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Sample records for ancient dna studies

  1. Authenticity in ancient DNA studies

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Willerslev, Eske

    2006-01-01

    Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist as ...

  2. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  3. Ancient DNA and Forensics Mutual Benefits a Practical Sampling and Laboratory Guide Through a Virtual Ancient DNA Study

    Directory of Open Access Journals (Sweden)

    Jan Cemper-Kiesslich

    2014-09-01

    In this review the authors give a general overview on the field of ancient DNA analysis focussing of the potentials and limits, fields of application, requirements for samples, laboratory setup, reaction design and equipment as well as a brief outlook on current developments, future perspectives and potential cross links with associated scientific disciplines. Key words: Human DNA, Ancient DNA, Forensic DNA typing, Molecular archaeology, Application.

  4. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes...... such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics......, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived...

  5. Paleo-Environmental Reconstruction Using Ancient DNA

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther

    The aim of this thesis has been to investigate and expand the methodology and applicability for using ancient DNA deposited in lake sediments to detect and determine its genetic sources for paleo-environmental reconstruction. The aim was furthermore to put this tool into an applicable context...... solving other scientifically interesting questions. Still in its childhood, ancient environmental DNA research has a large potential for still developing, improving and discovering its possibilities and limitations in different environments and for identifying various organisms, both in terms...... research on ancient and modern environmental DNA (Paper 1), secondly by setting up a comparative study (Paper 2) to investigate how an ancient plant DNA (mini)-barcode can reflect other traditional methods (e.g. pollen and macrofossils) for reconstructing floristic history. In prolongation of the results...

  6. Geologically ancient DNA: fact or artefact?

    DEFF Research Database (Denmark)

    Hebsgaard, Martin Bay; Phillips, Matthew J.; Willerslev, Eske

    2005-01-01

    Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and...

  7. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

    Foote, Andrew David; Hofreiter, Michael; Morin, Philip A.

    2012-01-01

    such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an oppor- tunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have...... focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes...... in distribution and range of marine mammal species; we review these studies and discuss the limitations of such ‘presence only’ studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also...

  8. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... yielded major progress with regard to both the phylogenetic positions of extinct species, as well as resolving population genetics questions in both extinct and extant species....

  9. Application of Ancient DNA Methods to the Study of the Transatlantic Slave Trade

    DEFF Research Database (Denmark)

    Sandoval Velasco, Marcela

    As one of a limited number of biomolecules recording evolutionary events, DNA provides an unparalleled means of investigating genetic processes. Over three decades, ancient DNA research has matured in many ways, growing alongside technological and methodological advancements. However, due to DNA...... means of investigating genetic processes. Over three decades, ancient DNA research has matured in many ways, growing alongside technological and methodological advancements. However, due to DNA preservation, degradation and contamination, ancient DNA research presents significant limitations...... preservation, degradation and contamination, ancient DNA research presents significant limitations and challenges. Until recently, it was thought that DNA did not survive more than few hundred thousand years, and that it was impossible to retrieve whole genome data from ancient samples preserved under...

  10. The study of human Y chromosome variation through ancient DNA.

    Science.gov (United States)

    Kivisild, Toomas

    2017-05-01

    High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

  11. Non-destructive sampling of ancient insect DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Elias, Scott; Gilbert, Tom

    2009-01-01

    BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological...... of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost......-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient...

  12. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

    DEFF Research Database (Denmark)

    Binladen, Jonas; Wiuf, Carsten Henrik; Gilbert, M. Thomas P.

    2006-01-01

    To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved...... in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from...... adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nu...

  13. Setting the stage - building and working in an ancient DNA laboratory.

    Science.gov (United States)

    Knapp, Michael; Clarke, Andrew C; Horsburgh, K Ann; Matisoo-Smith, Elizabeth A

    2012-01-20

    With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process. Copyright © 2011 Elsevier GmbH. All rights reserved.

  14. Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives

    Directory of Open Access Journals (Sweden)

    Michael Knapp

    2010-07-01

    Full Text Available The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA  research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.

  15. Ancient pathogen DNA in human teeth and petrous bones

    DEFF Research Database (Denmark)

    Margaryan, Ashot; Hansen, Henrik B.; Rasmussen, Simon

    2018-01-01

    Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petro...

  16. Stories in Genetic Code. The contribution of ancient DNA studies to anthropology and their ethical implications

    Directory of Open Access Journals (Sweden)

    Cristian M. Crespo

    2010-12-01

    Full Text Available For several decades, biological anthropology has employed different molecular markers in population research. Since 1990 different techniques in molecular biology have been developed allowing preserved DNA extraction and its typification in different samples from museums and archaeological sites. Ancient DNA studies related to archaeological issues are now included in the field of Archaeogenetics. In this work we present some of ancient DNA applications in archaeology. We also discuss advantages and limitations for this kind of research and its relationship with ethic and legal norms.

  17. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  18. A guide to ancient protein studies

    DEFF Research Database (Denmark)

    Hendy, Jessica; Welker, Frido; Demarchi, Beatrice

    2018-01-01

    Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from....... Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research...

  19. Fossil avian eggshell preserves ancient DNA

    DEFF Research Database (Denmark)

    Oskam, Charlotte L; Haile, James Seymour; McLay, Emma

    2010-01-01

    Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful...... isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids......, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has...

  20. Quantification and presence of human ancient DNA in burial place ...

    African Journals Online (AJOL)

    Quantification and presence of human ancient DNA in burial place remains of Turkey using real time polymerase chain reaction. ... A published real-time PCR assay, which allows for the combined analysis of nuclear or ancient DNA and mitochondrial DNA, was modified. This approach can be used for recovering DNA from ...

  1. Use of RAPD and PCR double amplification in the study of ancient DNA

    Directory of Open Access Journals (Sweden)

    F. Balzano

    2011-01-01

    Full Text Available This project analysed the DNA extracted from bones of ancient sheep which have been brought to light in Sardinian different archaeological sites. In order to better analyse this highly fragmented DNA, a double amplification technique was chosen. The first approach consisted of RAPD-PCR abd the second one in classic PCR. The RAPD-PCR amplified random fragments and allowed the production of numerous amplicons. The products of RAPD amplification have been amplified, more specifically, by the second PCR using primers for a sequence of 176 bp of mitochondrial D-loop region. These DNA fragments have been sequenced and the sequence analysis has confirmed that it belonged to Ovis aries. Consequently, this provedure can be considered a valid tool to perform amplification of degraded DNA, such as ancient DNA.

  2. Ancient DNA analysis of dental calculus.

    Science.gov (United States)

    Weyrich, Laura S; Dobney, Keith; Cooper, Alan

    2015-02-01

    Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

    DEFF Research Database (Denmark)

    Avila Arcos, Maria del Carmen; Cappellini, Enrico; Romero-Navarro, J. Alberto

    2011-01-01

    The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples...

  4. Using Ancient DNA to Understand Evolutionary and Ecological Processes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Cooper, Alan

    2014-01-01

    Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of ...

  5. Ancient and modern environmental DNA

    Science.gov (United States)

    Pedersen, Mikkel Winther; Overballe-Petersen, Søren; Ermini, Luca; Sarkissian, Clio Der; Haile, James; Hellstrom, Micaela; Spens, Johan; Thomsen, Philip Francis; Bohmann, Kristine; Cappellini, Enrico; Schnell, Ida Bærholm; Wales, Nathan A.; Carøe, Christian; Campos, Paula F.; Schmidt, Astrid M. Z.; Gilbert, M. Thomas P.; Hansen, Anders J.; Orlando, Ludovic; Willerslev, Eske

    2015-01-01

    DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field. PMID:25487334

  6. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Directory of Open Access Journals (Sweden)

    Andaine Seguin-Orlando

    Full Text Available Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

  7. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.

    Science.gov (United States)

    Yoshida, Kentaro; Sasaki, Eriko; Kamoun, Sophien

    2015-01-01

    The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

  8. Ancient DNA (aDNA): What is it? Why is it important?- Fact Sheet

    OpenAIRE

    Alexa Walker; George Nicholas; Daryl Pullman; Alan Goodman; Bioarchaeology and Genetics Working Group

    2014-01-01

    As genetic research is increasingly applied to new areas of study, including in archaeological and heritage contexts, a range of questions arise concerning the social, ethical, legal, and political implications of ancient DNA. This fact sheet explains the nature and challenges of aDNA research, and why information from it is important and relevant to people today.  

  9. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon Y. W.; Gilbert, Tom

    2012-01-01

    Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both...... quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

  10. Retroviral DNA Sequences as a Means for Determining Ancient Diets.

    Directory of Open Access Journals (Sweden)

    Jessica I Rivera-Perez

    Full Text Available For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.

  11. Combining bleach and mild predigestion improves ancient DNA recovery from bones

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Hanghøj, Kristian Ebbesen; Nistelberger, Heidi M.

    2017-01-01

    library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains...... aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high...

  12. Comparing ancient DNA preservation in petrous bone and tooth cementum

    DEFF Research Database (Denmark)

    Hansen, Henrik B.; Damgaard, Peter de Barros; Margaryan, Ashot

    2017-01-01

    Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA...... to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons...

  13. Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Tyler-Smith, Chris

    2016-01-11

    Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

  14. Use DNA to learn from the past: how modern and ancient DNA studies may help reveal the past and predict the future distribution of species

    Science.gov (United States)

    Edwards, M. E.; Alsos, I. G.; Sjögren, P.; Coissac, E.; Gielly, L.; Yoccoz, N.; Føreid, M. K.; Taberlet, P.

    2015-12-01

    Knowledge of how climate change affected species distribution in the past may help us predict the effect of ongoing environmental changes. We explore how the use of modern (AFLP fingerprinting techniques) and ancient DNA (metabarcoding P6 loop of chloroplast DNA) help to reveal past distribution of vascular plant species, dispersal processes, and effect of species traits. Based on studies of modern DNA combined with species distribution models, we show the dispersal routes and barriers to dispersal throughout the circumarctic/circumboreal region, likely dispersal vectors, the cost of dispersal in term of loss of genetic diversity, and how these relates to species traits, dispersal distance, and size of colonized region. We also estimate the expected future distribution and loss of genetic diversity and show how this relates to life form and adaptations to dispersal. To gain more knowledge on time lags in past range change events, we rely on palaeorecords. Current data on past distribution are limited by the taxonomic and time resolution of macrofossil and pollen records. We show how this may be improved by studying ancient DNA of lake sediments. DNA of lake sediments recorded about half of the flora surrounding the lake. Compared to macrofossil, the taxonomic resolution is similar but the detection rate is considerable improved. By taking into account main determinants of founder effect, dispersal vectors, and dispersal lags, we may improve our ability to forecast effects of climate change, whereas more studies on ancient DNA may provide us with knowledge on distribution time lags.

  15. The importance of studying inherited hematological disorders in ancient Anatolian populations

    Directory of Open Access Journals (Sweden)

    Yeşim Doğan Alakoç

    2011-12-01

    Full Text Available Before analysis of DNA from ancient remains was possible, anthropologists studied evolution and migration patterns using data obtained from population genetic studies on modern populations combined with data obtained from morphological evaluations of ancient remains. Currently, DNA analysis of ancient populations is making a valuable contribution to these efforts. Researchers that perform ancient DNA analysis prefer to study polymorphisms on the Y chromosome or mitochondrial DNA because the results are easier to statistically evaluate. To evaluate polymorphisms on diploid genomes, which are more informative, only mutations that have been extensively examined in modern populations should be chosen. The most extensively evaluated mutations are those related to prevalent inherited disorders. As such, beta-thalassemia, sickle cell anemia, FVL mutation of globin and the factor V genes are good candidates for DNA studies in ancient populations. These mutations are common in Anatolia, host to many civilizations since the Paleolithic period. This history makes Anatolia a good place for conducting research that could enhance our understanding of human evolution and migration patterns.

  16. Pros and cons of methylation-based enrichment methods for ancient DNA

    Science.gov (United States)

    Seguin-Orlando, Andaine; Gamba, Cristina; Sarkissian, Clio Der; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D.; Lopez, Patricio; McDonald, H. Gregory; Scott, Eric; Tikhonov, Alexei; Stafford,, Thomas W.; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. PMID:26134828

  17. Experimental conditions improving in-solution target enrichment for ancient DNA

    DEFF Research Database (Denmark)

    Cruz-Dávalos, Diana I.; Llamas, Bastien; Gaunitz, Charleen

    2017-01-01

    High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods ...

  18. The effect of ancient DNA damage on inferences of demographic histories

    DEFF Research Database (Denmark)

    Axelsson, Erik; Willerslev, Eske; Gilbert, Marcus Thomas Pius

    2008-01-01

    The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates o...... for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution....

  19. Fact Sheet- Ancient DNA: What is it? Why is it Important?

    OpenAIRE

    Alexa Walker; George Nicholas; Daryl Pullman; Alan Goodman; Bioarchaeology and Genetics Working Group

    2016-01-01

    As genetic research is increasingly applied to new areas of study, including in archaeological and heritage contexts, a range of questions arise concerning the social, ethical, legal, and political implications of ancient DNA. This fact sheet explains the nature and challenges of aDNA research, and why information from it is important and relevant to people today. 

  20. Comparison of Suitability of the Most Common Ancient DNA Quantification Methods.

    Science.gov (United States)

    Brzobohatá, Kristýna; Drozdová, Eva; Smutný, Jiří; Zeman, Tomáš; Beňuš, Radoslav

    2017-04-01

    Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA. Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site. The tested methods included ultraviolet (UV) absorbance, real-time quantitative polymerase chain reaction (qPCR) based on SYBR ® green detection, real-time qPCR based on a forensic kit, quantification via fluorescent dyes bonded to DNA, and fragmentary analysis. Differences between groups were tested using a paired t-test. Methods that measure total DNA present in the sample (NanoDrop ™ UV spectrophotometer and Qubit ® fluorometer) showed the highest concentrations. Methods based on real-time qPCR underestimated the quantity of aDNA. The most accurate method of aDNA quantification was fragmentary analysis, which also allows DNA quantification of the desired length and is not affected by PCR inhibitors. Methods based on the quantification of the total amount of DNA in samples are unsuitable for ancient samples as they overestimate the amount of DNA presumably due to the presence of microbial DNA. Real-time qPCR methods give undervalued results due to DNA damage and the presence of PCR inhibitors. DNA quantification methods based on fragment analysis show not only the quantity of DNA but also fragment length.

  1. High-Throughput DNA sequencing of ancient wood.

    Science.gov (United States)

    Wagner, Stefanie; Lagane, Frédéric; Seguin-Orlando, Andaine; Schubert, Mikkel; Leroy, Thibault; Guichoux, Erwan; Chancerel, Emilie; Bech-Hebelstrup, Inger; Bernard, Vincent; Billard, Cyrille; Billaud, Yves; Bolliger, Matthias; Croutsch, Christophe; Čufar, Katarina; Eynaud, Frédérique; Heussner, Karl Uwe; Köninger, Joachim; Langenegger, Fabien; Leroy, Frédéric; Lima, Christine; Martinelli, Nicoletta; Momber, Garry; Billamboz, André; Nelle, Oliver; Palomo, Antoni; Piqué, Raquel; Ramstein, Marianne; Schweichel, Roswitha; Stäuble, Harald; Tegel, Willy; Terradas, Xavier; Verdin, Florence; Plomion, Christophe; Kremer, Antoine; Orlando, Ludovic

    2018-03-01

    Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management. © 2018 John Wiley & Sons Ltd.

  2. Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample

    Directory of Open Access Journals (Sweden)

    Chang Seok Oh

    2010-03-01

    Full Text Available In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.

  3. Ancient bacteria show evidence of DNA repair

    DEFF Research Database (Denmark)

    Johnson, Sarah Stewart; Hebsgaard, Martin B; Christensen, Torben R

    2007-01-01

    -term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence...... geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long...... that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability....

  4. Evidence of ancient DNA reveals the first European lineage in Iron Age Central China.

    Science.gov (United States)

    Xie, C Z; Li, C X; Cui, Y Q; Zhang, Q C; Fu, Y Q; Zhu, H; Zhou, H

    2007-07-07

    Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.

  5. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments

    DEFF Research Database (Denmark)

    Hansen, Anders Johannes; Mitchell, D.L.; Wiuf, C.

    2006-01-01

    , and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate about hundred times faster than single stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen...... conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost...

  6. News from the west: ancient DNA from a French megalithic burial chamber.

    Science.gov (United States)

    Deguilloux, Marie-France; Soler, Ludovic; Pemonge, Marie-Hélène; Scarre, Chris; Joussaume, Roger; Laporte, Luc

    2011-01-01

    Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices. Copyright © 2010 Wiley-Liss, Inc.

  7. A new model for ancient DNA decay based on paleogenomic meta-analysis.

    Science.gov (United States)

    Kistler, Logan; Ware, Roselyn; Smith, Oliver; Collins, Matthew; Allaby, Robin G

    2017-06-20

    The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. DNA FROM ANCIENT STONE TOOLS AND BONES EXCAVATED AT BUGAS-HOLDING, WYOMING

    Science.gov (United States)

    Traces of DNA may preserve on ancient stone tools. We examined 24 chipped stone artifacts recovered from the Bugas-Holding site in northwestern Wyoming for the presence of DNA residues, and we compared DNA preservation in bones and stone tools from the same stratigraphic context...

  9. Pathogenic microbial ancient DNA: a problem or an opportunity?

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2006-01-01

    cloning. Yet these studies have used mobile insertion elements (e.g. IS 6110 in tuberculosis) or conserved loci (e.g. 16S) to detect the presence of pathogens, and very similar or identical sequences have been reported from environmental bacteria (Gilbert et al. 2004). For example, Rollo & Marota (1999......We agree with Donoghue & Spigelman (2005) that, although pathogen studies hold great potential, any discussion requires a critical assessment of the results to date. However, we did note, as did Pääbo et al. (2004), that the field of ancient pathogen DNA still lacks a series of well......-controlled and rigorous studies that address technical issues and reliability criteria. This is unfortunate, as the rapid evolutionary rate of many pathogens offers a unique means to establish the authenticity of ancient pathogen sequences-since they should clearly be ancestral to modern genetic diversity (e.g. Reid et...

  10. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA

    DEFF Research Database (Denmark)

    Malmström, Helena; Svensson, Emma M; Gilbert, M Thomas P

    2007-01-01

    concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail...... the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing...

  11. Ancient mitogenomics

    DEFF Research Database (Denmark)

    Ho, Simon Y. W.; Gilbert, Tom

    2010-01-01

    the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.......The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were...... obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe...

  12. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys.

    Science.gov (United States)

    Han, Lu; Zhu, Songbiao; Ning, Chao; Cai, Dawei; Wang, Kai; Chen, Quanjia; Hu, Songmei; Yang, Junkai; Shao, Jing; Zhu, Hong; Zhou, Hui

    2014-11-30

    The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

  13. Early history of European domestic cattle as revealed by ancient DNA.

    Science.gov (United States)

    Bollongino, R; Edwards, C J; Alt, K W; Burger, J; Bradley, D G

    2006-03-22

    We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.

  14. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  15. Ancient DNA from nomads in 2500-year-old archeological sites of Pengyang, China.

    Science.gov (United States)

    Zhao, Yong-Bin; Li, Hong-Jie; Cai, Da-Wei; Li, Chun-Xiang; Zhang, Quan-Chao; Zhu, Hong; Zhou, Hui

    2010-04-01

    Six human remains (dating approximately 2500 years ago) were excavated from Pengyang, China, an area occupied by both ancient nomadic and farming people. The funerary objects found with these remains suggested they were nomads. To further confirm their ancestry, we analyzed both the maternal lineages and paternal lineages of the ancient DNA. From the mitochondrial DNA, six haplotypes were identified as three haplogroups: C, D4 and M10. The haplotype-sharing populations and phylogenetic analyses revealed that these individuals were closely associated with the ancient Xiongnu and modern northern Asians. Single-nucleotide polymorphism analysis of Y chromosomes from four male samples that were typed as haplogroup Q indicated that these people had originated in Siberia. These results show that these ancient people from Pengyang present a close genetic affinity to nomadic people, indicating that northern nomads had reached the Central Plain area of China nearly 2500 years ago.

  16. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.

    Directory of Open Access Journals (Sweden)

    Henrik B Hansen

    Full Text Available Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively than parietal skull bone (average of 2.2%. Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001. This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA. In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.

  17. Natural transformation of bacteria by fragmented, damaged and ancient DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    with fullgenome comparisons that the process has general relevance in extant bacteria. Our findings reveal that the large environmental reservoir of short and damaged DNA retains capacity for natural transformation, even after thousands of years. This describes for the first time a process by which cells can...... transfer playing an important role early in the evolution of life. The published article explains the chemical structure behind an observed degradation difference between the two purine-nucleotides guanosine and adenosine in ancient DNA. We also point at new uses for high-through-put DNA sequencing...

  18. Parasitic infections and resource economy of Danish Iron Age settlement through ancient DNA sequencing.

    Science.gov (United States)

    Tams, Katrine Wegener; Jensen Søe, Martin; Merkyte, Inga; Valeur Seersholm, Frederik; Henriksen, Peter Steen; Klingenberg, Susanne; Willerslev, Eske; Kjær, Kurt H; Hansen, Anders Johannes; Kapel, Christian Moliin Outzen

    2018-01-01

    In this study, we screen archaeological soil samples by microscopy and analyse the samples by next generation sequencing to obtain results with parasites at species level and untargeted findings of plant and animal DNA. Three separate sediment layers of an ancient man-made pond in Hoby, Denmark, ranging from 100 BC to 200 AD, were analysed by microscopy for presence of intestinal worm eggs and DNA analysis were performed to identify intestinal worms and dietary components. Ancient DNA of parasites, domestic animals and edible plants revealed a change in use of the pond over time reflecting the household practice in the adjacent Iron Age settlement. The most abundant parasite found belonged to the Ascaris genus, which was not possible to type at species level. For all sediment layers the presence of eggs of the human whipworm Trichuris trichiura and the beef tapeworm Taenia saginata suggests continuous disposal of human faeces in the pond. Moreover, the continuous findings of T. saginata further imply beef consumption and may suggest that cattle were living in the immediate surrounding of the site throughout the period. Findings of additional host-specific parasites suggest fluctuating presence of other domestic animals over time: Trichuris suis (pig), Parascaris univalens (horse), Taenia hydatigena (dog and sheep). Likewise, alternating occurrence of aDNA of edible plants may suggest changes in agricultural practices. Moreover, the composition of aDNA of parasites, plants and vertebrates suggests a significant change in the use of the ancient pond over a period of three centuries.

  19. Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures.

    Science.gov (United States)

    Storey, Alice A; Athens, J Stephen; Bryant, David; Carson, Mike; Emery, Kitty; deFrance, Susan; Higham, Charles; Huynen, Leon; Intoh, Michiko; Jones, Sharyn; Kirch, Patrick V; Ladefoged, Thegn; McCoy, Patrick; Morales-Muñiz, Arturo; Quiroz, Daniel; Reitz, Elizabeth; Robins, Judith; Walter, Richard; Matisoo-Smith, Elizabeth

    2012-01-01

    Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.

  20. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo.

    Science.gov (United States)

    González-Oliver, A; Márquez-Morfín, L; Jiménez, J C; Torre-Blanco, A

    2001-11-01

    Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A. The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin. Copyright 2001 Wiley-Liss, Inc.

  1. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  2. DNA in ancient bone - where is it located and how should we extract it?

    DEFF Research Database (Denmark)

    Campos, Paula; Craig, Oliver E.; Turner-Walker, Gordon

    2012-01-01

    Despite the widespread use of bones in ancient DNA (aDNA) studies, relatively little concrete information exists in regard to how the DNA in mineralised collagen degrades, or where it survives in the material's architecture. While, at the macrostructural level, physical exclusion of microbes...... and other external contaminants may be an important feature, and, at the ultrastructural level, the adsorption of DNA to hydroxyapatite and/or binding of DNA to Type I collagen may stabilise the DNA, the relative contribution of each, and what other factors may be relevant, are unclear....... The question arises as to whether this may be due to post-collection preservation or just an artefact of the extraction methods used in these different studies? In an attempt to resolve these questions, we examine the efficacy of DNA extraction methods, and the quality and quantity of DNA recovered from both...

  3. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio

    2015-01-01

    samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions....

  4. Ancient DNA Reveals Late Pleistocene Existence of Ostriches in Indian Sub-Continent.

    Directory of Open Access Journals (Sweden)

    Sonal Jain

    Full Text Available Ancient DNA (aDNA analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating using confocal laser scanning microscopy (CLSM. DNA was isolated from five eggshell fragments and a 43 base pair (bp sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples. Phylogenetic analysis of the DNA sequence revealed a 92% identity of the fossil eggshells to Struthio camelus and their position basal to other palaeognaths, consistent with the vicariant speciation model. Our study provides the first molecular evidence for the presence of ostriches in India, complementing the continental drift theory of biogeographical movement of ostriches in India, and opening up a new window into the evolutionary history of ratites.

  5. Establishing the validity of domestication genes using DNA from ancient chickens

    Science.gov (United States)

    Girdland Flink, Linus; Allen, Richard; Barnett, Ross; Malmström, Helena; Peters, Joris; Eriksson, Jonas; Andersson, Leif; Dobney, Keith

    2014-01-01

    Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone. PMID:24753608

  6. Establishing the validity of domestication genes using DNA from ancient chickens.

    Science.gov (United States)

    Girdland Flink, Linus; Allen, Richard; Barnett, Ross; Malmström, Helena; Peters, Joris; Eriksson, Jonas; Andersson, Leif; Dobney, Keith; Larson, Greger

    2014-04-29

    Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼ 280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.

  7. Tracking down human contamination in ancient human teeth

    DEFF Research Database (Denmark)

    Sampietro, María Lourdes; Gilbert, M Thomas P; Lao, Oscar

    2006-01-01

    DNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results......DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation...

  8. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

    Science.gov (United States)

    Slatkin, Montgomery

    2016-01-01

    When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters—including drift times and admixture rates—for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ‘Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. PMID:27049965

  9. Ancient DNA: Saber-Toothed Cats Are the Same Beasts After All.

    Science.gov (United States)

    Meachen, Julie A

    2017-11-06

    Ancient DNA from the saber-toothed cat Homotherium reveals that the late Pleistocene species from Europe and North America were the same. Homotherium turns out to be only distantly related to the well-known saber-toothed Smilodon. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites.

    Science.gov (United States)

    Iñiguez, Alena Mayo; Reinhard, Karl; Carvalho Gonçalves, Marcelo Luiz; Ferreira, Luiz Fernando; Araújo, Adauto; Paulo Vicente, Ana Carolina

    2006-11-01

    Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further

  11. The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups

    Directory of Open Access Journals (Sweden)

    David G. Mahal

    2018-01-01

    Full Text Available Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.

  12. Tamil merchant in ancient Mesopotamia.

    Directory of Open Access Journals (Sweden)

    Malliya Gounder Palanichamy

    Full Text Available Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study representing all major populations of India. Our results although suggest that south India (Tamil Nadu and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade.

  13. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

  14. Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction.

    Directory of Open Access Journals (Sweden)

    Krithivasan Sankaranarayanan

    Full Text Available Fluid inclusions in evaporite minerals (halite, gypsum, etc. potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka, with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.

  15. Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction.

    Science.gov (United States)

    Sankaranarayanan, Krithivasan; Timofeeff, Michael N; Spathis, Rita; Lowenstein, Tim K; Lum, J Koji

    2011-01-01

    Fluid inclusions in evaporite minerals (halite, gypsum, etc.) potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka), with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.

  16. Ancient Biomolecules and Evolutionary Inference

    DEFF Research Database (Denmark)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando

    2018-01-01

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleo...

  17. Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania

    Science.gov (United States)

    Evin, Allowen; Flink, Linus Girdland; Bălăşescu, Adrian; Popovici, Dragomir; Andreescu, Radian; Bailey, Douglas; Mirea, Pavel; Lazăr, Cătălin; Boroneanţ, Adina; Bonsall, Clive; Vidarsdottir, Una Strand; Brehard, Stéphanie; Tresset, Anne; Cucchi, Thomas; Larson, Greger; Dobney, Keith

    2015-01-01

    Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory. PMID:25487340

  18. Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal.

    Directory of Open Access Journals (Sweden)

    David Penney

    Full Text Available Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.

  19. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

    2015-01-01

    DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage...... and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

  20. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears.

    Science.gov (United States)

    Fortes, Gloria G; Grandal-d'Anglade, Aurora; Kolbe, Ben; Fernandes, Daniel; Meleg, Ioana N; García-Vázquez, Ana; Pinto-Llona, Ana C; Constantin, Silviu; de Torres, Trino J; Ortiz, Jose E; Frischauf, Christine; Rabeder, Gernot; Hofreiter, Michael; Barlow, Axel

    2016-10-01

    Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago. © 2016 John Wiley & Sons Ltd.

  1. Toward a new history and geography of human genes informed by ancient DNA.

    Science.gov (United States)

    Pickrell, Joseph K; Reich, David

    2014-09-01

    Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene.

    Science.gov (United States)

    Hofman, Courtney A; Rick, Torben C; Fleischer, Robert C; Maldonado, Jesús E

    2015-09-01

    There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost

    DEFF Research Database (Denmark)

    Bellemain, Eva; Davey, Marie L.; Kauserud, Håvard

    2013-01-01

    The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 16000-32000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS...

  4. Perspectives for DNA studies on polar ice cores

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, E.

    2002-01-01

    Recently amplifiable ancient DNA was obtained from a Greenland ice core. The DNA revealed a diversity of fungi, plants, algae and protists and has thereby expanded the range of detectable organic material in fossil glacier ice. The results suggest that ancient DNA can be obtained from other ice c...

  5. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

    Science.gov (United States)

    Doerr, Daniel; Chauve, Cedric

    2017-01-01

    Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains. PMID:29114402

  6. Ancient DNA analyses of museum specimens from selected Presbytis (primate: Colobinae) based on partial Cyt b sequences

    Science.gov (United States)

    Aifat, N. R.; Yaakop, S.; Md-Zain, B. M.

    2016-11-01

    The IUCN Red List of Threatened Species has categorized Malaysian primates from being data deficient to critically endanger. Thus, ancient DNA analyses hold great potential to understand phylogeny, phylogeography and population history of extinct and extant species. Museum samples are one of the alternatives to provide important sources of biological materials for a large proportion of ancient DNA studies. In this study, a total of six museum skin samples from species Presbytis hosei (4 samples) and Presbytis frontata (2 samples), aged between 43 and 124 years old were extracted to obtain the DNA. Extraction was done by using QIAGEN QIAamp DNA Investigator Kit and the ability of this kit to extract museum skin samples was tested by amplification of partial Cyt b sequence using species-specific designed primer. Two primer pairs were designed specifically for P. hosei and P. frontata, respectively. These primer pairs proved to be efficient in amplifying 200bp of the targeted species in the optimized PCR conditions. The performance of the sequences were tested to determine genetic distance of genus Presbytis in Malaysia. From the analyses, P. hosei is closely related to P. chrysomelas and P. frontata with the value of 0.095 and 0.106, respectively. Cyt b gave a clear data in determining relationships among Bornean species. Thus, with the optimized condition, museum specimens can be used for molecular systematic studies of the Malaysian primates.

  7. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

    Science.gov (United States)

    Der Sarkissian, Clio; Pichereau, Vianney; Dupont, Catherine; Ilsøe, Peter C; Perrigault, Mickael; Butler, Paul; Chauvaud, Laurent; Eiríksson, Jón; Scourse, James; Paillard, Christine; Orlando, Ludovic

    2017-09-01

    Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management. © 2017 John Wiley & Sons Ltd.

  8. Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese.

    Science.gov (United States)

    Li, Jiawei; Zeng, Wen; Zhang, Ye; Ko, Albert Min-Shan; Li, Chunxiang; Zhu, Hong; Fu, Qiaomei; Zhou, Hui

    2017-12-04

    Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese. We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300-3800 years ago. Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.

  9. Ancient Resistome.

    Science.gov (United States)

    Olaitan, Abiola Olumuyiwa; Rolain, Jean-Marc

    2016-08-01

    Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.

