Результаты исследования древней ДНК (дДНК)

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Three-part ancestry for Europeans

Science 5 September 2014:
Vol. 345 no. 6201 pp. 1106-1107
DOI: 10.1126/science.345.6201.1106

Ann Gibbons

For years, the favored recipe for making a modern European ​was this: Start with DNA from a hunter-gatherer whose ancestors lived in Europe 45,000 years ago, then add genes from an early farmer who migrated to the continent about 9000 years ago. An extensive study of ancient DNA now points to a third ingredient: blood from an Asian nomad who blew into central Europe perhaps only about 4000 or 5000 years ago. This third major lineage originated somewhere in northwestern Asia, perhaps on the steppes of western Asia or in Eastern Europe. This is a "ghost lineage," because no pureblood member of this group survives today. But whoever these people were, their descendants successfully spread far and wide, for their genes show up not only in Europeans but also in Native Americans, according to a talk by paleogeneticist Johannes Krause of the University of Tübingen in Germany, who spoke at a biomolecular archaeology meeting last week. Those who heard the talk in a packed auditorium at the University of Basel were impressed by the genomic data's high resolution—it is the largest data set of ancient DNA ever presented in a single study—even though some aren't convinced about the exact details.​ 

http://www.sciencemag.org/content/345/6201/1106.short#xref-fn-1-1

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Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, Gabriel Renaud, Swapan Mallick et al.

Published online 17 September 2014.

We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1, 2, 3, 4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.

http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html
http://www.nature.com/nature/journal/v513/n7518/extref/nature13673-s1.pdf

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First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African

Alan G. Morris, Anja Heinze, Eva K.F. Chan, Andrew B. Smith and Vanessa M. Hayes.

Accepted September 3, 2014.

Abstract

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of Southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semi-desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-pastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330 year old male skeleton, confirmed via osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that pre-pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

http://gbe.oxfordjournals.org/content/early/2014/09/10/gbe.evu202.short

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Genome flux and stasis in a five millennium transect of European prehistory

Cristina Gamba,   Eppie R. Jones,   Matthew D. Teasdale,   Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle,   János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi.

Published 21 October 2014.

Abstract

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

http://www.nature.com/ncomms/2014/141021/ncomms6257/full/ncomms6257.html
http://www.ncbi.nlm.nih.gov/sra?term=SRP039766

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Genome sequence of a 45,000-year-old modern human from western Siberia

Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri et al.

Abstract

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.

http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html
http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf

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Genomic structure in Europeans dating back at least 36,200 years

Andaine Seguin-Orlando1, Thorfinn S. Korneliussen1, Martin Sikora1, Anna-Sapfo Malaspinas, Andrea Manica, Ida Moltke, Anders Albrechtsen, Amy Ko, Ashot Margaryan, Vyacheslav Moiseyev, Ted Goebel, Michael Westaway,   David Lambert, Valeri Khartanovich, Jeffrey D. Wall, Philip R. Nigst, Robert A. Foley, Marta Mirazon Lahr, Rasmus Nielsen,    Ludovic Orlando, Eske Willerslev.

Published Online November 6 2014

Abstract

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.

http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114
http://www.sciencemag.org/content/suppl/2014/11/05/science.aaa0114.DC1/Seguin-Orlando.SM.pdf

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Identification of the remains of King Richard III

Тuri E. King, Gloria Gonzalez Fortes, Patricia Balaresque, Mark G. Thomas, David Balding, Pierpaolo Maisano Delser, Rita Neumann, Walther Parson, Michael Knapp, Susan Walsh, Laure Tonasso, John Holt, Manfred Kayser, Jo Appleby, Peter Forster, David Ekserdjian, Michael Hofreiter   & Kevin Schürer

Published 02 December 2014

Abstract

In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard’s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.

http://www.nature.com/ncomms/2014/141202/ncomms6631/full/ncomms6631.html

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Mitochondrial DNA variation in the Viking age population of Norway

Maja Krzewińska, Gro Bjørnstad, Pontus Skoglund, Pall Isolfur Olason, Jan Bill, Anders Götherström, Erika Hagelberg.

