empuries samples, and the Armenian/Caucasian ones. And in the case of Ashkenazim and West Sicilians, there is a preference for a mixture of Italic + Armenian, over Mycenaean/Empuries. Populations that retain their Mycenaean/Empuries even after the addition of Italic and Armenian, are more likely to have actual ancient Aegean ancestry versus a coincidentally similar mixture.

Can you try adding Saudis or Yemenis in there and see what happens for the Aegean islanders, Jews, and Sicilians? Would it eat up some of the Levantine? Maybe try Berber, Levantine, and Arabian and remove the Egyptian?

Greekscholar
09-24-2019, 01:00 AM
Mainland Greeks likely have some Levantine input, as do all Southeast Europeans, but nowhere near on the level of the Aegean islanders or Sicilians.

What I do think though is there is overlap between the Mycenaean/Empuries samples, and the Armenian/Caucasian ones. And in the case of Ashkenazim and West Sicilians, there is a preference for a mixture of Italic + Armenian, over Mycenaean/Empuries. Populations that retain their Mycenaean/Empuries even after the addition of Italic and Armenian, are more likely to have actual ancient Aegean ancestry versus a coincidentally similar mixture.

Can you try adding Saudis or Yemenis in there and see what happens for the Aegean islanders, Jews, and Sicilians? Would it eat up some of the Levantine? Maybe try Berber, Levantine, and Arabian and remove the Egyptian?

Exactly. Whatever else can be said, that much is true for this model, at least. I will be honest and say the lack of North African AND Italic in the Greek samples is personally surprising. I was expecting to find at least a little bit of both in myself based on other admix. calculators, and it hasn't played out that way.

I think both the 'double dose' Greek samples and the various possible Levant populations are worthy of some experimentation.

Sikeliot
09-24-2019, 01:19 AM
Exactly. Whatever else can be said, that much is true for this model, at least. I will be honest and say the lack of North African AND Italic in the Greek samples is personally surprising. I was expecting to find at least a little bit of both in myself based on other admix. calculators, and it hasn't played out that way.

I think both the 'double dose' Greek samples and the various possible Levant populations are worthy of some experimentation.

I think you should try to add some Arabian populations and see what happens.

The explanation for the low Greek in Trapanese makes sense. The Arab conquest pushed a lot of the Greek Christian population eastward across the island, with many ending up in places like Enna or Messina. The Trapanese population is probably significantly descended from people who arrived from the Muslim world under Arab rule, and later Italian repopulation during Norman rule, rather than the ancient inhabitants.

Greekscholar
09-24-2019, 01:49 AM
So, here are some runs using just one Greek sample. Interestingly, the only major difference in average fit is if the lone Greek sample is Mycenaean. GRC_Peloponnese_N, Empuries2 and Minoan all produce pretty similar average fits. Also, I am happy to see the Levant_Canaanite_MBA average remain nearly unchanged, maybe this means it is mutually exclusive from the Greek samples? It seems ARM_LBA and Bell_Beaker_ITA suck up the difference. ARM_LBA would make sense, extra Asia Minor juice being added, but Bell Beaker?

https://imgur.com/HpHb7CF.jpeg

Sikeliot
09-24-2019, 01:55 AM
So, here are some runs using just one Greek sample. Interestingly, the only major difference in average fit is if the lone Greek sample is Mycenaean. GRC_Peloponnese_N, Empuries2 and Minoan all produce pretty similar average fits. Also, I am happy to see the Levant_Canaanite_MBA average remain nearly unchanged, maybe this means it is mutually exclusive from the Greek samples? It seems ARM_LBA and Bell_Beaker_ITA suck up the difference. ARM_LBA would make sense, extra Asia Minor juice being added, but Bell Beaker?

https://imgur.com/HpHb7CF.jpeg

Ashkenazim and Trapanese again lose their Greek input, and are almost half combined Armenia, Levant, and North African. Close to a "half and half" model Italic/MENA. Even East Sicily in some of the models above loses much of its Greek.

I'd like to see what happens if you use Saudis or Yemenis, to the Levantine component in each group.

I notice you have much less Armenian-like ancestry than the Cretan sample, which likely shows that the Aegean islands, with the exception of Crete, might have less of this. You also have a lot of Slavic, almost as much as mainlanders, but also much more Levantine than mainlanders.