  10. Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

    NARCIS (Netherlands)

    J. Draus-Barini (Jolanta); S. Walsh (Susan); E. Pośpiech (Ewelina); T. Kupiec (Tomasz); H. Głab (Henryk); W. Branicki (Wojciech); M.H. Kayser (Manfred)

    2013-01-01

    textabstractBackground: DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing

  11. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

    Science.gov (United States)

    Weyrich, Laura S; Duchene, Sebastian; Soubrier, Julien; Arriola, Luis; Llamas, Bastien; Breen, James; Morris, Alan G; Alt, Kurt W; Caramelli, David; Dresely, Veit; Farrell, Milly; Farrer, Andrew G; Francken, Michael; Gully, Neville; Haak, Wolfgang; Hardy, Karen; Harvati, Katerina; Held, Petra; Holmes, Edward C; Kaidonis, John; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Semal, Patrick; Soltysiak, Arkadiusz; Townsend, Grant; Usai, Donatella; Wahl, Joachim; Huson, Daniel H; Dobney, Keith; Cooper, Alan

    2017-04-20

    Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

  12. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement.

    Science.gov (United States)

    Søe, Martin Jensen; Nejsum, Peter; Fredensborg, Brian Lund; Kapel, Christian Moliin Outzen

    2015-02-01

    Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past.

  13. Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

    Science.gov (United States)

    Almathen, Faisal; Charruau, Pauline; Mohandesan, Elmira; Mwacharo, Joram M.; Orozco-terWengel, Pablo; Pitt, Daniel; Abdussamad, Abdussamad M.; Uerpmann, Margarethe; Uerpmann, Hans-Peter; De Cupere, Bea; Magee, Peter; Alnaqeeb, Majed A.; Salim, Bashir; Raziq, Abdul; Dessie, Tadelle; Abdelhadi, Omer M.; Banabazi, Mohammad H.; Al-Eknah, Marzook; Walzer, Chris; Faye, Bernard; Hofreiter, Michael; Peters, Joris; Hanotte, Olivier

    2016-01-01

    Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. PMID:27162355

  14. Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material.

    Science.gov (United States)

    Lech, T

    2016-05-06

    Historical parchments in the form of documents, manuscripts, books, or letters, make up a large portion of cultural heritage collections. Their priceless historical value is associated with not only their content, but also the information hidden in the DNA deposited on them. Analyses of ancient DNA (aDNA) retrieved from parchments can be used in various investigations, including, but not limited to, studying their authentication, tracing the development of the culture, diplomacy, and technology, as well as obtaining information on the usage and domestication of animals. This article proposes and verifies a procedure for aDNA recovery from historical parchments and its appropriate preparation for further analyses. This study involved experimental selection of an aDNA extraction method with the highest efficiency and quality of extracted genetic material, from among the multi-stage phenol-chloroform extraction methods, and the modern, column-based techniques that use selective DNA-binding membranes. Moreover, current techniques to amplify entire genetic material were questioned, and the possibility of using mitochondrial DNA for species identification was analyzed. The usefulness of the proposed procedure was successfully confirmed in identification tests of historical parchments dating back to the 13-16th century AD.

  15. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in viking-age settlement

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Nejsum, Peter; Fredensborg, Brian Lund

    2015-01-01

    Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully...... selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura, using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology...

  16. Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae).

    Science.gov (United States)

    Garrigos, Yareli Esquer; Hugueny, Bernard; Koerner, Kellie; Ibañez, Carla; Bonillo, Celine; Pruvost, Patrice; Causse, Romain; Cruaud, Corinne; Gaubert, Philippe

    2013-01-01

    Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so

  17. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    -eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (. Scrophulariaceae......We use 2nd generation sequencing technology on sedimentary ancient DNA (. sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty...... and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650calyrBP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less...

  18. Human evolution in Siberia: from frozen bodies to ancient DNA

    Directory of Open Access Journals (Sweden)

    Bouakaze Caroline

    2010-01-01

    Full Text Available Abstract Background The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations. This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia. Results High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. Conclusion We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baïkal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today.

  19. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Pichereau, Vianney; Dupont, Catherine

    2017-01-01

    Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro...... extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure......, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine...

  20. Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

    Science.gov (United States)

    Zhang, Quan-Chao; Li, Hong-Jie; Cui, Ying-Qiu; Xu, Zhi; Jin, Li; Zhou, Hui; Zhu, Hong

    2015-01-01

    The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area. PMID:25938511

  1. Optical dating of perennially frozen deposits associated with preserved ancient plant and animal DNA in north-central Siberia

    DEFF Research Database (Denmark)

    Arnold, L.J.; Roberts, R.G.; Macphee, R.D.E.

    2008-01-01

    We present chronological constraints on a suite of permanently frozen fluvial deposits which contain ancient DNA (aDNA) from the Taimyr Peninsula of north-central Siberia. The luminescence phenomenology of these samples is first discussed, focusing on the optically stimulated luminescence (OSL) d...... of providing a reliable chronometric framework for sedimentary aDNA records in permafrost environments. (C) 2007 Elsevier Ltd. All rights reserved Udgivelsesdato: 2008...

  2. Brief communication: Ancient nuclear DNA and kinship analysis: the case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain).

    Science.gov (United States)

    Gamba, Cristina; Fernández, Eva; Tirado, Mirian; Pastor, Francisco; Arroyo-Pardo, Eduardo

    2011-03-01

    The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler™ kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree-specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record. Copyright © 2010 Wiley-Liss, Inc.

  3. Resurrecting ancient animal genomes: the extinct moa and more.

    Science.gov (United States)

    Huynen, Leon; Millar, Craig D; Lambert, David M

    2012-08-01

    Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Biomolecular identification of ancient Mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe.

    Science.gov (United States)

    Müller, Romy; Roberts, Charlotte A; Brown, Terence A

    2014-02-01

    Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as "probable" or "possible." None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB. Copyright © 2013 Wiley Periodicals, Inc.

  5. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.

    Directory of Open Access Journals (Sweden)

    Bobbi M Johnson

    Full Text Available The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha. Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins

  6. King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times.

    Science.gov (United States)

    Heupink, Tim H; van den Hoff, John; Lambert, David M

    2012-08-23

    Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.

  7. Deciphering Equine Evolution and Spatial Ancestry with Ancient Data

    DEFF Research Database (Denmark)

    Jónsson, Hákon

    High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored to the s......High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored...... in the analysis of environmental bacterial sequences, which generally dominate ancient DNA extracts, and in the first pipeline completely devoted to the computational analysis of raw ancient DNA sequences. We then develop a spatially explicit method for determining which extant populations show the greatest...... genetic anity to ancient individuals, which often represents the key question in human paleogenomic projects. We applied the computational infrastructure developed to complete the genomic characterization of extant members of the genus Equus, which is composed of horses, asses and zebras. We sequenced...

  8. The characterization of Helicobacter pylori DNA associated with ancient human remains recovered from a Canadian glacier.

    Directory of Open Access Journals (Sweden)

    Treena Swanston

    2011-02-01

    Full Text Available Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of nearly half of the world's population. Genotypic characterization of H. pylori strains involves the analysis of virulence-associated genes, such as vacA, which has multiple alleles. Previous phylogenetic analyses have revealed a connection between modern H. pylori strains and the movement of ancient human populations. In this study, H. pylori DNA was amplified from the stomach tissue of the Kwäday Dän Ts'ìnchi individual. This ancient individual was recovered from the Samuel Glacier in Tatshenshini-Alsek Park, British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations and radiocarbon dated to a timeframe of approximately AD 1670 to 1850. This is the first ancient H. pylori strain to be characterized with vacA sequence data. The Tatshenshini H. pylori strain has a potential hybrid vacA m2a/m1d middle (m region allele and a vacA s2 signal (s region allele. A vacA s2 allele is more commonly identified with Western strains, and this suggests that European strains were present in northwestern Canada during the ancient individual's time. Phylogenetic analysis indicated that the vacA m1d region of the ancient strain clusters with previously published novel Native American strains that are closely related to Asian strains. This indicates a past connection between the Kwäday Dän Ts'ìnchi individual and the ancestors who arrived in the New World thousands of years ago.

  9. Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.

    Science.gov (United States)

    van der Kuyl, A C; Kuiken, C L; Dekker, J T; Perizonius, W R; Goudsmit, J

    1995-06-01

    Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

  10. A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA

    DEFF Research Database (Denmark)

    Kuch, Melanie; Gröcke, Darren R; Knyf, Martin C

    2007-01-01

    , which fall within haplogroups X and C, consistent with Northeastern Native populations today. In addition we have sexed the male using a novel-sexing assay and confirmed the authenticity of his Y chromosome with the presence of the Native American specific Y-QM3 single nucleotide polymorphism (SNP......). This is the first ancient nuclear SNP typed from a Native population in the Americas. In addition, using the same teeth we conducted a stable isotopes analysis of collagen and dentine to show that both individuals relied on marine sources (fresh and salt water fish, seals) with no hierarchy seen between them......, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots...

  11. Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians

    DEFF Research Database (Denmark)

    Malmström, Helena; Gilbert, M Thomas P; Thomas, Mark G

    2009-01-01

    of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern......]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations....

  12. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    Science.gov (United States)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

    2013-09-01

    We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

  13. Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's central coast during the Middle Horizon

    OpenAIRE

    Valverde, G.; Romero, M.; Espinoza, I.; Cooper, A.; Fehren-Schmitz, L.; Llamas, B.; Haak, W.

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650?1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, wh...

  14. Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

    Directory of Open Access Journals (Sweden)

    Lumibao Candice Y

    2011-01-01

    Full Text Available Abstract Background Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes. Results We successfully sequenced DNA from 64 samples (out of 126 comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments Conclusions An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.

  15. Ligation bias in Illumina next-generation DNA libraries

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...... for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.......Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by......-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate...

  16. Leprosy in a Lombard-Avar cemetery in central Italy (Campochiaro, Molise, 6th-8th century AD): ancient DNA evidence and demography.

    Science.gov (United States)

    Rubini, Mauro; Zaio, Paola; Spigelman, Mark; Donoghue, Helen D

    2017-09-01

    The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations. Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras. The individuals were from a site in Central Italy (6th-8th CE) and were examined for the presence of Mycobacterium leprae aDNA. In addition, an abridged life mortality table was constructed. Two individuals had typical leprosy palaeopathology, and one was positive for Mycobacterium leprae aDNA. However, the demographic profile shows a mortality curve similar to that of the standard, in contrast to a population that had been subjected to bubonic plague. This study shows that, in the historical population with leprosy, the risk factors for health seem to be constant and distributed across all age classes, similar to what is found today in the antibiotic era. There were no peaks of mortality equivalent to those found in fatal diseases such as the plague, probably due to the long clinical course of leprosy.

  17. Prehistoric introduction of domestic pigs onto the Okinawa Islands: ancient mitochondrial DNA evidence.

    Science.gov (United States)

    Watanobe, Takuma; Ishiguro, Naotaka; Nakano, Masuo; Takamiya, Hiroto; Matsui, Akira; Hongo, Hitomi

    2002-08-01

    Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes; 574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites) are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa islands in the early Yayoi-Heian period (1700-2000 BP), or earlier.

  18. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia.

    Science.gov (United States)

    Drancourt, M; Aboudharam, G; Signoli, M; Dutour, O; Raoult, D

    1998-10-13

    Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague ("plague teeth") and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human beta-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase beta-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.

  19. Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier.

    Directory of Open Access Journals (Sweden)

    Dan Bar Yaacov

    Full Text Available The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel into two subspecies, Chamaeleo chamaeleon recticrista (CCR and C. c. musae (CCM. CCR mostly inhabits the Mediterranean climate (northern Israel, while CCM inhabits the sands of the north-western Negev Desert (southern Israel. AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097, consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79, which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient local adaptation to mitochondrial-related traits.

  20. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Tomsho, Lynn P; Rendulic, Snjezana

    2007-01-01

    Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously...

  1. Multiple maternal origins of native modern and ancient horse populations in China.

    Science.gov (United States)

    Lei, C Z; Su, R; Bower, M A; Edwards, C J; Wang, X B; Weining, S; Liu, L; Xie, W M; Li, F; Liu, R Y; Zhang, Y S; Zhang, C M; Chen, H

    2009-12-01

    To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.

  2. Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA.

    Science.gov (United States)

    Marr, Melissa M; Brace, Selina; Schreve, Danielle C; Barnes, Ian

    2018-02-09

    Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.

  3. Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

    Science.gov (United States)

    Ahmed, Engy; Parducci, Laura; Unneberg, Per; Ågren, Rasmus; Schenk, Frederik; Rattray, Jayne E.; Han, Lu; Muschitiello, Francesco; Pedersen, Mikkel W.; Smittenberg, Rienk H.; Yamoah, Kweku Afrifa; Slotte, Tanja; Wohlfarth, Barbara

    2018-02-01

    The Lateglacial/early Holocene sediments from the ancient lake at Hässeldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hässeldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerød and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.

  4. Ancient Biomolecules and Evolutionary Inference.

    Science.gov (United States)

    Cappellini, Enrico; Prohaska, Ana; Racimo, Fernando; Welker, Frido; Pedersen, Mikkel Winther; Allentoft, Morten E; de Barros Damgaard, Peter; Gutenbrunner, Petra; Dunne, Julie; Hammann, Simon; Roffet-Salque, Mélanie; Ilardo, Melissa; Moreno-Mayar, J Víctor; Wang, Yucheng; Sikora, Martin; Vinner, Lasse; Cox, Jürgen; Evershed, Richard P; Willerslev, Eske

    2018-04-25

    Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  5. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses

    DEFF Research Database (Denmark)

    Lira, Jaime; Linderholm, Anna; Olaria, Carmen

    2010-01-01

    Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group...... wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times....

  6. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

    Directory of Open Access Journals (Sweden)

    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  7. Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis.

    Science.gov (United States)

    Fehren-Schmitz, Lars; Reindel, Markus; Cagigao, Elsa Tomasto; Hummel, Susanne; Herrmann, Bernd

    2010-02-01

    Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. 2009 Wiley-Liss, Inc.

  8. Illuminating the evolution of equids and rodents with next-generation sequencing of ancient specimens

    DEFF Research Database (Denmark)

    Mouatt, Julia Thidamarth Vilstrup

    enrichment methods and the massive throughput and latest advances within DNA sequencing, the field of ancient DNA has flourished in later years. Those advances have even enabled the sequencing of complete genomes from the past, moving the field into genomic sciences. In this thesis we have used these latest......The sequencing of ancient DNA provides perspectives on the genetic history of past populations and extinct species. However, ancient DNA research presents specific limitations mostly due to DNA survival, damage and contamination. Yet with stringent laboratory procedures, the sensitivity of target...... developments within ancient DNA research, including target enrichment capture and Next-Generation Sequencing, to address a range of evolutionary questions related to two major mammalian groups, equids and rodents. In particular we have resolved phylogenetic relationships within equids using complete mitochond...

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

    Science.gov (United States)

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

    2015-01-01

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

  10. Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna.

    Science.gov (United States)

    Volkov, Roman A; Panchuk, Irina I; Borisjuk, Nikolai V; Hosiawa-Baranska, Marta; Maluszynska, Jolanta; Hemleben, Vera

    2017-01-23

    Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies. Molecular cloning and nucleotide sequencing of A. belladonna 45S rDNA repeats revealed a general structure characteristic of other Solanaceae species, and a very high sequence similarity of two length variants, with the only difference in number of short IGS subrepeats. These results combined with the detection of three pairs of 45S rDNA loci on separate chromosomes, presumably inherited from both tetraploid and diploid ancestor species, example intensive sequence homogenization that led to substitution/elimination of rDNA repeats of one parent. Chromosome silver-staining revealed that only four out of six 45S rDNA sites are frequently transcriptionally active, demonstrating nucleolar dominance. For 5S rDNA, three size variants of repeats were detected, with the major class represented by repeats containing all functional IGS elements required for transcription, the intermediate size repeats containing partially deleted IGS sequences, and the short 5S repeats containing severe defects both in the IGS and coding sequences. While shorter variants demonstrate increased rate of based substitution, probably in their transition into pseudogenes, the functional 5S rDNA variants are nearly identical at the sequence level, pointing to their origin from a single parental species. Localization of the 5S rDNA genes on two chromosome pairs further supports uniparental

  11. Pre-Columbian Population Dynamics and Cultural Development in South Coast Perú as Revealed by Analysis of Ancient DNA

    OpenAIRE

    Fehren-Schmitz, Lars

    2012-01-01

    In this paper I report on a study whose principal aim is to understand the development and decline of the southern Peruvian Nasca culture in the upper Río Grande de Nasca drainage, and its cultural and biological affinities to the preceding Paracas culture. Ancient DNA analyses were conducted on over 300 pre-Columbian individuals from various cemeteries in southern Perú, from periods ranging from the Formative Period to the Middle Horizon. Our results show that the Nasca populations are close...

  12. Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus complex.

    Directory of Open Access Journals (Sweden)

    Xiuguang Mao

    Full Text Available The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2 and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.

  13. Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.

    Science.gov (United States)

    Naumova O, Y u; Rychkov S, Y u

    1998-03-01

    On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.

  14. Multiplexed SNP Typing of Ancient DNA Clarifies the Origin of Andaman mtDNA Haplogroups amongst South Asian Tribal Populations

    Science.gov (United States)

    Endicott, Phillip; Metspalu, Mait; Stringer, Chris; Macaulay, Vincent; Cooper, Alan; Sanchez, Juan J.

    2006-01-01

    The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups ∼30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity. PMID:17218991

  15. Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska.

    Science.gov (United States)

    West, Catherine; Hofman, Courtney A; Ebbert, Steve; Martin, John; Shirazi, Sabrina; Dunning, Samantha; Maldonado, Jesus E

    2017-10-01

    The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  16. Revising the recent evolutionary history of equids using ancient DNA.

    Science.gov (United States)

    Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

    2009-12-22

    The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

  17. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

    Science.gov (United States)

    Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

    2014-04-01

    Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

  18. Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.

    Directory of Open Access Journals (Sweden)

    Christina I Barrón-Ortiz

    Full Text Available Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus and a non-caballine (E. conversidens species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study.

  19. Diversity and survivability of microbial community in ancient permafrost sediment of northeast Siberia

    Science.gov (United States)

    Liang, R.; Lau, M.; Vishnivetskaya, T. A.; Lloyd, K. G.; Pfiffner, S. M.; Rivkina, E.; Onstott, T. C.

    2017-12-01

    The prevalence of microorganisms in frozen permafrost has been well documented in ancient sediment up to several million years old. However, the long term survivability and metabolic activity of microbes over geological timespans remain underexplored. Siberian permafrost sediment was collected at various depths (1.4m, 11.8 m and 24.8m) to represent a wide range of geological time from thousands to millions of years. Extracellular (eDNA) and intracellular DNA (iDNA) was simultaneously recovered for sequencing to characterize the potentially extinct and extant microbial community. Additionally, aspartic acid racemization assay (D/L Asp) was used to infer the metabolic activity of microbes in ancient permafrost. As compared with the young sample (1.4m), DNA yield and content of aspartic acid dramatically decreased in old samples (11.8m and 24.8m). However, D/L Asp and eDNA/iDNA significantly increased with the geological age. Such findings suggested that ancient microbiomes might be subjected to racemization or even DNA/proteins degradation at subzero temperature over the wide geological time scale. Preliminary characterization of microbial community indicated that the majority of sequences in old samples were identified as bacteria and only a small fraction was identified as archaea from the iDNA pool. While the eDNA and iDNA fractions shared similar dominant taxa at phylum level, the relative abundance of Proteobacteria in eDNA library was much higher than iDNA. By contrast, the phylum affiliated with Firmicutes was more numerically abundant in the iDNA fraction. More dramatic differences were observed between eDNA and iDNA library at lower taxonomic levels. Particularly, the microbial lineages affiliated with the genera Methanoregula, Desulfosporosinus and Syntrophomonas were only detected in the iDNA library. Such taxonomic difference between the relic eDNA and iDNA suggested that numerous species become locally "extinct" whereas many other taxa might survive in

  20. Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

    Full Text Available Although the functional consequences of mitochondrial DNA (mtDNA genetic backgrounds (haplotypes, haplogroups have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers". We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74% and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%. The variant defining Caucasian haplogroup J (C295T increased the binding of TFAM (Electro Mobility Shift Assay and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1, a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mtDNA

  1. Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Nejsum, Peter; Seersholm, Frederik Valeur

    2018-01-01

    , vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw...... or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from...

  2. Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies

    Science.gov (United States)

    Higgins, Denice; Rohrlach, Adam B.; Kaidonis, John; Townsend, Grant; Austin, Jeremy J.

    2015-01-01

    Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Futhermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard

  3. Investigation of ancient DNA from Western Siberia and the Sargat culture.

    Science.gov (United States)

    Bennett, Casey C; Kaestle, Frederika A

    2010-04-01

    Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis.

  4. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.

    Science.gov (United States)

    Paijmans, Johanna L A; Barnett, Ross; Gilbert, M Thomas P; Zepeda-Mendoza, M Lisandra; Reumer, Jelle W F; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F; Leonard, Jennifer A; Rohland, Nadin; Westbury, Michael V; Barlow, Axel; Hofreiter, Michael

    2017-11-06

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.

    Science.gov (United States)

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

    2015-01-01

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

  6. Moessbauer studies on ancient Jizhon plain Temmoku porcelains

    International Nuclear Information System (INIS)

    Yu Zhengfang; Zheng Yufang; Lin Yongqiang

    1994-01-01

    Three kinds of ancient Jizhou plain Temmoku wares and their several ware-making raw materials were studied by means of X-ray diffraction (XRD) and Moessbauer spectroscopy. The firing technique of ancient Jizhou Temmoku porcelains is discussed. (orig.)

  7. Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene.

    Science.gov (United States)

    Sheng, Gui-Lian; Barlow, Axel; Cooper, Alan; Hou, Xin-Dong; Ji, Xue-Ping; Jablonski, Nina G; Zhong, Bo-Jian; Liu, Hong; Flynn, Lawrence J; Yuan, Jun-Xia; Wang, Li-Rui; Basler, Nikolas; Westbury, Michael V; Hofreiter, Michael; Lai, Xu-Long

    2018-04-06

    The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cyt b and 12s rRNA, partial 16s rRNA and ND1 , and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  8. Ancient DNA from Giant Panda (Ailuropoda melanoleuca of South-Western China Reveals Genetic Diversity Loss during the Holocene

    Directory of Open Access Journals (Sweden)

    Gui-Lian Sheng

    2018-04-01

    Full Text Available The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae. Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  9. Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans.

    Science.gov (United States)

    Rawlence, Nicolas J; Kardamaki, Afroditi; Easton, Luke J; Tennyson, Alan J D; Scofield, R Paul; Waters, Jonathan M

    2017-07-26

    Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans ( Cygnus atratus ) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage ( C. sumnerensis , Poūwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction. © 2017 The Author(s).

  10. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication.

    Science.gov (United States)

    Kimura, Birgitta; Marshall, Fiona B; Chen, Shanyuan; Rosenbom, Sónia; Moehlman, Patricia D; Tuross, Noreen; Sabin, Richard C; Peters, Joris; Barich, Barbara; Yohannes, Hagos; Kebede, Fanuel; Teclai, Redae; Beja-Pereira, Albano; Mulligan, Connie J

    2011-01-07

    Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

  11. Insights into Modern Human Prehistory Using Ancient Genomes.

    Science.gov (United States)

    Yang, Melinda A; Fu, Qiaomei

    2018-03-01

    The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics

    NARCIS (Netherlands)

    Paijmans, Johanna L.A.; Barnett, Ross; Gilbert, M. Thomas P.; Zepeda-Mendoza, M. Lisandra; Reumer, Jelle W.F.; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F.; Leonard, Jennifer A.; Rohland, Nadin; Westbury, Michael V.; Barlow, Axel; Hofreiter, Michael

    2017-01-01

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of

  13. Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

    Science.gov (United States)

    Star, Bastiaan; Boessenkool, Sanne; Gondek, Agata T; Nikulina, Elena A; Hufthammer, Anne Karin; Pampoulie, Christophe; Knutsen, Halvor; André, Carl; Nistelberger, Heidi M; Dierking, Jan; Petereit, Christoph; Heinrich, Dirk; Jakobsen, Kjetill S; Stenseth, Nils Chr; Jentoft, Sissel; Barrett, James H

    2017-08-22

    Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod ( Gadus morhua ) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

  14. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

    Science.gov (United States)

    Delfin, Frederick; Min-Shan Ko, Albert; Li, Mingkun; Gunnarsdóttir, Ellen D; Tabbada, Kristina A; Salvador, Jazelyn M; Calacal, Gayvelline C; Sagum, Minerva S; Datar, Francisco A; Padilla, Sabino G; De Ungria, Maria Corazon A; Stoneking, Mark

    2014-01-01

    The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago. PMID:23756438

  15. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

    Science.gov (United States)

    Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

    2017-12-15

    Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

    Science.gov (United States)

    Müller, Romy; Roberts, Charlotte A; Brown, Terence A

    2014-04-22

    The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.

  17. A study on provenance relation between Jiaotanxia ancient Guan porcelain and Qingliangsi ancient Ru porcelain by NAA

    International Nuclear Information System (INIS)

    Li Rongwu; Feng Songlin; Huang Zhongxiang; Jia Xiuqin

    2004-01-01

    11 samples of ancient Chinese Ru porcelain from Qingliangsi kiln, 23 samples of ancient Chinese Guan porcelain from Jiaotanxia kiln and 4 samples of modern archaized Guan porcelain were obtained to determine the contents of elements in each of them by neutron activation analysis (NAA). The NAA data were further analyzed using fuzzy cluster analysis to obtain the fuzzy cluster trend diagrams for the bodies' samples and the glazes samples respectively. The analysis shows that the raw material origins of the Jiaotanxia ancient Chinese Guan porcelain bodies samples are very concentrated; those of the Qingliangsi ancient Chinese Ru porcelain bodies samples are a little dispersed; those of ancient Chinese Guan porcelain glazes samples are relatively concentrated; those of ancient Chinese Ru porcelain glazes samples are dispersed; and the origins of the raw material of ancient Chinese Guan porcelain glazes samples are obviously different from those of ancient Chinese Ru porcelain glazes samples. The bodies samples and glazes samples of Jiaotanxia ancient Chinese Guan porcelain and those of Qingliangsi ancient Chinese Ru porcelain have some difference but can be compared with each other. (authors)

  18. Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

    Science.gov (United States)

    D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.

    2016-01-01

    Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical population connectivity and genetic diversity showing: (1) a substantial loss of haplotypes, which is consistent with the hypothesis that condors were relatively abundant in the nineteenth century, but declined rapidly as a result of human-caused mortality; and (2) no evidence of historical population segregation, meaning that the available genetic data offer no cause to avoid releasing condors in unoccupied portions of their historical range.

  19. Letter to the editor: Genetics and the archaeology of ancient Israel.

    Science.gov (United States)

    Brody, Aaron J; King, Roy J

    2013-12-01

    This letter is a call for DNA testing on ancient skeletal materials from the southern Levant to begin a database of genetic information of the inhabitants of this crossroads region. In this region, during the Iron I period traditionally dated to circa 1200-1000 BCE, archaeologists and biblical historians view the earliest presence of a group that called itself Israel. They lived in villages in the varied hill countries of the region, contemporary with urban settlements in the coastal plains, inland valleys, and central hill country attributed to varied indigenous groups collectively called Canaanite. The remnants of Egyptian imperial presence in the region lasted until around 1150 BCE, postdating the arrival of an immigrant group from the Aegean called the Philistines circa 1175 BCE. The period that follows in the southern Levant is marked by the development of territorial states throughout the region, circa 1000-800 BCE. These patrimonial kingdoms, including the United Kingdom of Israel and the divided kingdoms of northern Israel and Judah, coalesced varied peoples under central leadership and newly founded administrative and religious bureaucracies. Ancient DNA testing will give us a further refined understanding of the individuals who peopled the region of the southern Levant throughout its varied archaeological and historic periods and provide scientific data that will support, refute, or nuance our sociohistoric reconstruction of ancient group identities. These social identities may or may not map onto genetic data, but without sampling of ancient DNA we may never know. A database of ancient DNA will also allow for comparisons with modern DNA samples collected throughout the greater region and the Mediterranean littoral, giving a more robust understanding of the long historical trajectories of regional human genetics and the genetics of varied ancestral groups of today's Jewish populations and other cultural groups in the modern Middle East and Mediterranean

  20. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    , the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two...... the ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least...

  1. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog.

    Directory of Open Access Journals (Sweden)

    Esther J Lee

    Full Text Available Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.

  2. Curiously modern DNA for a "250 million-year-old" bacterium.

    Science.gov (United States)

    Nickle, David C; Learn, Gerald H; Rain, Matthew W; Mullins, James I; Mittler, John E

    2002-01-01

    Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.

  3. Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations.

    Directory of Open Access Journals (Sweden)

    Nadezhda V Vorobieva

    Full Text Available BACKGROUND: The extant roe deer (Capreolus Gray, 1821 includes two species: the European roe deer (C. capreolus and the Siberian roe deer (C. pygargus that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia, where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan, Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. CONCLUSION/SIGNIFICANCE: Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian

  4. PIXE study on ancient pottery from Chinese Shanghai area

    International Nuclear Information System (INIS)

    Cheng, H.S.; Zhang, Z.Q.; Song, J.; Gao, M.H.; Zhu, D.; Lin, J.W.; Feng, S.L.

    2006-01-01

    Shanghai is the largest city in China, and it also has a very long history. Archaeologists have found that six thousand yeas ago, there were ancient people living at Songze, Qingpu County, Shanghai. This paper reports the study of ancient potteries unearthed from the Guangfulin site located at Songjiang, Shanghai. The potteries unearthed from Guangfulin site belonged to two different culture types: the Liangzhu culture type (local culture) and a new culture, which might be derived from elsewhere. PIXE has been used to measure the chemical compositions of samples and factor analysis was used. Experimental results show that the compositions of the pottery from the two phases are different from each other. It means that the raw materials used to make the ancient pottery originate from different places. This results support the idea suggested by archaeologists that a group of ancient people migrated to the Shanghai area from some other place 4000 years ago

  5. Application of PIXE to study ancient Iranian silver coins

    Energy Technology Data Exchange (ETDEWEB)

    Oliaiy, P.; Shokouhi, F.; Lamehi-Rachti, M.; Rahighi, J. [Van de Graaff Laboratory, AEOI, Tehran (Iran); Andami, P.; Dilmaghani, J.; Etezadi, M. [Tamashagah-e-Pool, General Office of Museums, MDFIR, Tehran (Iran)

    1999-07-01

    Ancient Iranian silver coins minted in various parts of the ancient Iran from Transoxiana to Mesopotamia over a time span of 460 years (247BC-208AD) during Parthians dynasty were analysed by PIXE with a 2.2 MeV proton beam. Forty seven silver coins owned by Tamashagah-e-Pool (museum of money) in Tehran were examined in this study. The possible correlation between the composition of coins and the minting time or the minting location of coins has been the prime objective of the present study. Elemental analysis of ancient coins could also reveal the direct relation with the political and economical situation and also with the metallurgy of the minting time. Results on the contents of principal component elements (Fe, Ni, Cu, As, Br, Ag, Sn, Sb, Ba, Au and Pb) are presented and discussed. (author)

  6. Microanalysis study on ancient Wiangkalong Pottery

    Science.gov (United States)

    Won-in, K.; Tancharakorn, S.; Dararutana, P.

    2017-09-01

    Wiangkalong is one of major ceramic production cities in northern of Thailand, once colonized by the ancient Lanna Kingdom (1290 A.D.). Ancient Wiangkalong potteries were produced with shapes and designs as similar as those of the Chinese Yuan and Ming Dynasties. Due to the complex nature of materials and objects, extremely sensitive, spatially resolved, multi-elemental and versatile analytical instruments using non-destructive and non-sampling methods to analyze theirs composition are need. In this work, micro-beam X-ray fluorescence spectroscopy based on synchrotron radiation was firstly used to characterize the elemental composition of the ancient Wiangkalong pottery. The results showed the variations in elemental composition of the body matrix, the glaze and the underglaze painting, such as K, Ca, Ti, V, Cr, Mn and Fe.

