Admixtools admixtools2 TUTORIAL for WINDOWS.

[Er Monnezza]

Yes, someone should inform Reich to switch over to g25, ffs, I mean all the cool kids in the 'east med' gang are using it, wtf does he need qpAdm for.

When Davidski wants to prove something, he unironically uses qpAdm and not Global25 (which remains a great tool anyway).

Also, I'd like a definition of the 'east med' terminology so I can understand wtf is the highbrow gang going on about, it seems everything from Abkhazia all the way to Cairo could be labelled as such, according to them.

No, according to the theorists of the "East Med Continuum", this area would extend from southern Italy to the Greek islands and Cyprus excluding mainland Greece and modern Turkey. I must admit, however, that this term has never convinced me much.

W/o anyone knowing about the sum of my different parental/maternal parts (that have nothing to do with either the East Med or the results listed) what conclusion can be reached? The same one with the Cretans, and/or the Dodecannese?

Using Global25 it can be seen that you have a somewhat high distance compared to the Cretan average (>3) and that you have too much CHG and too little Natufian. In short, one could speculate that you do not have fully Cretan origins despite having similar results.

1) The fact that the Greek categories (in g25 and elsewhere) are the only ones that are so numerous in those sheets (with Italians too, I guess) and that they refer to a historical snapshot of a period 100+ years past, most of the people with such autosomal profiles born in the early 20th century and long gone, while blatantly ignoring the current demographic reality of the country is a testament to the sheer idiocy of the small group of perpetrators responsible for those reference sheets and their crypto-racism that tries to disassociate the modern Greek profile from its Eastern/Anatolian demographic part through a process that renders the latter invisible.

In Italy there is also a recent demographic change. Since the 1950s, there were a total of 4 million people who moved from southern to northern Italy. Certainly the North Italian Global25 averages won't reflect this demographic change, but I do not expect them to because it is still too close to our own period. The same may apply to Greece.

 

[D.L.M]

Iberians have those categories too. Should the German average include recent assimilated Turks in it? What about the Northern Italian cluster with all the Southern Italian migration?


I am not in contact with your opponents.

 

[eupator]

Iberians have those categories too. Should the German average include recent assimilated Turks in it? What about the Northern Italian cluster with all the Southern Italian migration?

This can work in reverse, if we are picking historical snapshots, why that snapshot and not another? Which is the cut-off date? Why are the Bulgarian speakers more fit to fill in the Greek_Macedonia category and not the Rumelia Turks, who outnumbered them overwhelmingly and in some cases ever predated them?

If we are not using the current populations for our 'moderns' analysis, who gets to decide which should be the chosen historical snapshot and would they mind telling us which was the thought process behind such a decision?

 

[D.L.M]

This can work in reverse, if we are picking historical snapshots, why that snapshot and not another? Which is the cut-off date? Why are the Bulgarian speakers more fit to fill in the Greek_Macedonia category and not the Rumelia Turks, who outnumbered them overwhelmingly and in some cases ever predated them?

If we are not using the current populations for our 'moderns' analysis, who gets to decide which should be the chosen historical snapshot and would they mind telling us which was the thought process behind such a decision?

Maybe because the 20th century movement is pretty much 100% documented and these people know who they are. And when you include recent migrants it makes the waters more muddy when you want explore for example the Slavic admixture in Macedonia which is medieval in nature.

 

[eupator]

Maybe because the 20th century movement is pretty much 100% documented and these people know who they are. And when you include recent migrants it makes the waters more muddy when you want explore for example the Slavic admixture in Macedonia which is medieval in nature.

You mean 19th century, because the 20th century involves the great population exchanges of 1917-22, right in the beginning of the century.

As such, us Gen-X/Millenial grandchildren of both the 'mainland' groups and the 'anatolian' groups (the infants of 1922), who constitute the sheer majority of the modern population of Macedonia in Greece, are invisible in favor of late 19th century corpses of an imaginary narrative that serves what kind of purpose exactly?