Greekscholar
09-24-2019, 01:58 AM
I think you should try to add some Arabian populations and see what happens.

The explanation for the low Greek in Trapanese makes sense. The Arab conquest pushed a lot of the Greek Christian population eastward across the island, with many ending up in places like Enna or Messina. The Trapanese population is probably significantly descended from people who arrived from the Muslim world under Arab rule, and later Italian repopulation during Norman rule, rather than the ancient inhabitants.

Any ancient samples for these populations? I am trying to avoid mixing ancients and moderns.

Sikeliot
09-24-2019, 02:03 AM
Any ancient samples for these populations? I am trying to avoid mixing ancients and moderns.

I don't think so. I think you might have to use moderns for it. One modern population with all ancients probably will not cause an issue as Arabians have not changed much.

Greekscholar
09-24-2019, 02:10 AM
Ashkenazim and Trapanese again lose their Greek input, and are almost half combined Armenia, Levant, and North African. Close to a "half and half" model Italic/MENA. Even East Sicily in some of the models above loses much of its Greek.

I'd like to see what happens if you use Saudis or Yemenis, to the Levantine component in each group.

I notice you have much less Armenian-like ancestry than the Cretan sample, which likely shows that the Aegean islands, with the exception of Crete, might have less of this. You also have a lot of Slavic, almost as much as mainlanders, but also much more Levantine than mainlanders.

I am not taking myself too seriously in this model, I suspect there is a big difference in quality between these averaged samples and my Ancestry.com kit. I am interested in the basic idea that none of the Greeks are getting much in the way of North Africa or Bell Beaker, and I am certainly part of that trend.

Sikeliot
09-24-2019, 02:16 AM
I am not taking myself too seriously in this model, I suspect there is a big difference in quality between these averaged samples and my Ancestry.com kit. I am interested in the basic idea that none of the Greeks are getting much in the way of North Africa or Bell Beaker, and I am certainly part of that trend.

What do you think explains your consistently low Armenian and higher Slavic, when compared to the Cretans?

Greekscholar
09-24-2019, 02:21 AM
I don't think so. I think you might have to use moderns for it. One modern population with all ancients probably will not cause an issue as Arabians have not changed much.

Well, since you asked. Saudi alone doesn't seem to work. Saudi + Levant_Canaanite_MBA does seem to impact the Ashkenazim sample positively. Being a modern sample, the fact the other Jewish samples do not favor it, and seeing how much it cuts into the Levant amount, I am not sure if it means anything though.

https://imgur.com/yTjsefk.jpeg

Greekscholar
09-24-2019, 02:24 AM
What do you think explains your consistently low Armenian and higher Slavic, when compared to the Cretans?

I have to do some research on the difference between academic quality samples vs. commercial testing kits before I make any conclusions. I have done lots of runs, and my sample is by far the most likely to get 0% when new samples are added. It is possible that commercial testing kits are more likely to be "dumped" into a few target buckets, and maybe don't the SNP coverage (or something else technical and over my head) necessary to parse out all those small bits.

Sikeliot
09-24-2019, 02:26 AM
Well, since you asked. Saudi alone doesn't seem to work. Saudi + Levant_Canaanite_MBA does seem to impact the Ashkenazim sample positively. Being a modern sample, the fact the other Jewish samples do not favor it, and seeing how much it cuts into the Levant amount, I am not sure if it means anything though.

https://imgur.com/yTjsefk.jpeg


I notice including Saudi causes a dip in East Sicily's Levantine, and pushes some of it into Empuries.... West Sicily and Crete remain unaffected. This likely means that Levantine ancestry in West Sicily is more "true" Levantine than that in East Sicily, just as Greek ancestry in East Sicily is more "true" Greek. Ashkenazim obviously are not 10% Arabian, but it shows that they have more Arabian affinity than any of the Italian or Greek groups.

So Saudi as a source population for East Med peoples is ruled out, but we still can count Egyptian as a possible source for Jews/Sicilians.

Greekscholar
09-25-2019, 02:18 AM
Ok, so here is just me, with as good as fit as I could create. The key was adding the Baltic_EST_BA reference to differentiate the Slavic and using Minoan and Anatolia_Isparta_EBA, not Mycenaean and Empuries. Why do those ancient samples work better? I have no idea. Why does Baltic drastically improve my fit? I have no idea. I give a shout-out to Ancestry.com though. I chuckled at their 1% Baltic region they gave me.......noise I said. Now? I think they saw something there that is being reproduced by G25.

