Результаты исследования древней ДНК (дДНК)

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Из автореферата диссертации О. Балановского



Еще интересный спойлер, что готовится к публикации (или в работе?) исследование дДНК из разных по времени захоронений одного археологического комплекса (Деренбург) от неолита включая несколько срезов более позднего времени.

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The genetic impact of aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico // American Journal of Physical Anthropology, Article first published online: 17 OCT 2012 DOI: 10.1002/ajpa.22152

Jaime Mata-Míguez et al.

In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22152/abstract

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Complete mitochondrial DNA genome sequences from the first New Zealanders // Published online before print October 22, 2012, doi: 10.1073/pnas.1209896109
PNAS October 22, 2012

Knappa et al.

Abstract

The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

http://www.pnas.org/content/early/2012/10/17/1209896109

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Molecular genetic investigations on Austria's patron saint Leopold III // Forensic Science International: Genetics, Available online 8 November 2012

The successful marriage policy of margrave Leopold III increased the importance of the House of Babenberg in late medieval Austria (12th century). Historical documentation is inconclusive in providing evidence whether or not his eldest son Adalbert derived from an earlier relationship or from the marriage with King Henry IV's daughter Agnes of Waiblingen, with whom Leopold is considered to have had 17 children. As a matter of fact Adalbert was ignored in the line of succession in favor of a younger brother, Leopold IV, which has led to long term historical discussions. Human remains attributed to these individuals were subjected to DNA analysis. Autosomal, Y-chromosomal and mitochondrial DNA analyses brought successful results, which suggested that Leopold III, Agnes and Adalbert were related in parent–son constellation, in contrast to historical considerations. A possible mix-up of Adalbert's remains with those of his younger brother Ernst could not be confirmed by DNA analysis.

http://www.sciencedirect.com/science/article/pii/S1872497312002360


Sample-ID   DYS456   DYS389 I   DYS390   DYS389 II   DYS458   DYS19   DYS385   DYS393   DYS391   DYS439   DYS635   DYS392   YGATAH4   DYS437   DYS438   DYS448
AD   16   13   23   –   16   –   11, 14   13   (10), 11   –   23   13   12   15   12   19
L   16   13   23   28   16   –   11, 14   13   11   12   23   –   12   15   12   19

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Tracing the Origin of the East-West Population Admixture in the Altai Region (Central Asia).
Mercedes González-Ruiz1, Cristina Santos1, Xavier Jordana2, Marc Simón1, Carles Lalueza-Fox3, Elena Gigli3, Maria Pilar Aluja1, Assumpció Malgosa1*

Received: July 17, 2012; Accepted: October 2, 2012; Published: November 9, 2012

Abstract

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048904

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Так понимаю, эта работа выложена в открытый доступ совсем недавно... хотя написана в 2011-ом...

Mitochondrial DNA in ancient human populations of Europe.

http://digital.library.adelaide.edu.au/dspace/handle/2440/74221
http://digital.library.adelaide.edu.au/dspace/bitstream/2440/74221/1/02whole.pdf

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Origin and Diet of the Prehistoric Hunter-Gatherers on the Mediterranean Island of Favignana (Ègadi Islands, Sicily) // PLoS ONE 7(11): e49802. doi:10.1371/journal.pone.0049802

Mannino et al.

Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d’Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d’Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d’Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness-enhancing adaptations.

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049802

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http://www.bmj.com/content/345/bmj.e8268

Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study
BMJ 2012; 345 doi: http://dx.doi.org/10.1136/bmj.e8268 (Published 17 December 2012)
Cite this as: BMJ 2012;345:e8268

Zahi Hawass, egyptologist1, Somaia Ismail, professor of molecular biology23, Ashraf Selim, professor of radiology4, Sahar N Saleem, professor of radiology4, Dina Fathalla, molecular biologist3, Sally Wasef, molecular biologist5, Ahmed Z Gad, molecular biologist3, Rama Saad, molecular biologist3, Suzan Fares, molecular biologist3, Hany Amer, assistant professor of pharmacology6, Paul Gostner, radiologist7, Yehia Z Gad, professor of molecular genetics2, Carsten M Pusch, molecular biologist8, Albert R Zink, paleopathologist9

Abstract
Objective To investigate the true character of the harem conspiracy described in the Judicial Papyrus of Turin and determine whether Ramesses III was indeed killed.

Design Anthropological, forensic, radiological, and genetic study of the mummies of Ramesses III and unknown man E, found together and taken from the 20th dynasty of ancient Egypt (circa 1190-1070 BC).

Results Computed tomography scans revealed a deep cut in Ramesses III’s throat, probably made by a sharp knife. During the mummification process, a Horus eye amulet was inserted in the wound for healing purposes, and the neck was covered by a collar of thick linen layers. Forensic examination of unknown man E showed compressed skin folds around his neck and a thoracic inflation. Unknown man E also had an unusual mummification procedure. According to genetic analyses, both mummies had identical haplotypes of the Y chromosome and a common male lineage.

Conclusions This study suggests that Ramesses III was murdered during the harem conspiracy by the cutting of his throat. Unknown man E is a possible candidate as Ramesses III’s son Pentawere.

"Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a. The testing of polymorphic autosomal microsatellite loci provided similar results in at least one allele of each marker (table 2⇓). Although the mummy of Ramesses III’s wife Tiy was not available for testing, the identical Y chromosomal DNA and autosomal half allele sharing of the two male mummies strongly suggest a father-son relationship".

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Genetic Data Suggests that the Jinggouzi People are Associated with the Donghu, an Ancient Nomadic Group of North China // Human Biology 84(4):365-378. 2012
doi: http://dx.doi.org/10.3378/027.084.0402

Wang et al.

Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by a nomadic tribe in the 3rd century BC. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until the Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and to explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which was located in northern China, dated approximately 2500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C, and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms. Those haplogroups are common in North Asia and East Asia. The Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of the Donghu tribe and this might show some insight into the ancient nomadic society.

http://www.bioone.org/doi/abs/10.3378/027.084.0402?af=R

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Genetic comparison of the head of Henri IV and the presumptive blood from Louis XVI (both Kings of France).

Philippe Charliera, b, Iñigo Olaldec, Neus Soléc, Оscar Ramírezc, Jean-Pierre Babelond, Bruno Gallande, Francesc Calafellc, Carles Lalueza-Foxc.

    a Department of Forensic Medicine and Pathology, University Hospital R. Poincaré (AP-HP, UVSQ), 104 R. Poincaré boulevard, 92380 Garches, France
    b Laboratory of Medical Ethics and Forensic Medicine, University of Paris 5, 45 Saints Pères Street, 75006 Paris, France
    c Institut de Biologia Evolutiva, CSIC-UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
    d Académie des Inscriptions et Belles Lettres, Institut de France, quai Conti, 75007 Paris, France
    e Archives Nationales, 60 rue des Francs-Bourgeois, 75003 Paris, France

Abstract

A mummified head was identified in 2010 as belonging to Henri IV, King of France. A putative blood sample from the King Louis XVI preserved into a pyrographically decorated gourd was analyzed in 2011. Both kings are in a direct male-line descent, separated by seven generations. We have retrieved the hypervariable region 1 of the mitochondrial DNA as well as a partial Y-chromosome profile from Henri IV. Five STR loci match the alleles found in Louis XVI, while another locus shows an allele that is just one mutation step apart. Taking into consideration that the partial Y-chromosome profile is extremely rare in modern human databases, we concluded that both males could be paternally related. The likelihood ratio of the two samples belonging to males separated by seven generations (as opposed to unrelated males) was estimated as 246.3, with a 95% confidence interval between 44.2 and 9729. Historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample, and give another positive argument for the authenticity of the head of Henri IV.

http://www.sciencedirect.com/science/article/pii/S0379073812005361

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Fu et al
Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.


http://intl.pnas.org/content/early/2013/01/17/1221359110.abstract

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Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe // PLoS Genet 9(2): e1003296. doi:10.1371/journal.pgen.1003296,  Published: February 14, 2013

Sarkissian et al.

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296

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Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers

    Bohdan Gworysa,
    Joanna Rosińczuk-Tonderysb,
    Aleksander Chrószczc,
    Maciej Janeczekc,
    Andrzej Dwojakd,
    Justyna Bazanb, Corresponding author contact information, E-mail the corresponding author,
    Mirosław Furmaneke,
    Tadeusz Doboszf,
    Małgorzata Bonarf,
    Anna Jonkiszf,
    Ireneusz Całkosińskib

Abstract

So-called physiological stress markers are extremely valuable in assessing life conditions of old human populations. They constitute effects of adverse environmental conditions, which leave traces on skeleton. Those traces allow for partial assessment of life conditions not only in environmental and social but also cultural aspects for prehistoric populations. The aim of this study is to estimate the influence of general environmental conditions on human organism at the final stage of the Neolithic period – in the Corded Ware culture. Two skeletons discovered in a tumulus on the outskirts of Wroclaw in the Jagodno district have been subjected to assessment. Their age at the moment of death has been determined in both cases on the basis of multi-feature analysis of changes occurring in formation of particular morphologic features of skeleton and teeth. Attention has been paid to the obliteration degree of skull sutures and the surface state of chewing tooth crowns. A comprehensive DNA analysis has been conducted determining sex of the remains. Also bacteriological analysis of the research material has been conducted. Measurements of all available metric features of the skeletons have been performed with the use of the Martin method. Inventory and basic description of the finds accompanying skeleton remains have been carried out as well. Intensity of the following physiological stress markers have been defined and evaluated: Harris lines; cribra orbitalia; cribra cranii. Skull morphology, degree of suture obliteration, surface state of chewing tooth crowns and estimation of degree of bone development of postcranial skeleton indicate that both skeletons detailed age was about 16 – 18 years. Harris lines on the femur were formed in the 2nd and the 3rd year of life and on both tibias – in the 2nd year of life. Obtained results indicate that those people were expose to stress connected with food deficit when they were very young. Poor porotic changes on the skull and isotopic data suggest that their life quality increased at later age.

Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*.

http://www.sciencedirect.com/science/article/pii/S0305440313000459

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First insights into the metagenome of Egyptian mummies using next-generation sequencing

    Rabab Khairat,
    Markus Ball,
    Chun-Chi Hsieh Chang,
    Raffaella Bianucci,
    Andreas G. Nerlich,
    Martin Trautmann,
    Somaia Ismail,
    Gamila M. L. Shanab,
    Amr M. Karim,
    Yehia Z. Gad,
    … show all 11

Abstract

We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC–124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a “bacterial fingerprint”, discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.

http://link.springer.com/article/10.1007/s13353-013-0145-1

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Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

    Paul Brotherton,   
    Wolfgang Haak,   
    Jennifer Templeton,   
    Guido Brandt,   
    Julien Soubrier,   
    Christina Jane Adler,   
    Stephen M. Richards,   
    Clio Der Sarkissian,   
    Robert Ganslmeier,   
    Susanne Friederich,   
    Veit Dresely,   
    Mannis van Oven,   
    Rosalie Kenyon,   
    Mark B. Van der Hoek,   
    Jonas Korlach,   
    Khai Luong,   
    Simon Y.W. Ho,   
    Lluis Quintana-Murci,   
    Doron M. Behar,   
    Harald Meller   
    et al.

Abstract

    Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

http://www.nature.com/ncomms/journal/v4/n4/full/ncomms2656.html