 

[D.L.M]

You mean 19th century, because the 20th century involves the great population exchanges of 1917-22, right in the beginning of the century.

As such, us Gen-X/Millenial grandchildren of both the 'mainland' groups and the 'anatolian' groups (the infants of 1922), who constitute the sheer majority of the modern population of Macedonia in Greece, are invisible in favor of late 19th century corpses of an imaginary narrative that serves what kind of purpose exactly?

I think the regional associations are also related with the formation of the early Greek state for several reason. Did the Peloponnesians even call the Peloponnese, Peloponnese or Morea before 1831?

IDK why are you so emotionally invested at this? I don't really care, this is the first I am discussing it actually.

You can use one side to explore the history and genetics of your mainland ancestry and the other side your Anatolian ancestry with those divided components. It would be easier like that.

We both know that Anatolian admixture in European Greeks is not all from Hellenistic era, some of it came with Byzantines and some of it came with Ottoman Pontic migrants (before the population exchange), a good amount of it came with Roman Empire (total colonization of Corinth and Patras in Imperial Era). It is quite hard to investigate that in detail. I think you at least can recognize your Anatolian ancestry from 20th century in ratio with other centuries.

 

[eupator]

I think the regional associations are also related with the formation of the early Greek state for several reason. Did the Peloponnesians even call the Peloponnese, Peloponnese or Morea before 1831?

IDK why are you so emotionally invested at this? I don't really care, this is the first I am discussing it actually.

You can use one side to explore the history and genetics of your mainland ancestry and the other side your Anatolian ancestry with those divided components. It would be easier like that.

We both know that Anatolian admixture in European Greeks is not all from Hellenistic era, some of it came with Byzantines and some of it came with Ottoman Pontic migrants (before the population exchange), a good amount of it came with Roman Empire (total colonization of Corinth and Patras in Imperial Era). It is quite hard to investigate that in detail. I think you at least can recognize your Anatolian ancestry from 20th century in ratio with other centuries.

The categorization only makes sense through a racist perspective of history, based on the wish of the perpetrators of such categorization to render the Anatolian component invisible, like I said. It's very common theme in the diaspora, you will see the most ardent defenders of 'mainland Greek' purity being the diaspora Greeks, most of which not even being able to speak the language mind you, that still persist on such adherence, you may notice that diasporas are usually over-represented in these online communities for similar reasons.

You cannot fully grasp this because you are an outsider in this debate, similar debates may or may not exist within your own ethnic group.

If this lot had any academic sensibilities whatsoever, they would strive for a different kind categorization that would make more historical sense, like:

"Greek_Macedonia_modern", and/or
"Greek_Macedonia_19th_century_Slavic_speaker",
"Greek_Macedonia_19th_century_Rumelia_Turk",
"Greek_Macedonia_19th_century_Romanian_speaker",

etc.

 

[D.L.M]

The categorization only makes sense through a racist perspective of history, based on the wish of the perpetrators of such categorization to render the Anatolian component invisible, like I said. It's very common theme in the diaspora, you will see the most ardent defenders of 'mainland Greek' purity being the diaspora Greeks, most of which not even able to speak the language mind you, that still persist on such adherence, you may notice that diasporas are usually over-represented in these online communities for similar reasons.

You cannot fully grasp this because you are an outsider in this debate, similar debates may or may not exist within your own ethnic group.

If this lot had any academic sensibilities whatsoever, they would strive for a different kind categorization that would make more historical sense, like:

"Greek_Macedonia_modern", and/or
"Greek_Macedonia_19th_century_Slavic_speaker",
"Greek_Macedonia_19th_century_Rumelia_Turk",
"Greek_Macedonia_19th_century_Romanian_speaker",

etc.

A division of Slavic speakers would be good, IMO. Vlachs were not numerous enough in Macedonia and Turks were expelled I guess.

