Related post: Modelling the Roman era sample from Marathon Greece on qpAdm and G25
Study: A genetic history of the Balkans from Roman frontier to Slavic migrations
Post by Davidski about the study: https://eurogenes.blogspot.com/2024/01/romans-and-slavs-in-balkans-olalde-et.html
I used the reference/right populations as in that study but expanded upon them to decrease standard errors. If you have any criticism then tell me in the comments so i can improve the models.
The Balkan study didn't use a Balkan proxy for mainland Greeks even though they have a lot of Balkan Y-DNA from both sides of the Balkans, Arvanites/Albanians, Thracian etc, obviously in my models i have to take into account the Balkan admix. The models with South Slavic fit the best when rotating because they take into account the Balkan admx. They could have used a Balkan or South Slavic proxy if they added more right/reference populations + a lot of good quality Rome Imperial samples that are identical to Mugla West Anatolian samples to decrease the Standard Errors.The "Ottoman Turkish" proxy of the study is also sus, the paper claims that it is central Asian mixed but i can't find any models showcasing how much Central Asian admix it has. My qpAdm models don't fail without Central Asian/East Asian despite using Mongolia_North_N in the reference/right pops. It seems that they might have used some very low Turkic mixed sample that is mostly Byzantine Greek and just tagged it as Ottoman Turkish. If i somehow missed their models about the Turkic admix of the "Ottoman Turkish" samples then tell me in the comments.
If you are curious about the absence of Mycenaean as a source in the qpAdm chart, please scroll down to the qpAdm reference section below for a detailed overview of the models utilized. The selection criteria prioritized models based on their P-values, with preference given to those demonstrating the highest statistical significance. Furthermore, modern Greeks scored less than 5% excess Mycenaean when using the Roman era Aegean proxy.
The Aegean proxy in my analysis consist of samples from the Roman-era Mugla in West Anatolia, along with Imperial Rome samples that are identical to those from Mugla. Furthermore, the Marathon sample from 300 AD southern Greece is identical to those samples. It scores a total of 30-50% Mycenaean admix depending on the proxies used so Mugla samples might be an actual good representative of Roman era Southern Greeks until we get more samples.
Explaining more about the Roman era Aegean proxy here:
More work will be be done on these models, i will update them in the future.
qpAdm models:
Scroll down to see all the models i ran.
Keep in mind that because you cant use too many overlapping sources on qpAdm then some sources are forced to overcompensate for the lacking sources.
Sample of the Roman era Greek samples might be faulty, from one model i've made without them, the result was a bit closer to the G25 charts. I will remake the chart another time.
I rotated the sources
qpAdm references/outgroups:
qpAdm references/outgroups:
right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Tajikistan_Ksirov_Kushan', 'Croatia_EIA', 'Albania_BA_IA','Macedonia_Classical_Hellenistic', 'Bulgaria_EIA', 'Greece_Delphi_BA_Mycenaean', 'Greece_BA_Mycenaean', 'Lebanon_MBA.SG', 'Russia_Sunghir_Medieval.SG', 'Montenegro_Doclea_Roman.SG')
Aegean 1-200AD samples used https://pastebin.com/KdHE0uwT
G25 models:
I think G25 might be a bit better at making more complicated models and capturing small recent variations so check this post:
The qpAdm models above though confirm the main shifts that we see on G25
The Tajik like ancestry appear in the Levant during the Hellenistic and it also shows up in Cypriots
3 out of 8 of the Cypriot samples are outliers, 2 seem to be Maronite Cypriots while 1 is half mainland Greek. I don't know why they included them. I have seen dozens of Cypriot Greek samples from people whose all grandparents are native Cypriots and none of them were like those 3 samples. The Cypriot_Maronite_o samples can be modelled as 100% Lebanese Christian while the normal Cypriot Greek samples cannot.
