Слава, я нигеде не обнаружил чётки обоснований что аутосомы у этого случая из ME. Может быть тебе попадались? Как они вообще чётко верифицировать происхождение этих аутосом с ME. Сладётся мне что тампрменяется похожая методология как и в MTA или у Маргаряна, где показано по некторым случаям типа "поляк-финн".
Да, к своему стыду, пока ещё не углублялся в текст и в Supplementary, хотя самому очень интересно. У меня пока что всё на доверии тем добрым людям по моей ссылке выше, кто читал публикацию.)
Это первый L1189 римского периода с территории современной Сербии.
Один Z1842 римского периода с территории Италии уже есть в предыдущей публикации, посвящённой римлянам, но тоже так и не дошли руки до более-менее глубокого знакомства с этим образцом. Помню, что на PCA он был где-то в районе Восточного Средиземноморья.
Этот образец из ближневосточного кластера. Далал себе на память краткое резюме статьи. Вот его кусочек на эту тему:
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Период от основания Римских провинций на Балканах до кризиса империи 3 века н.э. (1-250 г.)Выделены 2 основных генетических кластера характеризующих населения римских дунайских провинций данного исторического периода:
1) Население местного происхождения - «балканский железный век» (моделируемый как 67% Эгейской бронзы + железный век Словении). Локальное происхождение данной группы подтверждается и распространенностью Y-хромосомой гаплогруппы E-V13. К Данныму кластеру относится 47% изученных образцов 1-550 г.г.
2) Пришлое население с ближневосточных генетическим профилем – «ближневосточный кластер» (близкородственные западно-анатолийскому халколиту).
Данная картина соответствует результатам, ранее полученным из итальянской провинции Лацио, где в имперский период также зафиксирован значительный приток населения из восточного Средиземноморья."
Уже вторая статья констатирует масштабный приток генов из восточного Средиземноморья в римские города в период расцвета империи. Отсюда, видимо, большинство ближневосточных игреков у восточных европейцев.
Пояснения из Suppl'а:
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qpWave tests for admixture
Given the high ancestry heterogeneity observed in PCA and ADMIXTURE, we used the qpWave 20 from AdmixTools v.6. (https://github.com/DReichLab/AdmixTools) to group individuals with similar ancestry profiles into relatively homogenous clusters, whose ancestry we could then model using qpAdm. By increasing sample size for each modeled cluster, we increase the power to reject non-fitting models, as compared to an approach where samples are modelled individually.
Using the set of outgroups shown in Table ST2, we first ran in qpWave all possible pairwise comparisons of high-quality individuals (>300,000 SNPs) from Viminacium, Mediana and Timacum Minus (Slog Necropolis), and all possible pairwise comparisons between high-quality individuals (>300,000 SNPs) from Timacum Minus (Kuline necropolis). We chose to run a separate analysis of Kuline due to a chronological gap of 400-500 years with the other necropolises.
The P-values of all pairwise qpWave tests are depicted is Figure S11. We observe 3 differentiated clusters that we named the Central/Northern European-related cluster (“CNE”), the Balkans Iron Age-related cluster (“Balkans IA”) and the Near Eastern-related cluster (“NE”) due to their position in PCA projections. Within each of these clusters, qpWave tests yielded high P-values indicating that individuals were symmetri-cally related to the populations in the outgroup set.
Next, we tested in qpWave the lower coverage individuals with <300,000 SNPs (excluding those with fewer than 15,000 SNPs) against the five clusters identified in the first step (Figure S11.B) and that were either assigned to one of these five clusters or to new clusters (Africa outlier and Steppe-related cluster) if they were not consistent with forming a clade with any of them. For borderline cases, we also considered PCA positions for aiding cluster assignment. Cluster assignment for each individual is shown in Table ST3. Finally, clusters defined in the two previous steps were tested against each other to check that they were differentially relative to the outgroup. None of the cluster significantly shared ancestry against the used set of outgroups.
qpAdm admixture modelling
In qpWave (Supplementary Section 11) we grouped individuals from Viminacium, Timacum Minus and Mediana into clusters. In the following section, we attempt to model the ancestry of each of these relatively homogenous clusters.
We used the same set of outgroups as for the qpWave tests (Table ST2): West_Africa_ancient, Sudan_EarlyChristian, Tianyuan, EHG, Iron_Gates_HG, Le-vant_N, Anatolia_N, Iran_N, Yamnaya_Samara, Alalakh_MLBA, Iberia_IA, Mycenae-an, Slovenia_EIA, Netherlands_IA, Russia_Ingria_IA, Steppe_IA, unless otherwise jus-tified for specific tests. This set of populations includes groups distantly related (both geographically and chronologically) to our Serbian ancient individuals, and more prox-imate groups that could form a clade with the true sources of ancestry in them.
