дДНК (гаплогруппа Q)

[Аббат Бузони]

I0434   SVP47   Samara_Eneolithic   5200-4000 BCE   Khvalynsk II, Volga River, Samara   Russia   Q1a   

Терминальный снип - F2676.
То есть это уровень Q-MEH2
Что не сильно информативно:(

Источники:
http://www.biorxiv.org/content/early/2015/10/10/016477.full-text.pdf+html
https://docs.google.com/spreadsheets/d/1Vjbp450AwI7R-Y9J1YGSm9FjJWu9s9lx1azjUJbS8hQ/edit#gid=1120645201

Получил доступ к БАМ и проверил "хвалынца". Параллельно его проверил уважаемый Семаргл.
Выводы совпали:
Q: V2083/F1237/M1077+
Q-L472: L528/F2676+

То есть - увы, в этом сиквенсе больше ничего нет, чтобы позволило идентифицировать этот образец по нижерасположенным субкладам.
Скорее всего - вымершая ветвь. Q1a*.

А где сейчас ближайшая к нему популяция с Q1a?

[Шад]

I0434   SVP47   Samara_Eneolithic   5200-4000 BCE   Khvalynsk II, Volga River, Samara   Russia   Q1a   

Терминальный снип - F2676.
То есть это уровень Q-MEH2
Что не сильно информативно:(

Источники:
http://www.biorxiv.org/content/early/2015/10/10/016477.full-text.pdf+html
https://docs.google.com/spreadsheets/d/1Vjbp450AwI7R-Y9J1YGSm9FjJWu9s9lx1azjUJbS8hQ/edit#gid=1120645201

Получил доступ к БАМ и проверил "хвалынца". Параллельно его проверил уважаемый Семаргл.
Выводы совпали:
Q: V2083/F1237/M1077+
Q-L472: L528/F2676+

То есть - увы, в этом сиквенсе больше ничего нет, чтобы позволило идентифицировать этот образец по нижерасположенным субкладам.
Скорее всего - вымершая ветвь. Q1a*.

А где сейчас ближайшая к нему популяция с Q1a?

Если вопрос по аутосомам, то лучше уточнить у Сергея.
А по Y, как мне кажется вопрос лишен смысла, так как датировка образца - 5200-4000 BCE, а датировка ветви - formed 29500 ybp, TMRCA 26100 ybp
Я уточнил у Семаргла - никаких пересечений даже по приватным снипам с базой YFull нет. Явная тупиковая ветвь. Хотя всегда есть шанс, что где-то бродят потомки:)

[Шад]

UPD от Srkz

Ситуация примерно, как с Y - смысла искать близость с современниками нет. Грубо он между EHG и ямниками.

[Аббат Бузони]

Известно из какого костяка брали ДНК? Реконструкций по Хвалынску II не мало.

[Srkz]

Известно из какого костяка брали ДНК? Реконструкций по Хвалынску II не мало.

Особые приметы: Следы четырех ударов на черепе, возраст 45-55, закопан без нужных в загробном мире предметов. Захоронение 17:
10434 / SVP47 (grave 17)
Male (confirmed genetically), age 45-55, positioned contracted on his side, with 4
pathological wounds on his skull, one of which probably was fatal. No grave gifts or animal
sacrifices accompanied the burial. His Q1a Y-chromosome haplotype is unique in the Samara
steppe series, but his U4a2 or U4d MtDNA haplotype are not unusual.

[Аббат Бузони]

Хвалынский II энеолитический могильник. Костяк 17.

[Аббат Бузони]

Сергей, а какие номера у R1b и R1a?

[rozenblatt]

Сергей, а какие номера у R1b и R1a?

10122 / SVP35 (grave 12)
Male (confirmed genetically), age 20-30, positioned on his back with raised knees, with 293
copper artifacts, mostly beads, amounting to 80% of the copper objects in the combined
cemeteries of Khvalynsk I and II. Probably a high-status individual, his Y-chromosome
haplotype, R1b1, also characterized the high-status individuals buried under kurgans in later
Yamnaya graves in this region, so he could be regarded as a founder of an elite group of
patrilineally related families. His MtDNA haplotype H2a1 is unique in the Samara series.