At any rate, every model I tried consistently said about 40/30/30 - Ancient Greek/Levant/Slavic. I figure the next step is to shell out 50 bucks or so to get my dad, Yia Yia, and aunt to get G25 coordinates and see what their results are. I am not having much luck with normal Google searching in trying to find out the difference in accuracy between commercial testing kits and the G25 reference panel. So, that remains a work in progress.

https://imgur.com/17VHnqa.jpeg

Dorkymon
09-25-2019, 07:19 PM
Here are Mainland Greece, and near by populations. Fit isn't bad considering the source samples were not chosen specifically for this group. Much more Slavic, and ancient Greek populations, less Levant and ARM_LBA.

https://imgur.com/bVS3VzH.jpeg

That's way too much Slavic in everyone, because a North Balkan population akin to Mycenaeans is missing. Try adding the i5769 Thracian from Bulgaria or perhaps this one plus Scythian_MDA.

Here's my take on Southeast Europeans:



Sample
Fit
BGR IA--I5769
Baltic EST MA
DEU MA--AED 106
DEU MA O--STR 300
HUN Avar Szolad
Han NChina
ITA Collegno MA O1--CL25
Scythian MDA
UKR Chernyakhiv Shyshaky
UKR Cimmerian--MJ12


Albanian:Average
1.1963
11.67
6.67
0
27.5
15.83
0.83
15
16.67
0
5.83


Bulgarian:Average
1.0402
9.17
15.83
0
11.67
20
0.83
17.5
11.67
5.83
7.5


Croatian:Average
0.8551
9.17
27.5
5
5.83
35
0
8.33
9.17
0
0


Custom:AGUser_Dorkymon
1.1503
0
21.67
0
15
11.67
3.33
0
3.33
26.67
18.33


Greek:Average
0.856
14.17
9.17
0
15.83
12.5
0
30.83
13.33
0
4.17


Greek_Crete:Average
2.0647
10
0.83
0
7.5
0
0.83
70.83
1.67
8.33
0


Romanian:Average
0.8678
7.5
15
0.83
15.83
25
0.83
8.33
13.33
5
8.33


Serbian:Average
1.1808
10.83
21.67
0
15
25
0
10.83
7.5
0
9.17



or if consolidated



Sample
Fit
North Balkan Iron Age-Medieval
South Balkan+Aegean Medieval
Slavic Migration Period-Medieval
SlavicThracic Mix (https://en.wikipedia.org/wiki/Chernyakhov_culture) Migration Period
Germanic/Mongol/etc.


Albanian:Average
1.1963
34.17
42.5
22.5
0
0.83


Bulgarian:Average
1.0402
28.34
29.17
35.83
5.83
0.83


Croatian:Average
0.8551
18.34
14.16
62.5
0
5


Custom:AGUser_Dorkymon
1.1503
21.66
15
33.34
26.67
3.33


Greek:Average
0.856
31.67
46.66
21.67
0
0


Greek_Crete:Average
2.0647
11.67
78.33
0.83
8.33
0.83


Romanian:Average
0.8678
29.16
24.16
40
5
1.66


Serbian:Average
1.1808
27.5
25.83
46.67
0
0

Greekscholar
09-25-2019, 10:53 PM
That's way too much Slavic in everyone, because a North Balkan population akin to Mycenaeans is missing. Try adding the i5769 Thracian from Bulgaria or perhaps this one plus Scythian_MDA.

Here's my take on Southeast Europeans:



Sample
Fit
BGR IA--I5769
Baltic EST MA
DEU MA--AED 106
DEU MA O--STR 300
HUN Avar Szolad
Han NChina
ITA Collegno MA O1--CL25
Scythian MDA
UKR Chernyakhiv Shyshaky
UKR Cimmerian--MJ12


