Результаты исследования древней ДНК (дДНК)

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Application of the iPLEXTM Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: Benefits for ancient population studies // ELECTROPHORESIS, Volume 32, Issue 3-4, pages 386–393, February 2011

Mendisco et al.

Abstract
Important developments in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique have generated new perspectives regarding SNP genotyping, which are particularly promising for ancient population-based studies. The main aim of the present study was to investigate the application of a MALDI-TOF MS-based SNP genotyping technique, called iPLEX® Gold, to analyze Amerindian ancient DNA samples. The first objective was to test the sensitivity of the method, which is recommended for DNA quantities between 10 and 5 ng, for ancient biological samples containing DNA molecules that were degraded and present in minute quantities. The second objective was to detail the advantages of this technique for studies on ancient populations. Two multiplexes were designed, allowing the major Amerindian mitochondrial and Y haplogroups to be determined simultaneously. This analysis has never been described before. Results demonstrated the reliability and accuracy of the method; data were obtained for both mitochondrial and nuclear DNA using picogram (pg) quantities of nucleic acid. This technique has the advantages of both MS and minisequencing techniques; thus, it should be included in the protocols for future ancient DNA studies.

http://onlinelibrary.wiley.com/doi/10.1002/elps.201000483/abstract

Образцы представлены Los Amarillos archeological site (по некоторым данным - преинкский период ~ 2500-1500 лет назад)

16223T - 16290T - 16319A - 16362C A2
16223T - 16325C - 16362C D1 // Q1a3a*
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*
16111T - 16125A - 16223T - 16290Y - 16319A - 16362C A2 // Q1a3a*
16223T - 16290T - 16319A - 16362C A2 // Q1a3a
16223T - 16325C - 16362C D1 // Q1a3a*
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*
16223T - 16290T - 16319A - 16362C A2
16223T - 16290T - 16319A - 16362C A2
16223T - 16325C - 16362C D1 // Q1a3a*
16182C - 16183C - 16189C - 16217C B2 // Q1a3*(xQ1a3a)
16183C - 16189Y - 16223T - 16298Y - 16311C - 16325C - 16327T C1b
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3*(xQ1a3a)
16111T - 16223T - 16290T - 16319A - 16362C A2 // Q1a3a*

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Genetic features of ancient West Siberian people of the Middle Ages, revealed by mitochondrial DNA haplogroup analysis // Journal of Human Genetics advance online publication 14 July 2011;   doi: 10.1038/jhg.2011.68

Sato et al.

In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U. This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia.

http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg201168a.html

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HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary // Journal of Human Genetics advance online publication 15 September 2011;   doi: 10.1038/jhg.2011.103

Guba et al.

Analysis of mitochondrial mutations in the HVS-I region is an effective method for ancient human populational studies. Discontinuous haplotype data between the first farmers and contemporary Europeans has been described before. Our contribution is based on a survey initiated on the Neolithic skeletons from Hungarian archaeological sites in the Alföld. This Lowland, the Hungarian Plain, is well excavated as an important region for spread of Neolithic culture from Near East and Balkans toward Central and Western Europe, started circa 8000 years ago. HVS-I sequences from nt15977 to nt16430 of 11 such specimens with sufficient mitochondrial DNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. After assigning all single-nucleotide polymorphisms, a novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined. On mitochondrial control mutations at nt16257 and nt16261, polymorphic PCRs were carried out to assess their distribution in remains. Neolithic data set was compared with contemporary Vác samples and references, resulting in higher frequency of N9a in Alföld as a remarkable genetic discontinuity. Our investigation is the first to study mutations form Neolithic of Hungary, resulting in an outcome of Far Eastern haplogroups in the Carpathian Basin. It is worth further investigation as a non-descendant theory, instead of a continuous population history, supporting genetic gaps between ancient and recent human populations.

http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg2011103a.html

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Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA // Journal of Human Genetics advance online publication 22 September 2011;   doi: 10.1038/jhg.2011.102

In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500–3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity.

http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg2011102a.html

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Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia // Article first published online: 27 SEP 2011, DOI: 10.1002/ajpa.21561

Adachi et al.

To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21561/abstract

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High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia // American Journal of Physical Anthropology, Article first published online: 12 OCT 2011, DOI: 10.1002/ajpa.21626

Casas-Vargas et al.

Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of “La Purnia” (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the “Río Suarez” to the “Río de Oro”, and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the “Chicamocha” river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21626/abstract

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The presence of nuclear families in prehistoric collective burials revisited: The bronze age burial of montanissell cave (Spain) in the light of aDNA // American Journal of Physical Anthropology, Article first published online: 30 SEP 2011, DOI: 10.1002/ajpa.21590

Simón et al.