 

[Archetype0ne]

Played further with the model from yesterday. Maybe ran 7-8 runs.
Only way to make Albanian work for me so far in a 3 way model, goes something like this:

Even then I am not sure what are the criteria for a model not to fail? Low se? High z-score?

 

[eupator]

Played further with the model from yesterday. Maybe ran 7-8 runs.
Only way to make Albanian work for me so far in a 3 way model, goes something like this:

Even then I am not sure what are the criteria for a model not to fail? Low se? High z-score?

Your model has a p-value of 0.056 (5.60e-2) which is strong (over 5%), so it's a pass. The s.e. are high but this could also be due to a bloated right list, which you might want to trim.

Check some of my admixtools1 runs and the right lists I used to use there, they were much smaller in size.

Edit: I have renamed some samples for ease of use, following this list.

 

[eupator]

I browsed through my admixtools1 pastebin and saw that I had an IA Albanian model:

A:
scale 1.414 1.414
HRV_IA 1.414 0.000
Turkey_OldHittitePeriod.SG 0.000 1.414


best coefficients: 0.657 0.343
totmean: 0.657 0.343
boot mean: 0.660 0.340
std. errors: 0.087 0.087

error covariance (* 1,000,000)
7504 -7504
-7504 7504


summ: Albanian.DG 2 0.329386 0.660 0.340 7504 -7504 7504

fixed pat wt dof chisq tail prob
00 0 13 14.655 0.329386 0.657 0.343
01 1 14 28.519 0.0121328 1.000 0.000
10 1 14 88.451 7.4372e-13 0.000 1.000
best pat: 00 0.329386 - -
best pat: 01 0.0121328 chi(nested): 13.864 p-value for nested model: 0.000196562

coeffs: 0.657 0.343

Right:

Mbuti.DG
Russia_Ust_Ishim.DG
China_Tianyuan
Goyet_Neanderthal.SG
Russia_Sunghir3.SG
Russia_Kostenki14.SG
Russia_MA1_HG.SG
SATP
Russia_DevilsCave_N.SG
Papuan.DG
Switzerland_Bichon.SG
Greece_Peloponnese_N
Balkan_HG
Tarim_EMBA1
ONG.SG

edit: p-value being 0.329386 if you missed it (32.9%).

 

[Archetype0ne]

I browsed through my admixtools1 pastebin and saw that I had an IA Albanian model:



Right:



edit: p-value being 0.329386 if you missed it (32.9%).

I was trying to somehow have a 3 way model with both a Slavic as well as Imperial Roman eastern shift.
For Slavic I tried everything I could think of, Migration Period CZE Early Slav, modern Polish, Avar Slavic Outlier, Sarmatian, Early Sarmatian Russia etc... nothing works. For the eastern shift it was easier but I had to dig back in time, as the Roman Era C4 cluster is too similar to the other proxies and causes the model to fail. So I settled with Israel IA. But for Slavic nothing works but the Ingria IA. Problem is Ingria IA... is Finno Urgic... not Slavic.
As for the base tried Mycenaean, HRV EBA-MBA, POP_CA, and found that the Maros L283 was good enough(not rly, .1se but as a 3 way model does the job well enough).

 

[eupator]

I was trying to somehow have a 3 way model with both a Slavic as well as Imperial Roman eastern shift.
For Slavic I tried everything I could think of, Migration Period CZE Early Slav, modern Polish, Avar Slavic Outlier, Sarmatian, Early Sarmatian Russia etc... nothing works. For the eastern shift it was easier but I had to dig back in time, as the Roman Era C4 cluster is too similar to the other proxies and causes the model to fail. So I settled with Israel IA. But for Slavic nothing works but the Ingria IA. Problem is Ingria IA... is Finno Urgic... not Slavic.
As for the base tried Mycenaean, HRV EBA-MBA, POP_CA, and found that the Maros L283 was good enough(not rly, .1se but as a 3 way model does the job well enough).

It's hard to find a medieval Slavic incursion sample to include in these Balkan models, you see Polish.DG works with my initial GREEKALPOP sample run, but that's a modern and it's different kettle of fish so to speak.