P 0.0448 good fit
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot_Maronite_o.HO Lebanese_Christian.HO 1 1.14e-13 8.79e12
P 0.000000388 rejected
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Lebanese_Christian.HO 1 1.14e-13 8.79e12
P 0.887 good fit
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot_mainlandmixed_o.HO Cypriot.HO 0.682 0.0877 7.78
2 Cypriot_mainlandmixed_o.HO Greek_Thessaloniki.HO 0.318 0.0877 3.62
P 0.919 good fit
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot_mainlandmixed_o.HO Cypriot.HO 0.602 0.119 5.04
2 Cypriot_mainlandmixed_o.HO Greek_Athens_10-20.WGA.HO 0.398 0.119 3.33
Cypriot outlier samples:
Cyprus2AJ19.HO M Cypriot_Maronite_o.HO
Cyprus21AJ19.HO M Cypriot_Maronite_o.HO
Cyprus13AJ19.HO M Cypriot_mainlandmixed_o.HO
qpAdm References/outgroups:
Important info:
I rotated the sources/references unless i specified otherwise
---------------------------------------------------------------
right = c('Mbuti.HO', 'Russia_Samara_EBA_Yamnaya', 'Russia_Karelia_HG', 'Serbia_IronGates_Mesolithic', 'Turkey_N', 'Iran_GanjDareh_N', 'Spain_IA', 'Greece_Minoan_Lassithi', 'Croatia_MLBA', 'Netherlands_EIA', 'Netherlands_MBA', 'Russia_IA_Ingria.SG', 'Latvia_BA', 'Turkey_EBA_II.SG', 'Israel_C', 'Armenia_EBA_KuraAraxes', 'Mongolia_North_N', 'Russia_MLBA_Sintashta', 'Iran_C_SehGabi', 'Tajikistan_Ksirov_Kushan', 'Croatia_EIA', 'Albania_BA_IA','Macedonia_Classical_Hellenistic', 'Bulgaria_EIA', 'Greece_Delphi_BA_Mycenaean', 'Greece_BA_Mycenaean', 'Lebanon_MBA.SG', 'Russia_Sunghir_Medieval.SG', 'Montenegro_Doclea_Roman.SG')
left = c('Aegean(Roman_era_1-200AD).SG', 'Greece_BA_Mycenaean', 'Montenegro_Doclea_Roman.SG')
target = c('Greek_Athens_10-20.WGA.HO')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop
P 0.204
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.441 0.0378 11.7
2 Greek_Thessaloniki.HO Macedonia_Classical_Hellenistic 0.0355 0.0560 0.633
3 Greek_Thessaloniki.HO Montenegro_Doclea_Roman.SG 0.523 0.0303 17.3
P 0.136
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.462 0.0196 23.6
2 Greek_Thessaloniki.HO Montenegro_Doclea_Roman.SG 0.538 0.0196 27.5
P 0.0771
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.478 0.0441 10.8
2 Greek_Thessaloniki.HO Greece_BA_Mycenaean -0.0186 0.0434 -0.429
3 Greek_Thessaloniki.HO Montenegro_Doclea_Roman.SG 0.541 0.0202 26.8
P 0.0759
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.478 0.0322 14.8
2 Greek_Thessaloniki.HO Albania_BA_IA -0.0343 0.0535 -0.642
3 Greek_Thessaloniki.HO Montenegro_Doclea_Roman.SG 0.557 0.0347 16.1
P 0.0687
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.444 0.0335 13.3
2 Greek_Thessaloniki.HO Bulgaria_EIA 0.0235 0.0336 0.697
3 Greek_Thessaloniki.HO Montenegro_Doclea_Roman.SG 0.533 0.0203 26.3
P 0.0850
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.578 0.0499 11.6
2 Greek_Thessaloniki.HO Greece_BA_Mycenaean 0.0140 0.0488 0.286
3 Greek_Thessaloniki.HO Russia_Sunghir_Medieval.SG 0.408 0.0183 22.3
P 0.112
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Thessaloniki.HO Aegean(Roman_era_1-200AD).SG 0.555 0.0447 12.4
2 Greek_Thessaloniki.HO Macedonia_Classical_Hellenistic 0.0545 0.0611 0.892
3 Greek_Thessaloniki.HO Russia_Sunghir_Medieval.SG 0.390 0.0267 14.6