10433 / SVP46 (grave 1)
Male (confirmed genetically), age 30-35, positioned on his back with raised knees, with a
copper ring and a copper bead. His R1a1 haplotype shows that this haplotype was present in
the region, although it is not represented later in high-status Yamnaya graves. His U5a1i
MtDNA haplotype is part of a U5a1 group well documented in the Samara series.

[Аббат Бузони]

Спасибо.


Хвалынский II энеолитический могильник. Костяк 12.  R1b1


Хвалынский II энеолитический могильник. Костяк 1. R1a1

[Шад]

Nour Moussa
Abstract
The study of Ancient DNA (aDNA), DNA recovered from archaeological and historic post mortem material, has complemented the study of anthropology and archaeology. There are several challenges in the retrieval and analysis of DNA from ancient specimens including exogenous contamination with modern DNA, polymerase chain reaction (PCR) inhibitors and DNA damage because of environmental factors. Despite all the obstacles, the extraction of aDNA is still possible through reliable extraction methods and highly sensitive PCR-based technologies that facilitated the use of aDNA analysis in revealing the maternal and paternal backgrounds of ancient populations. This dissertation examines prehistoric hunter-gatherer populations that inhabited Siberia, Russia, several thousand years ago. The Lake Baikal of Siberia was home to two temporally distinct populations from Early Neolithic, EN (8000-6800 cal BP) to Late Neolithic-Early Bronze Age, LN-EBA (5800-4000 cal BP). The EN group was separated from the LN-EBA group by a 1000-year gap (hiatus). Several cemeteries have been excavated as part of an international Baikal Archaeology Project (BAP). These include one EN cemetery (Shamanka II) and two LN-EBA cemeteries (Kurma XI and Khuzhir-Nuge XIV). Maternally inherited mitochondrial DNA (mtDNA) has been examined previously for two EN cemeteries (Lokomotiv and Shamanka II) and one of the LN-EBA cemeteries (Ust’-Ida). mtDNA has not been analyzed before from the Kurma XI cemetery. This dissertation hypothesis focused on the examination of mtDNA from Shamanka II and Kurma XI cemeteries and examination of Y-chromosomal DNA from the four excavated cemeteries (Lokomotiv, Shamanka II, Ust’-Ida and Kurma XI) to identify genetic discontinuity and/or continuity between and within the EN and LN-EBA of prehistoric populations. The project aims were; first, modification of published methods for sample preparation, DNA extraction and PCR amplification for aDNA research. Second, interpretation of mtDNA haplogroup distribution from Kurma XI in the context of other Lake Baikal cemeteries. Third, compare the genetic affinities of the prehistoric populations with the contemporary populations of the area through the maternal lineage. Finally, comprison of mtDNA and Y-chromosomal haplogroup distributions to determine maternal and paternal genetic affinities. Four different mtDNA haplogroups were found in Kurma XI individuals including A, D, F and Z. mtDNA haplogroup Z was not represented before in Lake Baikal’s prehistoric populations. In addition, six extra samples from Shamanka II were analyzed to reveal that Shamanka II and Lokomotiv did not share the same maternal background as was previously suggested. New mtDNA results from Kurma XI and Shamanka II suggested that each of the EN cemeteries and LN-EBA cemeteries had a different maternal origin; however, Kurma XI shared a similar maternal origin with Lokomotiv and also with Shamanka II. Through SNaPshot multiplex PCR amplification, Y-chromosomal haplogroups were obtained from male individuals in the four cemeteries. Individuals from Lokomotiv and Shamanka II were found to possess haplogroups K, R1a1 and C3, and individuals from Ust’-Ida and Kurma XI were found to belong to haplogroups Q, K and unidentified SNP (L914). For those individuals belonging to haplogroup Q, further experimentation to examine sub-haplogroups of Q revealed that these individuals belong to sub-haplogroup Q1a3. There was significant heterogeneity in the males from the Lokomotiv cemetery when compared to the other three cemeteries. Furthermore, the Y-chromosome results showed a discontinuity between the EN and the LN-EBA populations of Lake Baikal. Combining the maternal and the paternal results from the prehistoric populations of Lake Baikal suggested a patrilocal post-marital residence pattern, where females moved to their husbands’ birthplace after marriage. This research highlighted the utility of DNA analysis as an archaeological tool in conjunction with burial practices and artifacts in making inferences about the prehistoric population structure.

