Результаты исследования древней ДНК (дДНК)

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От Вячеслава Носевича в ФБ.
"О чем еще не знает не только Клесов, но даже и попгенетики: R1a1-M17 (М417 не тестировалась, но весьма вероятна) найдена еще и у охотника-собирателя в верховьях Западной Двины возрастом 6000 лет назад. И ныне присутствует у примерно половины обитателей того же региона. Тоже арии из Европы через Балканы, конечно, занесли!
Сведения об этом факте опубликованы (точнее сказать -похоронены) в региональном археологическом сборнике, который ни поп-, ни прочие генетики без специальной наводки в жизни искать не станут: Археология озерных поселений IV—II тыс. до н. э.: хронология культур и природно- климатические ритмы. — СПб.: ООО «Периферия», 2014. Статья: Чекунова Е.М., Ярцева Н.В., Чекунов М.К., Мазуркевич А.Н. Первые результаты генотипирования коренных жителей и человеческих костных останков из археологических памятников Верхнего Подвинья. С. 287-294. Таблица на с. 294."

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Результаты генотипирования палеоматериала из археологических материалов Верхнего Подвинья.

http://www.academia.edu/9559700/Archaeology_of_lake_settlements_IV-II_mil._BC

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Between the Baltic and Danubian Worlds: The Genetic Affinities of a Middle Neolithic Population from Central Poland

Wiesław Lorkiewicz, Tomasz Płoszaj, Krystyna Jędrychowska-Dańska, Elżbieta Żądzińska, Dominik Strapagiel,   Elżbieta Haduch, Anita Szczepanek, Ryszard Grygiel, Henryk W. Witas.

Published: February 25, 2015.

Abstract

For a long time, anthropological and genetic research on the Neolithic revolution in Europe was mainly concentrated on the mechanism of agricultural dispersal over different parts of the continent. Recently, attention has shifted towards population processes that occurred after the arrival of the first farmers, transforming the genetically very distinctive early Neolithic Linear Pottery Culture (LBK) and Mesolithic forager populations into present-day Central Europeans. The latest studies indicate that significant changes in this respect took place within the post-Linear Pottery cultures of the Early and Middle Neolithic which were a bridge between the allochthonous LBK and the first indigenous Neolithic culture of north-central Europe—the Funnel Beaker culture (TRB). The paper presents data on mtDNA haplotypes of a Middle Neolithic population dated to 4700/4600–4100/4000 BC belonging to the Brześć Kujawski Group of the Lengyel culture (BKG) from the Kuyavia region in north-central Poland. BKG communities constituted the border of the “Danubian World” in this part of Europe for approx. seven centuries, neighboring foragers of the North European Plain and the southern Baltic basin. MtDNA haplogroups were determined in 11 individuals, and four mtDNA macrohaplogroups were found (H, U5, T, and HV0). The overall haplogroup pattern did not deviate from other post-Linear Pottery populations from central Europe, although a complete lack of N1a and the presence of U5a are noteworthy. Of greatest importance is the observed link between the BKG and the TRB horizon, confirmed by an independent analysis of the craniometric variation of Mesolithic and Neolithic populations inhabiting central Europe. Estimated phylogenetic pattern suggests significant contribution of the post-Linear BKG communities to the origin of the subsequent Middle Neolithic cultures, such as the TRB.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118316

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Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Hannes Schroedera, María C. Ávila-Arcosa, Anna-Sapfo Malaspinasa, G. David Poznikd, Marcela Sandoval-Velascoa, Meredith L. Carpenterc, José Víctor Moreno-Mayara, Martin Sikoraa, Philip L. F. Johnsone, Morten Erik Allentofta, José Alfredo Samaniegoa, Jay B. Haviserf, Michael W. Deeg, Thomas W. Stafford, Jr.h, Antonio Salasi, Ludovic Orlandoa, Eske Willersleva, Carlos D. Bustamantec, and M. Thomas P. Gilberta.

Abstract

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

http://www.pnas.org/content/early/2015/03/05/1421784112.abstract?sid=59bcbd72-0b08-4efb-8308-d38372b5bf08
http://www.pnas.org/content/early/2015/03/05/1421784112.full.pdf?with-ds=yes
http://www.pnas.org/content/suppl/2015/03/05/1421784112.DCSupplemental/pnas.1421784112.sapp.pdf
http://www.ebi.ac.uk/ena/data/view/PRJEB8269

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Eight thousand years of natural selection in Europe

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Iain Mathieson, Manuel A. Rojo Guerra, Johannes Krause, David Anthony, Dorcas Brown, Carles Lalueza Fox, Wolfgang Haak, Nick Patterson, David Reich.