---------------------------------------------------------------------------------------
P 0.150
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.590 0.0216 27.3
2 Greek_Athens_10-20.WGA.HO Montenegro_Doclea_Roman.SG 0.410 0.0216 19.0
P 0.118
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.676 0.0420 16.1
2 Greek_Athens_10-20.WGA.HO Albania_BA_IA 0.0334 0.0662 0.504
3 Greek_Athens_10-20.WGA.HO Russia_Sunghir_Medieval.SG 0.291 0.0337 8.64
P 0.0844
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.652 0.0500 13.0
2 Greek_Athens_10-20.WGA.HO Macedonia_Classical_Hellenistic 0.0620 0.0715 0.868
3 Greek_Athens_10-20.WGA.HO Russia_Sunghir_Medieval.SG 0.286 0.0308 9.30
P 0.0881
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.561 0.0460 12.2
2 Greek_Athens_10-20.WGA.HO Macedonia_Classical_Hellenistic 0.0531 0.0762 0.697
3 Greek_Athens_10-20.WGA.HO Montenegro_Doclea_Roman.SG 0.386 0.0413 9.36
P 0.0707
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.677 0.0487 13.9
2 Greek_Athens_10-20.WGA.HO Greece_BA_Mycenaean 0.0168 0.0482 0.349
3 Greek_Athens_10-20.WGA.HO Russia_Sunghir_Medieval.SG 0.307 0.0189 16.2
P 0.0655
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.590 0.0474 12.5
2 Greek_Athens_10-20.WGA.HO Greece_BA_Mycenaean -0.00186 0.0455 -0.0409
3 Greek_Athens_10-20.WGA.HO Montenegro_Doclea_Roman.SG 0.412 0.0220 18.7
P 0.0837
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Greek_Athens_10-20.WGA.HO Aegean(Roman_era_1-200AD).SG 0.598 0.0361 16.6
2 Greek_Athens_10-20.WGA.HO Albania_BA_IA -0.0145 0.0659 -0.220
3 Greek_Athens_10-20.WGA.HO Montenegro_Doclea_Roman.SG 0.417 0.0434 9.60
---------------------------------------------------------------------------------------
P 0.341
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cretan.DG Aegean(Roman_era_1-200AD).SG 0.732 0.0338 21.7
2 Cretan.DG Montenegro_Doclea_Roman.SG 0.268 0.0338 7.92
P 0.278
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cretan.DG Aegean(Roman_era_1-200AD).SG 0.625 0.106 5.89
2 Cretan.DG Montenegro_Doclea_Roman.SG 0.298 0.0414 7.19
3 Cretan.DG Lebanon_MBA.SG 0.0774 0.0769 1.01
```c
```
---------------------------------------------------------------------------------------
P 0.0182
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.661 0.0608 10.9
2 Cypriot.HO Lebanon_MBA.SG 0.229 0.0537 4.25
3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0327 0.0230 1.42
4 Cypriot.HO Tajikistan_Ksirov_Kushan 0.0775 0.0269 2.88
P 0.00430
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.651 0.0661 9.85
2 Cypriot.HO Lebanon_MBA.SG 0.276 0.0545 5.07
3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0725 0.0181 4.00
P 0.00104
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.575 0.0950 6.05
2 Cypriot.HO Lebanon_MBA.SG 0.313 0.0691 4.53
3 Cypriot.HO Montenegro_Doclea_Roman.SG 0.112 0.0319 3.52
P 0.00389
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.621 0.0864 7.19
2 Cypriot.HO Lebanon_MBA.SG 0.248 0.0673 3.69
3 Cypriot.HO Montenegro_Doclea_Roman.SG 0.0567 0.0382 1.48
4 Cypriot.HO Tajikistan_Ksirov_Kushan 0.0741 0.0278 2.67
---------------------------------------------------------------------------------------
quick test for Turkic, didnt have Turkic on the right pops in the previous models.