Published 8 December 2014

Abstract

The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.

http://rstb.royalsocietypublishing.org/content/370/1660/20130384

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Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach

Yinqiu Cui, Li Song, Dong Wei, Yuhong Pang, Ning Wang, Chao Ning, Chunmei Li, Binxiao Feng, Wentao Tang, Hongjie Li, Yashan Ren et al.

DOI: 10.1098/rstb.2013.0378Published 8 December 2014

Abstract

The Yuan Dynasty (AD 1271–1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.

http://rstb.royalsocietypublishing.org/content/370/1660/20130378

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The ancient Yakuts: a population genetic enigma

Christine Keyser, Clémence Hollard, Angela Gonzalez, Jean-Luc Fausser, Eric Rivals, Anatoly Nikolayevich Alexeev, Alexandre Riberon, Eric Crubézy, Bertrand Ludes.

DOI: 10.1098/rstb.2013.0385Published 8 December 2014

Abstract

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.

http://rstb.royalsocietypublishing.org/content/370/1660/20130385

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Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles

F. Mendisco, M. H. Pemonge, E. Leblay, T. Romon, G. Richard, P. Courtaud, M. F. Deguilloux.

DOI: 10.1098/rstb.2013.0388Published 8 December 2014.

Abstract

The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence.

http://rstb.royalsocietypublishing.org/content/370/1660/20130388

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Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age

Shi-Zhu Gaо,Ye Zhang, Dong Wei, Hong-Jie Li, Yong-Bin Zhao, Yin-Qiu Cui and Hui Zhou.
Article first published online: 29 DEC 2014.

Abstract

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22690/abstract

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Collective burials among agro-pastoral societies in later Neolithic Germany: perspectives from ancient DNA

Esther J. Leea, Rebecca Renneberga, Melanie Hardera, Ben Krause-Kyoraa, Christoph Rinneb, Johannes Müllerb,   Almut Nebelc, Nicole von Wurmb-Schwarkd.

Abstract

Ancient DNA research has focused on the genetic patterns of the earliest farmers during the European Neolithic, especially with regards to the demographic changes in the transition from hunting and gathering to agriculture. However, genetic data is relatively lacking after this earliest transition period, when societies had fully adapted to new agrarian lifestyles specific to their local environment. During the later central European Neolithic (ca. 3600–2800 cal BC), large-scale collective burials and monumental architecture appeared within the landscape of many agricultural societies. This phenomenon has been argued to represent the emergence of a “collective” identity. With the aim of exploring genetic-based relations among individuals collectively buried, we obtained human skeletal remains of nearly 200 individuals from four later Neolithic collective burial sites in Germany: Calden, Odagsen, Groβenrode, and Panker. We successfully reproduced reliable mitochondrial DNA (mtDNA) haplotypes from eight Neolithic individuals, which were assigned to haplogroups H, HV0, and X2. Shared haplotypes observed among individuals within Calden and Odagsen suggest that genetic relations may have shaped the arrangement of the deceased within later Neolithic agricultural groups.

http://www.sciencedirect.com/science/article/pii/S0305440312003883

[Шад]

А.С. Пилипенко и другие

ГЕНОФОНД МИТОХОНДРИАЛЬНОЙ ДНК ДРЕВНЕТЮРКСКОГО НАСЕЛЕНИЯ АЛТАЯ

В генофонде мтДНК хунну резко доминируют восточно-евразийские гаплогруппы. Однако их основу составляют гаплогруппы A4, C и D. Гаплогруппы B (B4, B5) и некоторые подгруппы M представлены единичными линиями.

http://goo.gl/Xfjz4G

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Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , Guido Brandt, Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Bánffy , Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , Valery Khartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov , Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , Christina Roth , Anna Szécsényi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , David Anthony , Alan Cooper , Kurt Werner Alt , David Reich.

Abstract

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

http://biorxiv.org/content/early/2015/02/10/013433.full-text.pdf+html

http://0-www.nature.com.es.library.du.ac.bd/nature/journal/vaop/ncurrent/full/nature14317.html
http://www.ebi.ac.uk/ena/data/view/PRJEB8448