For my IA Albanian model, you can see there is room for improvement, especially with the s.e. that are high, those published papers aim for 5% and below, so it's up to you to refine it.

I wrote up this tutorial for admixtools2 for windows, so more people pick it up and work with it, because I don't have the time or patience to bang my head against the wall (hehe), I did some runs for myself and my folks, and some requests for friends (Armenians and Georgians) and called it mostly quits.

I am very interested to see what people come up with, the more the better, I don't have any predispositions.

 

[Archetype0ne]

I am out of upvotes, and found myself many times trying to upvote you mate. Cheers.

 

[D.L.M]

Can you estimate the Ancient Greek ancestry of Sicilians using LBA Sicilian samples? Because I have failed doing it with G25. Try throwing Etruscans and Daunians because Iron Age Campanians seem intermediate between Daunians and Campanians.

 

[Palermo Trapani]

Can you estimate the Ancient Greek ancestry of Sicilians using LBA Sicilian samples? Because I have failed doing it with G25. Try throwing Etruscans and Daunians because Iron Age Campanians seem intermediate between Daunians and Campanians.

ihype02: Here are some models for me using Dodecad12b. the first model is Jovialis K8 model which uses Minoan as the major source of ancestry to capture EEF related ancestry in modern Southern Italians (which is the major ancient ancestral source of modern Italians across the board, not only Southern mainland Italians/Sicilians). Obviously, the Yamnaya captures Steppe ancestry (Fernandes et al 2020 documented Steppe ancestry entering Sicily in the Bronze age), I get another Neolithic source from Central Italy (Antonio et al 2019 paper). The Iberomaurasian captures North African/Levant related ancestry which given the Pheonician/Carthagian period, Imperial Rome and in Sicily the Saracen period is part of modern Sicilian genetics at about 4.6% on average (Sazzini et al 2016).

So as I have said, I think Jovialis K8 model has support in the genetics literature on Southern Italy (Aneli et al 2022 paper published 17 January 2022 "The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context") and Raveane et al 2022 "Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy." So as you can see, Jovialis K8 model fits me quite well. Now, the 2nd two models I did the following. I replaced the Minoan source populations that Jovialis used for his K8 model with 1) All the Bronze age Sicilian samples from Fernandes et al 2020. The distance is 0.7474, which is very good but not as good as with Minoans as source population. 2) Only the LBA Sicilians from Fernandes et al 2020, the distance is now 1.3. So I would start with Jovialis K8 model and then replace the Minoan with the Bronze Age Siclian samples to see how your G25 model works regarding ancient Greek DNA in modern Sicily. I would also use other Southern Italian regions as well since all them in Jovilias's K8 model can be modeled with excellent fits using Minoans as a source population.

Cheers, hope this makes sense. PT

[TH="class: singleheader, colspan: 2, align: left"]Target: PalermoTrapani_ANCESTRY
Distance: 0.4939% / 0.49385911
[/TH]

[TD="class: singleleftcolumn, align: right"]71.8[/TD]
[TD="class: singlerightcolumn"]Minoan[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]20.7[/TD]
[TD="class: singlerightcolumn"]Yamnaya[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]3.8[/TD]
[TD="class: singlerightcolumn"]C_Italian_N[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]2.5[/TD]
[TD="class: singlerightcolumn"]Iberomaurusian[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]0.7[/TD]
[TD="class: singlerightcolumn"]C_Italian_ChL[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]0.5[/TD]
[TD="class: singlerightcolumn"]Remedello[/TD]

[TH="class: singleheader, colspan: 2, align: left"]Target: PalermoTrapani_ANCESTRY
Distance: 0.7474% / 0.74740674
[/TH]

