Результаты исследования древней ДНК (дДНК)

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Maternal Genetic Ancestry and Legacy of 10th Century AD Hungarians

Aranka Csosz, Anna Szecsenyi-Nagy, Veronika Csakyova, Peter Lango, Viktoria Bodis, Kitti Kohler, Gyongyver Tomory, Melinda Nagy, Balazs Gusztav Mende
doi: http://dx.doi.org/10.1101/056655

Abstract

The ancient Hungarians originated from the Ural region in today's central Russia and migrated across the Eastern European steppe, according to historical sources. The Hungarians conquered the Carpathian Basin 895-907 AD, and admixed with the indigenous communities. Here we present mitochondrial DNA results from three datasets: one from the Avar period (7-9th centuries) of the Carpathian Basin (n = 31); an almost four-fold enlarged dataset from the Hungarian conquest-period (n=101); and one from the contemporaneous Hungarian-Slavic contact zone (n = 23). We compare these mitochondrial DNA hypervariable segment sequences and haplogroup results with other ancient and modern Eurasian data. Whereas the analyzed Avars represents a certain group of the Avar society that shows East and South European genetic characteristics, the Hungarian conquerors' maternal gene pool is a mixture of West Eurasian and Central and North Eurasian elements. Comprehensively analyzing the results, both the linguistically recorded Finno-Ugric roots and historically documented Turkic and Central Asian influxes had possible genetic imprints in the conquerors' genetic composition. Our data allows a complex series of historic and population genetic events before the formation of the medieval population of the Carpathian Basin, and the maternal genetic continuity between 10-12th centuries and modern Hungarians.

http://biorxiv.org/content/early/2016/06/02/056655

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Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanováa Susanne Kreutzera Garrett Hellenthalb at al.
 
Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

http://www.pnas.org/content/early/2016/06/01/1523951113.abstract

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Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

Choongwon Jeong, Andrew T. Ozga, David B. Witonsky, Helena Malmström, Hanna Edlund, Courtney A. Hofman, Richard W. Hagan, Mattias Jakobsson, Cecil M. Lewis, Mark S. Aldenderfer, Anna Di Rienzo, and Christina Warinner

Abstract

The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×–7.25×, mean 2.16×) and mitochondrial genomes (20.8×–1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150–1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.

http://www.pnas.org/content/early/2016/06/16/1520844113.abstract

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The genetic structure of the world's first farmers

Iosif Lazaridis, Dani Nadel, Gary Rollefson, Deborah C. Merrett, Nadin Rohland, Swapan Mallick, Daniel Fernandes, Mario Novak, Beatriz Gamarra, Kendra Sirak, Sarah Connell, Kristin Stewardson, Eadaoin Harney, Qiaomei Fu, Gloria Gonzalez-Fortes, Songül Alpaslan Roodenberg, Gyorgy Lengyel, Fanny Bocquentin, Boris Gasparian, Janet M. Monge, Michael Gregg, Vered Eshed, Ahuva-Sivan Mizrahi, Christopher Meiklejohn, Fokke Gerritsen, Luminita Bejenaru, Matthias Blueher, Archie Campbell, Gianpero Cavalleri, David Comas, Philippe Froguel, Edmund Gilbert, Shona M. Kerr, Peter Kovacs, Johannes Krause, Darren McGettigan, Michael Merrigan, D. Andrew Merriwether, Seamus O'Reilly, Martin B. Richards, Ornella Semino, Michel Shamoon-Pour, Gheorghe Stefanescu, Michael Stumvoll, Anke Tonjes, Antonio Torroni, James F. Wilson, Loic Yengo, Nelli A. Hovhannisyan, Nick Patterson, Ron Pinhasi, David Reich

Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

http://biorxiv.org/content/early/2016/06/16/059311

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The genetics of an early Neolithic pastoralist from the Zagros, Iran

Marcos Gallego Llorente, Sarah Connell, Eppie R Jones, Deborah Merrett, Jeonsu Jeon, Anders Eriksson, Veronika Siska, Cristina Gamba, Chris Meiklejohn, Robert Beyer, Sungwon Jeon, Yung Sung Cho, Michael Hofreiter, Jong Bhak, Andrea Manica, Ron Pinhasi.

Abstract

The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding,ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in the region. Runs of homozygosity are of a similar length to those from Neolithic Anatolians, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity of early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.

http://biorxiv.org/content/early/2016/06/18/059568.full.pdf+html

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Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea

Won-Joon Lee, Eun Jin Woo, Chang Seok Oh, Jeong A. Yoo, Yi-Suk Kim, Jong Ha Hong, A. Young Yoon, Caroline M. Wilkinson, Jin Og Ju, Soon Jo Choi, Soong Doek Lee, Dong Hoon Shin

Abstract

In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin) were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE– 660 CE) of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes) than C4-based (maize, millet and other tropical grains). Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments) and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156632