P 0.00000279
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Cypriot.HO Aegean(Roman_era_1-200AD).SG 0.704 0.0776 9.08
2 Cypriot.HO Lebanon_MBA.SG 0.229 0.0649 3.53
3 Cypriot.HO Russia_Sunghir_Medieval.SG 0.0481 0.0244 1.97
4 Cypriot.HO Kazakhstan_Medieval_Nomad.SG 0.0183 0.00998 1.83
---------------------------------------------------------------------------------------
P 0.152
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Montenegro_Doclea_Roman.SG Aegean(Roman_era_1-200AD).SG 0.197 0.0423 4.65
2 Montenegro_Doclea_Roman.SG Croatia_EIA 0.118 0.0677 1.75
3 Montenegro_Doclea_Roman.SG Russia_Sunghir_Medieval.SG 0.685 0.0496 13.8
---------------------------------------------------------------------------------------
P 0.149
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Croatian.HO Montenegro_Doclea_Roman.SG 1 1.14e-13 8.79e12
---------------------------------------------------------------------------------------
P 0.0000798
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Montenegro_Doclea_Roman.SG Croatia_EIA 0.233 0.0579 4.02
2 Montenegro_Doclea_Roman.SG Russia_Sunghir_Medieval.SG 0.767 0.0579 13.2
---------------------------------------------------------------------------------------
P 0.0121
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Albanian.HO Aegean(Roman_era_1-200AD).SG 0.536 0.0464 11.5
2 Albanian.HO Albania_BA_IA 0.0594 0.0716 0.829
3 Albanian.HO Russia_Sunghir_Medieval.SG 0.405 0.0374 10.8
---------------------------------------------------------------------------------------
P 0.000771
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Albanian.HO Aegean(Roman_era_1-200AD).SG 0.450 0.0411 11.0
2 Albanian.HO Albania_BA_IA -0.0416 0.0710 -0.586
3 Albanian.HO Montenegro_Doclea_Roman.SG 0.591 0.0465 12.7
---------------------------------------------------------------------------------------
P 0.00204
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Albanian.HO Aegean(Roman_era_1-200AD).SG 0.432 0.0252 17.2
2 Albanian.HO Montenegro_Doclea_Roman.SG 0.568 0.0252 22.6
---------------------------------------------------------------------------------------
P 0.118
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.449 0.0227 19.8
2 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.551 0.0227 24.2
P 0.0473
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.453 0.0501 9.03
2 Bulgarian.HO Bulgaria_EIA -0.00536 0.0530 -0.101
3 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.553 0.0243 22.7
P 0.00666
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.256 0.0244 10.5
2 Bulgarian.HO Montenegro_Doclea_Roman.SG 0.744 0.0244 30.5
P 0.00106
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.317 0.0447 7.09
2 Bulgarian.HO Bulgaria_EIA -0.0727 0.0462 -1.57
3 Bulgarian.HO Montenegro_Doclea_Roman.SG 0.755 0.0262 28.8
P 0.0473
target left weight se z
<chr> <chr> <dbl> <dbl> <dbl>
1 Bulgarian.HO Aegean(Roman_era_1-200AD).SG 0.453 0.0501 9.03
2 Bulgarian.HO Bulgaria_EIA -0.00536 0.0530 -0.101
3 Bulgarian.HO Russia_Sunghir_Medieval.SG 0.553 0.0243 22.7
DNA samples from the Version v54.1.p1 Harvard dataset: https://reichdata.hms.harvard.edu/pub/datasets/amh_repo/curated_releases/
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