Abstract

The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.

http://biorxiv.org/content/early/2015/03/13/016477
http://biorxiv.org/content/biorxiv/early/2015/03/13/016477.full.pdf

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Mitochondrial DNA diversity in the gene pool of the Neolithic and Early Bronze Age Cisbaikalian human population

R. O. Trapezov, A. S. Pilipenko, V. I. Molodin

Abstract

This paper presents the results of a study of a mitochondrial DNA sample (N = 15) from the remains of representatives of the Neolithic and Early Bronze Age (VI–III millennia BC) Cisbaikalian human population. It was found that the mitochondrial gene pool of the ancient population under study contains lineages of East Eurasian haplogroups D, G2a C, Z, and F1b. The results of the comparative analysis of the group under study with ancient and modern Eurasian populations suggest that the development of autochtonous East Eurasian genetic components was the main mechanism of the formation of the population of the Baikal region. Genetic contacts with populations of neighboring regions of Central Asia also contributed to the formation of the gene pool of the Cisbaikalian population.

http://link.springer.com/article/10.1134/S2079059715010104
http://www.bionet.nsc.ru/vogis/download/18-3/07_Trapezov.pdf

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MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population

Aleksandr S. Pilipenko , Rostislav O. Trapezov, Anton A. Zhuravlev, Vyacheslav I. Molodin, Aida G. Romaschenko

Published: May 7, 2015

Abstract

Background

The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history.

Results and Conclusion

We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V—I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages’ phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127182

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Online Ancient Genome Repository

https://www.oagr.org.au/

Studies stored: 4
Datasets stored: 4
Files stored: 516
Data stored (at least): 697.8 GB


Пока скромно, но начало положено...

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Population genomics of Bronze Age Eurasia

Morten E. Allentoft et al.

Abstract

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html
http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html#supplementary-information
http://www.ebi.ac.uk/ena/data/view/PRJEB9021

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Mitochondrial DNA Suggests a Western Eurasian origin for Ancient (Proto-) Bulgarians

Nesheva, D V.; Karachanak-Yankova, S; Lari, M; Yordanov, Y; Galabov, A; Caramelli, David; and Toncheva, Draga

Abstract

Ancient (proto-) Bulgarians have long been thought to as a Turkic population. However, evidence found in the past three decades show that this is not the case. Until now, this evidence does not include ancient mitochondrial DNA (mtDNA) analysis. In order to fill this void, we have collected human remains from the VIII-X century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in Northeast Bulgaria and Tuhovishte (Satovcha region) in Southwest Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and Western Eurasian populations. Our results suggest a Western Eurasian matrilineal origin for proto-Bulgarians as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data which will further clarify proto-Bulgarian origins; thereby adding new clues to current understanding of European genetic evolution.

http://digitalcommons.wayne.edu/humbiol_preprints/69/

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The ancestry and affiliations of Kennewick Man

Morten Rasmussen, Martin Sikora, Anders Albrechtsen, Thorfinn Sand Korneliussen, J. Víctor Moreno-Mayar, G. David Poznik, Christoph P. E. Zollikofer, Marcia S. Ponce de León,   Morten E. Allentoft, Ida Moltke, Hákon Jónsson,   Cristina Valdiosera, Ripan S. Malhi, Ludovic Orlando, Carlos D. Bustamante, Thomas W. Stafford Jr, David J. Meltzer, Rasmus Nielsen   & Eske Willerslev.

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (bp)1. His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted2. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans2. In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature14625.html
http://www.ncbi.nlm.nih.gov/sra?term=SRS937952

Technical Report: Assessment of the genetic analyses of Rasmussen et al. (2015).
http://cdm16021.contentdm.oclc.org/cdm/ref/collection/p16021coll11/id/950

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An early modern human from Romania with a recent Neanderthal ancestor

Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel,   Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich & Svante Pääbo.

Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14558.html
http://www.ebi.ac.uk/ena/data/view/PRJEB8987

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Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

Anna-Sapfo Malaspinas et al.

Summary

Understanding the peopling of the Americas remains an important and challenging question. Here, we present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as ‘Botocudos’. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.

http://www.cell.com/current-biology/abstract/S0960-9822%2814%2901274-3
http://www.ebi.ac.uk/ena/data/view/PRJEB7622

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Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China

Chunxiang Li, Chao Ning, Erika Hagelberg, Hongjie Li, Yongbin Zhao, Wenying Li, Idelisi Abuduresule, Hong Zhu and Hui Zhou.

Received:   20 April 2015
Accepted:   22 June 2015
Published:   8 July 2015

Abstract
Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

http://www.biomedcentral.com/1471-2156/16/78
   

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Iron Age and Anglo-Saxon genomes from East England reveal British migration history

Stephan Schiffels, Wolfgang Haak, Pirita Paajanen, Bastien Llamas, Elizabeth Popescu, Louise Lou, Rachel Clarke, Alice Lyons, Richard Mortimer, Duncan Sayer, Chris Tyler-Smith, Alan Cooper, Richard Durbin
doi: http://dx.doi.org/10.1101/022723

Abstract

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo-Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo-Saxon period). We use present-day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today’s British are more similar to the Iron Age individuals than to most of the Anglo-Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo-Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo-Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

http://biorxiv.org/content/early/2015/07/17/022723