Mitochondrial DNA Analysis

The femur fragment (sample No. 321) was collected with a sterilized knife. This were then exposed to UV irradiation for 20 min, and subsequently immersed in 5.4% (w/v) sodium hypochlorite. When the samples were washed with distilled water and absolute ethanol, they were then air-dried and pulverized to a fine powder using a SPEX 6750 Freezer / Mill (SPEX SamplePrep, Metuchen, NJ) [15]. Bone powder (0.5 g) was incubated in 1 mL of lysis buffer (EDTA 50 mM, pH 8.0; 1 mg /mL of proteinase K; SDS 1%; 0.1 M DTT) at 56°C for 24 h. Total DNA was extracted with an equal volume of phenol / chloroform / isoamyl alcohol (25:24:1), and then was treated with chloroform / isoamyl alcohol (24:1). DNA isolation and purification was performed using a QIAmp PCR purification kit (Qiagen, Hilden, Germany). The purified DNA was eluted in 40 μl of EB buffer (Qiagen) [15].

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A PALEOGENETIC STUDY OF PAZYRYK PEOPLE BURIED AT AK-ALAKHA-1, THE ALTAI MOUNTAINS

А.С. Пилипенко, Р.О. Трапезов, Н.В. Полосьмак.

В статье представлены результаты молекулярно-генетического исследования останков двух носителей пазырыкской культуры, погребенных в кург. 1 могильника Ак-Алаха-1 (плато Укок, Горный Алтай, Россия), с использованием четырех систем генетических маркеров – митохондриальной ДНК, полиморфного фрагмента гена амелогенина, STR-локусов аутосом и Y-хромосомы. Установлен мужской пол обоих индивидов. Выявлены идентичные варианты митохондриальной ДНК и Y-хромосомы, что свидетельствует в пользу родства погребенных. Однако интегральное рассмотрение полученных генетических данных позволяет исключить прямое родство (отец – сын). Приведена филогенетическая и филогеографическая интерпретация данных по митохондриальной ДНК и Y-хромосоме. Исследование демонстрирует современные возможности палеогенетических методов и назревшую необходимость их широкого применения для объективизации археологических реконструкций.
 
https://www.researchgate.net/publication/301548191_Pilipenko_2015_A_PALEOGENETIC_STUDY_OF_PAZYRYK_PEOPLE_BURIED_AT_AK-ALAKHA-1_THE_ALTAI_MOUNTAINS_in_russian

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The Demographic Development of the First Farmers in Anatolia

Gülşah Merve Kılınç, Ayça Omrak, Füsun Özer, Torsten Günther, Ali Metin Büyükkarakaya, Erhan Bıçakçı, Douglas aird, Handan Melike Dönertaş, Ayshin Ghalichi, Reyhan Yaka, Dilek Koptekin, Sinan Can Açan, Poorya Parvizi, Maja Krzewińska, Evangelia A. Daskalaki, Eren Yüncü, Nihan Dilşad Dağtaş, Andrew Fairbairn, Jessica Pearson, Gökhan Mustafaoğlu, Yılmaz Selim Erdal, Yasin Gökhan Çakan.

Summary

The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [ 1–3 ]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [ 4 ]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

http://www.cell.com/current-biology/abstract/S0960-9822(16)30850-8

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Genomic insights into the peopling of the Southwest Pacific

     Pontus Skoglund,   Cosimo Posth,   Kendra Sirak,   Matthew Spriggs,   Frederique Valentin,   Stuart Bedford,   Geoffrey R. Clark,   Christian Reepmeyer,   Fiona Petchey,   Daniel Fernandes,   Qiaomei Fu,   Eadaoin Harney,   Mark Lipson,   Swapan Mallick,   Mario Novak,   Nadin Rohland,   Kristin Stewardson,   Syafiq Abdullah,   Murray P. Cox,   Françoise R. Friedlaender,   Jonathan S. Friedlaender,   Toomas Kivisild,   George Koki,   Pradiptajati Kusuma,   D. Andrew Merriwether   et al.

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago1 marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100–2,700 years before present) and one from Tonga (about 2,700–2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania2, 3, 4, 5. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19844.html#affil-auth

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Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula

While the amount of ancient Iberian genetic data has increased over the last years, few studies have focused on population dynamic processes beyond the immediate period of the Neolithic transition. In this study, the Iberian dataset was enlarged by SNP-based haplogroup information for 249 new Mesolithic to Early Bronze Age individuals and 187 reproduced HVR I sequences. These new data allow confident insights into post-Neolithisation population dynamic processes on the Iberian Peninsula and make it possible to compare the development of Iberian and Central European groups over a time span of about 4,000 years.
The results of this study reveal a strong genetic regionalization of Iberian groups throughout the Neolithic and partially in the Chalcolithic. A considerable amount of hunter-gatherer maternal heritage persisted during the Iberian Early Neolithic. The greatest amount of “Neolithic” lineages/haplogroups (HV, J, K, N1a, T2, V, and X) has been found in Northeast Spain and Aragón, suggesting these regions were the main entrance for Neolithic lineages into the Iberian Peninsula, while the amount of mitochondrial hunter-gatherer influence increases with growing distance from these regions, pointing to various forms of Neolithic transitions on the Iberian Peninsula. In some areas genetic continuity between Early and Late Neolithic seems highly likely (Ebro Valley) while other regions show large genetic differences to the preceding period (Central Portugal, Northern Meseta). Central Iberian Bell Beaker groups are genetically distinct to most other Chalcolithic groups.
Although a substantial number of Early Neolithic Iberian individuals share direct sequence hits to contemporary individuals of the Central European Linear pottery culture, the amount of hunter-gatherer mitochondrial heritage is considerably greater in all regions of the Iberian Peninsula than in Central Europe. No genetic connection between Iberian and Central European Bell Beakers or the Corded Ware culture could be found. When focusing on the distribution of sub-clades of haplogroup H, differences between the Iberian Peninsula and the groups from other parts of Europe were recognizable. In the Iberian samples set only sub-haplogroups H1 and H3 could be identified. While H1 was present in all Early and Later Neolithic groups from Central and Western Europe, H3 shows strong Western European affinities and is not detectable in Central Europe before the Middle Neolithic. While no strong differences in sub-haplogroup H variability among Iberian groups of different epochs could be detected, a clear shift between Central Europe´s Early and Middle Neolithic is recognizable.

https://publications.ub.uni-mainz.de/theses/frontdoor.php?source_opus=100000815&la=en

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Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

John Lindo, Alessandro Achilli, Ugo Perego, David Archer, Cristina Valdiosera, Barbara Petzelt, Joycelynn Mitchell, Rosita Worl, E. James Dixon, Terence Fifield, Morten Rasmussen, Eske Willerslev, Jerome Cybulski, Brian Kemp, Michael DeGiorgio, Ripan S. Malhi.

Abstract

Recent genome-wide studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific northwest coast proves an intriguing focus for these studies due to its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here we report the genome-wide sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to approximately 10,300 cal years before present (BP). We also analyze low coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from approximately 6075 to 1750 cal years BP. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal BP. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared to other North American individuals (i.e., Anzick-1 and Kennewick Man) from the late Pleistocene or early Holocene. Despite regional shifts in mitochondrial DNA haplogroups we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.

http://biorxiv.org/content/early/2016/12/13/093468

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Интересная информация для R1b и достойных представителей гаплогруппы I.


Rott et al., Early medieval stone-lined graves in Southern Germany: analysis of an emerging noble class

The paper's about kinship and social structure, and not geared for ancient population genetics. But the Y-chromosome haplogroups include R1b (7), I1 (2), I2b1 (2), and I2b, and the mitochondrial haplogroups include T2f (6), H2a2 (3), H1b, HV0*, U3a and U5a. Keep in mind that many of these samples are close relatives.

Abstract

Objectives

Stone-lined graves, which first appear in Bavarian territory during the 7th century AD, are assumed to be tombs of emerging nobility. While previous research on stone-lined grave goods supports their status as elite burials, an important factor defining nobility—kinship—has not been examined so far.
Materials and methods

Morphological analysis of the commingled skeletal remains of 21 individuals from three archaeological sites was carried out. Radiocarbon dating was conducted on these individuals to gain information on usage intervals of these graves. To test whether stone-lined graves can be considered family graves, analyses of mitochondrial HVR I, Y-chromosomal and autosomal STRs were carried out.
Results

Morphological examination revealed a surplus of males buried in stone-lined graves and radiocarbon dating points to usage of the tombs for several generations. According to aDNA analysis, kinship can be assumed both between and within stone-lined graves.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23170/full

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The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers

Eppie R. Jones, Gunita Zarina, Vyacheslav Moiseyev, Emma Lightfoot, Philip R. Nigst, Andrea Manica, Ron Pinhasi, Daniel G. Bradley.

Summary

The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300–4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.

http://www.cell.com/current-biology/fulltext/S0960-9822(16)31542-1

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Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

    Veronika Siska1,*, Eppie Ruth Jones1,2, Sungwon Jeon3, Youngjune Bhak3, Hak-Min Kim3, Yun Sung Cho3, Hyunho Kim4, Kyusang Lee5, Elizaveta Veselovskaya6, Tatiana Balueva6, Marcos Gallego-Llorente1, Michael Hofreiter7, Daniel G. Bradley2, Anders Eriksson1, Ron Pinhasi8,*,†, Jong Bhak3,4,*,†,‡ and Andrea Manica1,*,†

Abstract

Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.

http://advances.sciencemag.org/content/3/2/e1601877

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Две сводных таблицы по дДНК из разных исследований

Медный век - https://docs.google.com/spreadsheets/d/1SBEMpAR6bdCNvVRzRzYF19wEzK-5Eh4qfT5LtzEpK3o/edit#gid=500113463

Early Farmers - https://docs.google.com/spreadsheets/d/1kBrzFiTOynv13maME6EA3-PMWERXLSyL-B0HAy5ZDaM/edit#gid=0