Albanian:Average
1.1963
11.67
6.67
0
27.5
15.83
0.83
15
16.67
0
5.83


Bulgarian:Average
1.0402
9.17
15.83
0
11.67
20
0.83
17.5
11.67
5.83
7.5


Croatian:Average
0.8551
9.17
27.5
5
5.83
35
0
8.33
9.17
0
0


Custom:AGUser_Dorkymon
1.1503
0
21.67
0
15
11.67
3.33
0
3.33
26.67
18.33


Greek:Average
0.856
14.17
9.17
0
15.83
12.5
0
30.83
13.33
0
4.17


Greek_Crete:Average
2.0647
10
0.83
0
7.5
0
0.83
70.83
1.67
8.33
0


Romanian:Average
0.8678
7.5
15
0.83
15.83
25
0.83
8.33
13.33
5
8.33


Serbian:Average
1.1808
10.83
21.67
0
15
25
0
10.83
7.5
0
9.17



or if consolidated



Sample
Fit
North Balkan Iron Age-Medieval
South Balkan+Aegean Medieval
Slavic Migration Period-Medieval
SlavicThracic Mix (https://en.wikipedia.org/wiki/Chernyakhov_culture) Migration Period
Germanic/Mongol/etc.


Albanian:Average
1.1963
34.17
42.5
22.5
0
0.83


Bulgarian:Average
1.0402
28.34
29.17
35.83
5.83
0.83


Croatian:Average
0.8551
18.34
14.16
62.5
0
5


Custom:AGUser_Dorkymon
1.1503
21.66
15
33.34
26.67
3.33


Greek:Average
0.856
31.67
46.66
21.67
0
0


Greek_Crete:Average
2.0647
11.67
78.33
0.83
8.33
0.83


Romanian:Average
0.8678
29.16
24.16
40
5
1.66


Serbian:Average
1.1808
27.5
25.83
46.67
0
0



Thanks for the comments and suggestions. I will work with those other samples you suggested and see what I come up with. :) I discovered the need for the Baltic sample in experimenting with my own kit, I was wondering what other options were out there.

Greekscholar
09-27-2019, 12:42 AM
Thanks for the comments and suggestions. I will work with those other samples you suggested and see what I come up with. :) I discovered the need for the Baltic sample in experimenting with my own kit, I was wondering what other options were out there.

Ok, here are some models for South Balkan populations. You were absolutely correct that differentiating the Slavic component into various other groups greatly increases fit. That said, I don't really know much about many of these populations, so I can't say if they are truly ancestral, or perhaps just better proxies for the various Slavic and other groups they likely mixed with as they moved south into Greece. I will say following the general 40% Ancient Greek/30% Levant/30% Slavic rule that seems pretty iron-clad for my own sample, the model is at least in the ball park. Thoughts?

https://imgur.com/9PyMGGd.jpeg

Sikeliot
09-27-2019, 12:52 AM
Ok, here are some models for South Balkan populations. You were absolutely correct that differentiating the Slavic component into various other groups greatly increases fit. That said, I don't really know much about many of these populations, so I can't say if they are truly ancestral, or perhaps just better proxies for the various Slavic and other groups they likely mixed with as they moved south into Greece. I will say following the general 40% Ancient Greek/30% Levant/30% Slavic rule that seems pretty iron-clad for my own sample, the model is at least in the ball park. Thoughts?

The only way you would have Slavic ancestry is through migration from the mainland to the islands. Do you believe the Aegean islands have been settled, in the last 1000 years, from the mainland in a significant way?

Greekscholar
09-27-2019, 01:52 AM
The only way you would have Slavic ancestry is through migration from the mainland to the islands. Do you believe the Aegean islands have been settled, in the last 1000 years, from the mainland in a significant way?

Yes, you have asked me the question I love to talk about!

Fourni was abandoned because of pirates and was home to goats and only a few shepherd boys until at least 1838. These two primary source travel journals describe the state of the island (they are great reads for anyone interested in the Aegean Islands and Asia Minor during the time in question too.)

This one is from 1814, and was written by Edward Clarke. Fourni is mentioned on pg. 118 and 119. This traveler did not stop there, only commented that his crew was greatly afraid because of the pirates that lurk in the harbors.


https://books.google.com/books/about/Travels_in_Various_Countries_of_Europe_A.html?id=L kZEAAAAIAAJ&printsec=frontcover&source=kp_read_button#v=snippet&q=samos&f=false


1838 book - The ship the author chartered stopped in Fourni, pg. 155, and found a few boys herding goats and feared pirates were around every corner.


https://books.google.com/books?id=vOo_IT9-jF4C&q=fourni#v=snippet&q=nicaria&f=false

Because the island was resettled less than 200 years ago, there is still oral history that describes the founders. My family has preserved many of these stories on both continents. Long story short, the oral history told by islanders describe 12 families resettling the island - Condula (Kondila), Sklavos, Skordu, Achladis, Galanos, Tsourakis, Markakis, Amorianos (Amorganos,) Orphanos, Flitzanis, Grammatikos, and Spanos.