  7. Ancient DNA investigations: A review on their significance in ...

    African Journals Online (AJOL)

    However, its degradation and post-mortem chemical alteration make difficult its quantification and amplification. Moreover the study of aDNA is challenging due to the contamination by exogenous current DNA. Recently, the progress of molecular techniques and the use of sophisticated approaches greatly improved the ratio ...

  8. Application of neutron activation analysis in study of ancient ceramics

    International Nuclear Information System (INIS)

    Li Guoxia; Zhao Weijuan; Gao Zhengyao; Xie Jianzhong; Huang Zhongxiang; Jia Xiuqin; Han Song

    2000-01-01

    Trace-elements in ancient ceramics and imitative ancient ceramics were determined by neutron activation analysis (NAA). The NAA data are then analyzed by fuzzy cluster method and the trend cluster diagram is obtained. The raw material sources of ancient ceramics and imitative ancient ceramics are determined. The path for improving quality of imitative ancient ceramics is found

  9. Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

    DEFF Research Database (Denmark)

    Gilbert, Marcus Thomas Pius; Miller, Webb; Schuster, Stephan C.

    2008-01-01

    Debruyne et al. challenge the findings of our study and imply that we argue that hair shafts are an overall superior source of ancient DNA than bone. However, the authors are misreading and misinterpreting the conclusions of our study; we claim nothing further than that hair shaft represents...

  10. Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities

    Science.gov (United States)

    Haak, Wolfgang; Balanovsky, Oleg; Sanchez, Juan J.; Koshel, Sergey; Zaporozhchenko, Valery; Adler, Christina J.; Der Sarkissian, Clio S. I.; Brandt, Guido; Schwarz, Carolin; Nicklisch, Nicole; Dresely, Veit; Fritsch, Barbara; Balanovska, Elena; Villems, Richard; Meller, Harald; Alt, Kurt W.; Cooper, Alan

    2010-01-01

    In Europe, the Neolithic transition (8,000–4,000 b.c.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 b.c.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated b.c.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated b.c.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major

  11. Ancient DNA from European early neolithic farmers reveals their near eastern affinities.

    Directory of Open Access Journals (Sweden)

    Wolfgang Haak

    Full Text Available In Europe, the Neolithic transition (8,000-4,000 B.C. from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500-4,900 calibrated B.C. and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42 and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500-4,900 calibrated B.C.. We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394 and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting

  12. Ancient genomics in India: Clarifying the maternal origins of 160-year-old human remains

    Directory of Open Access Journals (Sweden)

    Esha Bandyopadhyay

    2017-10-01

    Full Text Available Sequencing DNA from archaeological remains has opened up new possibilities for furthering our understanding of the origins and evolutionary history of modern humans [1]. However, most ancient DNA (aDNA studies, thus far, have focused on ancient samples obtained from permafrozen and temperate regions, where preservation conditions are better suited for long-term DNA survival. Consequently, this has left a void in aDNA research in tropical regions such as South Asia. The primary aims of the present study were to (a test the feasibility of extracting DNA from historical samples (~160 years old from northern India, and (b correlate obtained mitochondrial DNA (mtDNA signatures with geographical origins of the individuals, as reported in historical records. A total of 30 molars were subjected to DNA extractions and Illumina indexed library preparation. All laboratory work was performed following strict aDNA standards in the clean laboratory at the Centre for Cellular and Molecular Biology, Hyderabad. Complete mtDNA genomes were targeted from all 30 samples following the DNA hybridization method outlined in Maricic et al., 2010 [2]. Captured libraries were sequenced on the Illumina HiSeq 2500 platform (100 bp paired-end mode at MedGenome Inc., Bangalore. Obtained sequences were trimmed for residual adapters using AdapterRemoval and mapped to the revised Cambridge Reference Sequence (rCRS using BWA. HaploGrep2 [3] was used to assign mtDNA haplogroups to each sample. We successfully obtained endogenous mtDNA sequences from all 30 samples, as confirmed by typical aDNA damage (cytosine deamination on the ends of DNA molecules. Coverage and depth of sequencing were in the range of 91-99.5% and 6X-371X, respectively. To ascertain the maternal origins of the individuals, mtDNA haplogroups of our samples were compared to a database compiled from published mtDNA sequences from modern South Asian individuals. Based on this, we were able to confirm northern

  13. Temporal Fluctuation in North East Baltic Sea Region Cattle Population Revealed by Mitochondrial and Y-Chromosomal DNA Analyses

    Science.gov (United States)

    Niemi, Marianna; Bläuer, Auli; Iso-Touru, Terhi; Harjula, Janne; Nyström Edmark, Veronica; Rannamäe, Eve; Lõugas, Lembi; Sajantila, Antti; Lidén, Kerstin; Taavitsainen, Jussi-Pekka

    2015-01-01

    Background Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. Results Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). Conclusions The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle. PMID:25992976

  14. Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia.

    Science.gov (United States)

    Rannamäe, E; Lõugas, L; Niemi, M; Kantanen, J; Maldre, L; Kadõrova, N; Saarma, U

    2016-04-01

    Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations. © 2016 Stichting International Foundation for Animal Genetics.

  15. Attitudes to Ancient Greek in Three Schools: A Case Study

    Science.gov (United States)

    Foster, Frances

    2018-01-01

    This study comes in response to recent changes in UK policy, whereby Ancient Greek and Latin have been included alongside modern languages as part of the curriculum at Key Stage 2. It aims to understand how Ancient Greek is surviving and thriving in three different types of schools. After a short overview of the history of Greek teaching in the…

  16. Comparison of two Neolithic mtDNA haplotypes from a Czech excavation site with the results of mitochondrial DNA studies on European Neolithic and Mesolithic individuals

    Czech Academy of Sciences Publication Activity Database

    Votrubová, J.; Emmerová, B.; Brzobohatá, Hana; Šumberová, Radka; Vaněk, D.

    2017-01-01

    Roč. 6, December (2017), „e125”-„e128” ISSN 1875-1768 R&D Projects: GA ČR GB14-36938G Institutional support: RVO:67985912 Keywords : ancient DNA * mtDNA * sequencing * haplotype * haplogroup Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology http://www.fsigeneticssup.com/article/S1875-1768(17)30162-2/pdf

  17. Ancient and modern environmental DNA

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Overballe-Petersen, Søren; Ermini, Luca

    2015-01-01

    woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene...

  18. Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China.

    Science.gov (United States)

    Wang, Haijing; Chen, Lu; Ge, Binwen; Zhang, Ye; Zhu, Hong; Zhou, Hui

    2012-08-01

    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.

  19. Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

    Science.gov (United States)

    Huang, Shi

    2009-01-01

    There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth. PMID:18600632

  20. Phylotyping and functional analysis of two ancient human microbiomes.

    Directory of Open Access Journals (Sweden)

    Raúl Y Tito

    Full Text Available BACKGROUND: The Human Microbiome Project (HMP is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. METHODOLOGY/PRINCIPAL FINDINGS: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.

  1. Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar

    Science.gov (United States)

    Malenica, Nenad; Šimon, Silvio; Besendorfer, Višnja; Maletić, Edi; Karoglan Kontić, Jasminka; Pejić, Ivan

    2011-09-01

    Reconstruction of the grapevine cultivation history has advanced tremendously during the last decade. Identification of grapevine cultivars by using microsatellite DNA markers has mostly become a routine. The parentage of several renowned grapevine cultivars, like Cabernet Sauvignon and Chardonnay, has been elucidated. However, the assembly of a complete grapevine genealogy is not yet possible because missing links might no longer be in cultivation or are even extinct. This problem could be overcome by analyzing ancient DNA from grapevine herbarium specimens and other historical remnants of once cultivated varieties. Here, we present the first successful genotyping of a grapevine herbarium specimen and the identification of the corresponding grapevine cultivar. Using a set of nine grapevine microsatellite markers, in combination with a whole genome amplification procedure, we found the 90-year-old Tribidrag herbarium specimen to display the same microsatellite profile as the popular American cultivar Zinfandel. This work, together with information from several historical documents, provides a new clue of Zinfandel cultivation in Croatia as early as the beginning of fifteenth century, under the native name Tribidrag. Moreover, it emphasizes substantial information potential of existing grapevine and other herbarium collections worldwide.

  2. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

    Directory of Open Access Journals (Sweden)

    Eveson J Paige

    2006-08-01

    Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

  3. Amplification success rate of DNA from museum skin collections: a case study of stoats from 18 museums

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália; Searle, J. B.

    2006-01-01

    Roč. 6, č. 4 (2006), s. 1014-1017 ISSN 1471-8278 Institutional research plan: CEZ:AV0Z60930519 Keywords : ancient DNA * mitochondrial DNA, * Mustela erminea * museum collections * polymerase chain reaction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.220, year: 2006

  4. Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.

    Science.gov (United States)

    Loog, Liisa; Thomas, Mark G; Barnett, Ross; Allen, Richard; Sykes, Naomi; Paxinos, Ptolemaios D; Lebrasseur, Ophélie; Dobney, Keith; Peters, Joris; Manica, Andrea; Larson, Greger; Eriksson, Anders

    2017-08-01

    Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Knife - Holders in Ancient Egyptian Tombs (Religious and Artistic Study

    Directory of Open Access Journals (Sweden)

    dr.Rasha Omran

    2015-01-01

    Full Text Available Studying ancient Egyptian tombs have long been an important source of information regarding many aspects of Egyptian religion. Walls of New Kingdom tombs are often decorated with plenty of painted religious scenes. While they were primarily private structures containing images selected by the person who expected to be housed there for eternity, the funerary monuments also reflect religious beliefs. While numerous researches focused on many of the religious scenes depicted on the walls of ancient Egyptian tombs, no one focused on the knife - holders' scenes. Hence, the current study focused on knife - holders scenes depicted on the walls of both royal and private tombs dating back to the New Kingdom at Thebes. The current study was undertaken to shed light on the meaning and the function of knife in Ancient Egypt. To study the role of the knife-holders in Ancient Egypt. To spot light on the actions and behaviors and locations of the knife-holders in Ancient Egyptian civilization. To spot light on the representations of the knife-holders on the walls of the ancient Egyptians tombs in the Valley of the Kings and Valley of the Queens as well as the private tombs at western Thebes. To focus on the shapes and positions of the Knife-holders in Ancient Egypt. To explain the difference between Knife - Holders and Demons. To achieve the objectives of the study, the required data were collected from periodicals, references presenting Knife Holders scenes. Preserving the scenes of knife - holders on the walls of the royal tombs in the Valley of the Kings and Valley of the Queens dating back to the New Kingdom as well as the private tombs at western Thebes that contributed to the interpretation of all the data gathered from literature. The preliminary results indicated that the term (Knife-Holders is an expression which indicates to tomb-guardians, demons or minor divinities. These minor deities were subordinate to the major gods and goddesses. They

  6. Towards next-generation biodiversity assessment using DNA metabarcoding

    DEFF Research Database (Denmark)

    Taberlet, Pierre; Coissac, Eric; Pompanon, Francois

    2012-01-01

    Virtually all empirical ecological studies require species identification during data collection. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA (soil......, water, faeces, etc.). It can be implemented for both modern and ancient environmental samples. The availability of next-generation sequencing platforms and the ecologists need for high-throughput taxon identification have facilitated the emergence of DNA metabarcoding. The potential power of DNA...

  7. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  8. Palaeoproteomics for human evolution studies

    Science.gov (United States)

    Welker, Frido

    2018-06-01

    The commonplace sequencing of Neanderthal, Denisovan and ancient modern human DNA continues to revolutionize our understanding of hominin phylogeny and interaction(s). The challenge with older fossils is that the progressive fragmentation of DNA even under optimal conditions, a function of time and temperature, results in ever shorter fragments of DNA. This process continues until no DNA can be sequenced or reliably aligned. Ancient proteins ultimately suffer a similar fate, but are a potential alternative source of biomolecular sequence data to investigate hominin phylogeny given their slower rate of fragmentation. In addition, ancient proteins have been proposed to potentially provide insights into in vivo biological processes and can be used to provide additional ecological information through large scale ZooMS (Zooarchaeology by Mass Spectrometry) screening of unidentifiable bone fragments. However, as initially with ancient DNA, most ancient protein research has focused on Late Pleistocene or Holocene samples from Europe. In addition, only a limited number of studies on hominin remains have been published. Here, an updated review on ancient protein analysis in human evolutionary contexts is given, including the identification of specific knowledge gaps and existing analytical limits, as well as potential avenues to overcome these.

  9. Earthquake Archaeology: a case study from Ancient Cnidus

    Science.gov (United States)

    Stewart, I. S.; Altunel, E.; Piccardi, L.

    2003-04-01

    Ancient earthquakes can leave their mark in the mythical practices and literary accounts of ancient peoples, the stratigraphy of their site histories, and the structural integrity of their constructions. The ancient Greek/Roman city of Cnidus in southwestern Turkey records all three. A spectacular exposed fault plane cliff bordering the northern edge of the city appears to have been an important revered site, bearing votive niches carved into the near-vertical slip plane and associated with a Sanctuary of Demeter that implies a connection to the underworld. Stratigraphic evidence for earthquake faulting can be found in the form of a destruction horizon of contorted soil, relics and human remains exposed in the original excavations of the Sanctuary of Demeter by Sir Charles Newton (1857-58) and in a destruction horizon of burnt soil and bone uncovered by the ongoing excavation of a colonnaded street. Structural damage to constructions is widespread across the site, with warped and offset walls in the Sanctuary of Demeter, collapsed buildings in several places, and a parallel arrangement of fallen columns in the colonnaded street. The most remarkable structural evidence for fault activity, however, is the rupture of the ancient city's famous Round Temple of Aphrodite, whose podium reveals a history of damage and which is unambiguously displaced across a bedrock fault. While these phenomena are equivocal when viewed in isolation, collectively they imply at least two damaging earthquakes at the site, one (possibly both) of which ruptured along the fault on which the city is found. The Cnidus case study highlights how reliable identification of archaeoseismic damage relies on compiling an assemblage of indicators rather than the discovery of a diagnostic "smoking gun".

  10. Mitochondrial DNA variation in the Viking age population of Norway.

    Science.gov (United States)

    Krzewińska, Maja; Bjørnstad, Gro; Skoglund, Pontus; Olason, Pall Isolfur; Bill, Jan; Götherström, Anders; Hagelberg, Erika

    2015-01-19

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  11. Balancing Acts Between Ancient and Modern Cities: The Ancient Greek Cities Project of C. A. Doxiadis

    Directory of Open Access Journals (Sweden)

    Mantha Zarmakoupi

    2015-12-01

    Full Text Available This paper examines the inception and development of the Ancient Greek Cities (AGC research project (1963–77 of Constantinos A. Doxiadis and addresses the novelty of its methodological approach to the study of classical urbanism. With the AGC project, Doxiadis launched a comprehensive study of the ancient Greek built environment to provide an overview of the factors involved in its shaping. The project produced 24 published volumes — the first two laying out the historical and methodological parameters of the ensuing 22 monographs with case studies — as well as 12 unpublished manuscripts, and through international conferences initiated a wider dialogue on ancient cities beyond the classical Greek world. It was the first interdisciplinary study that attempted to tackle the environmental factors, together with the social and economic ones, underpinning the creation, development and operation of ancient Greek cities. Doxiadis’s innovative approach to the analysis of the ancient city was indebted to his practice as an architect and town planner and was informed by his theory of Ekistics. His purpose was to identify the urban planning principles of ancient Greek settlements in order to employ them in his projects. This paper examines the concept and methodology of the AGC project as well as the ways in which Doxiadis used the study of ancient cities in relation to his contemporary urban/architectural agendas, and explains this important moment in the historiography of ancient Greek urbanism.

  12. Tech Talk for Social Studies Teachers: Ancient Egypt.

    Science.gov (United States)

    Pahl, Ronald H.

    1998-01-01

    Presents an annotated bibliography of 10 Web sites concerning ancient Egypt that have materials appropriate for social studies classes. Includes virtual tours of Egypt and specific temples, explorations of the pyramids, archaeological and geographic information, and information on the Egyptian "Book of the Dead." (MJP)

  13. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence ...

  14. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Science.gov (United States)

    Valverde, Guido; Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars; Llamas, Bastien; Haak, Wolfgang

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD), Wari (Middle Horizon, 800-1000 AD) and Ychsma (Late Intermediate Period, 1000-1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  15. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Directory of Open Access Journals (Sweden)

    Guido Valverde

    Full Text Available The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD, Wari (Middle Horizon, 800-1000 AD and Ychsma (Late Intermediate Period, 1000-1450 AD. We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  16. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    Science.gov (United States)

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  17. Multidisciplinary studies on ancient sandstone quarries of Western Sardinia (Italy).

    Science.gov (United States)

    Grillo, Silvana Maria; Del Vais, Carla; Naitza, Stefano

    2013-04-01

    The ancient coastal quarries of Mediterranean are increasingly considered geosites of multidisciplinary relevance. They are sites of historical-archaeological interest that show ancient techniques of stone extraction; they are significant for cultural heritage conservation and restoration, as sources of the stones used in ancient buildings and monuments; they are sites of geological relevance, as often retain important stratigraphic sections; they are also useful markers of secular changes in the sea level. A multisciplinary study is in progress on the ancient quarries of the Sinis region (western Sardinia island), integrating archaeological, geological, minero-petrographical data. In Sardinia, coastal quarries have been established from Punic and Roman times. Many of them exploited Quaternary sediments along the southern and western coasts of the island. They consist of middle-late Pleistocene marine conglomerates and carbonate sandstones, and of coastal (aeolian) carbonate sandstones. Sandstone blocks of different sizes have been widely used in ancient cities for buildings, defensive works, harbours, etc. Three main areas of stone extraction (San Giovanni di Sinis, Punta Maimoni, Is Arutas) have been so far recognized in the Sinis. GIS-supported mapping and documentation of the sites includes their geology and stratigraphy, the extension and layout of the quarries, and an evaluation of volumes of extracted rocks. Documented archaeological evidences include ancient extraction fronts, spoil heaps, working areas, working traces in the old fronts, transport routes of blocks, and traces of loading facilities. The study is aimed at reconstructing the relationships of the quarries with the urban areas of Sinis, as the ancient Punic-Roman city of Tharros. Consequently, a minero-petrographical characterization (optical microscopy, XRD) is performed on sandstones sampled in each quarry, and in historical buildings in Tharros and other centres of the region (Cabras

  18. Prediction of autosomal STR typing success in ancient and Second World War bone samples.

    Science.gov (United States)

    Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

    2017-03-01

    Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is

  19. Medicine in Ancient Assur

    DEFF Research Database (Denmark)

    Arbøll, Troels Pank

    This dissertation is a microhistorical study of a single individual named Kiṣir-Aššur who practiced medicine in the ancient city of Assur (modern northern Iraq) in the 7th century BCE. The study provides the first detailed analysis of one healer’s education and practice in ancient Mesopotamia...

  20. Towards the onset of fruit tree growing north of the Alps: ancient DNA from waterlogged apple (Malus sp.) seed fragments.

    Science.gov (United States)

    Schlumbaum, Angela; van Glabeke, Sabine; Roldan-Ruiz, Isabel

    2012-01-20

    Wild apples (Malus sp.) have been a major food source in the northern Alpine region since prehistory and their use is well understood. The onset of deliberate fruit tree growing in the area is, however, less clear. It is generally assumed that horticulture was practised in Roman times, but it might be even earlier. In the archaeological record seed testa and pericarp remains are particularly frequent at sites with waterlogged preservation such as lakeshore settlements or wells, pits and ditches, but the distinction between wild and domestic plants is not morphologically possible. With waterlogged remains being one main source of information about past fruit cultivation, we have tested the feasibility of analysing ancient DNA from waterlogged preserved bulk samples of testa fragments. We studied apple seeds from three Neolithic and three Roman sites with waterlogged preservation in the Alpine foreland. Chloroplast markers failed in all samples, but nuclear ITS1 (internal transcribed spacer region 1) of the ribosomal DNA was successfully typed in two Roman samples from the site Oedenburg/Biesheim-Kunheim (Haut-Rhin, F). The retrieved ITS1 sequences are identical to each other and are shared with wild Malus sylvestris and Malus sieversii, and with domestic apple cultivars, supporting the potential of using waterlogged remains for identifying the genetic status of apple diachronically. Copyright © 2011 Elsevier GmbH. All rights reserved.

  1. 800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Willerslev, Eske

    2007-01-01

    Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely...... in samples, which are recovered from warm environments and are relatively old (e.g. more than 100,000 years), these findings come as a great surprise. Here, we show that problems exist with the methodological approaches used in the study. First, the nested PCR technique as reported is nonsensical...... polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants. Udgivelsesdato: 2007-Feb-22...

  2. Paleo-oncology: the role of ancient remains in the study of cancer.

    Science.gov (United States)

    Halperin, Edward C

    2004-01-01

    Paleo-oncology is the study of carcinomas and sarcomas in ancient human populations and their hominid precursors. These populations are informative concerning the possible influences on cancer of morphologic and functional evolution, diet, lifestyle, and other environmental factors. The prevalence of cancer in ancient populations might have differed from that in modern humans, because of substantial differences in tobacco and alcohol use, diet, life expectancy, and the availability of treatment. The available physical data concerning cancer in antiquity includes evidence of its existence in animal fossils and ancient humans and their precursors. The difficulties of paleo-oncologic research include a limited soft tissue record. In evaluating cancer in ancient remains, one must also deal with the problem of pseudopathology: whether an observed tissue change is all antemortem pathologic lesion or a postmortem artifact. Future archeological discoveries and the application of improved diagnostic techniques may enable paleo-oncology to make further contributions to our understanding of cancer.

  3. The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545.

    Science.gov (United States)

    Hutchinson, William F; Culling, Mark; Orton, David C; Hänfling, Bernd; Lawson Handley, Lori; Hamilton-Dyer, Sheila; O'Connell, Tamsin C; Richards, Michael P; Barrett, James H

    2015-09-01

    A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts.

  4. The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545

    Science.gov (United States)

    Hutchinson, William F.; Culling, Mark; Orton, David C.; Hänfling, Bernd; Lawson Handley, Lori; Hamilton-Dyer, Sheila; O'Connell, Tamsin C.; Richards, Michael P.; Barrett, James H.

    2015-01-01

    A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts. PMID:26473047

  5. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    Science.gov (United States)

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

  6. Pathogens and host immunity in the ancient human oral cavity

    Science.gov (United States)

    Warinner, Christina; Matias Rodrigues, João F.; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y.; Tito, Raul Y.; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C.; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars; Samaniego Castruita, José Alfredo; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian; Olsen, Jesper V.; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M.; Collins, Matthew J.; Gilbert, M. Thomas P.; Rühli, Frank; Cappellini, Enrico

    2014-01-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize: (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) the first evidence of ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, “red-complex” pathogens, and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity, and diet, thereby extending the direct investigation of common diseases into the human evolutionary past. PMID:24562188

  7. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains

    DEFF Research Database (Denmark)

    Wales, Nathan; Andersen, Kenneth; Cappellini, Enrico

    2014-01-01

    Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate a...... extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated...... on the interactions between humans and past plant communities....

  8. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...... rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base...... elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested....

  9. Did the ancient Egyptians migrate to ancient Nigeria?

    Directory of Open Access Journals (Sweden)

    Jock M. Agai

    2014-01-01

    Full Text Available Literatures concerning the history of West African peoples published from 1900 to 1970 debate�the possible migrations of the Egyptians into West Africa. Writers like Samuel Johnson and�Lucas Olumide believe that the ancient Egyptians penetrated through ancient Nigeria but Leo�Frobenius and Geoffrey Parrinder frowned at this opinion. Using the works of these early�20th century writers of West African history together with a Yoruba legend which teaches�about the origin of their earliest ancestor(s, this researcher investigates the theories that the�ancient Egyptians had contact with the ancient Nigerians and particularly with the Yorubas.Intradisciplinary and/or interdisciplinary implications: There is an existing ideology�amongst the Yorubas and other writers of Yoruba history that the original ancestors of�the Yorubas originated in ancient Egypt hence there was migration between Egypt and�Yorubaland. This researcher contends that even if there was migration between Egypt and�Nigeria, such migration did not take place during the predynastic and dynastic period as�speculated by some scholars. The subject is open for further research.

  10. A novel SERRS sandwich-hybridization assay to detect specific DNA target.

    Directory of Open Access Journals (Sweden)

    Cécile Feuillie

    Full Text Available In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR. In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

  11. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru’s Central Coast during the Middle Horizon

    Science.gov (United States)

    Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars

    2016-01-01

    The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650–1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region’s demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500–700 AD), Wari (Middle Horizon, 800–1000 AD) and Ychsma (Late Intermediate Period, 1000–1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast. PMID:27248693

  12. A Spatio-Temporal Analysis of Mitochondrial DNA Haplogroup I

    Directory of Open Access Journals (Sweden)

    Revesz Peter Z.

    2016-01-01

    Full Text Available The recent recovery of ancient DNA from a growing number of human samples shows that mitochondrial DNA haplogroup I was introduced to Europe after the end of the Last Glacial Maximum. This paper provides a spatio-temporal analysis of the various subhaplogroups of mitochondrial DNA I. The study suggests that haplogroup I diversified into haplogroups I1, I2’3, I4 and I5 at specific regions in Eurasia and then spread southward to Crete and Egypt.

  13. Ancient Chinese Precedents in China

    National Research Council Canada - National Science Library

    Geddis, Robert

    1999-01-01

    ... classics from ancient china. The assumption is that since China's political and military leaders state openly that their strategy is based on traditional Chinese strategic concepts, a study of ancient classics on strategy...

  14. The provenance study of Chinese ancient architectonical colored glaze by INAA

    International Nuclear Information System (INIS)

    Cheng Lin; Feng Songlin; Li Rongwu; Lue Zhirong; Li Guoxia

    2008-01-01

    The colored glazes are very popular and famous in Chinese ancient architectures. In order to exactly locate the provenance of ancient architectonical colored glazes, 196 pieces of ancient colored glaze bodies and porcelain bodies fired in Xiyue Temple and Lidipo kiln are analyzed by INAA. The results of factor analysis and some archaeological questions are reported and discussed in this paper

  15. The provenance study of Chinese ancient architectonical colored glaze by INAA

    Energy Technology Data Exchange (ETDEWEB)

    Cheng Lin [Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Radiation Center, Beijing Normal University, Beijing 100875 (China); Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)], E-mail: chenglin@bnu.edu.cn; Feng Songlin [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Li Rongwu [Department of Physics, Beijing Normal University, Beijing 100049 (China); Lue Zhirong [Shan' xi Provincial Institute of Cultural Relics and Archaeology, Xi' an 710054 (China); Li Guoxia [Institute of Physical Engineering, Zhengzhou University, Zhengzhou 450052 (China)

    2008-12-15

    The colored glazes are very popular and famous in Chinese ancient architectures. In order to exactly locate the provenance of ancient architectonical colored glazes, 196 pieces of ancient colored glaze bodies and porcelain bodies fired in Xiyue Temple and Lidipo kiln are analyzed by INAA. The results of factor analysis and some archaeological questions are reported and discussed in this paper.

  16. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...

  17. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available BACKGROUND: Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. METHODOLOGY/PRINCIPAL FINDINGS: We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes. CONCLUSION: The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate

  18. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years.

    Science.gov (United States)

    Melchior, Linea; Kivisild, Toomas; Lynnerup, Niels; Dissing, Jørgen

    2008-05-28

    Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (Viking and Iron Age Danes. The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied.

  19. All that is gold does not glitter? Age, taxonomy, and ancient plant DNA quality

    Directory of Open Access Journals (Sweden)

    JinHee Choi

    2015-07-01

    Full Text Available More than 600 herbarium samples from four distantly related groups of flowering plants were used for DNA extraction and subsequent measurements of DNA purity and concentration. We did not find any significant relation between DNA purity and the age of the sample. However, DNA yields were different between plant groups studied. We believe that there there should be no reservations about “old” samples if the goal is to extract more DNA of better purity. We argue that the older herbarium samples are the mine for the future DNA studies, and have the value not less than the “fresh” specimens.

  20. A combined method for DNA analysis and radiocarbon dating from a single sample.

    Science.gov (United States)

    Korlević, Petra; Talamo, Sahra; Meyer, Matthias

    2018-03-07

    Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material.

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

    Directory of Open Access Journals (Sweden)

    Won-Joon Lee

    Full Text Available 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.

  2. Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.

    Directory of Open Access Journals (Sweden)

    Nathan Wales

    Full Text Available DNA extracted from ancient plant remains almost always contains a mixture of endogenous (that is, derived from the plant and exogenous (derived from other sources DNA. The exogenous 'contaminant' DNA, chiefly derived from microorganisms, presents significant problems for shotgun sequencing. In some samples, more than 90% of the recovered sequences are exogenous, providing limited data relevant to the sample. However, other samples have far less contamination and subsequently yield much more useful data via shotgun sequencing. Given the investment required for high-throughput sequencing, whenever multiple samples are available, it is most economical to sequence the least contaminated sample. We present an assay based on quantitative real-time PCR which estimates the relative amounts of fungal and bacterial DNA in a sample in comparison to the endogenous plant DNA. Given a collection of contextually-similar ancient plant samples, this low cost assay aids in selecting the best sample for shotgun sequencing.

  3. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910 in medieval central europe.

    Directory of Open Access Journals (Sweden)

    Annina Krüttli

    Full Text Available Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72% exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic

  4. The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data

    Directory of Open Access Journals (Sweden)

    Heike H. Zimmermann

    2017-10-01

    Full Text Available Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.

  5. Originating relation studies on ancient porcelains of chines Ru and Jun by NAA

    International Nuclear Information System (INIS)

    Zhao Weijuan; Xie Jianzhong; Gao Zhengyao; Li Guoxia; Li Rongwu; Zhang Bin

    2002-01-01

    50 samples of glazes and bodies of the ancient Chinese Ru porcelain, Jun porcelain and imitative ancient ceramics were analyzed by neutron activation analysis (NAA). The contents of 36 elements in each sample were measured. The NAA data were statistically treated by fuzzy cluster method and the trend cluster diagram was obtained. Their classes and raw material sources were determined. The results show that although these samples spanned hundreds of years, came from different kilns and had different glazes colors, the bodies of the ancient Chinese Ru porcelain and Jun porcelain belong to the same kind, the glazes of the ancient Chinese Ru porcelain is similar to the glazes of the ancient Chinese Jun porcelain. The originating places of the body raw material were concentrated, and that of the glaze raw materials were scattered, the source of the glaze raw material covered that the body raw material. The ancient Chinese Ru porcelain and Jun porcelain have basically the same raw material sources and the sources of raw material are stable in long time. It is found that most modern Jun porcelain samples are similar to the ancient Chinese Jun porcelain. Two modern Ru porcelain samples are similar to the ancient Chinese Ru porcelain, but another one drifts apart from the ancient Chinese Ru porcelain. Jingdezhen porcelain has no relation to Ru porcelain and Jun porcelain

  6. Study of provenance character on ancient porcelain of Yue Kiln at Silongkou with NAA

    International Nuclear Information System (INIS)

    Jihao Zhu; Songlin Feng; Dongyu Fan; Xiangqian Feng; Qing Xu; Yueming Shen; Zhenxi Zhuo; Wenjiang Zhang

    2007-01-01

    Chemical composition is an important information of studying the provenance character of ancient pottery and porcelain. The ancient celadon samples produced in Later Tang (850-907 A.D.) to Former Southern Song (1127-1279 A.D.) have been analyzed with NAA. Its provenance characteristic was compared with that of Hongzhou Kiln of Jiangxi Province and Yaozhou Kiln of Shanxi Province in this paper. The experimental data were studied with statistic methods. The results indicated that the chemical compositions of ancient porcelain body samples made in three kilns were different. The difference is able to be identified. The porcelain body materials of both Silongkou Yue Kiln and Hongzhou Kiln were similar. The samples of Yaozhou kiln in north of China existed obvious difference. (author)

  7. Exploring Ancient Skies A Survey of Ancient and Cultural Astronomy

    CERN Document Server

    Kelley, David H

    2011-01-01

    Exploring Ancient Skies brings together the methods of archaeology and the insights of modern astronomy to explore the science of astronomy as it was practiced in various cultures prior to the invention of the telescope. The book reviews an enormous and growing body of literature on the cultures of the ancient Mediterranean, the Far East, and the New World (particularly Mesoamerica), putting the ancient astronomical materials into their archaeological and cultural contexts. The authors begin with an overview of the field and proceed to essential aspects of naked-eye astronomy, followed by an examination of specific cultures. The book concludes by taking into account the purposes of ancient astronomy: astrology, navigation, calendar regulation, and (not least) the understanding of our place and role in the universe. Skies are recreated to display critical events as they would have appeared to ancient observers—events such as the supernova of 1054 A.D., the "lion horoscope," and the Star of Bethlehem. Explori...