[TD="class: singleleftcolumn, align: right"]38.5[/TD]
[TD="class: singlerightcolumn"]Anatolian_BA[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]19.0[/TD]
[TD="class: singlerightcolumn"]Sicily_LBA_Marcita[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]15.2[/TD]
[TD="class: singlerightcolumn"]Yamnaya[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]15.2[/TD]
[TD="class: singlerightcolumn"]Sicily_MBA_Buffa_Cave_II[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]11.7[/TD]
[TD="class: singlerightcolumn"]Sicily_EBA_lowcov_Vallone_Inferno[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]0.4[/TD]
[TD="class: singlerightcolumn"]Sicily_EBA_Contrada_Paolina_Castellucciana[/TD]

[TH="class: singleheader, colspan: 2, align: left"]Target: PalermoTrapani_ANCESTRY
Distance: 1.3025% / 1.30245948
[/TH]

[TD="class: singleleftcolumn, align: right"]45.9[/TD]
[TD="class: singlerightcolumn"]Anatolian_BA[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]37.2[/TD]
[TD="class: singlerightcolumn"]Sicily_LBA_Marcita[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]16.5[/TD]
[TD="class: singlerightcolumn"]Yamnaya[/TD]

[TD="class: barchartmode1 nonselectable, colspan: 2"][/TD]

[TD="class: singleleftcolumn, align: right"]0.4[/TD]
[TD="class: singlerightcolumn"]Iberomaurusian[/TD]

 

[Aspar]

Many thanks to Eupator for this straightforward and very useful demonstration on how to use this professional tool on Windows.
I tried models with some modern Balkan pops(Albanians, Bulgarians, Greeks_1, Greeks_2) and these are the best models I could obtain:

target      left                                  weight     se     z
  <chr>       <chr>                                  <dbl>  <dbl> <dbl>
1 Albanian.DG Bulgaria_IA                            0.793 0.0817  9.71
2 Albanian.DG Hungary_Avar_5_daughter.or.mother.AV1  0.207 0.0817  2.53
> results$popdrop
# A tibble: 3 x 13
  pat      wt   dof  chisq        p f4rank Bulgari~1 Hunga~2 feasi~3 best  dofdiff
  <chr> <dbl> <dbl>  <dbl>    <dbl>  <dbl>     <dbl>   <dbl> <lgl>   <lgl>   <dbl>
[B]1 00        0     2  0.458 7.95e- 1      1     0.793   0.207 TRUE    NA         NA[/B]
2 01        1     3  7.18  6.65e- 2      0     1      NA     TRUE    TRUE        0
3 10        1     3 97.8   4.60e-21      0    NA       1     TRUE    TRUE       NA

target       left                                  weight     se     z
  <chr>        <chr>                                  <dbl>  <dbl> <dbl>
1 Bulgarian.DG Bulgaria_IA                            0.479 0.0727  6.58
2 Bulgarian.DG Hungary_Avar_5_daughter.or.mother.AV1  0.341 0.0672  5.07
3 Bulgarian.DG Armenia_LBA.SG                         0.181 0.0725  2.49
> results$popdrop
# A tibble: 7 x 14
  pat      wt   dof    chisq        p f4rank Bulga~1 Hunga~2 Armen~3 feasi~4 best 
  <chr> <dbl> <dbl>    <dbl>    <dbl>  <dbl>   <dbl>   <dbl>   <dbl> <lgl>   <lgl>
[B]1 000       0     1   0.0349 8.52e- 1      2   0.479   0.341   0.181 TRUE    NA   [/B]
2 001       1     2   6.13   4.68e- 2      1   0.591   0.409  NA     TRUE    TRUE 
3 010       1     2  26.2    2.02e- 6      1   0.764  NA       0.236 TRUE    TRUE 
4 100       1     2  50.9    8.74e-12      1  NA       0.640   0.360 TRUE    TRUE 
5 011       2     3  34.7    1.38e- 7      0   1      NA      NA     TRUE    NA   
6 101       2     3  67.1    1.80e-14      0  NA       1      NA     TRUE    NA   
7 110       2     3 121.     5.08e-26      0  NA      NA       1     TRUE    NA