Where were they from? Well, using DNA genealogy, specifically Auto-clusters, I can say for sure that Ikaria, Samos, and Kalymnos are confirmed for my family (I know for sure 5 of those 12 families are my direct ancestors, I know at least one relative from all but one surname.) As for the mainland? One of the families (the cousin who took the Y-test, and the surname of the first male in my family to come to America) was said to be from the Peloponnese. I have not been able to find mainland cousin matches with enough cMs and family trees to make many conclusions. My cousin did have his Y-test come back I-Y18331. His closest match (identical........but who to date has only tested to 12 markers) is from the Peloponnese, as are the other members of the I-Y18331.

My soft conclusion for now is that the idea we have North African or Genoese/Venetian Italian ancestry looks very unlikely based on what I have uncovered. Mainland Greek looks much more likely based on G25 results, the family stories, the Y-group of my cousin, and the K15 PCA. How much? How many relatives? What percent? Those questions are likely impossible to answer. You've got a founder effect on Fourni that derives in part from two large founder effects (Ikaria and Kalymnos) so you end up in the wash once you reach about 3rd cousin level connections.

I have attached my Autocluster report to show you what I mean. The huge Red Square are all Ikarians. The Orange Square is Kalymnos. The Yellow Square is Fourni (a few mistaken Kalymniotes are placed there too.) You will see these are tight clusters, cousin to one, cousin to all, for each island. You will allows see in the gray blocks, that Ikaria and Kalymnos don't have many shared cousin connections. Look at Fourni. The people from there are connected to both Ikaria and Kalymnos. Keep in mind my closest relatives by cM are mostly in the Fourni cluster, then Ikaria, then Kalymnos. That said, many of those Fourniotes are very admixed at this point, 1/4 to 1/8 heritage from the island, but the ones that connect to nearly every sample (like I do, or they wouldn't be in my autocluster) are 100% from Fourni.

https://imgur.com/EocQzhH.jpeg

Sikeliot
09-27-2019, 02:26 AM
Yes, you have asked me the question I love to talk about!

Fourni was abandoned because of pirates and was home to goats and only a few shepherd boys until at least 1838. These two primary source travel journals describe the state of the island (they are great reads for anyone interested in the Aegean Islands and Asia Minor during the time in question too.)

The genetic diversity of the Aegean islands, even people on the same island plotting very differently implies to me that the Aegean islands are far from being "isolated" or "preserved" and there has likely been a lot of migration in the last 500 years between the islands, from the mainland to the islands, and from Anatolia or even Cyprus. I do tend to believe the "native" islanders should be closest to Sicilians or Cretans but you have a lot of ways you can mix people that they plot like this... half Peloponnese and half Cypriot would come out that way.

What I notice among the Dodecanese for instance, is that the smaller islands tend to be more "South Italian" like while people from some of the larger islands like Rhodes have more diversity.

Here is someone from the island of Leros I just got... I have never seen a result from there so this was interesting. Very close to the Aegean islands (Cyclades less so), Calabria, Campania, and to some extent Sicily and Cyprus.

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

Greekscholar
09-27-2019, 02:55 AM
The genetic diversity of the Aegean islands, even people on the same island plotting very differently implies to me that the Aegean islands are far from being "isolated" or "preserved" and there has likely been a lot of migration in the last 500 years between the islands, from the mainland to the islands, and from Anatolia or even Cyprus. I do tend to believe the "native" islanders should be closest to Sicilians or Cretans but you have a lot of ways you can mix people that they plot like this... half Peloponnese and half Cypriot would come out that way.

What I notice among the Dodecanese for instance, is that the smaller islands tend to be more "South Italian" like while people from some of the larger islands like Rhodes have more diversity.

Here is someone from the island of Leros I just got... I have never seen a result from there so this was interesting. Very close to the Aegean islands (Cyclades less so), Calabria, Campania, and to some extent Sicily and Cyprus.