  8. Ancient pathogen DNA in human teeth and petrous bones

    DEFF Research Database (Denmark)

    Margaryan, Ashot; Hansen, Henrik B.; Rasmussen, Simon

    2018-01-01

    pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y.pestis DNA in the teeth, whereas all the petrous bones failed to produce Y.pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10...

  9. Study of ancient pottery from Slovakia

    International Nuclear Information System (INIS)

    Lipka, J.; Fusek, G.; Sitek, J.; Hucl, M.; Rausz, J.; Gajdosova, M.

    1990-01-01

    Ancient pottery samples collected from south-west Slovakia were studied through subjective observation and by Moessbauer spectroscopy. This method is convenient for determining the provenance and the manufacture of pottery. Transformations, induced by firing the clay and characterized by Moessbauer spectroscopy, give valuable information regarding the manufacture as, for instance, the final temperature of firing in it. The relative abundance of Fe 2+ and Fe 3+ determines the atmosphere used to fire a pottery. It has been found that the determination of the firing atmosphere obtained through the subjective observation is in good agreement with that obtained using Moessbauer spectroscopy. An unfired and fired clay was also investigated. (orig.)

  10. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

    Science.gov (United States)

    Weiß, Clemens L; Schuenemann, Verena J; Devos, Jane; Shirsekar, Gautam; Reiter, Ella; Gould, Billie A; Stinchcombe, John R; Krause, Johannes; Burbano, Hernán A

    2016-06-01

    Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

  11. Characterising the potential of sheep wool for ancient DNA analyses

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted; Tranekjer, Lena D.; Mannering, Ulla

    2011-01-01

    can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads...... and content of DNA in hair shafts are known to vary, and it is possible that common treatments of wool such as dyeing may negatively impact the DNA. Using quantitative real-time polymerase chain reaction (PCR), we demonstrate that in general, short fragments of both mitochondrial and single-copy nuclear DNA...

  12. Keeping cool in the desert: a study of ancient underground villages in Tunisia

    Energy Technology Data Exchange (ETDEWEB)

    Cole, R.S.

    1981-07-01

    A preliminary report on a one-month study of passive solar structures in Tunisia describe ancient underground Roman homes in Bulla Reggia and similar inhabited Berber homes in Matmata. The research group gathered data on the passive-solar gain, compass orientations, and room measurements of the homes and on natural-lighting techniques, ventilation systems, earth-sheltered construction methods, cooling concepts, and domestic water-collecting systems used for these ancient dwellings. 1 figure.

  13. On Ancient Babylonian Algebra and Geometry

    Indian Academy of Sciences (India)

    ber system prevalent during the ancient Mesopotamian civilization. In this article, we study the ... civilization provides a better insight into the thought processes of the ancient Babylonian mathematicians. In this context, consider the following ...

  14. Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages.

    Science.gov (United States)

    Rixon, Frazer J; Schmid, Michael F

    2014-04-01

    Structural information can inform our understanding of virus origins and evolution. The herpesviruses and tailed bacteriophages constitute two large families of dsDNA viruses which infect vertebrates and prokaryotes respectively. A relationship between these disparate groups was initially suggested by similarities in their capsid assembly and DNA packaging strategies. This relationship has now been confirmed by a range of studies that have revealed common structural features in their capsid proteins, and similar organizations and sequence conservation in their DNA packaging machinery and maturational proteases. This concentration of conserved traits in proteins involved in essential and primordial capsid/packaging functions is evidence that these structures are derived from an ancient, common ancestor and is in sharp contrast to the lack of such evidence for other virus functions. Copyright © 2014. Published by Elsevier B.V.

  15. The provenance study of Chinese ancient color glaze from Shanxi by INAA and factor analysis

    International Nuclear Information System (INIS)

    Cheng, L.; Ding, X.L.; Feng, S.L.; Feng, X.Q.; Lu, Z.R.

    2005-01-01

    This paper reports the results of the provenance study of Chinese ancient color glaze in Shanxi. The minor and trace elements of body of color glaze in different dynasty from Xiyue temper kiln and that of Lidipo kiln in Ming Dynasty determined by INAA, some of ancient porcelain from Lidipo kiln were measured, also. The factor analysis showed that provenances of the ancient color glazes from Xiyue Temple that were produced during Song Dynasty to the early Qing Dynasty were in the place of the Xiyue kiln, and body material of ancient color have little been changed, on the other hand, that of Later Qing Dynasty were-produced from Lidipo kiln. Different color glazes were measured by SRXRF and it proved the colored elements were Fe and Cu.

  16. Tradition and Creativity. Toward a Study of Intericonicity in Ancient Egyptian Art

    OpenAIRE

    Laboury, Dimitri

    2017-01-01

    Although a key-concept in Art historical discourse and reasoning, creativity has almost always been avoided as an issue in the discussion of Ancient Egyptian Art, as if the notion was simply irrelevant in such a context. This surprising phenomenon has clearly deep roots in the history of the western vision of Ancient Egyptian Art (and civilization). Nonetheless, the investigation of some (actually quite rare) cases of true copies in Ancient Egyptian Art reveals that creativity operated within...

  17. Ancient Genomics and the Peopling of the Southwest Pacific

    Science.gov (United States)

    Skoglund, Pontus; Posth, Cosimo; Sirak, Kendra; Spriggs, Matthew; Valentin, Frederique; Bedford, Stuart; Clark, Geoffrey; Reepmeyer, Christian; Petchey, Fiona; Fernandes, Daniel; Fu, Qiaomei; Harney, Eadaoin; Lipson, Mark; Mallick, Swapan; Novak, Mario; Rohland, Nadin; Stewardson, Kristin; Abdullah, Syafiq; Cox, Murray P.; Friedlaender, Françoise R.; Friedlaender, Jonathan S.; Kivisild, Toomas; Koki, George; Kusuma, Pradiptajati; Merriwether, D. Andrew; Ricaut, Francois-X.; Wee, Joseph T. S.; Patterson, Nick; Krause, Johannes; Pinhasi, Ron; Reich, David

    2017-01-01

    The appearance of people associated with the Lapita culture in the South Pacific ~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 Papuans of the New Guinea region is unclear. We report genome-wide ancient DNA data from four individuals from Vanuatu (~3100-2700 years before present) and Tonga (~2700-2300 years before present), and co-analyze them with 778 present-day East Asians and Oceanians. Today, indigenous peoples of the South Pacific harbor a mixture of ancestry from Papuans and a population of East Asian origin that does not exist in unmixed form today, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five percent 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, prior to the further expansion into Remote Oceania2–5. However, our finding that the ancient individuals had little to no Papuan ancestry implies later human population movements that spread Papuan ancestry through the South Pacific after the islands’ first peopling. PMID:27698418

  18. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia

    OpenAIRE

    Drancourt, Michel; Aboudharam, Gérard; Signoli, Michel; Dutour, Olivier; Raoult, Didier

    1998-01-01

    Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on...

  19. Science and Library in the Ancient Age

    Directory of Open Access Journals (Sweden)

    Hasan Sacit Keseroğlu

    2016-09-01

    Full Text Available Science assumes its contemporary identity as a result of the stages of magic, religion and reason. The religious stage starts with the invention of writing and this stage leaves its place to reason with Thales in Ancient Greece. Knowledge eludes from religious beliefs. Ways to reach accurate, reliable and realistic knowledge are sought, along with the answer for what knowledge is. Therefore, beginning of the science is taken into consideration together with science and philosophy. The purpose of this study is to approach knowledge and science of the ancient age in Mesopotamia, Egypt and Ancient Greece in general terms and to determine the relationship between the knowledge produced in those places and libraries established. The hypothesis has been determined as “Egypt and Mesopotamia at the starting point of the history of science and science, and libraries in Ancient Greece have developed parallelly to each other.” The scope of the study has been limited to Mesopotamia, Egypt and Ancient Greece; and Ancient Greece has been explained, with descriptive method, in the frame of the topics of Ionia, Athens, Hellenistic Period and Rome. Many archives and libraries have been established in the ancient age. The difference between an archive and a library has been mentioned first, and then, various libraries have been introduced such as Nineveh in Mesopotamia, Alexandria in Ancient Greece and many others in Egypt. It has been clearly distinguished that there had been a very tight relationship between knowledge production and library, especially with the Library of Alexandria.

  20. Apps for Ancient Civilizations

    Science.gov (United States)

    Thompson, Stephanie

    2011-01-01

    This project incorporates technology and a historical emphasis on science drawn from ancient civilizations to promote a greater understanding of conceptual science. In the Apps for Ancient Civilizations project, students investigate an ancient culture to discover how people might have used science and math smartphone apps to make their lives…

  1. Analytical study of ancient pottery from the archaeological site of Aiani, northern Greece

    International Nuclear Information System (INIS)

    Iordanidis, A.; Garcia-Guinea, J.; Karamitrou-Mentessidi, G.

    2009-01-01

    The present study is a multi-analytical approach on the characterization of several potsherd samples, dated from prehistoric to hellenistic times, from Aiani, ancient Upper Macedonia, northern Greece. In particular, X-ray Diffraction (XRD), X-ray Fluorescence (XRF) and Environmental Scanning Electron Microscopy, coupled with Energy Dispersive X-ray system (ESEM-EDX) were used for the determination of the morphological, chemical and mineralogical characteristics of the potsherds. The preliminary results indicated a rather local provenance of the analyzed ancient pottery samples and a finer texture and thus better ceramic manufacture as getting to hellenistic era. The use of a silicious or calcerous raw material is probably related to the specific utilization of each ceramic vessel in ancient times. The presence of gehlenite or pyroxene minerals in the ceramic matrix indicated higher firing temperatures, while lower temperatures were deduced when finding phylosilicate minerals. The preliminary results of this study do not necessarily imply that all the pottery of this area, belonging to the same chronological type, have similar physicochemical characteristics

  2. High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens

    DEFF Research Database (Denmark)

    Murray, Dáithí C.; Pearson, Stuart G.; Fullagar, Richard

    2012-01-01

    DNA analysis identified unreported plant and animal taxa, some of which are locally extinct or endemic. The survival and preservation of DNA in hot, arid environments is a complex and poorly understood process that is both sporadic and rare, but the survival of DNA through desiccation may be important......The study of arid palaeoenvironments is often frustrated by the poor or non-existent preservation of plant and animal material, yet these environments are of considerable environmental importance. The analysis of pollen and macrofossils isolated from herbivore middens has been an invaluable source...

  3. Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic.

    Science.gov (United States)

    Mendum, Tom A; Schuenemann, Verena J; Roffey, Simon; Taylor, G Michael; Wu, Huihai; Singh, Pushpendra; Tucker, Katie; Hinds, Jason; Cole, Stewart T; Kierzek, Andrzej M; Nieselt, Kay; Krause, Johannes; Stewart, Graham R

    2014-04-08

    Leprosy has afflicted humankind throughout history leaving evidence in both early texts and the archaeological record. In Britain, leprosy was widespread throughout the Middle Ages until its gradual and unexplained decline between the 14th and 16th centuries. The nature of this ancient endemic leprosy and its relationship to modern strains is only partly understood. Modern leprosy strains are currently divided into 5 phylogenetic groups, types 0 to 4, each with strong geographical links. Until recently, European strains, both ancient and modern, were thought to be exclusively type 3 strains. However, evidence for type 2 strains, a group normally associated with Central Asia and the Middle East, has recently been found in archaeological samples in Scandinavia and from two skeletons from the medieval leprosy hospital (or leprosarium) of St Mary Magdalen, near Winchester, England. Here we report the genotypic analysis and whole genome sequencing of two further ancient M. leprae genomes extracted from the remains of two individuals, Sk14 and Sk27, that were excavated from 10th-12th century burials at the leprosarium of St Mary Magdalen. DNA was extracted from the surfaces of bones showing osteological signs of leprosy. Known M. leprae polymorphisms were PCR amplified and Sanger sequenced, while draft genomes were generated by enriching for M. leprae DNA, and Illumina sequencing. SNP-typing and phylogenetic analysis of the draft genomes placed both of these ancient strains in the conserved type 2 group, with very few novel SNPs compared to other ancient or modern strains. The genomes of the two newly sequenced M. leprae strains group firmly with other type 2F strains. Moreover, the M. leprae strain most closely related to one of the strains, Sk14, in the worldwide phylogeny is a contemporaneous ancient St Magdalen skeleton, vividly illustrating the epidemic and clonal nature of leprosy at this site. The prevalence of these type 2 strains indicates that type 2F strains

  4. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death.

    Science.gov (United States)

    Schuenemann, Verena J; Bos, Kirsten; DeWitte, Sharon; Schmedes, Sarah; Jamieson, Joslyn; Mittnik, Alissa; Forrest, Stephen; Coombes, Brian K; Wood, James W; Earn, David J D; White, William; Krause, Johannes; Poinar, Hendrik N

    2011-09-20

    Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.

  5. Moessbauer study of ancient iron smelting slag in Japan

    International Nuclear Information System (INIS)

    Nakanishi, A.

    2008-01-01

    For an investigation of the ancient iron manufacturing technique, a reproducing experiment was carried out by archaeologists, where ancient type of iron smelting furnace was built and iron sand with high titanium contents was used as the raw material. During the operation of furnace, a large amount of slag flowed away from the furnace. In order to investigate the possibility for the estimation about the operative condition of furnace and the raw material, 57 Fe Moessbauer spectroscopy was applied for characterizing these slags and it was found that these slags mainly consisted of ferropseudobrookite (FeTi 2 O 5 ).

  6. Quantification and presence of human ancient DNA in burial place ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... burial place remains of Turkey using real time ... DNA was isolaled from fossil bone tissue remains with Bio Robot EZ1 and ... the increase in the amount of DNA as it is amplified. The ... species or human blood in this work.

  7. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds.

    Science.gov (United States)

    Lagerholm, Vendela K; Sandoval-Castellanos, Edson; Vaniscotte, Amélie; Potapova, Olga R; Tomek, Teresa; Bochenski, Zbigniew M; Shepherd, Paul; Barton, Nick; Van Dyck, Marie-Claire; Miller, Rebecca; Höglund, Jacob; Yoccoz, Nigel G; Dalén, Love; Stewart, John R

    2017-04-01

    Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum. © 2016 John Wiley & Sons Ltd.

  8. Detection and analysis of ancient segmental duplications in mammalian genomes.

    Science.gov (United States)

    Pu, Lianrong; Lin, Yu; Pevzner, Pavel A

    2018-05-07

    Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer. © 2018 Pu et al.; Published by Cold Spring Harbor Laboratory Press.

  9. A code of ethics for evidence-based research with ancient human remains.

    Science.gov (United States)

    Kreissl Lonfat, Bettina M; Kaufmann, Ina Maria; Rühli, Frank

    2015-06-01

    As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article. © 2015 Wiley Periodicals, Inc.

  10. 800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?

    Science.gov (United States)

    Binladen, Jonas; Gilbert, M Thomas P; Willerslev, Eske

    2007-02-22

    Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely in samples, which are recovered from warm environments and are relatively old (e.g. more than 100,000 years), these findings come as a great surprise. Here, we show that problems exist with the methodological approaches used in the study. First, the nested PCR technique as reported is nonsensical--one of the second round 'nested' primers falls outside the amplicon of the first round PCR. More worryingly, the binding region of one of the first round primers (Elcytb320R) falls within the short 43 base pair reported mammoth sequence, specifically covering two of the three reportedly diagnostic Elephas polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants.

  11. [Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA].

    Science.gov (United States)

    Pérez, Luz Adriana; Rodríguez, Freddy; Langebaek, Carl Henrik; Groot, Helena

    2016-09-01

    Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.

  12. Natural analogue study on backfill materials from ancient Chinese constructions for LILW disposal. Appendix 5: China (b)

    International Nuclear Information System (INIS)

    Cunli, G.; Zhiwen, F.; Xiuzhen, L.; Yawen, H.; Anxi, C.; Jinsheng, Z.

    2001-01-01

    Full text: The objective of this work was to contribute to the demonstration of the long term safety of low-and-intermediate level radioactive waste (LILW) disposal using information from a natural analogue study on ancient Chinese constructions. The work firstly compared LILW near surface disposal facilities with Chinese ancient tombs in respects of siting, engineering structures, design and construction procedures and indicates that they are both based upon multi-barrier principle. After extensive literature and field survey, three materials were collected from two Chinese ancient tombs and one ancient architectures for further laboratory study. The three materials were studied in laboratories from the point of view of radioactive waste disposal in near surface facilities to obtain information concerning their basic physical and chemical properties, engineering properties and radionuclide adsorption abilities. The results show that the two materials from the ancient tombs have low permeability and strong adsorption for 60 Co and 134 Cs. The saturated permeabilities of the two ancient materials are in the order of 10 -1 0 m/s and the distribution coefficients for the two radionuclides are all in the order of 10 1 m 3 /kg. The conclusion was that the then current LILW disposal option in near-surface would be effective for a long term period of time, and clay materials, as backfill materials for LILW near-surface disposal facilities would very effective in preventing water intrusion and retarding radionuclide release even over a long term of period. Overall the LILW disposal option was considered to be safe in long term. (author)

  13. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe.

    Science.gov (United States)

    Horn, Susanne; Prost, Stefan; Stiller, Mathias; Makowiecki, Daniel; Kuznetsova, Tatiana; Benecke, Norbert; Pucher, Erich; Hufthammer, Anne K; Schouwenburg, Charles; Shapiro, Beth; Hofreiter, Michael

    2014-04-01

    After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.

  14. Urology and the scientific method in ancient Egypt.

    Science.gov (United States)

    Gordetsky, Jennifer; O'Brien, Jeanne

    2009-03-01

    To examine the practice of urology in ancient Egypt using various sources, including the Edwin Smith and Ebers Papyri. The sources of knowledge of ancient Egyptian medicine include medical papyri, paleopathology, art, and hieroglyphic carvings. A brief overview of the medical system in ancient Egypt was completed, in addition to an examination of the training and specialization of the physician in the ancient world. Urologic diseases treated in ancient Egypt and some of the first documented urologic surgeries are presented. Finally, we studied the role of the physician-priest and the intertwined use of religion and magic in ancient Egyptian medicine. The same medical conditions urologists treat in the office today were methodically documented thousands of years ago. Medical papyri show evidence that the ancient Egyptians practiced medicine using a scientific method based on the clinical observation of disease. This has been exemplified by the Edwin Smith Surgical Papyrus, a collection of surgical cases that gives a diagnosis, treatment, and prognosis for each ailment, and the discovery of medical specialization in ancient Egypt, giving us perhaps the world's first urologists. Intertwined with the scientific method was also the rich mysticism and religion of ancient Egypt, which were integral components of the healing process. We present an overview of the practice of urology in ancient Egypt, in terms of both pharmacologic and surgical intervention, as well as with a look into the religion of medicine practiced at that time.

  15. Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA.

    Science.gov (United States)

    Li, Hongjie; Zhao, Xin; Zhao, Yongbin; Li, Chunxiang; Si, Dayong; Zhou, Hui; Cui, Yinqiu

    2011-12-01

    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.

  16. Mechanisms in ancient Chinese books with illustrations

    CERN Document Server

    Hsiao, Kuo-Hung

    2014-01-01

    This book presents a unique approach for studying mechanisms and machines with drawings that were depicted unclearly in ancient Chinese books. The historical, cultural and technical backgrounds of the mechanisms are explained, and various mechanisms described and illustrated in ancient books are introduced. By utilizing the idea for the conceptual design of modern mechanisms, all feasible designs of ancient mechanisms with uncertain members and joints that meet the technical standards of the subjects’ time periods are synthesized systematically. Ancient Chinese crossbows (the original crossbow and repeating crossbows), textile mechanisms (silk-reeling mechanism, spinning mechanisms, and looms), and many other artisan's tool mechanisms are used as illustrated examples.  Such an approach provides a logical method for the reconstruction designs of ancient mechanisms with uncertain structures. It also provides an innovative direction for researchers to further identify the original structures of mechanisms...

  17. Non-destructive study of ancient documents and books by means of ion beams

    International Nuclear Information System (INIS)

    Ruvalcaba S, J.L.; Monroy, M.

    2004-01-01

    In this work, a non destructive methodology for the analysis of ancient manuscripts and books using an external beam system and the techniques Particle Induced X-ray Emission Spectroscopy (PIXE) and Rutherford Backscattering Spectrometry (RBS) is presented. This application shows the analytical features of the particle accelerator based techniques for the characterization of this kind of historical materials. This methodology was used for the analysis of inks of an European book from XVII century. This is the first study in Mexico of an ancient book using simultaneously PIXE and RBS non-vacuum techniques. (Author) 21 refs., 9 figs

  18. Deep sequencing of RNA from ancient maize kernels

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rasmussen, Morten

    2013-01-01

    The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited - perhaps due to dogma associated with the fragility of RNA. We hy...... maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication....

  19. Study of provenance properties on ancient porcelain of Yue Kiln at Si-long-kou with NAA

    International Nuclear Information System (INIS)

    Feng Songlin; Fan Dongyu; Feng Xiangqian; Cheng Lin; Lei Yong; Xu Qing; Quan Huishan; Shen Yueming; Zhou Zhexi; Zhang Wenjiang

    2005-01-01

    Chinese ancient porcelain history has lasted about three thousands years from Shang Dynasty (1100∼1600 BC). A large amount of ancient porcelain sherds with accuracy provenance and ages were excavated from a lot of kiln sites in China. Archaeologists and ceramic experts have recognized and researched it with excavated stratum, utensil shape, body quality, glaze color and painting pattern. However, the appearance characteristic of some ancient porcelain manufactured in different kilns is similar. Therefore, it is still difficult to identify the provenance and ages of the samples excavated from some sites using traditional methods. Up, to now, many problems of Chinese ancient porcelain are confused for archaeologist and collecting experts. The elemental composition of ancient porcelain shows certain information of provenance and age. Especially, the sorts and contents of the elements in porcelain didn't change, so it is very useful to determine the provenance of ancient porcelain with elemental composition characteristics. Provenance characteristic is the important scientific information to identify ancient porcelain wares excavated from sites and graves. The porcelain samples of Si-Long-Kou Yue kiln in Zhejiang Province of china have been analyzed with NAA in this paper. The provenance characteristic was compared with it of Hong-Zhou kiln of Jiang-Xi Province and Yao-Zhou kiln of Shan-Xi Province. The experimental data were studied with statistic methods. The results show that the chemical compositions of porcelain body samples for three kilns were different. The difference was been able identified. The porcelain body materials of both Si-Long-Kou Yue kiln and Hong-Zhou kiln of Jiang-Xi were similar. The samples of Yao-Zhou kiln in north of China existed obvious difference.

  20. Ancient DNA extracted from Danish aurochs (Bos primigenius)

    DEFF Research Database (Denmark)

    Nielsen, Peter Gravlund; Aaris-Sørensen, Kim; Hofreiter, Michael

    2012-01-01

    study of genetic variation of Danish aurochs. In addition, for all specimens we address correlations between the ability to obtain DNA sequences and various parameters such as the age of the sample, the collagen content, the museum storage period, Danish geography and whether the specimens were found...... in an archeological or geological context. We find that aurochs from southern Scandinavia display a star-shaped population genetic structure, that is indicative of a local and relatively recent diversification from a few ancestral haplotypes that may have originated in the ancestral Western European population before...... migration northwards during the retreat of the glaciers. Scenarios suggesting several invasions of genetically distinct aurochs are not supported by these analyses. Rather, our results suggest that a single continuous migration northward occurred. Our findings also suggest, although with only limited...

  1. DNA and bone structure preservation in medieval human skeletons.

    Science.gov (United States)

    Coulson-Thomas, Yvette M; Norton, Andrew L; Coulson-Thomas, Vivien J; Florencio-Silva, Rinaldo; Ali, Nadir; Elmrghni, Samir; Gil, Cristiane D; Sasso, Gisela R S; Dixon, Ronald A; Nader, Helena B

    2015-06-01

    Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Detecting Ancient Tuberculosis

    Directory of Open Access Journals (Sweden)

    Angela M. Gernaey

    1998-12-01

    Full Text Available Some diseases have played a more significant role in human development than others. Here we describe the results of a trial to diagnose ancient tuberculosis using chemical methods. Palaeo-epidemiological studies of the disease are compromised, but it has become apparent that tuberculosis (TB is a 'population-density dependent' disease. From modern studies, it is also apparent that the prevalence of TB can be used as an indicator of the level of poverty within the studied population. Mid-shaft rib samples from articulated individuals recovered from the former Newcastle Infirmary Burial Ground (1753-1845 AD were examined for mycolic acids that are species-specific for Mycobacterium tuberculosis. The 24% of ribs positive for mycolic acids correlated with the documented 27% tuberculosis prevalence. Mycolic acid biomarkers have the potential to provide an accurate trace of the palaeo-epidemiology of tuberculosis in ancient populations, thereby providing an indication of the overall level of poverty - a useful adjunct for archaeology.

  3. Puzzling sequences: studying microbial genomes from 'Ötzi'

    International Nuclear Information System (INIS)

    Rattei, T.

    2012-01-01

    Ancient remains, and mummies in particular, are of central value for archaeological research. The Tyrolean iceman “Ötzi” was conserved in a glacier of the Ötztal Alps about 5000 years ago. Aside from morphological and phenotypical classification, the determination of DNA sequences and the subsequent genome analyses have been first applied to mitochondrial DNA and then been extended to genomic DNA. Typically also ancient microbial DNA is sequenced. These sequences allow the identification of pathogens as well as studying the evolution of microorganisms. The talk will explain the metagenomic aspects of the “Ötzi” genome project and discuss the first results. (author)

  4. Development and trends in synchrotron studies of ancient and historical materials

    International Nuclear Information System (INIS)

    Bertrand, Loïc; Cotte, Marine; Stampanoni, Marco; Thoury, Mathieu; Marone, Federica; Schöder, Sebastian

    2012-01-01

    Synchrotron photon-based methods are increasingly being used for the physico-chemical study of ancient and historical materials (archaeology, palaeontology, conservation sciences, palaeo-environments). In particular, parameters such as the high photon flux, the small source size and the low divergence attained at the synchrotron make it a very efficient source for a range of advanced spectroscopy and imaging techniques, adapted to the heterogeneity and great complexity of the materials under study. The continuous tunability of the source — its very extended energy distribution over wide energy domains (meV to keV) with a high intensity — is an essential parameter for techniques based on a very fine tuning of the probing energy to reach high chemical sensitivity such as XANES, EXAFS, STXM, UV/VIS spectrometry, etc. The small source size attained (a few micrometres) at least in the vertical plane leads to spatial coherence of the photon beams, giving rise in turn to a series of imaging methods already crucial to the field. This review of the existing literature shows that microfocused hard X-ray spectroscopy (absorption, fluorescence, diffraction), full-field X-ray tomography and infrared spectroscopy are the leading synchrotron techniques in the field, and presents illustrative examples of the study of ancient and historical materials for the various methods. Fast developing analytical modalities in scanning spectroscopy (STXM, macro-XRF scanning) and novel analytical strategies regarding optics, detectors and other instrumental developments are expected to provide major contributions in the years to come. Other energy domains are increasingly being used or considered such as far-infrared and ultraviolet/visible for spectroscopy and imaging. We discuss the main instrumental developments and perspectives, and their impact for the science being made on ancient materials using synchrotron techniques.

  5. Melanesian mtDNA complexity.

    Directory of Open Access Journals (Sweden)

    Jonathan S Friedlaender

    Full Text Available Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA sequences from hypervariable regions 1 and 2 (HVR1 and HVR2 from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups. Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP, and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal Austronesian influence in this region remains unresolved.

  6. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.

    Science.gov (United States)

    Bennett, E Andrew; Champlot, Sophie; Peters, Joris; Arbuckle, Benjamin S; Guimaraes, Silvia; Pruvost, Mélanie; Bar-David, Shirli; Davis, Simon J M; Gautier, Mathieu; Kaczensky, Petra; Kuehn, Ralph; Mashkour, Marjan; Morales-Muñiz, Arturo; Pucher, Erich; Tournepiche, Jean-François; Uerpmann, Hans-Peter; Bălăşescu, Adrian; Germonpré, Mietje; Gündem, Can Y; Hemami, Mahmoud-Reza; Moullé, Pierre-Elie; Ötzan, Aliye; Uerpmann, Margarete; Walzer, Chris; Grange, Thierry; Geigl, Eva-Maria

    2017-01-01

    Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.

  7. Study on the provenance of ancient porcelain excavated in Maojiawan ruin by WDXRF analysis

    International Nuclear Information System (INIS)

    Xie Guoxi

    2007-01-01

    In order to determine the provenance of two different kinds of ancient celadons which were excavated in Maojiawan ruin located in Beijing of China and named FLQ (imitated celadon) and WLNQ which is celadon outside and blue-white inside, ten components of each sample's body and glaze were measured by the wave length dispersive X-ray fluorescence (WDXRF) analysis. Multivariates statistical analysis was used to analyze and compare the experiment data with those of LQY (ancient celadon) made in Zhejiang and ancient Jingdezhen porcelain (JDZ) made in Jingdezhen. The results show that the two different kinds of ancient celadons have the same provenance as JDZ, that is, they were produced in Jingdezhen. (authors)

  8. Ancient Greek with Thrasymachus: A Web Site for Learning Ancient Greek.

    Science.gov (United States)

    Barker, Alison

    2001-01-01

    Discusses a project that was begun as an attempt by two teachers of Ancient Greek to provide supplementary materials to accompany "Thrasymachus," a first-year textbook for learning ancient Greek. Provides a brief history and description of the project, the format of each chapter, a chronology for completion of materials for each chapter in the…

  9. Preliminary Study of Ancient Town Protection and Rural Tourism Development of Caoshi Town in Hengdong County, Hunan Province

    OpenAIRE

    Liu, Tian-zhao; Yang, Zai-tian; Liu Pei-lin

    2012-01-01

    The typical style and features of mountains and waters in Caoshi Ancient Town, have hitherto been well preserved. Caoshi Ancient Town boasts superior base of the natural eco-environment and deep-rooted background of regional culture, where mountains, waters, shoals, towns and other landscape elements are merged harmoniously, the transportation and geographical conditions have been fundamentally changed. Ancient towns, old temples, ancient forests, ancient wells and ancient piers are unique in...

  10. Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling.

    Directory of Open Access Journals (Sweden)

    Thi-Nguyen-Ny Tran

    Full Text Available BACKGROUND: The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. METHODOLOGY/PRINCIPAL FINDINGS: We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279-modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%. Third, we classified 10 of 18 teeth (56% collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I in human ancient and modern dental pulp, respectively. CONCLUSIONS/SIGNIFICANCE: Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.

  11. Classification of Ancient Mammal Individuals Using Dental Pulp MALDI-TOF MS Peptide Profiling

    Science.gov (United States)

    Tran, Thi-Nguyen-Ny; Aboudharam, Gérard; Gardeisen, Armelle; Davoust, Bernard; Bocquet-Appel, Jean-Pierre; Flaudrops, Christophe; Belghazi, Maya; Raoult, Didier; Drancourt, Michel

    2011-01-01

    Background The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets. Methodology/Principal Findings We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively. Conclusions/Significance Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals. PMID:21364886

  12. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Epp, Laura S.; Haile, James Seymour

    2012-01-01

    the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified....

