Результаты исследования древней ДНК (дДНК)

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Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight

Dong, Yu; Li, Chunxiang; Luan, Fengshi; Li, Zhenguang; Li, Hongjie; Cui, Yinqiu; Zhou, Hui; and Malhi, Ripan S.

Abstract

To gain insight into the social organization of a population associated with the Dawenkou period, ancient DNA analysis of 18 individuals from human remains from Fujia site, Shandong Province, China was completed. Directly radiocarbon dated to 4800–4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y-chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage were de-emphasized compared to the bonds of descent at Fujia.

http://digitalcommons.wayne.edu/humbiol_preprints/73/

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A common genetic origin for early farmers from Mediterranean Cardial and Central European LBK cultures

Abstract

The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: an initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK tradition, which followed the Danube River into Central Europe. While genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400 year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.
http://mbe.oxfordjournals.org/content/early/2015/09/02/molbev.msv181.full.pdf+html
http://mbe.oxfordjournals.org/content/suppl/2015/09/02/msv181.DC1/cardial_supplementary_MBE_submission.pdf

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Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

Torsten Günthera,1, Cristina Valdioseraa,b,c,1, Helena Malmströma, Irene Ureñac,d, Ricardo Rodriguez-Varelac,d, Óddny Osk Sverrisdóttira, Evangelia A. Daskalakia,e, Pontus Skoglunda,e,f, Thijessen Naidooa, Emma M. Svenssona,g, José María Bermúdez de Castroh, Eudald Carbonelli, Michael Dunnj, Jan Storåe, Eneko Iriartek, Juan Luis Arsuagac,d, José-Miguel Carreteroc,k, Anders Götherströme, and Mattias Jakobssona,l,2

Abstract

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

http://www.pnas.org/content/early/2015/09/02/1509851112
http://www.ebi.ac.uk/ena/data/view/PRJEB9783

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Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage

Montserrat Hervella, Mihai Rotea, Neskuts Izagirre, Mihai Constantinescu, Santos Alonso, Mihai Ioana, Cătălin Lazăr, Florin Ridiche, Andrei Dorian Soficaru, Mihai G. Netea, Concepcion de-la-Rua.

Abstract

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128810

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/Афанасьев_Г.Е._Ван_Л._Вень_Ш._Вэй_Л._Добровольская_М.В._Коробов_Д.С._Решетова_И.К._Ли_Х._Тун_С._Хазарские_конфедераты_в_бассейне_Дона_Тезисы_докладов_на_Всероссийской_научной_конференции_Естественнонаучные_методы_исследования_и_парадигма_современной_археологии_._М._ИА_РАН._2015.



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Eight thousand years of natural selection in Europe - take 2

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Nick Patterson, Songul Alpaslan Roodenberg, Eadaoin Harney, Kristin Stewardson, Daniel Fernandes, Mario Novak, Kendra Sirak, Cristina Gamba, Eppie R. Jones, Bastien Llamas, Stanislav Dryomov, Joseph Pickrell, Juan Luis Arsuaga, Jose Maria Bermudez de Castro, Eudald Carbonell, Fokke Gerritsen, Aleksandr Khokhlov, Pavel Kuznetsov, Marina Lozano, Harald Meller, Oleg Mochalov, Vayacheslav Moiseyev, Manuel A. Rojo Guerra, Jacob Roodenberg, Josep Maria Verges, Johannes Krause, Alan Cooper, Kurt W. Alt, Dorcas Brown, David Anthony, Carles Lalueza-Fox, Wolfgang Haak, Ron Pinhasi, David Reich.

doi: http://dx.doi.org/10.1101/016477

Abstract: The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

http://www.biorxiv.org/content/early/2015/10/10/016477.abstract?%3Fcollection=

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Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent

M. Gallego Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica.

Abstract
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

http://www.sciencemag.org/content/early/2015/10/07/science.aad2879.abstract

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Uncovering the sources of DNA found on the Turin Shroud

Gianni Barcaccia, Giulio Galla, Alessandro Achilli, Anna Olivieri & Antonio Torroni.