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

There may be a few islands, or parts of islands (think Ikaria and parts of Crete) that were largely spared from depopulation/repopulation events. Small islands nearly had to have been subject to these forces, and for the NE Aegean islands, Samos, Mytilene, Fourni, Chios, to name a few, it is an easily researched historical fact. That said, even a high Slavic islander like myself clearly clusters in the Continuum populations, and I have never found an Island Greek who did not. So, while mainland input seems certain at some level, I can't say I have ever seen it actually shift a person out the Continuum range.

I hate to keep saying this, but we just need more samples, especially G25, for different islands. I was really impressed that it was able to differentiate between Southern Italian/Island Greek populations using Slavic vs. Bell Beaker and Guanche samples. I still feel there are Greeks that will have some traces of more recent Italian ancestry (the Crete reference sample is not nearly as firm in its rejection of Bell Beaker as mine is) but until we can break down individuals or (not holding my breathe) academic samples from different islands, it is really hard to say much more.

Sikeliot
09-27-2019, 02:57 AM
There may be a few islands, or parts of islands (think Ikaria and parts of Crete) that were largely spared from depopulation/repopulation events. Small islands nearly had to have been subject to these forces, and for the NE Aegean islands, Samos, Mytilene, Fourni, Chios, to name a few, it is an easily researched historical fact. That said, even a high Slavic islander like myself clearly clusters in the Continuum populations, and I have never found an Island Greek who did not. So, while mainland input seems certain at some level, I can't say I have ever seen it actually shift a person out the Continuum range.

I hate to keep saying this, but we just need more samples, especially G25, for different islands. I was really impressed that it was able to differentiate between Southern Italian/Island Greek populations using Slavic vs. Bell Beaker and Guanche samples. I still feel there are Greeks that will have some traces of more recent Italian ancestry (the Crete reference sample is not nearly as firm in its rejection of Bell Beaker as mine is) but until we can break down individuals or (not holding my breathe) academic samples from different islands, it is really hard to say much more.


I have never seen a Lesbos or Lemnos Greek on GEDmatch but from what I see on 23andme, they should be the most 'mainland' like of the Aegean islanders apart from, possibly, some people in the Cyclades.

Based on what I see so far, I'd say Ikaria seems the most South Italian-like overall in a homogenous sense in that I have never seen someone from there who deviates far from the average.

Sikeliot
09-27-2019, 03:14 AM
Here is an interesting Eurogenes K36. She is from Terrasini, Palermo province, Sicily right near the border with Trapani (this is an area with low Greek input historically).

She seems further than average from the South Italian and Aegean averages, but she matches higher than average with Levantines (as much as does the person from Leros). There seem to be many factors influencing membership in the Eastern Mediterranean cluster.

https://i.imgur.com/w3buiSQ.png

Sikeliot
09-28-2019, 01:02 AM
What is interesting is I have some Cretan results who are more mainland shifted than that average. Here are the results in Eurogenes K36 for one of them. Let me know if you'd like to see other calculators.

They look at first glance equidistant but when you see they are as close to Bulgaria as to the Crete average or Sicily, that tells you they are mainland shifted. They are from Chania.


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

xripkan
10-29-2019, 04:50 PM
Whoops. I think ITA_Collegno_MA is "Middle Ages" not "Metal Age." I swapped it out for Bell_Beaker_ITA. Fit improves, but Greek sources crash hard for non-Greek target populations, seemingly replaced by ARM_LBA. This is probably wrong, isn't it?


https://imgur.com/I0bYQsy.jpg

My results

Distance 0.02475555

ARM_LBA 6.2
Bell_Beaker_ITA 0
CZE_Early_Slav 35.4
Canary_Islands_Guanche 0
GRC_Mycenaean 19.6
Iberia_Northeast_Empuries2 27.2
Levant_Canaanite_MBA 11.6

xripkan
10-29-2019, 04:59 PM
My results based on Dorkymon's model

Distance 0.02066849

BGR_IA 0
Baltic_EST_MA 9.8
DEU_MA_o_STR300 34.2
DEU_MA _AED106 0
HUN_Avar_Szolad 0
Han_NChina 1.2
ITA_Collegno_MA_o1 15.8
Scythian_MDA 28.8
UKR_Chernyakhiv_Shyshaky 0
UKR_Cimmerian 10.2

or

North Balkan Iron Age-Medieval 39
South Balkan+Aegean Medieval 50
Slavic Migration Period-Medieval 9.8
SlavicThracic Mix Migration Period 0
Mongols 1.2