target     left           weight     se     z
  <chr>      <chr>           <dbl>  <dbl> <dbl>
1 Greek_2.DG Greek_Emporion  0.605 0.0897  6.75
2 Greek_2.DG Armenia_LBA.SG  0.395 0.0897  4.40
> results$popdrop
# A tibble: 3 x 13
  pat      wt   dof chisq        p f4rank Greek_Em~1 Armen~2 feasi~3 best  dofdiff
  <chr> <dbl> <dbl> <dbl>    <dbl>  <dbl>      <dbl>   <dbl> <lgl>   <lgl>   <dbl>
[B]1 00        0     2  10.2 6.06e- 3      1      0.605   0.395 TRUE    NA         NA[/B]
2 01        1     3  40.8 7.14e- 9      0      1      NA     TRUE    TRUE        0
3 10        1     3  72.6 1.18e-15      0     NA       1     TRUE    TRUE       NA

target     left                                  weight     se     z
  <chr>      <chr>                                  <dbl>  <dbl> <dbl>
1 Greek_1.DG Bulgaria_IA                            0.501 0.0939  5.34
2 Greek_1.DG Hungary_Avar_5_daughter.or.mother.AV1  0.267 0.0788  3.38
3 Greek_1.DG Armenia_LBA.SG                         0.233 0.0986  2.36
> results$popdrop
# A tibble: 7 x 14
  pat      wt   dof  chisq        p f4rank Bulgari~1 Hunga~2 Armen~3 feasi~4 best 
  <chr> <dbl> <dbl>  <dbl>    <dbl>  <dbl>     <dbl>   <dbl>   <dbl> <lgl>   <lgl>
1 000       0     1  0.849 3.57e- 1      2     0.501   0.267   0.233 TRUE    NA   
[B]2 001       1     2  9.27  9.70e- 3      1     0.675   0.325  NA     TRUE    TRUE [/B]
3 010       1     2 16.3   2.89e- 4      1     0.679  NA       0.321 TRUE    TRUE 
4 100       1     2 44.4   2.27e-10      1    NA       0.473   0.527 TRUE    TRUE 
5 011       2     3 27.6   4.48e- 6      0     1      NA      NA     TRUE    NA   
6 101       2     3 84.9   2.67e-18      0    NA       1      NA     TRUE    NA   
7 110       2     3 83.8   4.59e-18      0    NA      NA       1     TRUE    NA

I know 'se' are a bit higher than 5% but it seems to me that 'p-value' is fine. Eupator what do you think?

 

[eupator]

You can probably trim the std. errors a bit more just by fine tuning the right list, but the p-values look good.

Keep in mind that the Greek reference samples are quite diverse in both 1240 and HO (the Greek_2.DG might be a Pontic from Thessaloniki) and sometimes cannot used be as averages very well. This might apply to others in the modern lists.

 

[eupator]

what do you think?

The moderns seem to work quite easily,

this is a run of mine using proximal neighbors as sources:

> results$weights
# A tibble: 2 × 5
  target left              weight     se     z
  <chr>  <chr>              <dbl>  <dbl> <dbl>
[B]1 eptr    Albanian           0.510 0.0742 [/B] 6.87[B]
2 eptr    Armenian_Hemsheni  0.490 0.0742  [/B]6.60
> results$popdrop
# A tibble: 3 × 13
  pat      wt   dof chisq        p f4rank Albanian Armenian_Hemsheni
  <chr> <dbl> <dbl> <dbl>    <dbl>  <dbl>    <dbl>             <dbl>
1 00        0     9  10.1 [B]3.40e- 1[/B]      1    0.510             0.490
2 01        1    10 185.  2.38e-34      0    1                NA    

