Результаты исследования древней ДНК (дДНК)

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Archaeogenomic evidence reveals prehistoric matrilineal dynasty

Douglas J. Kennett, Stephen Plog, Richard J. George, Brendan J. Culleton, Adam S. Watson, Pontus Skoglund, Nadin Rohland, Swapan Mallick, Kristin Stewardson, Logan Kistler, Steven A. LeBlanc, Peter M. Whiteley, David Reich & George H. Perry.

Abstract

For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother–daughter and grandmother–grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for ∼330 years.

http://www.nature.com/articles/ncomms14115

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Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations

Amy Goldberga, Torsten Güntherb, Noah A. Rosenberga, and Mattias Jakobssonb Author Affiliations

Abstract

Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically–inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

http://www.pnas.org/content/early/2017/02/17/1616392114.abstract
http://www.pnas.org/content/suppl/2017/02/20/1616392114.DCSupplemental/pnas.1616392114.sapp.pdf

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Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots
Alexey G. Nikitin,    Inna Potekhina,    Nadin Rohland,    Swapan Mallick,    David Reich,    Malcolm Lillie
Published: February 24, 2017
    http://dx.doi.org/10.1371/journal.pone.0172952

Abstract

The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400–2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950–2,500 BCE).

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http://www.biorxiv.org/content/early/2017/03/02/112714

Extensive farming in Estonia started through a sex-biased migration from the Steppe

Lehti Saag, Liivi Varul, Christiana Lyn Scheib, Jesper Stenderup, Morten E Allentoft, Lauri Saag, Luca Pagani, Maere Reidla, Kristiina Tambets, Ene Metspalu, Aivar Kriiska, Eske Willerslev, Toomas Kivisild, Mait Metspalu

doi: https://doi.org/10.1101/112714

Abstract

Farming-based economies appear relatively late in Northeast Europe and the extent to which they involve genetic ancestry change is still poorly understood. Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry, but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry.

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Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe

Martina Unterländer, Friso Palstra, Iosif Lazaridis, Aleksandr Pilipenko, Zuzana Hofmanová, Melanie Groß, Christian Sell, Jens Blöcher, Karola Kirsanow, Nadin Rohland, Benjamin Rieger, Elke Kaiser, Wolfram Schier, Dimitri Pozdniakov, Aleksandr Khokhlov, Myriam Georges, Sandra Wilde, Adam Powell, Evelyne Heyer, Mathias Currat, David Reich, Zainolla Samashev, Hermann Parzinger, Vyacheslav I. Molodin & Joachim Burger

Abstract

During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.

http://www.nature.com/articles/ncomms14615

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Complete mitochondrial sequences from Mesolithic Sardinia

Alessandra Modi, Francesca Tassi, Roberta Rosa Susca, Stefania Vai, Ermanno Rizzi, Gianluca De Bellis, Carlo Lugliè, Gloria Gonzalez Fortes, Martina Lari, Guido Barbujani, David Caramelli & Silvia Ghirotto

Abstract

Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.

http://www.nature.com/articles/srep42869

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Mitochondrial DNA diversity in a Transbaikalian Xiongnu population

    Aleksandr S. Pilipenko, Stepan V. Cherdantsev, Rostislav O. Trapezov, Anton A. Zhuravlev, Vladimir N. Babenko, Dmitri V. Pozdnyakov, Prokopiy B. Konovalov, Natalia V. Polosmak

First Online:    10 March 2017

DOI: 10.1007/s12520-017-0481-x

Abstract

Xiongnu was a confederation of nomadic pastoral tribes (~200 bc–100 ad) that founded the first nomadic empire in Central Asia. According to archeological and historical data, the tribes played a key role in ethnic and cultural processes in Central Asia and adjacent regions of Eurasia. Genetic studies of the Xiongnu published to date have focused on remains from burial grounds in present-day Mongolia, in the southern part of the ancient Xiongnu area. However, paleoanthropological materials from numerous Xiongnu cemeteries and settlements in Transbaikalia (the southern region of Eastern Siberia, Russia) in the northern part of the Xiongnu Empire have not been examined genetically. Here, we analyzed mitochondrial DNA variation in a Transbaikalian Xiongnu population based on ancient DNA obtained from skeletal remains (n = 18) at four burial grounds to complement available Xiongnu genetic diversity data. We detected 16 mitochondrial DNA haplotypes belonging to seven East Eurasian haplogroups (A, B5, C, D4, G2a, N9a, and Y) in the Transbaikalian Xiongnu series. We observed substantial similarity between Transbaikalian and Mongolian Xiongnu series with respect to main haplogroup composition and frequencies. We observed several mitochondrial DNA clusters (N9a, Y, B5, and A16) and 11 of 16 haplotypes that were previously undetected in the Xiongnu gene pool. We also observed high similarity between the Xiongnu and contemporary indigenous populations of eastern Central Asia, particularly Mongolian-speaking groups. These findings extend our knowledge of Xiongnu genetic diversity.
http://link.springer.com/article/10.1007/s12520-017-0481-x

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-017-0924-0

Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC

    Maciej ChyleńskiEmail author, Anna Juras, Edvard Ehler, Helena Malmström, Janusz Piontek, Mattias Jakobsson, Arkadiusz Marciniak and Miroslawa Dabert

DOI: 10.1186/s12862-017-0924-0

Received: 15 November 2016
Accepted: 23 February 2017
Published: 16 March 2017

Abstract
Background

Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities.