Ancient populations have commonly been thought to have lived in small groups where extreme endogamy was the norm. To contribute to this debate, a genetic analysis has been carried out on a collective burial with eight primary inhumations from Montanissell Cave in the Catalan pre-Pyrenees. Radiocarbon dating clearly placed the burial in the Bronze Age, around 3200 BP. The composition of the group—two adults (one male, one female), one young woman, and five children from both sexes—seemed to represent the structure of a typical nuclear family. The genetic evidence proves this assumption to be wrong. In fact, at least five out of the eight mitochondrial haplotypes were different, denying the possibility of a common maternal ancestor for all of them. Nevertheless, 50% of the inhumations shared haplogroup J, so the possibility of a maternal relationship cannot be ruled out. Actually, combining different analyses performed using ancient and living populations, the probability of having four related J individuals in Montanissell Cave would range from 0.9884 to 0.9999. Owing to the particularities of this singular collective burial (small number of bodies placed altogether in a hidden cave, the evidence of non-simultaneous interments, close dating and unusual grave goods), we suggest that it might represent a small group with a patrilocal mating system.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21590/abstract

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Ancient DNA suggests the leading role played by men in the Neolithic dissemination // Published online before print October 31, 2011, doi: 10.1073/pnas.1113061108, PNAS October 31, 2011

Lacan et al.

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

http://www.pnas.org/content/early/2011/10/24/1113061108.abstract

G2a (P15) - 5/6 (83,3%)
E1b1b1a1b (V13) - 1/6 (16,6%)

DYS456 DYS389I DYS390 DYS389II DYS458 DYS19 DYS385 DYS393 DYS391 DYS439 DYS635 DYS392 H4 DYS437 DYS438 DYS448   
15   12   (23)   (29)   18   15    (14/14)     13   10   11   (21)   X   12   16   10   X    G2a 
15   12   23   X   18   15    14/14     13   10   11   21   (11)   12   16   10   22    G2a 
15   12   23   29   18   15    14/14     13   10   11   21   11   12   16   10   (22)    G2a 
15   12   (23)   29   (18)   (15)    (14/14)     13   (10)   11   X   X   12   16   X   22    G2a 
15   12   X   X   18   (15)   X/X   13   (10)   (11)   X   X   12   (16)   X   X    G2a
16   13   24   (31)   16   13    16/19     13   (10)   11   22   11   10   (14)   10   20    E1b1b1a1b 

16093C, 16224C, 16311C // K1a
16093C, 16224C, 16311C // K1a
16093C, 16224C, 16311C // K1a
CRS // H3
16126C, 16294T, 16296T, 16304C // T2b
16126C, 16294T, 16296T, 16304C // T2b
16051G, 16189C, 16270T // U5

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Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers // Molecular Ecology, Article first published online: 25 NOV 2011, DOI: 10.1111/j.1365-294X.2011.05361.x

GAMBA et al.

The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations—N* and X1—are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (FST∼0.13, P < 10−5), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.

http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05361.x/abstract

5475–5305 cal. BCE

N* - 3/7
K - 1/7
H - 1/7
U5 - 1/7
X1 - 1/7

5329–4999 cal. BCE

H - 2/3
K - 1/3

4250–3700 cal. BCE

K - 1/3
H20 - 1/3
N* - 1/3

[Centurion]

Население западносибирской лесостепи в эпоху бронзы (V–начало I тысячелетия до н. э.) по данным анализа генофонда митохондриальной ДНК // ГЕНОМИКА

А.С. Пилипенко[1], А.А. Журавлев[1], Р.О. Трапезов[1], А.Г. Ромащенко[1], В.И. Молодин[2]
1 Институт цитологии и генетики СО РАН, Новосибирск
2 Институт археологии и этнографии СО РАН, Новосибирск

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Finding the founder of Stockholm - a kinship study based on Y-chromosomal, autosomal and mitochondrial DNA // Ann Anat. 2012 Jan 20;194(1):138-45. Epub 2011 Apr 5

Malmström et al.