https://era.library.ualberta.ca/files/wm117r51m#.V8fk6YU3_x5

[Шад]

A Genetic Analysis of Human Remains from the Bronze Age (2nd Millennium BC) Cemetery Bertek-56 in the Altai Mountains (in Russian)
Pilipenko et al., 2016

Article in Archaeology Ethnology and Anthropology of Eurasia 44(4):141-149 · December 2016
DOI: 10.17746/1563-0102.2016.44.4.141-149
https://www.researchgate.net/publication/311562402_A_Genetic_Analysis_of_Human_Remains_from_the_Bronze_Age_2nd_Millennium_BC_Cemetery_Bertek-56_in_the_Altai_Mountains_in_Russian

Abstract
Bone samples from two individuals (an adult and a child) buried at a Middle Bronze Age cemetery Bertek-56 on the Ukok Plateau, Altai, were subjected to a genetic analysis. The results are interpreted with reference to archaeological and craniometric data. Four systems of genetic markers were analyzed: mitochondrial DNA, the polymorphic part of amelogenin gene, autosomal STR-loci, and STR-loci of Y-chromosome. Complete information on these genetic markers was obtained for the adult individual. For the child, data on mitochondrial DNA, amelogenin gene, and partial profi les of autosomal and Y-chromosomal STR-loci are available. Both individuals were shown to be male and unrelated. The boy’s mitochondrial DNA belongs to the Western Eurasian haplogroup K (subgroup K1a24a), and that of the adult male, to the Eastern Eurasian haplogroup C. Using the predictor program, the Y-chromosomal haplotype of the adult individual (17 Y-chromosomal STR-loci) was identifi ed as Eastern Eurasian haplogroup Q. Phylogenetic and phylogeographic analysis of the results suggests that the Bertek population originated from an admixture of two genetically contrasting groups, one with Eastern Eurasian, the other with Western Eurasian features. These results are consistent with those of the archaeological and craniometric analysis indicating the admixture of autochthonous groups with immigrants from western Eurasia

В работе опубликован (см. таблица 2) гаплотип (второй индивид, взрослый), который явно можно отнести к гаплогруппе Q.
Далее мы параллельно с уважаемым Nimissin пришли к выводу, что он - Q-M120. Что, в принципе, совпадает с мнениями авторов, которые обнаружили совпадающие гаплотипы в YHRD (коллекции по Северо-Восточному Китаю и Корее).
Из дополнения уважаемого Nimissin:

The second sample (adult man) from Table 2 undoubtedly belongs to Q-M120.
13-14-30-24-9-14-14-15,21-12-11-14-19-16-16-22-10.

Two modern Mongolian samples were genotyped by Di Cristofaro et al. (2013) as Q-M120:
Mongol-Central
14-14-30-24-9-14-14-15,23-12-10-14-19-15-16-22-10,
Mongol-NorthWest
13-14-31-24-9-14-14-16,21-12-10-14-19-17-16-22-10.
Mongolian from Ulaanbaatar (Y23 without SNP)
13-14-30-24-9-14-15-15,20-12-12-14-19-15-16-22-10-18-24-12-13-20-10.

Я в своих выводах опирался на базу гаплотипов FTDNA и данные Jean A Trejaut et al 2014 по народу Akha (этот гаплотип Q-M120 был занесен в базу Семаргла). 

В ходе этого небольшого исследования мы также подтвердили GATAH4 <=10 (NIST) или 9 (FTDNA) в качестве признака не только Q1b, но и Q-M120.

[sahaliyan]

A Genetic Analysis of Human Remains from the Bronze Age (2nd Millennium BC) Cemetery Bertek-56 in the Altai Mountains (in Russian)
Pilipenko et al., 2016

Article in Archaeology Ethnology and Anthropology of Eurasia 44(4):141-149 · December 2016
DOI: 10.17746/1563-0102.2016.44.4.141-149
https://www.researchgate.net/publication/311562402_A_Genetic_Analysis_of_Human_Remains_from_the_Bronze_Age_2nd_Millennium_BC_Cemetery_Bertek-56_in_the_Altai_Mountains_in_Russian