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Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago


Abstract

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|'hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) 'hot spot' for the evolution of our species.

http://biorxiv.org/content/early/2017/06/05/145409

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The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods

Abstract

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006852

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Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada

Summary

Situated at the furthest northeastern edge of Canada, the island of Newfoundland (approximately 110,000 km2) and Labrador (approximately 295,000 km2) today constitute a province characterized by abundant natural resources but low population density. Both landmasses were covered by the Laurentide ice sheet during the Last Glacial Maximum (18,000 years before present [YBP]); after the glacier retreated, ice patches remained on the island until ca. 9,000 calibrated (cal) YBP [1]. Nevertheless, indigenous peoples, whose ancestors had trekked some 5,000 km from the west coast, arrived approximately 10,000 cal YBP in Labrador and ca. 6,000 cal YBP in Newfoundland [2, 3]. Differential features in material culture indicate at least three settlement episodes by distinct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk. Newfoundland has remained home to indigenous peoples until present day with only one apparent hiatus (3,400–2,800 YBP). This record suggests abandonment, severe constriction, or local extinction followed by subsequent immigrations from single or multiple source populations, but the specific dynamics and the cultural and biological relationships, if any, among these successive peoples remain enigmatic [4]. By examining the mitochondrial genome diversity and isotopic ratios of 74 ancient remains in conjunction with the archaeological record, we have provided definitive evidence for the genetic discontinuity between the maternal lineages of these populations. This northeastern margin of North America appears to have been populated multiple times by distinct groups that did not share a recent common ancestry, but rather one much deeper in time at the entry point into the continent.

http://www.cell.com/current-biology/fulltext/S0960-9822(17)31091-6

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https://www.nature.com/articles/s41598-018-20705-6

A mosaic genetic structure of the human population living in the South Baltic region during the Iron Age

    Ireneusz Stolarek, Anna Juras, Luiza Handschuh, Malgorzata Marcinkowska-Swojak, Anna Philips, Michal Zenczak, Artur Dębski, Hanna Kóčka-Krenz, Janusz Piontek, Piotr Kozlowski & Marek Figlerowicz

    Scientific Reportsvolume 8, Article number: 2455 (2018)
    doi:10.1038/s41598-018-20705-6

Received:    30 October 2017
Accepted:    23 January 2018
Published online:    06 February 2018

Abstract

Despite the increase in our knowledge about the factors that shaped the genetic structure of the human population in Europe, the demographic processes that occurred during and after the Early Bronze Age (EBA) in Central-East Europe remain unclear. To fill the gap, we isolated and sequenced DNAs of 60 individuals from Kowalewko, a bi-ritual cemetery of the Iron Age (IA) Wielbark culture, located between the Oder and Vistula rivers (Kow-OVIA population). The collected data revealed high genetic diversity of Kow-OVIA, suggesting that it was not a small isolated population. Analyses of mtDNA haplogroup frequencies and genetic distances performed for Kow-OVIA and other ancient European populations showed that Kow-OVIA was most closely linked to the Jutland Iron Age (JIA) population. However, the relationship of both populations to the preceding Late Neolithic (LN) and EBA populations were different. We found that this phenomenon is most likely the consequence of the distinct genetic history observed for Kow-OVIA women and men. Females were related to the Early-Middle Neolithic farmers, whereas males were related to JIA and LN Bell Beakers. In general, our findings disclose the mechanisms that could underlie the formation of the local genetic substructures in the South Baltic region during the IA.

Несмотря на увеличение наших знаний о факторах, которые сформировали генетическую структуру населения в Европе, демографические процессы, происходившие во время и после раннего бронзового века (РБВ) в Центральной и Восточной Европе, остаются неясными. Чтобы заполнить пробел, мы выделили и секвенировали ДНК из 60 человек из Ковалевко, двухритуального кладбища вельбаркской культуры железного века (ЖВ), расположенного между реками Одер и Висла (популяция Kow-OVIA). Собранные данные свидетельствуют о высоком генетическом разнообразии Kow-OVIA, предполагая, что это не была маленькая изолированная популяция. Анализ частот гаплогруппы мтДНК и генетических расстояний, проведенных для Kow-OVIA и других древнеевропейских популяций, показал, что Kow-OVIA наиболее тесно связан с популяцией железного века Ютландии (JIA). Однако связь обеих популяций с предшествующими популяциями позднего неолита (ПН) и РБВ популяциям была различной. Мы обнаружили, что это явление, скорее всего, является следствием различной генетической истории, наблюдаемой для женщин и мужчин Kow-OVIA. Женщины были связаны с земледельцами раннего и среднего неолита, тогда как мужчины были связаны с железным веком Ютландии JIA и ПН культурой колоколовидных кубков. В целом наши выводы раскрывают механизмы, которые могли бы стать основой формирования локальных генетических подструктур в южном балтийском регионе во время железного века.

МтДНК вельбаркской культуры, из Польши, неожиданно оказалось что у мужчин и женщин мтДНК сильно разныею