  13. Molecules in the mud: Combining ancient DNA and lipid biomarkers to reconstruct vegetation response to climate variability during the Last Interglacial and the Holocene on Baffin Island, Arctic Canada

    Science.gov (United States)

    Crump, S. E.; Sepúlveda, J.; Bunce, M.; Miller, G. H.

    2017-12-01

    Modern ecological studies are revealing that the "greening" of the Arctic, resulting from a poleward shift in woody vegetation ranges, is already underway. The increasing abundance of shrubs in tundra ecosystems plays an important role in the global climate system through multiple positive feedbacks, yet uncertainty in future predictions of terrestrial vegetation means that climate models are likely not capturing these feedbacks accurately. Recently developed molecular techniques for reconstructing past vegetation and climate allow for a closer look at the paleo-record in order to improve our understanding of tundra community responses to climate variability; our current research focus is to apply these tools to both Last Interglacial and Holocene warm times. Here we present initial results from a small lake on southern Baffin Island spanning the last 7.2 ka. We reconstruct climate with both bulk geochemical and biomarker proxies, primarily using biogenic silica and branched glycerol dialkyl glycerol tetraethers (brGDGTs) as temperature indicators. We assess shifts in plant community using multivariate analysis of sedimentary ancient DNA (sedaDNA) metabarcoding data. This combination of approaches reveals that the vegetation community has responded sensitively to early Holocene warmth, Neoglacial cooling, and possibly modern anthropogenic warming. To our knowledge, this represents the first combination of a quantitative, biomarker-based climate reconstruction with a sedaDNA-based paleoecological reconstruction, and offers a glimpse at the potential of these molecular techniques used in tandem.

  14. Radiocarbon dating study of ancient iron artifacts with accelerator mass spectrometry

    International Nuclear Information System (INIS)

    Igaki, Kenzo; Nakamura, Toshio; Hirasawa, Masahiro; Kato, Masako; Sano, Masamichi.

    1994-01-01

    In order to study the correlation between the highly resistive property against corrosion and the production method of the ancient iron artifacts, it is essentially necessary to determine the accurate ages of them. 14 C dating with accelerator mass spectrometry was applied to the two ancient artifacts, a Japanese sword of wrought iron with a production age ranged from the Kamakura to the Muromachi period, estimation based on the fabrication technique, and a planning adze of cast iron with no definite origin. The former was dated as 880±150 y.B.P., corresponding to the calendar age ranged from AD 1021 to AD 1263, and the latter as 1720±160 y.B.P. with the calendar age ranged from AD 119 to AD 457 and from AD 483 to AD 508. These calibrated 14 C ages for both iron artifacts are consistent with the relevant ages conjectured by historical considerations. (author)

  15. µ-XRF Studies on the Colour Brilliance in Ancient Wool Carpets

    Directory of Open Access Journals (Sweden)

    Markus Meyer

    2017-01-01

    Full Text Available Many handmade ancient and recent oriental wool carpets show outstanding brilliance and persistence of colour that is not achieved by common industrial dyeing procedures. Anthropologists have suggested the influence of wool fermentation prior to dyeing as key technique to achieve the high dyeing quality. By means of μ-XRF elemental mapping of mordant metals we corroborate this view and show a deep and homogenous penetration of colourants into fermented wool fibres. Furthermore we are able to apply this technique and prove that the fermentation process for ancient specimens cannot be investigated by standard methods due to the lack of intact cuticle layers. This finding suggests a broad range of further investigations that will contribute to a deeper understanding of the development of traditional dyeing techniques. Spectroscopic studies add information on the oxidation states of the metal ions within the respective mordant-dye-complexes and suggest a partial charge transfer as basis for a significant colour change when Fe mordants are used.

  16. Study of the circumstance influence on the elemental distribution in ancient animal bone using μ-XRF

    International Nuclear Information System (INIS)

    Yan Lingtong; Feng Songlin; Li Li; Xu Wei; Feng Xiangqian; Xie Guoxi

    2010-01-01

    Elemental analysis of archaeological bone plays an important role in the study of the dietary habits of ancient animals. The elemental characteristic of diagenetic skeletons depends on the surrounding circumstance. The study of environmental influence on the elemental concentration of ancient bone is significant. In this paper, the diagenetic influence on archaeological skeletons is analyzed by microbeam X-ray fluorescence (μ-XRF). The results show that the enamel is an excellent barrier to the diagenesis and the element Sr in bone isn't susceptible to contamination from the buried environment. (authors)

  17. The rights of patients as consumers: An ancient view.

    Science.gov (United States)

    Barapatre, Nishant Bhimraj; Joglekar, Vishnu Prabhakar

    2016-01-01

    As far as the rights of consumers are concerned, the International Organization of Consumer's Union (IOCU) in 1983 has specified about the eight rights of a consumer. The Consumer Protection Act (CPA), 1986 then prescribed six "Rights of Consumers," which are protected under the act. However, these rights can be observed in the ancient Indian texts such as Brihat-trayee , Narad Smruti , and Kautilya Arthashastra ., in the form of rights given to patients. For the purpose of present study, the implemented methodology includes - (1) study of the consumer rights described by IOCU and CPA, (2) detailed review of literature for observance of replication of these consumer rights in the ancient Indian texts and (3) a comparative study of the present consumer rights with the rights of patients observed in ancient Indian texts. This study shows that the substance of consumer rights is not a recent evolution, but the foundation of these rights has been laid well beforehand in the ancient times, which were provided to the patients by medical profession as well as by the rulers. The current scenario of protection of consumer rights is the replication of this ancient practice only.

  18. Knife - Holders in Ancient Egyptian Tombs (Religious and Artistic Study)

    OpenAIRE

    dr.Rasha Omran

    2015-01-01

    Studying ancient Egyptian tombs have long been an important source of information regarding many aspects of Egyptian religion. Walls of New Kingdom tombs are often decorated with plenty of painted religious scenes. While they were primarily private structures containing images selected by the person who expected to be housed there for eternity, the funerary monuments also reflect religious beliefs. While numerous researches focused on many of the religious scenes depicted on the walls of anci...

  19. PIXE study on the provenance of Chinese ancient porcelain

    International Nuclear Information System (INIS)

    Zhu, D.; Cheng, H.S.; Lin, J.W.; Yang, F.J.

    2006-01-01

    This paper reports the PIXE study on the provenance of Chinese ancient porcelain made in 7-10th century. The chemical compositions of Jun celadon samples made at Juntai, Linru and Hunyuan kilns, the white-glazed porcelain samples made at Ding, Huangye and Dangyangyu kilns, and the Ru celadon samples made at Qiangliang Temple were measured by external-beam PIXE, and the factor analysis was applied for identifying their provenances. Experimental results show that the porcelain products made at different kilns can be distinguished according to the compositional differences measured by PIXE

  20. PIXE study on the provenance of Chinese ancient porcelain

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, D. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China); Cheng, H.S. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China)]. E-mail: hscheng@fudan.edu.cn; Lin, J.W. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China); Yang, F.J. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China)

    2006-08-15

    This paper reports the PIXE study on the provenance of Chinese ancient porcelain made in 7-10th century. The chemical compositions of Jun celadon samples made at Juntai, Linru and Hunyuan kilns, the white-glazed porcelain samples made at Ding, Huangye and Dangyangyu kilns, and the Ru celadon samples made at Qiangliang Temple were measured by external-beam PIXE, and the factor analysis was applied for identifying their provenances. Experimental results show that the porcelain products made at different kilns can be distinguished according to the compositional differences measured by PIXE.

  1. PIXE study on the provenance of Chinese ancient porcelain

    Science.gov (United States)

    Zhu, D.; Cheng, H. S.; Lin, J. W.; Yang, F. J.

    2006-08-01

    This paper reports the PIXE study on the provenance of Chinese ancient porcelain made in 7-10th century. The chemical compositions of Jun celadon samples made at Juntai, Linru and Hunyuan kilns, the white-glazed porcelain samples made at Ding, Huangye and Dangyangyu kilns, and the Ru celadon samples made at Qiangliang Temple were measured by external-beam PIXE, and the factor analysis was applied for identifying their provenances. Experimental results show that the porcelain products made at different kilns can be distinguished according to the compositional differences measured by PIXE.

  2. My journey to DNA repair.

    Science.gov (United States)

    Lindahl, Tomas

    2013-02-01

    I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases I, III and IV. I discovered the mammalian exonucleases DNase III (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O(6)-methylguanine (O(6)mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation. Copyright © 2013. Production and hosting by Elsevier Ltd.

  3. A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

    Science.gov (United States)

    Caramelli, David; Milani, Lucio; Vai, Stefania; Modi, Alessandra; Pecchioli, Elena; Girardi, Matteo; Pilli, Elena; Lari, Martina; Lippi, Barbara; Ronchitelli, Annamaria; Mallegni, Francesco; Casoli, Antonella; Bertorelle, Giorgio; Barbujani, Guido

    2008-01-01

    Background DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. Methodology/Principal Findings We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. Conclusions/Significance: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans. PMID:18628960

  4. A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences.

    Directory of Open Access Journals (Sweden)

    David Caramelli

    Full Text Available BACKGROUND: DNA sequences from ancient specimens may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal and early modern (Cro-Magnoid Europeans. METHODOLOGY/PRINCIPAL FINDINGS: We typed the mitochondrial DNA (mtDNA hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23 and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. CONCLUSIONS/SIGNIFICANCE: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

  5. Bacterial natural transformation by highly fragmented and damaged DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake......DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often DNA is recognized as nutrient source...... of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations...

  6. Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

    Directory of Open Access Journals (Sweden)

    Vincent J. Lynch

    2015-02-01

    Full Text Available A major challenge in biology is determining how evolutionarily novel characters originate; however, mechanistic explanations for the origin of new characters are almost completely unknown. The evolution of pregnancy is an excellent system in which to study the origin of novelties because mammals preserve stages in the transition from egg laying to live birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved endometrial expression during the origins of mammalian pregnancy, including genes that mediate maternal-fetal communication and immunotolerance. Furthermore, thousands of cis-regulatory elements that mediate decidualization and cell-type identity in decidualized stromal cells are derived from ancient mammalian transposable elements (TEs. Our results indicate that one of the defining mammalian novelties evolved from DNA sequences derived from ancient mammalian TEs co-opted into hormone-responsive regulatory elements distributed throughout the genome.

  7. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted

    2011-01-01

    Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

  8. Mitochondrial DNA variation in the Viking age population of Norway

    OpenAIRE

    Krzewińska, Maja; Bjørnstad, Gro; Skoglund, Pontus; Olason, Pall Isolfur; Bill, Jan; Götherström, Anders; Hagelberg, Erika

    2015-01-01

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. ...

  9. Chinese herbal dose in ancient and modern times: a comparative study.

    Science.gov (United States)

    He, Shimin

    2013-04-01

    Appropriate dose guarantees Chinese herb's safety and effectiveness. There are adult dose criteria for Chinese herbs in decoction in the Pharmacopoeia of the People's Republic of China (2010 Edition) at present. But Chinese herbs have been frequently used in much higher doses than the dose criteria. This study has been conducted to test the dependability of the dose criteria. Twenty Chinese herbs were selected as representatives and their adult doses in decoction in Bei Ji Qian Jin Yao Fang, a famous ancient literature, have been reviewed and compared with those in the Pharmacopoeia of the People's Republic of China (2010 Edition). The adult dose criteria for all these 20 Chinese herbs in the Pharmacopoeia of the People's Republic of China (2010 Edition) haven't covered those in Bei Ji Qian Jin Yao Fang. Furthermore, maximal adult doses in the dose criteria are much lower than those in Bei Ji Qian Jin Yao Fang. The dose criteria in the Pharmacopoeia of the People's Republic of China (2010 Edition) are not comprehensive enough. Studying ancient literatures is an effective method to gain precious Chinese herbs' dose data and helps for new dose criteria's establishment in the future.

  10. Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology

    Directory of Open Access Journals (Sweden)

    Nguyen-Hieu Tung

    2012-09-01

    Full Text Available Abstract Background Theoretical models suggest that DNA degradation would sharply limit the PCR-based detection of both eukaryotic and prokaryotic DNA within ancient specimens. However, the relative extent of decay of eukaryote and prokaryote DNA over time is a matter of debate. In this study, the murine macrophage cell line J774, alone or infected with Mycobacterium smegmatis bacteria, were killed after exposure to 90°C dry heat for intervals ranging from 1 to 48 h in order to compare eukaryotic cells, extracellular bacteria and intracellular bacteria. The sizes of the resulting mycobacterial rpoB and murine rpb2 homologous gene fragments were then determined by real-time PCR and fluorescent probing. Findings The cycle threshold (Ct values of PCR-amplified DNA fragments from J774 cells and the M. smegmatis negative controls (without heat exposure varied from 26–33 for the J774 rpb2 gene fragments and from 24–29 for M. smegmatis rpoB fragments. After 90°C dry heat incubation for up to 48 h, the Ct values of test samples increased relative to those of the controls for each amplicon size. For each dry heat exposure time, the Ct values of the 146-149-bp fragments were lower than those of 746-747-bp fragments. During the 4- to 24-h dry heat incubation, the non-infected J774 cell DNA was degraded into 597-bp rpb2 fragments. After 48 h, however, only 450-bp rpb2 fragments of both non-infected and infected J774 cells could be amplified. In contrast, the 746-bp rpoB fragments of M. smegmatis DNA could be amplified after the 48-h dry heat exposure in all experiments. Infected and non-infected J774 cell DNA was degraded more rapidly than M. smegmatis DNA after dry heat exposure (ANOVA test, p  Conclusion In this study, mycobacterial DNA was more resistant to dry-heat stress than eukaryotic DNA. Therefore, the detection of large, experimental, ancient mycobacterial DNA fragments is a suitable approach for paleomicrobiological studies.

  11. Ancient DNA: Would the Real Neandertal Please Stand up?

    DEFF Research Database (Denmark)

    Cooper, Alan; Drummond, Alexei J.; Willerslev, Eske

    2004-01-01

    Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contri...

  12. GENERATION OF GEOMETRIC ORNAMENTS IN ANCIENT MOSAIC ART

    Directory of Open Access Journals (Sweden)

    SASS Ludmila

    2015-06-01

    Full Text Available The paper examines geometrical ornaments from ancient mosaic.We studied the geometric generation by using Computer Aided Graphics for three examples of ancient mosaic: a mosaic of Ancient Corinth, a mosaic of the sacred geometry Flower of Life (exposed in the National Museum of Israel and a mosaic of fortress Masada - Israel. The technique of drawing ancient mosaic is recomposed using computer aided graphics. A program has been developed that can help draw a petal-type arc (semicircle of the mosaic that is the Byzantine church of Masada. Based on these mosaics, other variants of aesthetic images in monochrome or black and white and polychrome were drawn, all of which can be materialized in decorative art to embellish various surfaces: walls, floors, pools, fountains, etc.

  13. Ancient origin and maternal inheritance of blue cuckoo eggs.

    Science.gov (United States)

    Fossøy, Frode; Sorenson, Michael D; Liang, Wei; Ekrem, Torbjørn; Moksnes, Arne; Møller, Anders P; Rutila, Jarkko; Røskaft, Eivin; Takasu, Fugo; Yang, Canchao; Stokke, Bård G

    2016-01-12

    Maternal inheritance via the female-specific W chromosome was long ago proposed as a potential solution to the evolutionary enigma of co-existing host-specific races (or 'gentes') in avian brood parasites. Here we report the first unambiguous evidence for maternal inheritance of egg colouration in the brood-parasitic common cuckoo Cuculus canorus. Females laying blue eggs belong to an ancient (∼2.6 Myr) maternal lineage, as evidenced by both mitochondrial and W-linked DNA, but are indistinguishable at nuclear DNA from other common cuckoos. Hence, cuckoo host races with blue eggs are distinguished only by maternally inherited components of the genome, which maintain host-specific adaptation despite interbreeding among males and females reared by different hosts. A mitochondrial phylogeny suggests that blue eggs originated in Asia and then expanded westwards as female cuckoos laying blue eggs interbred with the existing European population, introducing an adaptive trait that expanded the range of potential hosts.

  14. The last Viking King: a royal maternity case solved by ancient DNA analysis

    DEFF Research Database (Denmark)

    Dissing, Jørgen; Binladen, Jonas; Hansen, Anders

    2006-01-01

    Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases...... doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D...

  15. Aiding the Interpretation of Ancient Documents

    DEFF Research Database (Denmark)

    Roued-Cunliffe, Henriette

    How can Decision Support System (DSS) software aid the interpretation process involved in the reading of ancient documents? This paper discusses the development of a DSS prototype for the reading of ancient texts. In this context the term ‘ancient documents’ is used to describe mainly Greek...... tool it is important first to comprehend the interpretation process involved in reading ancient documents. This is not a linear process but rather a recursive process where the scholar moves between different levels of reading, such as ‘understanding the meaning of a character’ or ‘understanding...

  16. Complexities of Nitrogen Isotope Biogeochemistry in Plant-Soil Systems: Implications for the Study of Ancient Agricultural and Animal Management Practices

    Directory of Open Access Journals (Sweden)

    Paul eSzpak

    2014-06-01

    Full Text Available Nitrogen isotopic studies have potential to shed light on the structure of ancient ecosystems, agropastoral regimes, and human-environment interactions. Until relatively recently, however, little attention was paid to the complexities of nitrogen transformations in ancient plant-soil systems and their potential impact on plant and animal tissue nitrogen isotopic compositions. This paper discusses the importance of understanding nitrogen dynamics in ancient contexts, and highlights several key areas of archaeology where a more detailed understanding of these processes may enable us to answer some fundamental questions. This paper explores two larger themes that are prominent in archaeological studies using stable nitrogen isotope analysis: (1 agricultural practices (use of animal fertilizers, burning of vegetation or shifting cultivation, and tillage and (2 animal domestication and husbandry (grazing intensity/stocking rate and the foddering of domestic animals with cultigens. The paucity of plant material in ancient deposits necessitates that these issues are addressed primarily through the isotopic analysis of skeletal material rather than the plants themselves, but the interpretation of these data hinges on a thorough understanding of the underlying biogeochemical processes in plant-soil systems. Building on studies conducted in modern ecosystems and under controlled conditions, these processes are reviewed, and their relevance discussed for ancient contexts.

  17. Mitochondrial phylogenomics of modern and ancient equids.

    Science.gov (United States)

    Vilstrup, Julia T; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra C A; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K; Ovodov, Nikolai D; Clary, Joel; Helgen, Kristofer M; Fleischer, Robert C; Cooper, Alan; Shapiro, Beth; Orlando, Ludovic

    2013-01-01

    The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).

  18. Mitochondrial Phylogenomics of Modern and Ancient Equids

    Science.gov (United States)

    Vilstrup, Julia T.; Seguin-Orlando, Andaine; Stiller, Mathias; Ginolhac, Aurelien; Raghavan, Maanasa; Nielsen, Sandra C. A.; Weinstock, Jacobo; Froese, Duane; Vasiliev, Sergei K.; Ovodov, Nikolai D.; Clary, Joel; Helgen, Kristofer M.; Fleischer, Robert C.; Cooper, Alan; Shapiro, Beth; Orlando, Ludovic

    2013-01-01

    The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya). PMID:23437078

  19. Mitochondrial phylogenomics of modern and ancient equids.

    Directory of Open Access Journals (Sweden)

    Julia T Vilstrup

    Full Text Available The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga. Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya.

  20. Mitochondrial DNA from El Mirador cave (Atapuerca, Spain reveals the heterogeneity of Chalcolithic populations.

    Directory of Open Access Journals (Sweden)

    Daniel Gómez-Sánchez

    Full Text Available Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500-4,050 years BP out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760-4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

  1. The eye and its diseases in Ancient Egypt

    DEFF Research Database (Denmark)

    Andersen, S. Ry

    1997-01-01

    Ophthalmology, History of ophthalmology, eyes in the Ancient Egypt, eye disease in Ancient Egypt, porotic hyperostosis, mummification......Ophthalmology, History of ophthalmology, eyes in the Ancient Egypt, eye disease in Ancient Egypt, porotic hyperostosis, mummification...

  2. Molecular analysis of ancient caries

    Science.gov (United States)

    Simón, Marc; Montiel, Rafael; Smerling, Andrea; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A.; Jiménez-Marín, Andrea R.; Malgosa, Assumpció

    2014-01-01

    An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains. PMID:25056622

  3. Dwarfs in ancient Egypt.

    Science.gov (United States)

    Kozma, Chahira

    2006-02-15

    Ancient Egypt was one of the most advanced and productive civilizations in antiquity, spanning 3000 years before the "Christian" era. Ancient Egyptians built colossal temples and magnificent tombs to honor their gods and religious leaders. Their hieroglyphic language, system of organization, and recording of events give contemporary researchers insights into their daily activities. Based on the record left by their art, the ancient Egyptians documented the presence of dwarfs in almost every facet of life. Due to the hot dry climate and natural and artificial mummification, Egypt is a major source of information on achondroplasia in the old world. The remains of dwarfs are abundant and include complete and partial skeletons. Dwarfs were employed as personal attendants, animal tenders, jewelers, and entertainers. Several high-ranking dwarfs especially from the Old Kingdom (2700-2190 BCE) achieved important status and had lavish burial places close to the pyramids. Their costly tombs in the royal cemeteries and the inscriptions on their statutes indicate their high-ranking position in Egyptian society and their close relation to the king. Some of them were Seneb, Pereniankh, Khnumhotpe, and Djeder. There were at least two dwarf gods, Ptah and Bes. The god Ptah was associated with regeneration and rejuvenation. The god Bes was a protector of sexuality, childbirth, women, and children. He was a favored deity particularly during the Greco-Roman period. His temple was recently excavated in the Baharia oasis in the middle of Egypt. The burial sites and artistic sources provide glimpses of the positions of dwarfs in daily life in ancient Egypt. Dwarfs were accepted in ancient Egypt; their recorded daily activities suggest assimilation into daily life, and their disorder was not shown as a physical handicap. Wisdom writings and moral teachings in ancient Egypt commanded respect for dwarfs and other individuals with disabilities. Copyright (c) 2005 Wiley-Liss, Inc.

  4. Moessbauer studies on ancient pottery from a neolithic site in Tung Wan, Hong Kong

    International Nuclear Information System (INIS)

    Zheng Yufang; Tang Chung

    1994-01-01

    Twelve ceramic sherds unearthed from different archaeological layers at a neolithic site in Tung Wan, Hong Kong, were studied by means of X-ray diffraction (XRD) and Moessbauer spectroscopy. The results show that the firing techniques used for ancient pottery wares at different layers were very different. For the oldest sherds (4000-3000 B.C.) from layer No. 4, the original firing temperature was low and craftmanship was inferior. For the sherds (1650-250 B.C.) from layer No. 2, the original firing temperature was above 1000 C. In addition, the results indicate that the ancient pottery wares from the ruins might not have been manufactured in the Tung Wan region. (orig.)

  5. Three Thousand Years of Continuity in the Maternal Lineages of Ancient Sheep (Ovis aries) in Estonia

    Science.gov (United States)

    Rannamäe, Eve; Lõugas, Lembi; Speller, Camilla F.; Valk, Heiki; Maldre, Liina; Wilczyński, Jarosław; Mikhailov, Aleksandr; Saarma, Urmas

    2016-01-01

    Although sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mitochondrial hypervariable region in 115 ancient sheep from 71 sites in Estonia (c. 1200 BC–AD 1900s), 19 ancient samples from Latvia, Russia, Poland and Greece (6800 BC–AD 1700), as well as 44 samples of modern Kihnu native sheep breed. Our analyses revealed: (1) 49 mitochondrial haplotypes, associated with sheep haplogroups A and B; (2) high haplotype diversity in Estonian ancient sheep; (3) continuity in mtDNA haplotypes through time; (4) possible population expansion during the first centuries of the Middle Ages (associated with the establishment of the new power regime related to 13th century crusades); (5) significant difference in genetic diversity between ancient populations and modern native sheep, in agreement with the beginning of large-scale breeding in the 19th century and population decline in local sheep. Overall, our results suggest that in spite of the observed fluctuations in ancient sheep populations, and changes in the natural and historical conditions, the utilisation of local sheep has been constant in the territory of Estonia, displaying matrilineal continuity from the Middle Bronze Age through the Modern Period, and into modern native sheep. PMID:27732668

  6. Ancient analogues concerning stability and durability of cementitious wasteform

    International Nuclear Information System (INIS)

    Jiang, W.; Roy, D.M.

    1994-01-01

    The history of cementitious materials goes back to ancient times. The Greeks and Romans used calcined limestone and later developed pozzolanic cement by grinding together lime and volcanic ash called open-quotes pozzolanclose quotes which was first found near Port Pozzuoli, Italy. The ancient Chinese used lime-pozzolanic mixes to build the Great Wall. The ancient Egyptians used calcined impure gypsum to build the Great Pyramid of Cheops. The extraordinary stability and durability of these materials has impressed us, when so much dramatically damaged infrastructure restored by using modern portland cement now requires rebuilding. Stability and durability of cementitious materials have attracted intensive research interest and contractors' concerns, as does immobilization of radioactive and hazardous industrial waste in cementitious materials. Nuclear waste pollution of the environment and an acceptable solution for waste management and disposal constitute among the most important public concerns. The analogy of ancient cementitious materials to modern Portland cement could give us some clues to study their stability and durability. This present study examines selected results of studies of ancient building materials from France, Italy, China, and Egypt, combined with knowledge obtained from the behavior of modern portland cement to evaluate the potential for stability and durability of such materials in nuclear waste forms

  7. Ancient Egyptian Medicine: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Samuel Adu-Gyamfi

    2015-12-01

    Full Text Available Our present day knowledge in the area of medicine in Ancient Egypt has been severally sourced from medical papyri several of which have been deduced and analyzed by different scholars. For educational purposes it is always imperative to consult different literature or sources in the teaching of ancient Egypt and medicine in particular. To avoid subjectivity the author has found the need to re-engage the efforts made by several scholars in adducing evidences from medical papyri. In the quest to re-engage the efforts of earlier writers and commentaries on the medical papyri, we are afforded the opportunity to be informed about the need to ask further questions to enable us to construct or reconstruct both past and modern views on ancient Egyptian medical knowledge. It is this vocation the author sought to pursue in the interim, through a preliminary review, to highlight, comment and reinvigorate in the reader or researcher the need for a continuous engagement of some pertinent documentary sources on Ancient Egyptian medical knowledge for educational and research purposes. The study is based on qualitative review of published literature. The selection of those articles as sources was based on the focus of the review, in order to purposively select and comment on articles that were published based either on information from a medical papyrus or focused on medical specialization among the ancient Egyptians as well as ancient Egyptian knowledge on diseases and medicine. It was found that the Egyptians developed relatively sophisticated medical practices covering significant medical fields such as herbal medicine, gynecology and obstetrics, anatomy and physiology, mummification and even the preliminary form of surgery. These practices, perhaps, were developed as remedies for the prevailing diseases and the accidents that might have occurred during the construction of their giant pyramids. It must be stated that they were not without flaws. Also, the

  8. Genetic polymorphisms in prehistoric Pacific islanders determined by analysis of ancient bone DNA.

    Science.gov (United States)

    Hagelberg, E; Clegg, J B

    1993-05-22

    A previously characterized Asian-specific mitochondrial DNA (mtDNA) length mutation has been detected in DNA isolated from prehistoric human bones from Polynesia, including Hawaii, Chatham Islands and Society Islands. In contrast, the Asian mutation was absent in skeletal samples from the Melanesian archipelagos of New Britain and Vanuatu and in the oldest samples from Fiji, Tonga and Samoa in the central Pacific (2700-1600 years BP) although it was present in a more recent prehistoric sample from Tonga. These results, augmented by informative DNA sequence data from the hypervariable region of mtDNA, fail to support current views that the central Pacific was settled directly by voyagers from island Southeast Asia, the putative ancestors of modern Polynesians. An earlier occupation by peoples from the neighbouring Melanesian archipelagos seems more likely.

  9. Mortar alteration: experimental study and ancient analogues

    International Nuclear Information System (INIS)

    Rassineux, Francois

    1987-01-01

    As the durability of cemented matrices is a matter of great importance in numerous domains, notably for the long term reliability of surface storages of radioactive wastes, the objective of this research thesis is to define mechanisms of evolution of cemented matrices when in contact with diluted aqueous solutions. The author notably studied the influence of the lixiviation mode on the evolution of two mortars having different compositions (pH, CO 2 pressure, system containment, and cement mineralogical nature appear to be the main governing parameters), the alteration (dissolution is the prevailing process in the interaction between cemented matrices and a diluted solution such as rain water), and ancient binders (archaeological binders containing mineral phases such as hydrated calcium silicates or hydro-grossulars). The obtained results lead to the definition of alteration mechanisms in modern cements, and highlight factors governing the durability of these materials when submitted to meteoric alteration [fr

  10. Is the ancient permafrost bacteria able to keep DNA stable?

    Indian Academy of Sciences (India)

    Navya

    nucleotide substitutions per nucleotide site per year for mitochondrial DNA. DISCUSSION ... Despite the nature of mutations, we think the degree of variability in mutation rates is still an ..... Saccharomyces cerevisiae. Microbiology. 150 ...

  11. Ancient and Current Chaos Theories

    Directory of Open Access Journals (Sweden)

    Güngör Gündüz

    2006-07-01

    Full Text Available Chaos theories developed in the last three decades have made very important contributions to our understanding of dynamical systems and natural phenomena. The meaning of chaos in the current theories and in the past is somewhat different from each other. In this work, the properties of dynamical systems and the evolution of chaotic systems were discussed in terms of the views of ancient philosophers. The meaning of chaos in Anaximenes’ philosophy and its role in the Ancient natural philosophy has been discussed in relation to other natural philosophers such as of Anaximander, Parmenides, Heraclitus, Empedocles, Leucippus (i.e. atomists and Aristotle. In addition, the fundamental concepts of statistical mechanics and the current chaos theories were discussed in relation to the views in Ancient natural philosophy. The roots of the scientific concepts such as randomness, autocatalysis, nonlinear growth, information, pattern, etc. in the Ancient natural philosophy were investigated.

  12. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    Science.gov (United States)

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Ancient humans and the origin of modern humans.

    Science.gov (United States)

    Kelso, Janet; Prüfer, Kay

    2014-12-01

    Recent advances in sequencing technologies and molecular methods have facilitated the sequencing of DNA from ancient human remains which has, in turn, provided unprecedented insight into human history. Within the past 4 years the genomes of Neandertals and Denisovans, as well as the genomes of at least two early modern humans, have been sequenced. These sequences showed that there have been several episodes of admixture between modern and archaic groups; including admixture from Neandertals into modern human populations outside of Africa, and admixture from Denisovans into modern human populations in Oceania. Recent results indicate that some of these introgressed regions may have been advantageous for modern humans as they expanded into new regions outside of Africa. Copyright © 2014. Published by Elsevier Ltd.

  14. Study on distinguishing of Chinese ancient porcelains by neutron activation and fuzzy cluster analysis

    International Nuclear Information System (INIS)

    Wang An

    1992-01-01

    By means of the method of neutron activation, the contents of trace elements in some samples of Chinese ancient porcelains from different places of production were determined. The data were analysed by fuzzy cluster analysis. On the basis of the above mentioned works, a method with regard to the distinguishing and determining of Chinese ancient porcelain was suggested

  15. Thermoluminescence and X-ray diffraction studies on sliced ancient porcelain samples

    International Nuclear Information System (INIS)

    Leung, P.L.; Yang, B.

    1999-01-01

    The thermal activation characteristics (TACs) of the sensitivity of the '110 deg. C' peak in 14 sliced ancient Chinese porcelain samples are studied. Comparing with the TACs of natural quartz and synthetic mullite, the relation between the TACs and the composition of the sample is discussed with reference to the X-ray diffraction (XRD) spectra. It is suggested that in some cases, contribution of the porcelain components other than quartz to the TACs is not negligible

  16. Thermoluminescence and X-ray diffraction studies on sliced ancient porcelain samples

    Energy Technology Data Exchange (ETDEWEB)

    Leung, P.L.; Yang, B. E-mail: yangbr@bnu.edu.cn

    1999-09-01

    The thermal activation characteristics (TACs) of the sensitivity of the '110 deg. C' peak in 14 sliced ancient Chinese porcelain samples are studied. Comparing with the TACs of natural quartz and synthetic mullite, the relation between the TACs and the composition of the sample is discussed with reference to the X-ray diffraction (XRD) spectra. It is suggested that in some cases, contribution of the porcelain components other than quartz to the TACs is not negligible.