Abstract
Historical records claim that Birger Magnusson (died 1266), famous regent of Sweden and the founder of Stockholm, was buried in Varnhem Abbey in Västergötland. After being lost for centuries, his putative grave was rediscovered during restoration work in the 1920s. Morphological analyses of the three individuals in the grave concluded that the older male, the female and the younger male found in the grave were likely to be Birger, his second wife Mechtild of Holstein and his son Erik from a previous marriage. More recent evaluations of the data from the 1920s seriously questioned these conclusions, ultimately leading to the reopening and reexamination of the grave in 2002. Ancient DNA-analyses were performed to investigate if the relationship between the three individuals matched what we would expect if the individuals were Birger, Erik and Mechtild. We used pyrosequencing of Y-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions, massive clonal data, the c-statistics, and real-time quantitative data. We show that the males carry the same Y-chromosomal haplogroup and thus we cannot reject a father-son type of relation. Further, as shown by the mtDNA analyses, none of the individuals are maternally related. We conclude that the graves indeed belong to Birger, Erik and Mechtild, or to three individuals with the exact same kind of biological relatedness.

http://www.ncbi.nlm.nih.gov/pubmed/21596538?dopt=Abstract

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Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany // American Journal of Physical Anthropology, Article first published online: 3 MAY 2012, DOI: 10.1002/ajpa.22074

Lee et al.

he transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800–2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22074/abstract

[Centurion]

Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe // Journal of Human Genetics advance online publication 7 June 2012;   doi: 10.1038/jhg.2012.69

Nikitin et al.

Recent studies of ancient mitochondrial DNA (mtDNA) lineages have revealed the presence of East Eurasian mtDNA haplogroups in the Central European Neolithic. Here we report the finding of East Eurasian lineages in ancient mtDNA from two Neolithic cemeteries of the North Pontic Region (NPR) in Ukraine. In our study, comprehensive haplotyping information was obtained for 7 out of 18 specimens. Although the majority of identified mtDNA haplogroups belonged to the traditional West Eurasian lineages of H and U, three specimens were determined to belong to the lineages of mtDNA haplogroup C. This find extends the presence of East Eurasian lineages in Neolithic Europe from the Carpathian Mountains to the northern shores of the Black Sea and provides the first genetic account of Neolithic mtDNA lineages from the NPR.

http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg201269a.html

[Centurion]

Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers // Current Biology, 28 June 2012

Sánchez-Quinto et al.

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic [1,2,3,4,5,6,7,8,9,10] is poorly understood, both due to the scarcity of human remains from that period [11,12,13,14,15,16,17,18] and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns [19,20,21,22]. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain) [23]. The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

http://www.cell.com/current-biology/abstract/S0960-9822(12)00650-1

[Шад]

В некрополе Эгин-Гол (приграничный район Монголии) около 50% гаплогрупп хуннов -R1a1.

Раскопки, проведенные на территории Монголии, подарили археологам и генетикам очень ценные находки. Обнаруженные учеными человеческие останки, возможно, помогут пролить свет на происхождение древнего кочевого народа хунну. Китайскими и монгольскими археологами, которые в течение последних пяти лет проводят раскопки на территории Монголии...Так, недавно директор Института археологии Внутренней Монголии Чэнь Юнчжи сообщил, что совместная археологическая группа сделала очень интересную находку — скелет пожилого мужчины.Останки старика были обнаружены недалеко от склепа Дуурлинг Нарз (Duurlig Nars), где обычно проводились захоронения представителей высоких чинов, одним из которых он возможно и являлся.В его скелете были замечены неясные мутации Y-хромосом (мужских половых хромосом). А исследование структуры ДНК показало, что мужчина, судя повсему, "иноземец" — он, скорее всего, принадлежал к иной этнической группе. Что, возможно, указывает на его принадлежность к Хуннской Империи, господствовавшей на этой территории примерно в 200-100-е годы до нашей эры...Останкам, обнаруженным на востоке Монголии неподалеку от северной границы Китая, предположительно две тысячи лет. Судя по анализу ДНК, ученые считают, что это либо потомок европейских кровей, либо выходец из западной Азии. Однако он занимал важное положение в Хуннской Империи, как полагает генетик Киунг-Йонг Ким и его коллеги из Сеульского национального университета (Южная Корея), которые присоединились к исследованиям.

...проанализировали костные останки из трех захоронений Хуннского времени, могильник Дуурлиг Нарс, аймак Кентей, C.-В. Монголия. Два мужчины и одна женщина, судя по инвентарю (золотые штучки и пр.), принадлежали к знати. У одного из мужиков (300-100 г. до н.э.) по днк у-хромосомы определили гаплогруппу R1a1, что указывает на его западные корни и возможное индоевропейское происхождение его самого или предков. Ранее R1a1 идентифицировали у андроновцев из захоронений на территории Красноярского края. По материнской мтднк у этого индивида тоже западный маркер U2e1. У второго мужчины определили вполне восточно-азиатскую гаплогруппу С3с.

Источник