Abstract
Bone samples from two individuals (an adult and a child) buried at a Middle Bronze Age cemetery Bertek-56 on the Ukok Plateau, Altai, were subjected to a genetic analysis. The results are interpreted with reference to archaeological and craniometric data. Four systems of genetic markers were analyzed: mitochondrial DNA, the polymorphic part of amelogenin gene, autosomal STR-loci, and STR-loci of Y-chromosome. Complete information on these genetic markers was obtained for the adult individual. For the child, data on mitochondrial DNA, amelogenin gene, and partial profi les of autosomal and Y-chromosomal STR-loci are available. Both individuals were shown to be male and unrelated. The boy’s mitochondrial DNA belongs to the Western Eurasian haplogroup K (subgroup K1a24a), and that of the adult male, to the Eastern Eurasian haplogroup C. Using the predictor program, the Y-chromosomal haplotype of the adult individual (17 Y-chromosomal STR-loci) was identifi ed as Eastern Eurasian haplogroup Q. Phylogenetic and phylogeographic analysis of the results suggests that the Bertek population originated from an admixture of two genetically contrasting groups, one with Eastern Eurasian, the other with Western Eurasian features. These results are consistent with those of the archaeological and craniometric analysis indicating the admixture of autochthonous groups with immigrants from western Eurasia

В работе опубликован (см. таблица 2) гаплотип (второй индивид, взрослый), который явно можно отнести к гаплогруппе Q.
Далее мы параллельно с уважаемым Nimissin пришли к выводу, что он - Q-M120. Что, в принципе, совпадает с мнениями авторов, которые обнаружили совпадающие гаплотипы в YHRD (коллекции по Северо-Восточному Китаю и Корее).
Из дополнения уважаемого Nimissin:

The second sample (adult man) from Table 2 undoubtedly belongs to Q-M120.
13-14-30-24-9-14-14-15,21-12-11-14-19-16-16-22-10.

Two modern Mongolian samples were genotyped by Di Cristofaro et al. (2013) as Q-M120:
Mongol-Central
14-14-30-24-9-14-14-15,23-12-10-14-19-15-16-22-10,
Mongol-NorthWest
13-14-31-24-9-14-14-16,21-12-10-14-19-17-16-22-10.
Mongolian from Ulaanbaatar (Y23 without SNP)
13-14-30-24-9-14-15-15,20-12-12-14-19-15-16-22-10-18-24-12-13-20-10.

Я в своих выводах опирался на базу гаплотипов FTDNA и данные Jean A Trejaut et al 2014 по народу Akha (этот гаплотип Q-M120 был занесен в базу Семаргла). 

В ходе этого небольшого исследования мы также подтвердили GATAH4 <=10 (NIST) или 9 (FTDNA) в качестве признака не только Q1b, но и Q-M120.

There are full match samples in Han Chinese of Henan,Shandong,,Zhejiang and Chengdu,and more 1-2 steps samples,this is amazing

[Nimissin]

В настоящее время в Китае частота гаплогруппы Q-M120 составляет около 3 % (Guo et al., 2014).
В работе Zhao et al. (2014) "Ancient DNA Evidence Reveals that the Y Chromosome Haplogroup Q1a1 Admixed into the Han Chinese 3,000 Years Ago" было показано, что 3000 лет назад среди древнего населения археологического памятника Hengbei (на Лессовом плато) частота гаплогруппы Q-M120 составляла около 40 %. Причем эта гаплогруппа была обнаружена в образцах из погребений аристократов и простолюдинов, а среди образцов из захоронений рабов - отсутствовала. Эти люди жили на рубеже II и I тысячелетий до нашей эры, в эпоху династии Чжоу, известной своими бронзами.

[Шад]

There are full match samples in Han Chinese of Henan,Shandong,,Zhejiang and Chengdu,and more 1-2 steps samples,this is amazing

@sahaliyan
Can you identify the articles, where the full match samples have been mentioned? Or is their number in YHRD?

[sahaliyan]

There are full match samples in Han Chinese of Henan,Shandong,,Zhejiang and Chengdu,and more 1-2 steps samples,this is amazing

@sahaliyan
Can you identify the articles, where the full match samples have been mentioned? Or is their number in YHRD?

I think most of those samples already in YHRD