  17. Thermoluminescence and X-ray diffraction studies on sliced ancient porcelain samples

    Science.gov (United States)

    Leung, P. L.; Yang, B.

    1999-09-01

    The thermal activation characteristics (TACs) of the sensitivity of the '110°C' peak in 14 sliced ancient Chinese porcelain samples are studied. Comparing with the TACs of natural quartz and synthetic mullite, the relation between the TACs and the composition of the sample is discussed with reference to the X-ray diffraction (XRD) spectra. It is suggested that in some cases, contribution of the porcelain components other than quartz to the TACs is not negligible.

  18. Radiocarbon dating of ancient Japanese documents

    International Nuclear Information System (INIS)

    Oda, H.

    2001-01-01

    History is a reconstruction of past human activity, evidence of which is remained in the form of documents or relics. For the reconstruction of historic period, the radiocarbon dating of ancient documents provides important information. Although radiocarbon age is converted into calendar age with the calibration curve, the calibrated radiocarbon age is still different from the historical age when the document was written. The difference is known as 'old wood effect' for wooden cultural property. The discrepancy becomes more serious problem for recent sample which requires more accurate age determination. Using Tandetron accelerator mass spectrometer at Nagoya University, we have measured radiocarbon ages of Japanese ancient documents, sutras and printed books written dates of which are clarified from the paleographic standpoint. The purpose is to clarify the relation between calibrated radiocarbon age and historical age of ancient Japanese document by AMS radiocarbon dating. This paper reports 23 radiocarbon ages of ancient Japanese documents, sutras and printed books. The calibrated radiocarbon ages are in good agreement with the corresponding historical ages. It was shown by radiocarbon dating of the ancient documents that Japanese paper has little gap by 'old wood effect'; accordingly, ancient Japanese paper is a suitable sample for radiocarbon dating of recent historic period. (author)

  19. The History and Practice of Ancient Astronomy

    CERN Document Server

    Evans, James

    1998-01-01

    The History and Practice of Ancient Astronomy combines new scholarship with hands-on science to bring readers into direct contact with the work of ancient astronomers. While tracing ideas from ancient Babylon to sixteenth-century Europe, the book places its greatest emphasis on the Greek period, when astronomers developed the geometric and philosophical ideas that have determined the subsequent character of Western astronomy. The author approaches this history through the concrete details of ancient astronomical practice. Carefully organized and generously illustrated, the book can teach reade

  20. Application of nuclear analysis techniques in ancient chinese porcelain

    International Nuclear Information System (INIS)

    Feng Songlin; Xu Qing; Feng Xiangqian; Lei Yong; Cheng Lin; Wang Yanqing

    2005-01-01

    Ancient ceramic was fired with porcelain clay. It contains various provenance information and age characteristic. It is the scientific foundation of studying Chinese porcelain to analyze and research the ancient ceramic with modern analysis methods. According to the property of nuclear analysis technique, its function and application are discussed. (authors)

  1. An investigation into the ancient abortion laws: comparing ancient Persia with ancient Greece and Rome.

    Science.gov (United States)

    Yarmohammadi, Hassan; Zargaran, Arman; Vatanpour, Azadeh; Abedini, Ehsan; Adhami, Siamak

    2013-01-01

    Since the dawn of medicine, medical rights and ethics have always been one of mankind's concerns. In any civilisation, attention paid to medical laws and ethics depends on the progress of human values and the advancement of medical science. The history of various civilisations teaches that each had its own views on medical ethics, but most had something in common. Ancient civilisations such as Greece, Rome, or Assyria did not consider the foetus to be alive and therefore to have human rights. In contrast, ancient Persians valued the foetus as a living person equal to others. Accordingly, they brought laws against abortion, even in cases of sexual abuse. Furthermore, abortion was considered to be a murder and punishments were meted out to the mother, father, and the person performing it.

  2. The Ancient Greece's roots of Olimpism

    Directory of Open Access Journals (Sweden)

    Bubka Sergej Nazarovich

    2011-10-01

    Full Text Available The paper focused on the phenomena of sport in Ancient Greece along with history, traditions, religion, education, culture and art. Economic and political conditions are analysed which promote or hamper development of Olympic Games in Ancient Greece. Exceptional stability of Ancient Olympic games during more than eleven centuries are noted as well as their influence on the life of Greek polices of those days. Hellenistic period needs of individual consideration.

  3. Suicide in ancient Greece.

    Science.gov (United States)

    Laios, K; Tsoukalas, G; Kontaxaki, M-I; Karamanou, M; Androutsos, G

    2014-01-01

    The theme of suicide appears several times in ancient Greek literature. However, each such reference acquires special significance depending on the field from which it originates. Most of the information found in mythology, but the suicide in a mythological tale, although in terms of motivation and mental situation of heroes may be in imitation of similar incidents of real life, in fact is linked with the principles of the ancient Greek religion. In ancient drama and mainly in tragedies suicide conduces to the tragic hypostasis of the heroes and to the evolution of the plot and also is a tool in order to be presented the ideas of poets for the relations of the gods, the relation among gods and men and the relation among the men. In ancient Greek philosophy there were the deniers of suicide, who were more concerned about the impact of suicide on society and also these who accepted it, recognizing the right of the individual to put an end to his life, in order to avoid personal misfortunes. Real suicides will be found mostly from historical sources, but most of them concern leading figures of the ancient world. Closer to the problem of suicide in the everyday life of antiquity are ancient Greek medicines, who studied the phenomenon more general without references to specific incidents. Doctors did not approve in principal the suicide and dealt with it as insane behavior in the development of the mental diseases, of melancholia and mania. They considered that the discrepancy of humors in the organ of logic in the human body will cause malfunction, which will lead to the absurdity and consequently to suicide, either due to excessive concentration of black bile in melancholia or due to yellow bile in mania. They believed that greater risk to commit suicide had women, young people and the elderly. As therapy they used the drugs of their time with the intention to induce calm and repression in the ill person, therefore they mainly used mandragora. In general, we would say

  4. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years

    DEFF Research Database (Denmark)

    Melchior, Linea; Kivisild, Toomas; Lynnerup, Niels

    2008-01-01

    -PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained...

  5. Ancient Egypt in our Cultural Heritage?

    Directory of Open Access Journals (Sweden)

    Vera Vasiljević

    2016-02-01

    Full Text Available Inspiration derived from ancient Egypt is usually expressed through the Egyptian motifs in arts and popular culture of the 19th and 20th centuries, as well as through the non-scientific interpretations of the culture, very much based upon the Renaissance ones. The number and variety of material and non-material traces of this fascination are most expressed in the countries where, along with the early support for the institutional development of Egyptology, there existed economically potent educated middle classes (Western and Central Europe, USA, but may also be traced elsewhere. The public fascination by ancient Egypt has not ceased by the times of foundation of Egyptology, marked by the decipherment of the hieroglyphic script in 1822. Until the end of the 20th century Egyptologists have rarely dealt with the prelude to their discipline, limiting their interest to the critical approach to ancient sources and to noting the attempts to interpret the hieroglyphic script and the function of pyramids. However, the rising importance of the reception studies in other disciplines raised the interest of Egyptologists for the "fascination of Egypt", thus changing the status of various modes of expressing "Egyptomania" – they have thus become a part of the cultural heritage, registered, documented, preserved and studied. The research of this kind is only beginning in Serbia. The line of inquiry enhances the knowledge of the scope, manifestations and roles of the interest in Egypt, not limited by the national or political borders. On the other hand, the existence of the cultural heritage similar to the wider European view of ancient Egypt – short remarks by Jerotej Račanin, Kandor by Atanasije Stojković, the usage of architectural motifs derived from Egypt, the emergence of small private collections, to mention several early examples – all show that the research into the reception of ancient Egypt may contribute to the knowledge about the history

  6. Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice.

    Directory of Open Access Journals (Sweden)

    Alice Beau

    Full Text Available In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment. If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace. At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i the occidental origin of the Michelsberg groups and (ii the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

  7. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  8. AN INTERESTING CASE OF ANCIENT SCHWANNOMA

    Directory of Open Access Journals (Sweden)

    Binu

    2015-01-01

    Full Text Available INTRODUCTION : Schwannoma is a common benign tumour of nerve sheath. Degenerating type of schwannoma is called ancient schwannoma. Ancient schwannomas of scalp are rare and are often misdiagnosed as sebaceous cyst or dermoid cyst. CASE REPORT : We present a thirty two year old male presented with scalp swel ling of eight years duration. X - ray showed no intracranial extension. He underwent excision of the tumour and histopathology was reported as ancient schwannoma. DISCUSSION : Histopathologically , ancient schwannomas charecterised by cellular Antoni type A ar eas and less cellular Antoni type - B areas. 9 th , 7 th , 11 th , 5 th and 4 th cranial nerves are often affected and may be associated with multiple neuro fibramatosis (Von - Recklinghausen’s disease. Impact : Case is presented for its rarity and possible pre - operative misdiagnosis

  9. Is the ancient permafrost bacteria able to keep DNA stable?

    Indian Academy of Sciences (India)

    lated strains was extracted by using a Fast DNA kit for soil (BIO 101, Vista, USA) based .... lites, but its movement is extremely slow (Burt and Williams. 1976). A bacterium of ... Despite the nature of mutations, we think the degree of variability in ...

  10. Anthropology. Response to Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

    Science.gov (United States)

    Kemp, Brian M; Lindo, John; Bolnick, Deborah A; Malhi, Ripan S; Chatters, James C

    2015-02-20

    Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations. Copyright © 2015, American Association for the Advancement of Science.

  11. Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina).

    Science.gov (United States)

    Carnese, Fransisco R; Mendisco, Fanny; Keyser, Christine; Dejean, Cristina B; Dugoujon, Jean-Michel; Bravi, Claudio M; Ludes, Bertrand; Crubézy, Eric

    2010-03-01

    Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans).

  12. [Herbological study of the botanical origin of Chinese crude drugs "Du-hua" and "Qiang-hua" in ancient China].

    Science.gov (United States)

    Mikage, Masayuki; Ochimori, Akane

    2007-01-01

    The Chinese crude drug Qiang-hua was listed as an alias of Du-hua in Shen-nong-ben-cao-jing, an herbal journal written during the Han Dynasty, China. Du-hua and Qiang-hua are recognized as different herbs in China these days; the main botanical origin of Du-hua is Angelica spp. and that of Qiang-hua is Notopterygium spp., of the family Umbelliferae. To make clear the botanical origins of Du-hua and Qiang-hua in ancient China, the authors made a herbological study. The findings were as follows: the name of Qiang-hua was given to the genuine Du-hua, which is produced in Qiang Province, an ancient province located in northwest China; the botanical origin of Qiang-hua is presumed to be Notopterygium incisum Ting ex H.T. Chang and N. forbesii Boissieu based on both the morphology and habitat written in ancient herbal journals. Both species are prescribed as having the plant origin of Qiang-hua in the present Chinese Pharmacopoeia. Therefore, we concluded that Du-hua and Qiang-hua were essentially the same drug, and were originally derived from the Notopterygium species in ancient China.

  13. Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle

    NARCIS (Netherlands)

    Gargani, Maria; Pariset, Lorraine; Lenstra, Johannes A; De Minicis, Elisabetta; Valentini, Alessio

    2015-01-01

    Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations.

  14. Second-harmonic generation imaging of collagen in ancient bone.

    Science.gov (United States)

    Thomas, B; McIntosh, D; Fildes, T; Smith, L; Hargrave, F; Islam, M; Thompson, T; Layfield, R; Scott, D; Shaw, B; Burrell, C L; Gonzalez, S; Taylor, S

    2017-12-01

    Second-harmonic generation imaging (SHG) captures triple helical collagen molecules near tissue surfaces. Biomedical research routinely utilizes various imaging software packages to quantify SHG signals for collagen content and distribution estimates in modern tissue samples including bone. For the first time using SHG, samples of modern, medieval, and ice age bones were imaged to test the applicability of SHG to ancient bone from a variety of ages, settings, and taxa. Four independent techniques including Raman spectroscopy, FTIR spectroscopy, radiocarbon dating protocols, and mass spectrometry-based protein sequencing, confirm the presence of protein, consistent with the hypothesis that SHG imaging detects ancient bone collagen. These results suggest that future studies have the potential to use SHG imaging to provide new insights into the composition of ancient bone, to characterize ancient bone disorders, to investigate collagen preservation within and between various taxa, and to monitor collagen decay regimes in different depositional environments.

  15. Study on Anti-seismic Strengthening of the Ancient Stone Archway

    Directory of Open Access Journals (Sweden)

    Zhang Ding

    2016-01-01

    Full Text Available Chinese ancient stone archways are in flat structure. And joints of their members are of half tenons and mortises. Under the influence of the earthquake, the resisting ability of archway’s uneven sides is relatively poor and the relevant members have little reliable joints. This paper is to analyze seismic strengthening feasibility of Tiantai mountain stone archway which is damaged from the earthquake and to research on the aspects of the loading mode, structure layout and soundness. On the premise of guaranteeing the authenticity and beauty, we use earthquake damaging mechanism of stone archways and the modern anti-seismic structure designing theory and modern building materials. We also follow the way of the modern construction technology and ancient construction and strengthen the anti-seismic way of the resisting ability of Tiantai mountain stone archway’s uneven sides and joints of tenons and mortises. The best anti-seismic strengthening schemes are put forward as well.

  16. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

    Science.gov (United States)

    Moody, Michael L; Rieseberg, Loren H

    2012-07-01

    The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

  17. Trepanation in Ancient China.

    Science.gov (United States)

    Hobert, Leah; Binello, Emanuela

    2017-05-01

    Trepanation, the process of making a burr hole in the skull to access the brain, is an ancient form of a primitive craniotomy. There is widespread evidence of contributions made to this practice by ancient civilizations in Europe, Africa, and South America, where archaeologists have unearthed thousands of trepanned skulls dating back to the Neolithic period. Little is known about trepanation in China, and it is commonly believed that the Chinese used only traditional Chinese medicine and nonsurgical methods for treating brain injuries. However, a thorough analysis of the available archeological and literary evidence reveals that trepanation was widely practiced throughout China thousands of years ago. A significant number of trepanned Chinese skulls have been unearthed showing signs of healing and suggesting that patients survived after surgery. Trepanation was likely performed for therapeutic and spiritual reasons. Medical and historical works from Chinese literature contain descriptions of primitive neurosurgical procedures, including stories of surgeons, such as the legendary Hua Tuo, and surgical techniques used for the treatment of brain pathologies. The lack of translation of Chinese reports into the English language and the lack of publications on this topic in the English language may have contributed to the misconception that ancient China was devoid of trepanation. This article summarizes the available evidence attesting to the performance of successful primitive cranial surgery in ancient China. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. The TL dating of ancient porcelain

    International Nuclear Information System (INIS)

    Leung, P.L.; Stokes, M.J.; Wang Weida; Xia Junding; Zhou Zhixin

    1997-01-01

    The age determination of ancient porcelain using the pre-dose technique in TL dating was reported. The variation of beta dose with depth below the surface of the porcelain slice, the thermal activation characteristic (TAC) for 110 degree C peak, the measurement of paleodose and the estimation of annual dose were studied. The results show that this technique is suitable for authenticity testing of ancient porcelain, but both accuracy and precision for porcelain dating are worse than those for pottery, because porcelain differs from pottery on composition, structure and firing temperature. Besides, some complicated factors in the pre-dose technique would be the possible cause of the greater errors

  19. Linen in Ancient Egypt

    Directory of Open Access Journals (Sweden)

    dr.Rehab Mahmoud Ahmed Elsharnouby

    2014-01-01

    Full Text Available Egypt was famous through the Ancient Near East for both weaving linen cloth and the produced quantities. Cloth was sent as expensive gifts from one king to another and given to a laborer as wages in return for his work. Cloth was regarded as an essential element in everyday life as it could be used for everything: clothing, bedding, trappings for animals, or sails of a ship. It was in fact one of the most widely used item throughout Ancient Egypt. Although other textile fibers were used in Pharaonic Egypt, namely, sheep's wool, goat hair and a form of coir, the majority of textiles were made from the plant Linum usitatissimum, flax. Cloth made from this fiber is defined as linen. The research starts with a brief definition of the flax, and then reviews the scenes representing the sowing and the harvesting of its seeds. It also focuses on the way of removing the seeds heads, the preparing of the flax for spinning: retting, beating and scutching. After that, it deals with transforming flax into orderly lengths, and rolling it into balls or coils. The researcher as well studies the Ancient Egyptian spinning techniques: grasped spindle, support spindle and drop spinning; the different types of weaving: tabby weaves, basket weaves, tapestry weaves and warps-patterned weave and the types of looms that were in use in Egypt, namely, the horizontal and vertical looms.

  20. Endocrinology in ancient Sparta.

    Science.gov (United States)

    Tsoulogiannis, Ioannis N; Spandidos, Demetrios A

    2007-01-01

    This article attempts to analyze the crucial link between the plant Agnus castus and human health, particularly hormonal status, with special reference to the needs of the society of ancient Sparta. The ancient Spartans used Agnus both as a cure for infertility and as a remedy to treat battle wounds. These special properties were recognized by the sanctuary of Asclepios Agnita, which was located in Sparta, as well as by medical practitioners in Sparta during the classical, Hellenistic and Roman ages.

  1. Ancient Human Parasites in Ethnic Chinese Populations.

    Science.gov (United States)

    Yeh, Hui-Yuan; Mitchell, Piers D

    2016-10-01

    Whilst archaeological evidence for many aspects of life in ancient China is well studied, there has been much less interest in ancient infectious diseases, such as intestinal parasites in past Chinese populations. Here, we bring together evidence from mummies, ancient latrines, and pelvic soil from burials, dating from the Neolithic Period to the Qing Dynasty, in order to better understand the health of the past inhabitants of China and the diseases endemic in the region. Seven species of intestinal parasite have been identified, namely roundworm, whipworm, Chinese liver fluke, oriental schistosome, pinworm, Taenia sp. tapeworm, and the intestinal fluke Fasciolopsis buski . It was found that in the past, roundworm, whipworm, and Chinese liver fluke appear to have been much more common than the other species. While roundworm and whipworm remained common into the late 20th century, Chinese liver fluke seems to have undergone a marked decline in its prevalence over time. The iconic transport route known as the Silk Road has been shown to have acted as a vector for the transmission of ancient diseases, highlighted by the discovery of Chinese liver fluke in a 2,000 year-old relay station in northwest China, 1,500 km outside its endemic range.

  2. Views of Ancient Egypt. Teacher's Guide. School Arts: Looking/Learning.

    Science.gov (United States)

    Downs, Linda; Brenner, Carla

    This teaching guide discusses ancient Egyptian culture, the lithographs made by Napoleon's scientists in 1798-99 to study and record every aspect of Egypt, the world's subsequent fascination with Egypt, ancient Egyptian architecture, Egyptian writing, and archeologists' illustrations of Egypt. The guide suggests activities for elementary school,…

  3. DNA:DNA hybridization studies on the pink-pigmented facultative methylotrophs.

    Science.gov (United States)

    Hood, D W; Dow, C S; Green, P N

    1987-03-01

    The genomic relatedness among 36 strains of pink-pigmented facultatively methylotrophic bacteria (PPFMs) was estimated by determination of DNA base composition and by DNA:DNA hybridization studies. A reproducible hybridization system was developed for the rapid analysis of multiple DNA samples. Results indicated that the PPFMs comprise four major and several minor homology groups, and that they should remain grouped in a single genus, Methylobacterium.

  4. Health benefits of ancient grains. Comparison among bread made with ancient, heritage and modern grain flours in human cultured cells.

    Science.gov (United States)

    Valli, Veronica; Taccari, Annalisa; Di Nunzio, Mattia; Danesi, Francesca; Bordoni, Alessandra

    2018-05-01

    Nowadays the higher nutritional value of whole grains compared to refined grains is recognized. In the last decade, there has been a renewed interest in the ancient wheat varieties for producing high-value food products with enhanced health benefits. This study compared two ancient grains, two heritage grains, and four modern grains grown in the same agronomic conditions considering not only their chemical characteristics, but also their biological effects. Whole grain flours were obtained and used to make bread. Bread was in vitro digested, the digesta were supplemented to HepG2 cells, and the biological effects of supplementation were evaluated. In addition, cells previously supplemented with the different digested bread types were then exposed to inflammatory agents to evidence possible protective effects of the pre-treatments. Despite the impossibility to discriminate bread made with different grains based on their chemical composition, results herein reported evidence that their supplementation to cultured cells exerts different effects, confirming the potential health benefits of ancient grains. This research represents an advancement for the evaluation of the apparent positive effects of ancient grains and the formulation of cereal-based products with added nutritional value. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Dreams in ancient Greek Medicine.

    Science.gov (United States)

    Laios, K; Moschos, M M; Koukaki, E; Vasilopoulos, E; Karamanou, M; Kontaxaki, M-I; Androutsos, G

    2016-01-01

    Dreams preoccupied the Greek and Roman world in antiquity, therefore they had a prominent role in social, philosophical, religious, historical and political life of those times. They were considered as omens and prophetic signs of future events in private and public life, and that was particularly accentuated when elements of actions which took place in the plot of dreams were associated directly or indirectly with real events. This is why it was important to use them in divination, and helped the growth of superstition and folklore believes. Medicine as a science and an anthropocentric art, could not ignore the importance of dreams, having in mind their popularity in antiquity. In ancient Greek medicine dreams can be divided into two basic categories. In the first one -which is related to religious medicine-dreams experienced by religionists are classified, when resorted to great religious sanctuaries such as those of Asclepius (Asclepieia) and Amphiaraos (Amfiaraeia). These dreams were the essential element for healing in this form of religious medicine, because after pilgrims underwent purifications they went to sleep in a special dwelling of the sanctuaries called "enkoimeterion" (Greek: the place to sleep) so that the healing god would come to their dreams either to cure them or to suggest treatment. In ancient Greek literature there are many reports of these experiences, but if there may be phenomena of self-suggestion, or they could be characterized as propaganda messages from the priesthood of each sanctuary for advertising purposes. The other category concerns the references about dreams found in ancient Greek medical literature, where one can find the attempts of ancient Greek physicians to interpret these dreams in a rational way as sings either of a corporal disease or of psychological distress. This second category will be the object of our study. Despite the different ways followed by each ancient Greek physician in order to explain dreams, their

  6. Archaeological Studies of the Ancient Turkestan Site: results of 2011-2012 excavations

    Directory of Open Access Journals (Sweden)

    Smagulov Yerbulat A.

    2013-03-01

    Full Text Available The results of the 2011-12 excavations on the Eski-Turkestan site conducted by the Turkestani archaeological expedition (Institute of archaeology named after A. Margulan are presented. The site contains the remains of the ancient town of Yasy (modern town of Turkestan, South Kazakhstan oblast. The aim of the excavations was to study the earliest layers of the settlement, the primary stages of the city formation, and to identify construction elements of the ancient citadel in particular. It has been established that the most ancient nucleus of the city was located under Kultobe hill on the eastern edge of the settlement. The oldest architectural object of the citadel is a cruciform construction with powerful rammed clay defensive walls having narrow loopholes, preserved to a height of over 3 m. The three rooms were connected by arched doorways. In the second construction horizon, a building with long narrow rooms around a small open courtyard had been added to this "castle". During this period, around the perimeter of the citadel powerful rammed clay and mud-brick defensive walls had been erected, with the space between them and the extended castle being just partially built up. These two periods can be dated to the 1st–3rd centuries AD. This stage comes to an end with defeat and a fire. In the fire layer, numerous ceramic vessels in disassembling have been found. Individual unique finds have been made, and alabaster idols are of special interest. The restoration of the fortification wall and a new stage of the citadel development refer to the 9th-11th centuries. At the base of the new wall, pots with sacrificial food have been discovered, one of them bearing a runic inscription.

  7. Second-harmonic generation imaging of collagen in ancient bone

    Directory of Open Access Journals (Sweden)

    B. Thomas

    2017-12-01

    Full Text Available Second-harmonic generation imaging (SHG captures triple helical collagen molecules near tissue surfaces. Biomedical research routinely utilizes various imaging software packages to quantify SHG signals for collagen content and distribution estimates in modern tissue samples including bone. For the first time using SHG, samples of modern, medieval, and ice age bones were imaged to test the applicability of SHG to ancient bone from a variety of ages, settings, and taxa. Four independent techniques including Raman spectroscopy, FTIR spectroscopy, radiocarbon dating protocols, and mass spectrometry-based protein sequencing, confirm the presence of protein, consistent with the hypothesis that SHG imaging detects ancient bone collagen. These results suggest that future studies have the potential to use SHG imaging to provide new insights into the composition of ancient bone, to characterize ancient bone disorders, to investigate collagen preservation within and between various taxa, and to monitor collagen decay regimes in different depositional environments.

  8. Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains.

    Science.gov (United States)

    Gould, Billie A; León, Blanca; Buffen, Aron M; Thompson, Lonnie G

    2010-09-01

    Around the world, tropical glaciers and ice caps are retreating at unprecedented rates because of climate change. In at least one location, along the margin of the Quelccaya Ice Cap in southeastern Peru, ancient plant remains have been continually uncovered since 2002. We used genetic analysis to identify plants that existed at these sites during the mid-Holocene. • We examined remains between 4576 and 5222 yr old, using PCR amplification, cloning, and sequencing of a fragment of the chloroplast trnL intron. We then matched these sequences to sequences in GenBank. • We found evidence of at least five taxa characteristic of wetlands, which occur primarily at lower elevations in the region today. • A diverse community most likely existed at these locations the last time they were ice-free and thus has the potential to reestablish with time. This is the first genetic analysis of vegetation uncovered by receding glacial ice, and it may become one of many as ancient plant materials are newly uncovered in a changing climate.

  9. Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon.

    Science.gov (United States)

    Paffetti, Donatella; Vettori, Cristina; Caramelli, David; Vernesi, Cristiano; Lari, Martina; Paganelli, Arturo; Paule, Ladislav; Giannini, Raffaello

    2007-08-16

    Phylogeographic analyses on the Western Euroasiatic Fagus taxa (F. orientalis, F. sylvatica, F. taurica and F. moesiaca) is available, however, the subdivision of Fagus spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of Fagus Eurasiatic taxa. For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the Fagus spp. present during the Last Interglacial period in Italy. In this work we aim at testing if the trnL-trnF chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different Quercus taxa, can be employed in distinguishing the Fagus species and in identifying the ancient pollen. 86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the trnL-trnF region to verify the efficiency of this cpDNA region in identifying the Fagus spp.. Furthermore, Fagus crenata (2 populations), Fagus grandifolia (2 populations), Fagus japonica, Fagus hayatae, Quercus species and Castanea species were analysed to better resolve the phylogenetic inference. Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different Fagus species. Considering a short fragment of 176 base pairs within the trnL intron, 2 transversions were found able in distinguishing the F. orientalis complex taxa (F. orientalis, F. taurica and F. moesiaca) from the remaining Fagus spp. (F. sylvatica, F. japonica, F. hayataea, F. crenata and F. grandifolia). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded. The sequences data indicate that the DNA recovered from ancient pollen belongs to the F. orientalis complex since

  10. Provenance study of ancient Chinese Yaozhou porcelain by neutron activation analysis

    International Nuclear Information System (INIS)

    Li, R.W.; Zhao, W.J.; Li, G.X.; Xie, J.Z.; Guo, M.; Gao, Z.Y.; Feng, S.L.; Fan, D.Y.; Zhang, Y.; Cai, Z.F.; Zhuo, Z.X.

    2004-01-01

    The glaze samples of ancient Chinese Yaozhou porcelain were analyzed by neutron activation analysis (NAA). The contents of 29 elements for each sample were measured. the scattergram of the coloring elements shows some informations of soueces of raw materials. (authors)

  11. Lake Tanganyika--a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae?

    Directory of Open Access Journals (Sweden)

    Juliane D Weiss

    Full Text Available A long history of research focused on the East Africa cichlid radiations (EAR revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika ("ancient mouthbrooders" was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor

  12. Ancient Chinese literature reveals pathways of eggplant domestication.

    Science.gov (United States)

    Wang, Jin-Xiu; Gao, Tian-Gang; Knapp, Sandra

    2008-12-01

    Changes in key traits occurring during the processes of plant domestication have long been subjects of debate. Only in the case of genetic analysis or with extensive plant remains can specific sets of changes be documented. Historical details of the plant domestication processes are rare and other evidence of morphological change can be difficult to obtain, especially for those vegetables that lack a substantial body of archaeological data. Botanical records chronicled in the ancient literature of established ancient civilizations, such as that of China, are invaluable resources for the study and understanding of the process of plant domestication. Here, the considerable body of ancient Chinese literature is used to explore the domestication process that has occurred with the eggplant (Solanum melongena), an important vegetable in Old World. Information about eggplant domestication in the ancient Chinese literature was retrieved using a variety of methods. The information obtained was then sorted by taxon, examined and taxonomic identifications verified. It was found that the earliest record of the eggplant documented in ancient Chinese literature was in a work from 59 bc. As far as is known, this is the earliest reliable and accurately dated record of eggplant in cultivation. The analysis reveals that the process of domestication of the eggplant in China involved three principal aspects of fruit quality: size, shape and taste. These traits were actively and gradually selected; fruit size changed from small to large, taste changed from not palatable to what was termed at the time sweetish, and that over time, a wider variety of fruit shapes was cultivated. The results indicate that, in addition to data gleaned from archaeology and genetics, evidence as to changes in key traits occurring during the process of plant domestication and selective forces responsible for these changes can be traced through the ancient literature in some civilizations.

  13. Perseus Project: Interactive Teaching and Research Tools for Ancient Greek Civilization.

    Science.gov (United States)

    Crane, Gregory; Harward, V. Judson

    1987-01-01

    Describes the Perseus Project, an educational program utilizing computer technology to study ancient Greek civilization. Including approximately 10 percent of all ancient literature and visual information on architecture, sculpture, ceramics, topography, and archaeology, the project spans a range of disciplines. States that Perseus fuels student…

  14. Role of radiation physics in the study and authentication of ancient gold work

    International Nuclear Information System (INIS)

    Guerra, M.F.

    2014-01-01

    Ancient gold items are important expressions of different aspects of past civilisations. By using non-destructive techniques of analysis and exam it is possible to obtain data kept within the objects morphology and within the materials employed, providing information, among others, on the manufacturing technologies, on the functions attributed to the objects, and on the sources of raw material exploited. This paper aims to give an overview of the questions raised by cultural heritage objects made with gold, and the role of science-based techniques applied to their study and authentication. Two examples serve to illustrate this: one concerns 19th century restorations of Etruscan objects and the other the provenance of Merovingian gold. - Highlights: ► An overview of the application of radiation techniques for the analysis of ancient gold work is given. ► We focused on non-destructive SEM-EDS, IBA techniques, X-radiography, and optical microscopy. ► Exam is illustrated by the authentication of Etruscan gold jewellery kept in museum collections. ► Fingerprinting gold is illustrated by the elemental analysis of Merovingian items from tombs in Gaul

  15. The conscious of Nightmares in ancient China

    OpenAIRE

    西林, 眞紀子

    2006-01-01

    The analaysis concerns Nightmares in ancient China. People in ancient China were very afraid of Nightmares. Nightmares are described in the『春秋左氏傳』etc. The exocis Nightmares is described in the『周禮』. The ceremony "難" of exocis Nightmares in the『禮記』. In the characters Meng (夢) had the conscious of Nightmares in ancient China. The analaysis is about the characters 'Meng', about the characters of the relationship 'Meng'

  16. Unriddling of ancient-medieval culture by PIXE

    International Nuclear Information System (INIS)

    Uda, M.