results$weights
# A tibble: 2 × 5
  target left              weight     se     z
  <chr>  <chr>              <dbl>  <dbl> <dbl>
[B]1 eptr  Bulgarian          0.423 0.0662  [/B]6.39[B]
2 eptr  Armenian_Hemsheni  0.577 0.0662  [/B]8.71
> results$popdrop
# A tibble: 3 × 13
  pat      wt   dof chisq        p f4rank Bulgarian Armenian_Hemsheni
  <chr> <dbl> <dbl> <dbl>    <dbl>  <dbl>     <dbl>             <dbl>
1 00        0     9  16.0 [B]6.64e- 2[/B]      1     0.423             0.577
2 01        1    10 397.  3.67e-79      0     1                NA    
3 10        1    10 257.  1.87e-49      0    NA                 1    

results$weights
# A tibble: 2 × 5
  target left      weight     se     z
  <chr>  <chr>      <dbl>  <dbl> <dbl>
[B]1 eptr  Bulgarian  0.448 0.0600  [/B]7.47[B]
2 eptr  Armenian   0.552 0.0600 [/B] 9.20
> results$popdrop
# A tibble: 3 × 13
  pat      wt   dof chisq        p f4rank Bulgarian Armenian feasible
  <chr> <dbl> <dbl> <dbl>    <dbl>  <dbl>     <dbl>    <dbl> <lgl>   
1 00        0     9  10.1 [B]3.46e- 1 [/B]     1     0.448    0.552 TRUE    
2 01        1    10 406.  3.92e-81      0     1       NA     TRUE    
3 10        1    10 318.  2.65e-62      0    NA        1     TRUE  

results$weights
# A tibble: 2 × 5
  target left     weight     se     z
  <chr>  <chr>     <dbl>  <dbl> <dbl>
[B]1 eptr  Albanian  0.590 0.0679  [/B]8.69[B]
2 eptr  Georgian  0.410 0.0679  [/B]6.04
> results$popdrop
# A tibble: 3 × 13
  pat      wt   dof chisq        p f4rank Albanian Georgian feasible
  <chr> <dbl> <dbl> <dbl>    <dbl>  <dbl>    <dbl>    <dbl> <lgl>   
1 00        0     9  16.2[B] 6.30e- 2 [/B]     1    0.590    0.410 TRUE    
2 01        1    10 230.  8.89e-44      0    1       NA     TRUE    
3 10        1    10 468.  3.12e-94      0   NA        1     TRUE

Right:

right = c('Mbuti.DG', 'ONG.SG', 'EHG', 'CHG', 'Balkan_HG', 'Iberomaurusian', 'WSHG', 'Mongolia_North_N', 'Turkey_Epipaleolithic', 'Iran_N', 'PPN')

 

[Aspar]

You can probably trim the std. errors a bit more just by fine tuning the right list, but the p-values look good.

Keep in mind that the Greek reference samples are quite diverse in both 1240 and HO (the Greek_2.DG might be a Pontic from Thessaloniki) and sometimes cannot used be as averages very well. This might apply to others in the modern lists.

You certainly seem on point about Greek_2:

pop1       pop2              est      se
  <chr>      <chr>           <dbl>   <dbl>
1 Greek_2.DG Armenian.DG -0.00374  0.00283
2 Greek_2.DG Cretan.DG    0.00119  0.00285
3 Greek_2.DG Georgian.DG  0.000170 0.00284
4 Greek_2.DG Greek_1.DG  -0.00652  0.00388

pop1        pop2             est      se
  <chr>       <chr>          <dbl>   <dbl>
1 Georgian.DG Armenian.DG 0.00358  0.00174
2 Georgian.DG Cretan.DG   0.00652  0.00175
3 Georgian.DG Greek_1.DG  0.00608  0.00276
4 Georgian.DG Greek_2.DG  0.000170 0.00284

I'm not sure how to interpret the negative values but genetic distance wise Greek_2.DG is closer to Georgian.DG than to Cretan.DG. Also Greek_2.DG is closer to Georgian.DG than Armenian.DG is. Therefore I also think Greek_2 is actually of Pontic origin.
What's interesting is that as per my model above he can be modeled as 60.5% Greek_Emporium and 39.5% Armenia_LBA. I didn't expect so much Ancient Greek ancestry compared to Armenia_LBA TBH.