We tested all possible 1-way, 2-way and 3-way combinations of populations in our outgroup population set, using them as sources and leaving the remaining populations as outgroups in the model. We then checked whether a 1-way model was sufficient to ex-plain the ancestry in the test population. If no 1-way model showed a good fit (p-value > 0.05), we looked for plausible 2-way models, and, if the 2-way model was still not fit-ting, we looked for 3-way models. We computed standard errors for qpAdm tests using a weighted block jackknife over 5-Mb blocks.
Near Eastern cluster
There are no 1-way models nor 2-way models fitting the ancestry of this group. The only model that worked (P-value = 0.096) using this set of outgroups is:
0.90 (±0.022)Mycenenan + 0.082 (±0.015) Iran_N + 0.019 (±0.017) Netherlands_IA
This model suggests that the ancestry in this group deviates from Mycenaean-related ancestry in the direction of Iran Neolithic-related ancestry, but it does not provide good information about the proximal ancestry of this cluster. Furthermore, the ancestry proportion assigned to Netherlands_IA is very low (barely different from 0), and the 2-way model featuring Iran_N and Mycenaean with Netherlands_IA in the outgroups fails with P-value=0.007, likely indicating that to model this cluster of individuals one needs more central or northern European-related ancestry than that included in the model Iran_N+Mycenaean, but not as much as that present in Netherlands_IA. A plausible reason no other models work is that, even though this group clearly has a shift towards Anatolian Late Chalcolithic-Early Bronze Age groups in PCA, only one post-Neolithic Near Eastern group is included in the initial outgroup set, the Alalakh Middle-Late Bronze age group from Northern Levant, which is not a good proxy fom the ancestry in this cluster. Therefore, we tested 1-way models featuring an Anatolian Chalcolithic (LC) or Early Bronze Age (EBA) population as the only source (from West to East: Anatolia_Barcin_LC, Anatolia_Gondurle_EBA, Anatolia_CamlibelTarlasi_LC, Anatolia_Ikiztepe_LC, Anatolia_Arslantepe_LC, Anatolia_Arslantepe_EBA). Using the full set of outgroups in Table ST2, we obtained the results depicted in Table ST4.
Only the Late Chalcolithic individual from Barcın (near the Sea of Marmara) was a plausible proxy for the ancestry in this Near Eastern-related cluster of Roman-period Serbian individuals, although chronologically it is thousands of years earlier. To improve the fit of these models and based on the findings that Chalcolithic and Bronze Age populations from Anatolia had different levels of Iran Neolithic-related ancestry 53, we ran the same models again but added Iran Neolithic as a source together with the Anatolian groups, to account for possible differences in Iran Neolithic-related ancestry between the available Anatolian populations and the true source of ancestry in our test population.
We confirm that adding a small proportion of Iran Neolithic-related ancestry provides a good fit with Anatolia_Barcin_LC as the main ancestry source, while the other Anatoli-an sources continue to provide poor fits. Given that Anatolia_Barcin_LC is represented by a single individual with ~576K SNPs, we checked whether the good fit for this group could be due to a reduced power to reject poorly-fitting models, as compared to the other Anatolian groups that include several individuals 62. We thus tested the same model of Anatolian group + Iran_N but using single individuals with similar numbers of available SNPs as Anatolia_Barcin_LC.
In all cases, even when using individuals with substantially fewer SNPs than the Anato-lia_Barcin_LC individual, models are strongly rejected. This confirms that the well-fitting model for Anatolia_Barcin_LC is not a consequence of limited power to reject poorly-fitting models due to this group including only one individual.
To understand why Anatolia_Barcin_LC + Iran_N provides a good fit but models fea-turing other Anatolian groups + Iran_N are strongly rejected, we added as a third source the Balkans Iron Age-related cluster of Serbian Roman-period individuals modelled in the previous section (Supplementary section 12.1), to account for European-related an-cestry that could be missing in the Anatolian groups providing poor fits, but present in Anatolia_Barcin_LC and our test population (the Near Eastern-related cluster of Ro-man-period Serbian individuals)
The fit greatly improved by including the Balkans IA cluster as a source, suggesting that these Anatolian populations are missing a European/Balkan ancestry component that is present in Anatolia_Barcin_LC. and in the Near Eastern-related cluster of Serbian indi-viduals which is also chronologically more plausible.
To sum up, the individuals with Near Eastern affinities in Viminacium (the Near Eastern cluster) can be modelled as deriving the vast majority of their ancestry ultimately from groups related to Late Chalcolithic western Anatolians, although with slightly more Iran-Neolithic-related ancestry than the samples with currently available data. Even when including the modeling Indigenous Balkan populations, they must still derive roughly half their ancestry from groups related to Anatolians related to those from the Chalcolithic and Bronze Age. In the future, genomic data from Hellenistic and Roman Anatolia will provide more proximate sources for the ancestry of this cluster."