    1997-01-01

    Some examples are given for unriddling of ancient-medieval culture by PIXE. Effectiveness of PIXE to analyze art and archaeological objects is also explained. Objects employed here are 1) red, yellow, blue and white pigments painted on sun-dried bricks excavated in Egypt, 2) ancient glass beads used in the Near East, 3) South American mummy hair, 4) ancient slag excavated from Kansai-district, Japan 5) ink used by Galileo Galilei and 6) Renaissance style enameled gold jewelry. (author)

  17. Provenance study of ancient Chinese Yaozhou porcelain by neutron activation analysis

    Science.gov (United States)

    Li, G. X.; Y Gao, Z.; Li, R. W.; Zhao, W. J.; Xie, J. Z.; Feng, S. L.; Zhuo, Z. X.; Y Fan, D.; Zhang, Y.; Cai, Z. F.; Liu, H.

    2003-09-01

    This paper reports our study of the provenance of ancient Chinese Yaozhou porcelain. The content of 29 elements in the Yaozhou porcelain samples was measured by neutron activation analysis (NAA). The NAA data were further analysed using fuzzy cluster analysis to obtain the trend fuzzy cluster diagrams. These samples with different glaze colour, ranging over more than 700 years, were fired in different kilns. Our analysis indicates the relatively concentrated distribution of the sources of the raw material for the Yaozhou porcelain body samples. They can be classified into two independent periods, i.e. the Tang (AD 618-907) and the Five Dynasties (AD 907-960) period, and the Song (AD 960-1279) and Jin (AD 1115-1234) period. Our analysis also indicates that the sources of the raw material for the ancient Yaozhou porcelain glaze samples are quite scattered and those for the black glaze in the Tang Dynasty are very concentrated. The sources of the raw material for the celadon glaze and the white glaze in the Tang Dynasty are widely distributed and those for the celadon glaze in the Song Dynasty are close to those of the bluish white glaze in the Jin Dynasty, and they are very concentrated. The sources of the raw material for the porcelain glazes cover those of the porcelain bodies.

  18. Beringian paleoecology inferred from permafrost-preserved fungal DNA

    DEFF Research Database (Denmark)

    Lydolph, Magnus C; Jacobsen, Jonas; Arctander, Peter

    2005-01-01

    of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark......-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition...

  19. Moessbauer studies on ancient Chinese pottery of Yangshao Culture Period

    International Nuclear Information System (INIS)

    Yu Zhengfang; Zheng Qi; Zheng Yufang; Zhongshan Univ., Guangzhou

    1988-01-01

    Eleven pieces of ancient Chinese pottery (4770 B.C. - 2960 B.C.) of Yangshao Culture Period collected from the Xi'an area have been studied by means of Moessbauer spectroscopy. The samples were refired up to 1100 0 C in steps of 100 0 C for 2 h in air. The highest temperature up to which the Moessbauer pattern remains basically unchanged can be identified with the original firing temperature. The result indicates that the firing temperatures for most of the sherds were between 900-1000 0 C. The function of the grit contained in the pottery has been discussed. The crimson and reddish painted materials on the surface of sherds have been studied, respectively. The first appearance of pottery can probably be traced back to an even earlier period. (orig.)

  20. Moessbauer studies on ancient Chinese pottery of Yangshao Culture Period

    Energy Technology Data Exchange (ETDEWEB)

    Zhengfang, Yu; Qi, Zheng; Yufang, Zheng

    1988-02-01

    Eleven pieces of ancient Chinese pottery (4770 B.C. - 2960 B.C.) of Yangshao Culture Period collected from the Xi'an area have been studied by means of Moessbauer spectroscopy. The samples were refired up to 1100/sup 0/C in steps of 100/sup 0/C for 2 h in air. The highest temperature up to which the Moessbauer pattern remains basically unchanged can be identified with the original firing temperature. The result indicates that the firing temperatures for most of the sherds were between 900-1000/sup 0/C. The function of the grit contained in the pottery has been discussed. The crimson and reddish painted materials on the surface of sherds have been studied, respectively. The first appearance of pottery can probably be traced back to an even earlier period.

  1. Problem-oriented approach to Ancient philosophy

    Directory of Open Access Journals (Sweden)

    Berstov, Igor

    2007-06-01

    Full Text Available Igor Berestov and Marina Wolf of the Institute of philosophy and law, Novosibirsk, discuss various methodological difficulties typical of studies in the history of Ancient Greek philosophy and try to develop their own problem-oriented approach.

  2. The value of ancient architecture for educational program of masters of architectural space design

    Directory of Open Access Journals (Sweden)

    Prishchepa Aleksandr

    2017-01-01

    Full Text Available The existence of archaeological sites of ancient Greek colony-towns and medieval fortresses gives a real insight into the interaction of all spheres of human activity in ancient times. Ancient Greek Emporium is a vivid example of the architecture, art, archaeology and urban planning synthesis. Archaeological excavations provide an opportunity to study the artefacts of the ancient world belonging to several fields, such as sculpture, decorative arts, fashion design and household. Studying history of archaeology right on the place of excavation of an ancient city masters can imagine the scale of buildings, streets layout and location of business, administrative and residential buildings. It allows students to form professional way of thinking in a short period in order to gather the material and work on the master thesis.

  3. Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes

    DEFF Research Database (Denmark)

    Epp, L. S.; Gussarova, C.; Boessenkool, S.

    2015-01-01

    temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte, algal (in particular diatom) and copepod DNA retrieved from a sediment core spanning...... phases, and distinct temporal changes in plant presence were recovered. The plant DNA was mostly in agreement with expected vegetation history, but very early occurrences of vascular plants, including the woody Empetrum nigrum, document terrestrial vegetation very shortly after glacial retreat. Our study...... core. Our DNA record was stratigraphically coherent, with no indication of leaching between layers, and our cross-taxon comparisons were in accordance with previously inferred local ecosystem changes. Authentic ancient plant DNA was retrieved from nearly all layers, both from the marine and the limnic...

  4. Genetic Drift. The ancient Egyptian dwarfs of the Walters Art Museum.

    Science.gov (United States)

    Kozma, Chahira

    2010-10-01

    The ancient Egyptians left an impressive artistic legacy documenting many aspects of their society including the existence of dwarfs as highly valued members. In previous publications in the Journal, I discussed dwarfs and skeletal dysplasia in ancient Egypt. In this study, I examined the ancient Egyptian representations of dwarfs of the Walters Art Museum in Baltimore, Maryland. One of the highlights of the collection is a group of five ivory figurines from Predynastic Times (pre 3500-3100 BCE) depicting a couple, a man with a child, and two females. Representations from other periods include ordinary as well as dwarf deities. The dwarf gods, Bes and Ptah, are frequently depicted holding or biting snakes or standing on crocodiles symbolizing their ability to ward off dangers. A couple of statuettes from the Greco-Roman Period that, in contrast to earlier Egyptian Periods, depict harsh physical anomalies, twisted bodies, and facial pain. The artistic impression can be interpreted as either tragic or humorous. The grotesque depiction of dwarfs during the Greco-Roman Period in ancient Egypt is believed to be due to a greater infusion of Hellenistic influence. This study provides a microcosm of the legacy of dwarfs in ancient Egypt and supports the premise that dwarfs were accepted and integrated in the ancient Egyptian society, and with a few exceptions, their disorder was not depicted as a physical handicap. Copyright © 2010 Wiley-Liss, Inc.

  5. Anticancer activity of botanical compounds in ancient fermented beverages (review).

    Science.gov (United States)

    McGovern, P E; Christofidou-Solomidou, M; Wang, W; Dukes, F; Davidson, T; El-Deiry, W S

    2010-07-01

    Humans around the globe probably discovered natural remedies against disease and cancer by trial and error over the millennia. Biomolecular archaeological analyses of ancient organics, especially plants dissolved or decocted as fermented beverages, have begun to reveal the preliterate histories of traditional pharmacopeias, which often date back thousands of years earlier than ancient textual, ethnohistorical, and ethnological evidence. In this new approach to drug discovery, two case studies from ancient Egypt and China illustrate how ancient medicines can be reconstructed from chemical and archaeological data and their active compounds delimited for testing their anticancer and other medicinal effects. Specifically, isoscopoletin from Artemisia argyi, artemisinin from Artemisia annua, and the latter's more easily assimilated semi-synthetic derivative, artesunate, showed the greatest activity in vitro against lung and colon cancers. In vivo tests of these compounds previously unscreened against lung and pancreatic cancers are planned for the future.

  6. Genetic data from algae sedimentary DNA reflect the influence of environment over geography.

    Science.gov (United States)

    Stoof-Leichsenring, Kathleen R; Herzschuh, Ulrike; Pestryakova, Luidmila A; Klemm, Juliane; Epp, Laura S; Tiedemann, Ralph

    2015-08-11

    Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur in similar environments and less-related lineages in dissimilar environments, in our case different vegetation and co-varying climatic and limnic variables across treeline transects. Thus our study reveals that environmental conditions rather than geographic distance is reflected by diatom-relatedness patterns in space and time. We tentatively speculate that the detected relatedness pattern in Staurosira across the treeline could be a result of adaptation to diverse environmental conditions across the arctic boreal treeline, however, a geographically-driven divergence and subsequent repopulation of ecologically different habitats might also be a potential explanation for the observed pattern.

  7. Genomic insights into the origin of farming in the ancient Near East

    Science.gov (United States)

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

    2016-01-01

    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. PMID:27459054

  8. DNA-binding, DNA cleavage and cytotoxicity studies of two anthraquinone derivatives.

    Science.gov (United States)

    Gholivand, M B; Kashanian, S; Peyman, H

    2012-02-15

    The interaction of native calf thymus DNA (CT-DNA) with two anthraquinones including quinizarin (1,4-dihydroxy anthraquinone) and danthron (1,8-dihydroxy anthraquinone) in a mixture of 0.04M Brittone-Robinson buffer and 50% of ethanol were studied at physiological pH by spectrofluorometric and cyclic voltammetry techniques. The former technique was used to calculate the binding constants of anthraquinones-DNA complexes at different temperatures. Thermodynamic study indicated that the reactions of both anthraquinone-DNA systems are predominantly entropically driven. Furthermore, the binding mechanisms on the reaction of the two anthraquinones with DNA and the effect of ionic strength on the fluorescence property of the system have also been investigated. The results of the experiments indicated that the binding modes of quinizarin and danthron with DNA were evaluated to be groove binding. Moreover, the cytotoxic activity of both compounds against human chronic myelogenous leukemia K562 cell line and DNA cleavage were investigated. The results indicated that these compounds slightly cleavage pUC18 plasmid DNA and showed minor antitumor activity against K562 (human chronic myeloid leukemia) cell line. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone.

    Science.gov (United States)

    Douka, Katerina; Slon, Viviane; Stringer, Chris; Potts, Richard; Hübner, Alexander; Meyer, Matthias; Spoor, Fred; Pääbo, Svante; Higham, Tom

    2017-06-01

    The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. [Ancient Greek in modern language of medicine].

    Science.gov (United States)

    Marković, Vera

    2007-01-01

    In order to standardize language of medicine, it is essential to have a good command of ancient Greek and Latin. We cannot deny a huge impact of ancient Greek medicine on medical terminology. Compounds of Greek origin related to terms for organs, illnesses, inflammations, surgical procedures etc. have been listed as examples. They contain Greek prefixes and suffixes transcribed into Latin and they have been analysed. It may be concluded that the modern language of medicine basically represents the ancient Greek language transcribed into Latin.

  11. The provenance investigation on ancient chinese Ru porcelains by NAA

    International Nuclear Information System (INIS)

    Gao Zhengyao; Wang Jie; Chen Songhua

    1997-01-01

    The 28 samples of glazes and bodies of ancient Chinese Ru porcelains are analyzed by neutron activation. The 36 element contents in each sample are determined. The neutron activation analysis (NAA) data are analyzed by fuzzy cluster. The trend cluster diagram is obtained. The result shows that the ancient Chinese Ru porcelains were most probably from the same raw material source though they were from different time, fired in different kilns and in different colors. The near provenance relation between ancient Jun porcelain and ancient Ru porcelain is preliminarily analyzed. The two modern Ru porcelains approximate to ancient Ru porcelains, one becomes estranged from ancient Ru porcelains. Jingdezhen porcelain is unconcerned with Ru porcelains

  12. mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization.

    Directory of Open Access Journals (Sweden)

    Henryk W Witas

    Full Text Available Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa and Tell Masaikh (ancient Kar-Assurnasirpal Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya. They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5.

  13. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

    Science.gov (United States)

    Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

  14. Ancient Greek in modern language of medicine

    Directory of Open Access Journals (Sweden)

    Marković Vera

    2007-01-01

    Full Text Available In order to standardize language of medicine, it is essential to have a good command of ancient Greek and Latin. We cannot deny a huge impact of ancient Greek medicine on medical terminology. Compounds of Greek origin related to terms for organs, illnesses, inflammations, surgical procedures etc. have been listed as examples. They contain Greek prefixes and suffixes transcribed into Latin and they have been analyzed. It may be concluded that the modern language of medicine basically represents the ancient Greek language transcribed into Latin.

  15. An Evaluation of the Historical Importance of Fertility and Its Reflection in Ancient Mythology.

    Science.gov (United States)

    Behjati-Ardakani, Zohreh; Akhondi, Mohammad Mehdi; Mahmoodzadeh, Homa; Hosseini, Seyed Hasan

    2016-01-01

    Myths are reflective of human concerns and needs during ancient times. By reviewing them, it turns out that many human problems today, have a historical background. Among the main themes of ancient mythologies, fertility and reproduction have various representations in ancient civilizations. The purpose of this paper was to review myths and common symbols of fertility and reproduction in ancient civilizations and evaluate the reasons of their continuous importance in different cultures. The data in this review study was obtained by scrutinizing the related literature. The gathered data indicated the multiplicity and variety of fertility symbols in ancient myths. Most ancient fertility symbols were inspired by the nature and some of them like earth and water were common in mythology of different civilizations. Therefore, the symbols consolidate the concept of conformity between human reproductive concerns and the nature's necessities.

  16. Cosmologies of the ancient Mediterranean world

    Directory of Open Access Journals (Sweden)

    John T. Fitzgerald

    2013-07-01

    Full Text Available Cosmology is concerned with the order of the universe and seeks to provide an account, not only of that order, but also of the mind or reason behind it. In antiquity, the cosmos was usually understood religiously, such that the cosmologies of the ancient Mediterranean world were either religious in nature or constituted a reaction to a religiously conceived understanding of the structures of the universe. The oldest form in which ancient cosmologies occur is myth, which, owing to its elasticity as a form, enabled them to be appropriated, adapted and used by different groups. In addition, different cosmologies co-existed within the same ancient culture, each having an authoritative status. This article provides an introductory overview of these cosmological myths and argues that a comparative approach is the most fruitful way to study them. Emphasis is given to certain prominent cosmological topics, including theogony (the genesis of the divine or the relationship of the divine to the cosmos, cosmogony (the genesis of the cosmos, and anthropogony (the origin of humans within the cosmos. Although these myths vary greatly in terms of content and how they envision the origin of the cosmos, many of them depict death as part of the structure of the universe.

  17. Exploring Ancient Skies An Encyclopedic Survey of Archaeoastronomy

    CERN Document Server

    Kelley, David H

    2005-01-01

    Exploring Ancient Skies brings together the methods of archaeology and the insights of modern astronomy to explore the science of astronomy as it was practiced in various cultures prior to the invention of the telescope. The book reviews an enormous and growing body of literature on the cultures of the ancient Mediterranean, the Far East, and the New World (particularly Mesoamerica), putting the ancient astronomical materials into their archaeological and cultural contexts. The authors begin with an overview of the field and proceed to essential aspects of naked-eye astronomy, followed by an examination of specific cultures. The book concludes by taking into account the purposes of ancient astronomy: astrology, navigation, calendar regulation, and (not least) the understanding of our place and role in the universe. Skies are recreated to display critical events as they would have appeared to ancient observers - events such as the supernova of 1054, the 'lion horoscope' or the 'Star of Bethlehem.' Exploring An...

  18. Cathair Crobh Dearg: From Ancient Beliefs to the Rounds 2017

    Directory of Open Access Journals (Sweden)

    Frédéric Armao

    2017-10-01

    Full Text Available This paper will study the case of the stone enclosure of Cathair Crobh Dearg, Co. Kerry (also referred to as the City and Dá Chích Anann (or the Paps of Anu, the twin mountains that can be seen from the enclosure. The site is mentioned in ancient mythological texts as well as more modern accounts in connection with the Irish festival of Bealtaine, in early May. The author relied on archaeological evidence, an analysis of ancient documents, a number of manuscripts from the Irish National Folklore Collection, as well as personal visits to the site in order to try and understand the nature, and possibly origin, of both contemporary rituals and ancient beliefs.

  19. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

    Science.gov (United States)

    Gaucher, Eric A.; Thomson, J. Michael; Burgan, Michelle F.; Benner, Steven A.

    2003-01-01

    Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55-65 degrees C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria, the distribution of thermophily in derived bacterial lineages, the inferred G + C content of ancient ribosomal RNA, and the geological record combined with assumptions concerning molecular clocks. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.

  20. Twins in Ancient Greece: a synopsis.

    Science.gov (United States)

    Malamitsi-Puchner, Ariadne

    2016-01-01

    This brief outline associates twins with several aspects of life in Ancient Greece. In Greek mythology twins caused ambivalent reactions and were believed to have ambivalent feelings for each other. Very often, they were viewed as the representatives of the dualistic nature of the universe. Heteropaternal superfecundation, which dominates in ancient myths, explains on one hand, the god-like qualities and, on the other hand, the mortal nature of many twins. An assumption is presented that legends referring to twins might reflect the territorial expansions of Ancient Greeks in Northern Mediterranean, around the Black Sea, in Asia Minor, as well as North East Africa. In conclusion, in Greek antiquity, twins have been used as transitional figures between myth and reality.

  1. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Directory of Open Access Journals (Sweden)

    Verena J Schuenemann

    2018-05-01

    Full Text Available Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  2. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

    Science.gov (United States)

    Schuenemann, Verena J; Avanzi, Charlotte; Krause-Kyora, Ben; Seitz, Alexander; Herbig, Alexander; Inskip, Sarah; Bonazzi, Marion; Reiter, Ella; Urban, Christian; Dangvard Pedersen, Dorthe; Taylor, G Michael; Singh, Pushpendra; Stewart, Graham R; Velemínský, Petr; Likovsky, Jakub; Marcsik, Antónia; Molnár, Erika; Pálfi, György; Mariotti, Valentina; Riga, Alessandro; Belcastro, M Giovanna; Boldsen, Jesper L; Nebel, Almut; Mays, Simon; Donoghue, Helen D; Zakrzewski, Sonia; Benjak, Andrej; Nieselt, Kay; Cole, Stewart T; Krause, Johannes

    2018-05-01

    Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

  3. Mycorrhizal symbiosis: ancient signalling mechanisms co-opted

    NARCIS (Netherlands)

    Geurts, R.; Vleeshouwers, V.G.A.A.

    2012-01-01

    Mycorrhizal root endosymbiosis is an ancient property of land plants. Two parallel studies now provide novel insight into the mechanism driving this interaction and how it is used by other filamentous microbes like pathogenic oomycetes.

  4. The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars.

    Science.gov (United States)

    Marlow, Jeffrey J; Larowe, Douglas E; Ehlmann, Bethany L; Amend, Jan P; Orphan, Victoria J

    2014-04-01

    This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO2 partial pressures. In all scenarios, AOM is exergonic, ranging from -31 to -135 kJ/mol CH4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.

  5. A phase-transition model for the rise and collapse of ancient civilizations: A pre-ceramic Andean case study

    Science.gov (United States)

    Flores, J. C.

    2015-12-01

    For ancient civilizations, the shift from disorder to organized urban settlements is viewed as a phase-transition simile. The number of monumental constructions, assumed to be a signature of civilization processes, corresponds to the order parameter, and effective connectivity becomes related to the control parameter. Based on parameter estimations from archaeological and paleo-climatological data, this study analyzes the rise and fall of the ancient Caral civilization on the South Pacific coast during a period of small ENSO fluctuations (approximately 4500 BP). Other examples considered include civilizations on Easter Island and the Maya Lowlands. This work considers a typical nonlinear third order evolution equation and numerical simulations.

  6. The last Viking King: a royal maternity case solved by ancient DNA analysis.

    Science.gov (United States)

    Dissing, Jørgen; Binladen, Jonas; Hansen, Anders; Sejrsen, Birgitte; Willerslev, Eske; Lynnerup, Niels

    2007-02-14

    The last of the Danish Viking Kings, Sven Estridsen, died in a.d. 1074 and is entombed in Roskilde Cathedral with other Danish kings and queens. Sven's mother, Estrid, is entombed in a pillar across the chancel. However, while there is no reasonable doubt about the identity of Sven, there have been doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D-loop were PCR amplified, cloned and a number of clones with each segment were sequenced. Also a segment containing the H/non-H specific nucleotide 7028 was sequenced. Consensus sequences were determined and D-loop results were replicated in an independent laboratory. This allowed the assignment of King Sven Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases where the sequence has been altered by a germ line mutation. Therefore, the observation of two sequence differences makes it highly unlikely that the entombed woman was the mother of Sven. In addition, physical examination of the skeleton and the teeth strongly indicated that this woman was much younger (approximately 35 years) at the time of death than the 70 years history records tell. Although the entombed woman cannot be the Estrid, she may well be one of Sven's two daughters-in-law who were also called Estrid and who both became queens.

  7. Studying DNA Looping by Single-Molecule FRET

    OpenAIRE

    Le, Tung T.; Kim, Harold D.

    2014-01-01

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can als...

  8. The Ancient Kemetic Roots of Library and Information Science.

    Science.gov (United States)

    Zulu, Itibari M.

    This paper argues that the ancient people of Kemet (Egypt), "the black land," built and operated the first major libraries and institutions of higher education in the world. Topics of discussion include the Ancient Egyptians as an African people; a chronology of Ancient Kemet; literature in Kemet; a history of Egyptian Librarianship; the…

  9. DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas

    Directory of Open Access Journals (Sweden)

    Gavery Mackenzie R

    2010-08-01

    Full Text Available Abstract Background DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (Crassostrea gigas. Results Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in C. gigas genes and demonstrated that this species possesses intragenic methylation. In silico analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the C. gigas genome, and that specific functional categories of genes have significantly different levels of methylation. Conclusions The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in Crassostrea gigas, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.

  10. Studies on protozoa in ancient remains - A Review

    Directory of Open Access Journals (Sweden)

    Liesbeth Frías

    2013-02-01

    Full Text Available Paleoparasitological research has made important contributions to the understanding of parasite evolution and ecology. Although parasitic protozoa exhibit a worldwide distribution, recovering these organisms from an archaeological context is still exceptional and relies on the availability and distribution of evidence, the ecology of infectious diseases and adequate detection techniques. Here, we present a review of the findings related to protozoa in ancient remains, with an emphasis on their geographical distribution in the past and the methodologies used for their retrieval. The development of more sensitive detection methods has increased the number of identified parasitic species, promising interesting insights from research in the future.

  11. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.

    Science.gov (United States)

    Ozga, Andrew T; Nieves-Colón, Maria A; Honap, Tanvi P; Sankaranarayanan, Krithivasan; Hofman, Courtney A; Milner, George R; Lewis, Cecil M; Stone, Anne C; Warinner, Christina

    2016-06-01

    Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Ancient and modern women in the "Woman's World".

    Science.gov (United States)

    Hurst, Isobel

    2009-01-01

    Under the editorship of Oscar Wilde, the "Woman's World" exemplified the popular dissemination of Hellenism through periodical culture. Addressing topics such as marriage, politics, and education in relation to the lives of women in the ancient world, the magazine offered an unfamiliar version of the reception of ancient Greece and Rome in late-Victorian aestheticism, one that was accessible to a wide readership because it was often based on images rather than texts. The classical scholar Jane Ellen Harrison addressed herself to this audience of women readers, discussing the similarities between modern collegiate life and the "woman's world" that enabled Sappho to flourish in ancient Greece. The "Woman's World" thus questions gender stereotypes by juxtaposing ancient and modern women, implicitly endorsing varied models of womanhood.

  13. Defining Astrology in Ancient and Classical History

    Science.gov (United States)

    Campion, Nicholas

    2015-05-01

    Astrology in the ancient and classical worlds can be partly defined by its role, and partly by the way in which scholars spoke about it. The problem is complicated by the fact that the word is Greek - it has no Babylonian or Egyptian cognates - and even in Greece it was interchangeable with its cousin, 'astronomy'. Yet if we are to understand the role of the sky, stars and planets in culture, debates about the nature of ancient astrology, by both classical and modern scholars, must be taken into account. This talk will consider modern scholars' typologies of ancient astrology, together with ancient debates from Cicero in the 1st century BC, to Plotinus (204/5-270 AD) and Isidore of Seville (c. 560 - 4 April 636). It will consider the implications for our understanding of astronomy's role in culture, and conclude that in the classical period astrology may be best understood through its diversity and allegiance to competing philosophies, and that its functions were therefore similarly varied.

  14. The fingerprint element analysis on provenance of ancient chinese Jun porcelain

    International Nuclear Information System (INIS)

    Gao Zhengyao; Chen Songhua; Wang Jie; Huang Zhongxiang; Jia Xiuqin; Han Song

    1997-01-01

    Forty-three samples of ancient Jun porcelains and so on were chosen. Neutron activation analysis (NAA) was used to measure the 36 trace elements in every sample. Seven elements were chosen as the 'fingerprint elements'. The provenance of the glazes and bodies of ancient Chinese Jun porcelain were investigated by the fingerprint element analysis method. The result shows that although the ancient Chinese Jun porcelain samples have been leapt over six hundred years, and glaze colors are utterly different and are from many different kilns, there are long term, stable and same mainly raw material source. The near provenance relation between ancient Jun porcelain and ancient Ru porcelain is preliminarily analyzed. A few modern Jun porcelains approximate from ancient Jun porcelains, the majority become estranged from ancient Jun porcelain

  15. HGIS AND ARCHIVE RESEARCHES: A TOOL FOR THE STUDY OF THE ANCIENT MILL CHANNEL OF CESENA (ITALY

    Directory of Open Access Journals (Sweden)

    G. Bitelli

    2016-06-01

    Full Text Available The present study aims to demonstrate the usefulness of GIS to support archive searches and historical studies (e.g. related to industrial archaeology, in the case of an ancient channel for mill powering near Cesena (Emilia-Romagna, Italy, whose history is weaved together with the history of the Compagnia dei Molini di Cesena mill company, the most ancient limited company in Italy. Several historical maps (about 40 sheets in total inherent the studied area and 80 archive documents (drawings, photos, specifications, administrative acts, newspaper articles, over a period of more than 600 years, were collected. Once digitized, historical maps were analysed, georeferenced and mosaicked where necessary. Subsequently, in all the maps the channel with its four mills and the Savio river were vectorized. All the additional archive documents were digitized, catalogued and stored. Using the QGIS open source platform, a Historical GIS was created, encompassing the current cartographic base and all historical maps, with their vectorized elements; each archive document was linked to the proper historical map, so that the document can be immediately retrieved and visualized. In such a HGIS, the maps form the base for a spatial and temporal navigation, facilitated by a specific interface; the external documents linked to them complete the description of the represented elements. This simple and interactive tool offers a new approach to archive searches, as it allows reconstruction in space and time of the evolution of the ancient channel and the history of this important mill company.

  16. Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

    Science.gov (United States)

    Klyosov, A A

    2011-05-01

    This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the

  17. Recovering mitochondrial DNA lineages of extinct Amerindian nations in extant homopatric Brazilian populations.

    Science.gov (United States)

    Gonçalves, Vanessa F; Parra, Flavia C; Gonçalves-Dornelas, Higgor; Rodrigues-Carvalho, Claudia; Silva, Hilton P; Pena, Sergio Dj

    2010-12-01

    Brazilian Amerindians have experienced a drastic population decrease in the past 500 years. Indeed, many native groups from eastern Brazil have vanished. However, their mitochondrial mtDNA haplotypes, still persist in Brazilians, at least 50 million of whom carry Amerindian mitochondrial lineages. Our objective was to test whether, by analyzing extant rural populations from regions anciently occupied by specific Amerindian groups, we could identify potentially authentic mitochondrial lineages, a strategy we have named 'homopatric targeting'. We studied 173 individuals from Queixadinha, a small village located in a territory previously occupied by the now extinct Botocudo Amerindian nation. Pedigree analysis revealed 74 unrelated matrilineages, which were screened for Amerindian mtDNA lineages by restriction fragment length polymorphism. A cosmopolitan control group was composed of 100 individuals from surrounding cities. All Amerindian lineages identified had their hypervariable segment HVSI sequenced, yielding 13 Amerindian haplotypes in Queixadinha, nine of which were not present in available databanks or in the literature. Among these haplotypes, there was a significant excess of haplogroup C (70%) and absence of haplogroup A lineages, which were the most common in the control group. The novelty of the haplotypes and the excess of the C haplogroup suggested that we might indeed have identified Botocudo lineages. To validate our strategy, we studied teeth extracted from 14 ancient skulls of Botocudo Amerindians from the collection of the National Museum of Rio de Janeiro. We recovered mtDNA sequences from all the teeth, identifying only six different haplotypes (a low haplotypic diversity of 0.8352 ± 0.0617), one of which was present among the lineages observed in the extant individuals studied. These findings validate the technique of homopatric targeting as a useful new strategy to study the peopling and colonization of the New World, especially when direct

  18. Legacy of the Ancient World: An Educational Guide. Understanding Ancient Culture through Art at the Tampa Museum of Art.

    Science.gov (United States)

    Whitelaw, R. Lynn

    Among the many contributions made by Ancient Greeks and Romans to contemporary life, are those which influence art, architecture, literature, philosophy, mathematics and science, theater, athletics, religion, and the founding of democracy. The Tampa Museum of Art's classical collection offers a unique opportunity to learn about Ancient Greeks and…

  19. Lipids of aquatic sediments, recent and ancient

    Science.gov (United States)

    Eglinton, G.; Hajibrahim, S. K.; Maxwell, J. R.; Quirke, J. M. E.; Shaw, G. J.; Volkman, J. K.; Wardroper, A. M. K.

    1979-01-01

    Computerized gas chromatography-mass spectrometry (GC-MS) is now an essential tool in the analysis of the complex mixtures of lipids (geolipids) encountered in aquatic sediments, both 'recent' (less than 1 million years old) and ancient. The application of MS, and particularly GC-MS, has been instrumental in the rapid development of organic geochemistry and environmental organic chemistry in recent years. The techniques used have resulted in the identification of numerous compounds of a variety of types in sediments. Most attention has been concentrated on molecules of limited size, mainly below 500 molecular mass, and of limited functionality, for examples, hydrocarbons, fatty acids and alcohols. Examples from recent studies (at Bristol) of contemporary, 'recent' and ancient sediments are presented and discussed.

  20. AMS radiocarbon dating of ancient Japanese sutras

    CERN Document Server

    Oda, H; Nakamura, T; Fujita, K

    2000-01-01

    Radiocarbon ages of ancient Japanese sutras whose historical ages were known paleographically were measured by means of accelerator mass spectrometry (AMS). Calibrated radiocarbon ages of five samples were consistent with the corresponding historical ages; the 'old wood effect' is negligible for ancient Japanese sutras. Japanese paper has been made from fresh branches grown within a few years and the interval from trimming off the branches to writing sutra on the paper is within one year. The good agreement between the calibrated radiocarbon ages and the historical ages is supported by such characteristics of Japanese paper. It is indicated in this study that Japanese sutra is a suitable sample for radiocarbon dating in the historic period because of little gap by 'old wood effect'.

  1. AMS radiocarbon dating of ancient Japanese sutras

    International Nuclear Information System (INIS)

    Oda, Hirotaka; Yoshizawa, Yasukazu; Nakamura, Toshio; Fujita, Keiko

    2000-01-01

    Radiocarbon ages of ancient Japanese sutras whose historical ages were known paleographically were measured by means of accelerator mass spectrometry (AMS). Calibrated radiocarbon ages of five samples were consistent with the corresponding historical ages; the 'old wood effect' is negligible for ancient Japanese sutras. Japanese paper has been made from fresh branches grown within a few years and the interval from trimming off the branches to writing sutra on the paper is within one year. The good agreement between the calibrated radiocarbon ages and the historical ages is supported by such characteristics of Japanese paper. It is indicated in this study that Japanese sutra is a suitable sample for radiocarbon dating in the historic period because of little gap by 'old wood effect'

  2. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.