Other than that, Greek_1 seems some Northern Greek folk, perhaps from Macedonia?? Similar to Greek_2 of course which again should be a Macedonian sample but unlike it, Greek_1 seems to pack significant Slavic ancestry, again as per the model above, 67.5% Bulgaria_IA and 32.5% AV2. The model with Greek_Emporium is rejected. Greek_1 is also some 12.5% more 'Slavic' than the Albanian.DG, which can be modeled as 79.3% Bulgaria_IA and 20.7% AV2, and closer to the 'Slavic' percentages of the Bulgarian.DG, around 34.1%. It's further away from Cretan.DG than Bulgarian.DG is:

pop1      pop2             est      se
  <chr>     <chr>          <dbl>   <dbl>
1 Cretan.DG Armenian.DG  0.00369 0.00168
2 Cretan.DG Bulgarian.DG 0.00126 0.00173
3 Cretan.DG Greek_1.DG   0.00175 0.00299
4 Cretan.DG Greek_2.DG   0.00118 0.00285

pop1       pop2               est      se
  <chr>      <chr>            <dbl>   <dbl>
1 Greek_1.DG Albanian.DG  -0.00111  0.00429
2 Greek_1.DG Bulgarian.DG -0.000884 0.00292
3 Greek_1.DG Cretan.DG     0.00176  0.00300
4 Greek_1.DG Greek_2.DG   -0.00653  0.00389

Again, I don't know how to interpret the negative values but if that means closer related than the positive ones then Greek_2.DG is closest to Greek_1.DG. I'm not sure I'm reading this correctly but why would Greek_2.DG be closer to Greek_1.DG than Albanians.DG or Bulgarian.DG are? Perhaps some elevated West Asian ancestry in Greek_1.DG which qpAdm failed to capture or perhaps Greek_2.DG isn't fully Pontic Greek but has some minor mainland Greek Macedonian ancestry?
When I take into account Armenian.DG fst distances then there isn't anything irregular and Greek_1.DG is even further away from Armenian.DG than Bulgarian.DG is:

pop1        pop2              est      se
  <chr>       <chr>           <dbl>   <dbl>
1 Armenian.DG Bulgarian.DG  0.00522 0.00168
2 Armenian.DG Cretan.DG     0.00369 0.00168
3 Armenian.DG Greek_1.DG    0.00697 0.00295
4 Armenian.DG Greek_2.DG   -0.00371 0.00283

What's interesting about Bulgarian.DG is it requires some 18.1% of Armenia_LBA on top of 47.9% Bulgaria_IA and 34.1% AV2 unlike Albanian.DG and Greek_1.DG. His closest is Greek_1.DG which is nothing surprising but I'm not sure how to explain the fact that Cretan.DG and Greek_2.DG are closer to Bulgarian.DG than Albanian.DG is?

pop1         pop2              est      se
  <chr>        <chr>           <dbl>   <dbl>
1 Bulgarian.DG Albanian.DG  0.00954  0.00338
2 Bulgarian.DG Cretan.DG    0.00125  0.00173
3 Bulgarian.DG Greek_1.DG  -0.000884 0.00292
4 Bulgarian.DG Greek_2.DG   0.00197  0.00282

As for the Albanians, the model above seems realistic when taking into account their yDna. Anything above 25% Slavic admixture doesn't seem realistic to me.

pop1        pop2              est      se
  <chr>       <chr>           <dbl>   <dbl>
1 Albanian.DG Bulgarian.DG  0.00954 0.00338
2 Albanian.DG Cretan.DG     0.0105  0.00342
3 Albanian.DG Greek_1.DG   -0.00111 0.00429
4 Albanian.DG Greek_2.DG    0.00744 0.00433

Again, the fact that Greek_2.DG is closer to Albanian.DG than Bulgarian.DG is, seems to tell about some other Greek ancestry in Greek_2.DG on top of the Pontic one.