Abstract

The Turin Shroud is traditionally considered to be the burial cloth in which the body of Jesus Christ was wrapped after his death approximately 2000 years ago. Here, we report the main findings from the analysis of genomic DNA extracted from dust particles vacuumed from parts of the body image and the lateral edge used for radiocarbon dating. Several plant taxa native to the Mediterranean area were identified as well as species with a primary center of origin in Asia, the Middle East or the Americas but introduced in a historical interval later than the Medieval period. Regarding human mitogenome lineages, our analyses detected sequences from multiple subjects of different ethnic origins, which clustered into a number of Western Eurasian haplogroups, including some known to be typical of Western Europe, the Near East, the Arabian Peninsula and the Indian sub-continent. Such diversity does not exclude a Medieval origin in Europe but it would be also compatible with the historic path followed by the Turin Shroud during its presumed journey from the Near East. Furthermore, the results raise the possibility of an Indian manufacture of the linen cloth.

http://www.nature.com/articles/srep14484

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Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia

Justin C. Tackneya, Ben A. Potterb, Jennifer Raffc, Michael Powersd, W. Scott Watkinse, Derek Warnerd, Joshua D. Reutherb,f, Joel D. Irishg, and Dennis H. O’Rourkea.


Abstract

Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

http://www.pnas.org/content/early/2015/10/21/1511903112

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Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists

Chao Ning, Shizhu Gao, Boping Deng, Hongxiang Zheng, Dong Wei, Haoze Lv, Hongjie Li, Li Song, Yong Wu, Hui Zhou and Yinqiu Cui.

Abstract

The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga–Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.

http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg2015128a.html

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The complete mitogenome of a 500-year-old Inca child mummy
Alberto Gómez-Carballa, Laura Catelli, Jacobo Pardo-Seco, Federico Martinón-Torres, Lutz Roewer, Carlos Vullo & Antonio Salas

Received:17 June 2015
Accepted:16 October 2015
Published online:12 November 2015

Abstract

In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5–23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings.

http://www.nature.com/articles/srep16462

Inca child mummy reveals lost genetic history of South America
http://news.sciencemag.org/archaeology/2015/11/inca-child-mummy-reveals-lost-genetic-history-south-america

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Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Eppie R. Jones,   Gloria Gonzalez-Fortes, Sarah Connell, Veronika Siska, Anders Eriksson, Rui Martiniano, Russell L. McLaughlin, Marcos Gallego Llorente,   Lara M. Cassidy, Cristina Gamba, Tengiz Meshveliani, Ofer Bar-Yosef, Werner Müller, Anna Belfer-Cohen, Zinovi Matskevich, Nino Jakeli, Thomas F. G. Higham, Mathias Currat, David Lordkipanidze, Michael Hofreiter et al.

Abstract

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html
http://www.ebi.ac.uk/ena/data/view/PRJEB11364

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Genome-wide patterns of selection in 230 ancient Eurasians

Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Nick Patterson, Songül Alpaslan Roodenberg, Eadaoin Harney,   Kristin Stewardson, Daniel Fernandes,   Mario Novak, Kendra Sirak,   Cristina Gamba,   Eppie R. Jones,   Bastien Llamas,   Stanislav Dryomov, Joseph Pickrell, Juan Luís Arsuaga, José María Bermúdez de Castro, Eudald Carbonell,   Fokke Gerritsen, Aleksandr Khokhlov, Pavel Kuznetsov, Marina Lozano,   Harald Meller, Oleg Mochalov et al.

Abstract

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16152.html

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Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

Lara M. Cassidya, Rui Martinianoa, Eileen M. Murphyb, Matthew D. Teasdalea, James Malloryb, Barrie Hartwellb, and Daniel G. Bradleya.


Abstract

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

http://www.pnas.org/content/early/2015/12/22/1518445113

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Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman

V. Coia, G. Cipollini, P. Anagnostou, F. Maixner, C. Battaggia, F. Brisighelli, A Gómez-Carballa, G. Destro Bisol, A. Salas & A. Zink.

Abstract

The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.

http://www.nature.com/articles/srep18932