    2008-01-01

    We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data...... that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re......-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

  3. On the acoustics of ancient Greek and Roman theaters.

    Science.gov (United States)

    Farnetani, Andrea; Prodi, Nicola; Pompoli, Roberto

    2008-09-01

    The interplay of architecture and acoustics is remarkable in ancient Greek and Roman theaters. Frequently they are nowadays lively performance spaces and the knowledge of the sound field inside them is still an issue of relevant importance. Even if the transition from Greek to Roman theaters can be described with a great architectural detail, a comprehensive and objective approach to the two types of spaces from the acoustical point of view is available at present only as a computer model study [P. Chourmouziadou and J. Kang, "Acoustic evolution of ancient Greek and Roman theaters," Appl. Acoust. 69, re (2007)]. This work addresses the same topic from the experimental point of view, and its aim is to provide a basis to the acoustical evolution from Greek to Roman theater design. First, by means of in situ and scale model measurements, the most important features of the sound field in ancient theaters are clarified and discussed. Then it has been possible to match quantitatively the role of some remarkable architectural design variables with acoustics, and it is seen how this criterion can be used effectively to define different groups of ancient theaters. Finally some more specific wave phenomena are addressed and discussed.

  4. Comparing particle-size distributions in modern and ancient sand-bed rivers

    Science.gov (United States)

    Hajek, E. A.; Lynds, R. M.; Huzurbazar, S. V.

    2011-12-01

    Particle-size distributions yield valuable insight into processes controlling sediment supply, transport, and deposition in sedimentary systems. This is especially true in ancient deposits, where effects of changing boundary conditions and autogenic processes may be detected from deposited sediment. In order to improve interpretations in ancient deposits and constrain uncertainty associated with new methods for paleomorphodynamic reconstructions in ancient fluvial systems, we compare particle-size distributions in three active sand-bed rivers in central Nebraska (USA) to grain-size distributions from ancient sandy fluvial deposits. Within the modern rivers studied, particle-size distributions of active-layer, suspended-load, and slackwater deposits show consistent relationships despite some morphological and sediment-supply differences between the rivers. In particular, there is substantial and consistent overlap between bed-material and suspended-load distributions, and the coarsest material found in slackwater deposits is comparable to the coarse fraction of suspended-sediment samples. Proxy bed-load and slackwater-deposit samples from the Kayenta Formation (Lower Jurassic, Utah/Colorado, USA) show overlap similar to that seen in the modern rivers, suggesting that these deposits may be sampled for paleomorphodynamic reconstructions, including paleoslope estimation. We also compare grain-size distributions of channel, floodplain, and proximal-overbank deposits in the Willwood (Paleocene/Eocene, Bighorn Basin, Wyoming, USA), Wasatch (Paleocene/Eocene, Piceance Creek Basin, Colorado, USA), and Ferris (Cretaceous/Paleocene, Hanna Basin, Wyoming, USA) formations. Grain-size characteristics in these deposits reflect how suspended- and bed-load sediment is distributed across the floodplain during channel avulsion events. In order to constrain uncertainty inherent in such estimates, we evaluate uncertainty associated with sample collection, preparation, analytical

  5. Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

    Directory of Open Access Journals (Sweden)

    Ulrike H. Taron

    2018-03-01

    Full Text Available High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples, a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang, for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.

  6. Resurrection of DNA function in vivo from an extinct genome.

    Directory of Open Access Journals (Sweden)

    Andrew J Pask

    2008-05-01

    Full Text Available There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine, obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

  7. The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa.

    Science.gov (United States)

    Budde, K B; González-Martínez, S C; Hardy, O J; Heuertz, M

    2013-07-01

    Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.

  8. Architecture Of Uzbekistan Of The Ancient Period Style Features And Composition Laws

    Directory of Open Access Journals (Sweden)

    Nurmukhamedova Shoira Zahidovna

    2015-08-01

    Full Text Available Specific features of the development of architecture in Uzbekistan in ancient period are considered in the paper. The author emphasizes the role of building materials and structures studies the composition of ancient settlements in Khorezm and Bactria reveals a high level of military architecture and planning principles of residential and castle structures.

  9. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

    Directory of Open Access Journals (Sweden)

    Mayra Eduardoff

    2017-09-01

    Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

  10. Luminescence dating of flash flood deposits: a new approach for the chronological study of ancient irrigation perimeters in southern Yemen

    International Nuclear Information System (INIS)

    Balescu, S.; Lamothe, M.; Coque-Delhuille, B.

    1998-01-01

    This study is an attempt to assess the age of ancient irrigation silts from Southern Yemen using the optically stimulated luminescence (OSL) of the constituent K-feldspar grains. This OSL dating method is tested on the al-Haraja irrigation sequence (Wadi Bayhan) which overlies an archaeological occupation level previously dated at 2 203±123 years BP by 14 C. The OSL age estimates range between 2 097±177 years at the bottom of the sequence and 1 555±150 years at the top. This study demonstrates the potential of the luminescence dating method to provide chronological information on the deposition of ancient silts following irrigation in arid environment where 14 C datable material is rare. (authors)

  11. Fingerprint elements scatter analysis on ancient chinese Ru porcelains samples

    International Nuclear Information System (INIS)

    Gao Zhengyao; Wang Jie; Chen Xiande

    1997-01-01

    Altogether 28 samples, mainly including glazes and bodies of ancient Chinese Ru porcelain, were analyzed by NAA technique and the contents of 36 elements were compared. The scatter analysis for nine fingerprint-elements indicates that almost all ancient Chinese Ru porcelain samples had nearly identical and long-term stable source of raw materials although they were fired in different kilns, at varying time and with distinct colors, and moreover, the source of raw materials for modern Ru porcelain seems to approach that for ancient one. The close provenance relation between ancient Jun porcelain and ancient Ru porcelain is also preliminarily verified. The glaze material of Jingdezhen white porcelain is totally different from all other samples. It shows that the former came from a separate source

  12. Atherosclerosis across 4000 years of human history: the Horus study of four ancient populations.

    Science.gov (United States)

    Thompson, Randall C; Allam, Adel H; Lombardi, Guido P; Wann, L Samuel; Sutherland, M Linda; Sutherland, James D; Soliman, Muhammad Al-Tohamy; Frohlich, Bruno; Mininberg, David T; Monge, Janet M; Vallodolid, Clide M; Cox, Samantha L; Abd el-Maksoud, Gomaa; Badr, Ibrahim; Miyamoto, Michael I; el-Halim Nur el-Din, Abd; Narula, Jagat; Finch, Caleb E; Thomas, Gregory S

    2013-04-06

    Atherosclerosis is thought to be a disease of modern human beings and related to contemporary lifestyles. However, its prevalence before the modern era is unknown. We aimed to evaluate preindustrial populations for atherosclerosis. We obtained whole body CT scans of 137 mummies from four different geographical regions or populations spanning more than 4000 years. Individuals from ancient Egypt, ancient Peru, the Ancestral Puebloans of southwest America, and the Unangan of the Aleutian Islands were imaged. Atherosclerosis was regarded as definite if a calcified plaque was seen in the wall of an artery and probable if calcifications were seen along the expected course of an artery. Probable or definite atherosclerosis was noted in 47 (34%) of 137 mummies and in all four geographical populations: 29 (38%) of 76 ancient Egyptians, 13 (25%) of 51 ancient Peruvians, two (40%) of five Ancestral Puebloans, and three (60%) of five Unangan hunter gatherers (p=NS). Atherosclerosis was present in the aorta in 28 (20%) mummies, iliac or femoral arteries in 25 (18%), popliteal or tibial arteries in 25 (18%), carotid arteries in 17 (12%), and coronary arteries in six (4%). Of the five vascular beds examined, atherosclerosis was present in one to two beds in 34 (25%) mummies, in three to four beds in 11 (8%), and in all five vascular beds in two (1%). Age at time of death was positively correlated with atherosclerosis (mean age at death was 43 [SD 10] years for mummies with atherosclerosis vs 32 [15] years for those without; phuman beings raises the possibility of a more basic predisposition to the disease. National Endowment for the Humanities, Paleocardiology Foundation, The National Bank of Egypt, Siemens, and St Luke's Hospital Foundation of Kansas City. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Museum theriological collections for the study of genetic diversity

    Directory of Open Access Journals (Sweden)

    Ettore Randi

    2008-02-01

    Full Text Available Abstract Molecular methods to analyse DNA variability are opening new perspectives in the role played by museums in biodiversity research. DNA can be extracted from specific tissue collections, as well as from traditional voucher specimens. Ancient and museum DNA research produce valuable information for defining the phylogenetic positions of extinct taxa, the reconstruction of molecular and organismal evolution in extinct species, the characterization of extinct populations, including animal diets or microbial infections. Historical DNA samples are important sources of information also for conservation and evolutionary studies. In this paper, the methods used for ancient DNA analysis and the main results reported in published studies are reviewed. Riassunto Le collezioni teriologiche museali e lo studio della variabilità genetica. I metodi di analisi del DNA aprono nuove prospettive per il ruolo dei musei nello studio della biodiversità. Il DNA può essere estratto da collezioni di tessuti, oppure dai tradizionali materiali museali. Le ricerche che utilizzano DNA antico e museale possono produrre informazioni utili per definire la posizione filogenetica di taxa, la ricostruzione dell’evoluzione molecolare e fenotipica di specie e la caratterizzazione di popolazioni estinte, incluse l’identificazione della dieta e la presenza di malattie infettive. L’analisi del DNA estratto da campioni storici può fornire informazioni importanti anche per ricerche di biologia della conservazione. Si analizzano i metodi utilizzati per l’analisi del DNA antico, corredati da un breve excursus dei risultati delle principali ricerche disponibili in letteratura.

  14. Genomic gigantism: DNA loss is slow in mountain grasshoppers.

    Science.gov (United States)

    Bensasson, D; Petrov, D A; Zhang, D X; Hartl, D L; Hewitt, G M

    2001-02-01

    Several studies have shown DNA loss to be inversely correlated with genome size in animals. These studies include a comparison between Drosophila and the cricket, Laupala, but there has been no assessment of DNA loss in insects with very large genomes. Podisma pedestris, the brown mountain grasshopper, has a genome over 100 times as large as that of Drosophila and 10 times as large as that of Laupala. We used 58 paralogous nuclear pseudogenes of mitochondrial origin to study the characteristics of insertion, deletion, and point substitution in P. pedestris and Italopodisma. In animals, these pseudogenes are "dead on arrival"; they are abundant in many different eukaryotes, and their mitochondrial origin simplifies the identification of point substitutions accumulated in nuclear pseudogene lineages. There appears to be a mononucleotide repeat within the 643-bp pseudogene sequence studied that acts as a strong hot spot for insertions or deletions (indels). Because the data for other insect species did not contain such an unusual region, hot spots were excluded from species comparisons. The rate of DNA loss relative to point substitution appears to be considerably and significantly lower in the grasshoppers studied than in Drosophila or Laupala. This suggests that the inverse correlation between genome size and the rate of DNA loss can be extended to comparisons between insects with large or gigantic genomes (i.e., Laupala and Podisma). The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila. The main factor contributing to the difference in the rates of DNA loss estimated for grasshoppers, crickets, and Drosophila appears to be deletion size. Large deletions are relatively rare in Podisma and Italopodisma.

  15. Ancient inland human dispersals from Myanmar into interior East Asia since the Late Pleistocene.

    Science.gov (United States)

    Li, Yu-Chun; Wang, Hua-Wei; Tian, Jiao-Yang; Liu, Li-Na; Yang, Li-Qin; Zhu, Chun-Ling; Wu, Shi-Fang; Kong, Qing-Peng; Zhang, Ya-Ping

    2015-03-26

    Given the existence of plenty of river valleys connecting Southeast and East Asia, it is possible that some inland route(s) might have been adopted by the initial settlers to migrate into the interior of East Asia. Here we analyzed mitochondrial DNA (mtDNA) HVS variants of 845 newly collected individuals from 14 Myanmar populations and 5,907 published individuals from 115 populations from Myanmar and its surroundings. Enrichment of basal lineages with the highest genetic diversity in Myanmar suggests that Myanmar was likely one of the differentiation centers of the early modern humans. Intriguingly, some haplogroups were shared merely between Myanmar and southwestern China, hinting certain genetic connection between both regions. Further analyses revealed that such connection was in fact attributed to both recent gene flow and certain ancient dispersals from Myanmar to southwestern China during 25-10 kya, suggesting that, besides the coastal route, the early modern humans also adopted an inland dispersal route to populate the interior of East Asia.

  16. Study on provenance of ancient pottery excavated from Huating Ruins, Xinyi County by INAA

    International Nuclear Information System (INIS)

    Xu Anwu; Wang Changsui; Chi Jinqi; Satoshi Koshimizu; Kazai Manabu; Kushihara Koichi

    1997-01-01

    The ancient pottery excavated from Huating Ruins, Xinyi Country, Jiangsu Province, was measured and studied by INAA. The data were manipulated by multivariate statistic analysis, such as cluster and factor analysis. It has been shown that the specimens can be divided into two groups, which are related to Liangzhu Culture area and Dawenkou Culture area respectively. The result seems to support the viewpoint that the pottery specimens of Liangzhu Culture from Huating Ruins belong to war trophies

  17. CHANT (CHinese ANcient Texts): a comprehensive database of all ancient Chinese texts up to 600 AD

    OpenAIRE

    Ho, Che Wah

    2006-01-01

    The CHinese ANcient Texts (CHANT) database is a long-term project which began in 1988 to build up a comprehensive database of all ancient Chinese texts up to the sixth century AD. The project is near completion and the entire database, which includes both traditional and excavated materials, will be released on the CHANT Web site (www.chant.org) in mid-2002. With more than a decade of experience in establishing an electronic Chinese literary database, we have gained much insight useful to the...

  18. A multidisciplinary study of archaeological grape seeds

    Science.gov (United States)

    Cappellini, Enrico; Gilbert, M. Thomas P.; Geuna, Filippo; Fiorentino, Girolamo; Hall, Allan; Thomas-Oates, Jane; Ashton, Peter D.; Ashford, David A.; Arthur, Paul; Campos, Paula F.; Kool, Johan; Willerslev, Eske; Collins, Matthew J.

    2010-02-01

    We report here the first integrated investigation of both ancient DNA and proteins in archaeobotanical samples: medieval grape ( Vitis vinifera L.) seeds, preserved by anoxic waterlogging, from an early medieval (seventh-eighth century A.D.) Byzantine rural settlement in the Salento area (Lecce, Italy) and a late (fourteenth-fifteenth century A.D.) medieval site in York (England). Pyrolysis gas chromatography mass spectrometry documented good carbohydrate preservation, whilst amino acid analysis revealed approximately 90% loss of the original protein content. In the York sample, mass spectrometry-based sequencing identified several degraded ancient peptides. Nuclear microsatellite locus (VVS2, VVMD5, VVMD7, ZAG62 and ZAG79) analysis permitted a tentative comparison of the genetic profiles of both the ancient samples with the modern varieties. The ability to recover microsatellite DNA has potential to improve biomolecular analysis on ancient grape seeds from archaeological contexts. Although the investigation of five microsatellite loci cannot assign the ancient samples to any geographic region or modern cultivar, the results allow speculation that the material from York was not grown locally, whilst the remains from Supersano could represent a trace of contacts with the eastern Mediterranean.

  19. The ancient materials speak volumes for the future

    International Nuclear Information System (INIS)

    Anon.

    2010-01-01

    Study the ancient materials inform us not only for the processes used at the time but also for their possible behaviour in the future. The archaeo-materials and alteration anticipation laboratory (LAPA, CEA Saclay) is engaged each day in studying these materials. (O.M.)

  20. Truth Obviousness in Ancient Greek Philosophy

    Directory of Open Access Journals (Sweden)

    Halyna I. Budz

    2013-01-01

    Full Text Available The article examines the features of the axiomatic approach to the truth understanding in ancient Greek philosophy. Truth in the works by ancient philosophers has axiomatic essence, basing on divine origin of truth. As the truth has a divine origin, it is in reality. The reality, created by Gods is the solemn reality. Therefore, understanding of reality by man is the display of divine reality, which is true and clever. In of the context of ancient Greek philosophy, to know truth is to know something, existing in reality, in other words, something, truly existing, eternal reality. Consequently, to know truth is it to know the substantial reality base. That’s why the justification of the reality origin is the axiomatic doctrine of truth at the same time, because only fundamental principle “truly” exists and is the truth itself. The idea of fundamental principle in ancient Greek philosophy is the axiom, universal principle, which is the base of reality as a substance from ontological perspective and is realized as the truth from gnosiological perspective. Fundamental principle, as Greeks understand it, coincides with the truth, in other words, reality and thinking are identical. The idea of reality source is the universal criterion of world perception at the same time, in other words, it is the truth, which is perceived axiomatically.

  1. Reflections on Tutoring Ancient Greek Philosophy: A Case Study of Teaching First-Year Undergraduates in the UK

    Science.gov (United States)

    Vázquez, Daniel

    2014-01-01

    This is a case study of my reflections on teaching a first-year undergraduate tutorial on Ancient Greek Philosophy in the UK. This study draws upon the notion of reflective practice as an essential feature of teaching, in this case applied to Higher Education. My aim is to show how a critical engagement with my teaching practices and the overall…

  2. Ancient Terrestrial Carbon: Lost and Found

    Science.gov (United States)

    Freeman, K. H.

    2017-12-01

    Carbon fluxes in terrestrial environments dominate the global carbon cycle. The fluxes of terrestrial carbon are strongly tied to regional climate due to the influences of temperature, water, and nutrient dynamics on plant productivity. However, climate also influences the destruction of terrestrial organic matter, through weathering, erosion, and biomass loss via fire and oxidative microbial processes. Organic geochemical methods enable us to interrogate past terrestrial carbon dynamics and learn how continental processes might accelerate, or mitigate carbon transfer to the atmosphere, and the associated greenhouse warming. Terrestrial soil systems represent the weathering rind of the continents, and are inherently non-depositional and erosive. The production, transport, and depositional processes affecting organics in continental settings each impart their own biases on the amount and characteristics of preserved carbon. Typically, the best archives for biomarker records are sediments in ancient lakes or subaqueous fans, which represents a preservation bias that tends to favor wetter environments. Paleosols, or ancient soils, formed under depositional conditions that, for one reason or another, truncated soil ablation, erosion, or other loss processes. In modern soils, widely ranging organic carbon abundances are almost always substantially greater than the trace amounts of carbon left behind in ancient soils. Even so, measureable amounts of organic biomarkers persist in paleosols. We have been investigating processes that preserve soil organic carbon on geologic timescales, and how these mechanisms may be sensitive to past climate change. Climate-linked changes in temperature, moisture, pH, and weathering processes can impact carbon preservation via organo-mineral sorption, soil biogeochemistry, and stability based on the physical and chemical properties of organic compounds. These will be discussed and illustrated with examples from our studies of Cenozoic

  3. DNA cards: determinants of DNA yield and quality in collecting genetic samples for pharmacogenetic studies.

    Science.gov (United States)

    Mas, Sergi; Crescenti, Anna; Gassó, Patricia; Vidal-Taboada, Jose M; Lafuente, Amalia

    2007-08-01

    As pharmacogenetic studies frequently require establishment of DNA banks containing large cohorts with multi-centric designs, inexpensive methods for collecting and storing high-quality DNA are needed. The aims of this study were two-fold: to compare the amount and quality of DNA obtained from two different DNA cards (IsoCode Cards or FTA Classic Cards, Whatman plc, Brentford, Middlesex, UK); and to evaluate the effects of time and storage temperature, as well as the influence of anticoagulant ethylenediaminetetraacetic acid on the DNA elution procedure. The samples were genotyped by several methods typically used in pharmacogenetic studies: multiplex PCR, PCR-restriction fragment length polymorphism, single nucleotide primer extension, and allelic discrimination assay. In addition, they were amplified by whole genome amplification to increase genomic DNA mass. Time, storage temperature and ethylenediaminetetraacetic acid had no significant effects on either DNA card. This study reveals the importance of drying blood spots prior to isolation to avoid haemoglobin interference. Moreover, our results demonstrate that re-isolation protocols could be applied to increase the amount of DNA recovered. The samples analysed were accurately genotyped with all the methods examined herein. In conclusion, our study shows that both DNA cards, IsoCode Cards and FTA Classic Cards, facilitate genetic and pharmacogenetic testing for routine clinical practice.

  4. Colour Perception in Ancient World

    Science.gov (United States)

    Nesterov, D. I.; Fedorova, M. Yu

    2017-11-01

    How did the human thought form the surrounding color information into the persistent semantic images of a mythological, pseudoscientific and religious nature? The concepts associated with colour perception are suggested. The existence of colour environment does not depend on the human consciousness. The colour culture formation is directly related to the level of the human consciousness development and the possibility to influence the worldview and culture. The colour perception of a person goes through the stages similar to the development of colour vision in a child. Like any development, the colour consciousness has undergone stages of growth and decline, evolution and stagnation. The way of life and difficult conditions for existence made their own adjustments to the development of the human perception of the surrounding world. Wars have been both a powerful engine of progress in all spheres of life and a great destructive force demolishing the already created and preserved heritage. The surrounding world has always been interesting for humans, evoked images and fantasies in the consciousness of ancient people. Unusual and inexplicable natural phenomena spawned numerous legends and myths which was reflected in the ancient art and architecture and, accordingly, in a certain manifestation of colour in the human society. The colour perception of the ancient man, his pragmatic, utilitarian attitude to colour is considered as well as the influence of dependence on external conditions of existence and their reflection in the colour culture of antiquity. “Natural Science” conducts research in the field of the colour nature and their authorial interpretation of the Hellenic period. Several authorial concepts of the ancient world have been considered.

  5. Unique parasite aDNA in moa coprolites from New Zealand suggests mass parasite extinctions followed human-induced megafauna extinctions

    Science.gov (United States)

    Lafferty, Kevin D.; Hopkins, Skylar R.

    2018-01-01

    Having split early from Gondwana, Zealandia (now modern New Zealand) escaped discovery until the late 13th century, and therefore remains an important glimpse into a human-free world. Without humans or other land mammals, diverse and peculiar birds evolved in isolation, including several flightless moa species, the giant pouakai eagle (Harpagornis moorei), the kiwi (Apteryx mantelli), and the kakapo parrot (Strigops habroptila). This unique community has fascinated paleoecologists, who have spent almost two centuries devising new ways to glean information from ancient bird remains. In PNAS, Boast et al. (1) apply one recent technological advance, ancient DNA (aDNA) metabarcoding, to confirm previous discoveries and report new details about moa and kakapo diets, parasites, and niches. Their efforts confirm Zealandia was a lot different before humans arrived.

  6. DNA hydration studied by neutron fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix.

  7. DNA hydration studied by neutron fiber diffraction

    International Nuclear Information System (INIS)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J.

    1994-01-01

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix

  8. Dacic Ancient Astronomical Research in Sarmizegetuza

    Directory of Open Access Journals (Sweden)

    Emanuel George Oprea

    2015-11-01

    Full Text Available The actual Romanian territory belongs to Carpatho-Danubian Space and to Ancient Europe. The Ancient European Society was a vast cultural entity based on a theocratic, matriarchal society, peaceful and art creating.Temples of Sarmizegetusa have given rise to several theories over time, proven by historians with the most diverse arguments. The largest complex of temples and sanctuaries was founded in Sarmizegetusa Regia, the Dacian’s main fortress and ancient capital of Dacia in the time of King Decebalus. The mysterious form of settlements has led researchers to the conclusion that the locations were astronomical observation shrines. Among the places of Dacian worship in Orastie Mountains the most impressive is the Great Circular Sanctuary, used to perform some celestial observations, and also as original solar calendar. This paper had the purpose to re-discover the Dacian Civilization and Dacian cosmogony based on the accumulated knowledge upon our country’s past.

  9. Did the ancient egyptians discover Algol?

    Science.gov (United States)

    Jetsu, L.; Porceddu, S.; Porceddu, S.; Lyytinen, J.; Kajatkari, P.; Markkanen, T.; Toivari-Viitala, J.

    2013-02-01

    Fabritius discovered the first variable star, Mira, in 1596. Holwarda determined the 11 months period of Mira in 1638. Montanari discovered the next variable star, Algol, in 1669. Its period, 2.867 days, was determined by Goodricke (178). Algol was associated with demon-like creatures, "Gorgon" in ancient Greek and "ghoul" in ancient Arab mythology. This indicates that its variability was discovered much before 1669 (Wilk 1996), but this mythological evidence is ambiguous (Davis 1975). For thousands of years, the Ancient Egyptian Scribes (AES) observed stars for timekeeping in a region, where there are nearly 300 clear nights a year. We discovered a significant periodicity of 2.850 days in their calendar for lucky and unlucky days dated to 1224 BC, "the Cairo Calendar". Several astrophysical and astronomical tests supported our conclusion that this was the period of Algol three millennia ago. The "ghoulish habits" of Algol could explain this 0.017 days period increase (Battersby 2012).

  10. Finding hidden chemistry in ancient egyptian artifacts: Pigment degradation taught in a chemical engineering course

    OpenAIRE

    Giménez Izquierdo, Francisco Javier

    2015-01-01

    The main objective of this work was to show the application of the study of ancient technology and science on teaching (and learning) chemistry in Chemical Engineering Undergraduate studies. Degradation patterns of pigments used in Ancient Egypt were incorporated in the syllabus of the course entitled

  11. DNA methylation analysis from saliva samples for epidemiological studies.

    Science.gov (United States)

    Nishitani, Shota; Parets, Sasha E; Haas, Brian W; Smith, Alicia K

    2018-06-18

    Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.

  12. High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice.

    Science.gov (United States)

    Amanzougaghene, Nadia; Mumcuoglu, Kosta Y; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

    2016-01-01

    The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.

  13. Removal of natural organic dyes from wool-implications for ancient textile provenance studies

    DEFF Research Database (Denmark)

    Frei, Karin Margarita; Vanden Berghe, Ina; Frei, Robert

    2010-01-01

    Ancient wool textiles recovered from archaeological sites are in many cases originally dyed with natural organic dyestuffs from vegetable sources. These include among others woad (Isatis tinctoria L.), weld (Reseda luteola L.), and madder (Rubia tinctorum L.). These dyestuffs could be a threat...

  14. Studying DNA looping by single-molecule FRET.

    Science.gov (United States)

    Le, Tung T; Kim, Harold D

    2014-06-28

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

  15. Finding Hidden Chemistry in Ancient Egyptian Artifacts: Pigment Degradation Taught in a Chemical Engineering Course

    Science.gov (United States)

    Gime´nez, Javier

    2015-01-01

    The main objective of this work was to show the application of the study of ancient technology and science on teaching (and learning) chemistry in Chemical Engineering Undergraduate studies. Degradation patterns of pigments used in Ancient Egypt were incorporated in the syllabus of the course entitled "Technological and Scientific…

  16. Ancient Wisdom, Applied Knowledge for a Sustainable Future

    Science.gov (United States)

    Peterson, K.; Philippe, R. Elde; Dardar, T. M. Elde

    2017-12-01

    Ancient wisdom informs traditional knowledges that guide Indigenous communities on how to interact with the world. These knowledges and the ancient wisdom have been the life-giving forces that have prevented the complete genocide of Indigenous peoples, and is also the wisdom that is rejuvenating ancient ways that will take the world into a future that embraces the seventh generation philosophy.. Western scientists and agency representatives are learning from the work and wisdom of Native Americans. This presentation will share the ways in which the representatives of two Tribes along the coast of Louisiana have been helping to educate and apply their work with Western scientists.

  17. Radiocarbon ages of Sorori ancient rice of Korea

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyeong Ja, E-mail: kjkim@kigam.re.kr [Korea Institute of Geoscience and Mineral Resources, Daejeon (Korea, Republic of); Lee, Yung-Jo; Woo, Jong-Yoon [Institute of Korean Prehistory, Cheongju (Korea, Republic of); Jull, A.J. Timothy [NSF Arizona AMS Laboratory, University of Arizona, Tucson, AZ 85721 (United States)

    2013-01-15

    Samples of Sorori ancient rice were excavated in 1998 from the Sorori Paleolithic site located at Sorori, Oksan-myeon, Cheong-won County in Chungcheongbuk-do, Korea. We have made new radiocarbon measurements for Sorori samples in 2009 at the NSF Arizona AMS Laboratory. Both ancient rice samples and surrounded peat from the Sorori site were dated. The AMS results confirmed that the ages of the rice and peat soil were 12,520 {+-} 150 and 12,552 {+-} 90 BP, respectively. These radiocarbon ages are consistent with the previously published data of quasi rice measured at Seoul National University and confirm that the Sorori rice is the oldest ancient rice currently reported.

  18. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

    Science.gov (United States)

    Schuenemann, Verena J.; Peltzer, Alexander; Welte, Beatrix; van Pelt, W. Paul; Molak, Martyna; Wang, Chuan-Chao; Furtwängler, Anja; Urban, Christian; Reiter, Ella; Nieselt, Kay; Teßmann, Barbara; Francken, Michael; Harvati, Katerina; Haak, Wolfgang; Schiffels, Stephan; Krause, Johannes

    2017-01-01

    Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level. PMID:28556824

  19. Digital Study and Web-based Documentation of the Colour and Gilding on Ancient Marble Artworks

    OpenAIRE

    Siotto, Eliana; Palma, Gianpaolo; Potenziani, Marco; Scopigno, Roberto

    2015-01-01

    Greek and Roman marble artworks have been deeply studied from a typological and stylistic point of view, while there is still a limited knowledge on the pigments, dyes, binders and technical expedients used by Roman artists. In a renewed scientific interest towards the ancient polychromy (colour and gilding), a digital methodological and multidisciplinary approach can provide valuable information to better investigate and understand this fundamental aspect and to get a complete sense on Greek...

  20. An Ancient Inca Tax and Metallurgy in Peru

    Science.gov (United States)

    Journal of Chemical Education, 2007

    2007-01-01

    The discovery of ancient Inca tax rulers and other metallurgical objects in Peru show that the ancient civilizations of the country smelted metals. The analysis shows that the smelters in Peru switched from the production of copper to silver after a tax was imposed on them by the Inca rulers.

  1. Ancient drainages divide cryptic species in Australia's arid zone: morphological and multi-gene evidence for four new species of Beaked Geckos (Rhynchoedura).

    Science.gov (United States)

    Pepper, Mitzy; Doughty, Paul; Hutchinson, Mark N; Scott Keogh, J

    2011-12-01

    Deserts and other arid zones remain among the least studied biomes on Earth. Emerging genetic patterns of arid-distributed biota suggest a strong link between diversification history and both the onset of aridification and more recent cycles of severe aridification. A previous study based on 1 kb of mtDNA of the monotypic gecko genus Rhynchoedura identified five allopatric clades across the vast Australian arid zone. We supplemented this data with 2.2kb from three nuclear loci and additional mtDNA sequences. Phylogenetic relationships estimated from the mtDNA data with ML and Bayesian methods were largely concordant with relationships estimated with the nDNA data only, and mtDNA and nDNA data combined. These analyses, and coalescent-based species-tree inference methods implemented with (∗)BEAST, largely resolve the relationships among them. We also carried out an examination of 19 morphological characters for 268 museum specimens from across Australia, including all 197 animals for which we sequenced mtDNA. The mtDNA clades differ subtly in a number of morphological features, and we describe three of them as new species, raise a fourth from synonymy, and redescribe it and the type species, Rhynchoedura ornata. We also describe a morphologically distinctive new species from Queensland based on very few specimens. The distribution of arid zone clades across what is now relatively homogeneous sand deserts seems to be related to a topographic divide between the western uplands and eastern lowlands, with species' distributions correlated with dryland rivers and major drainage divides. The existence of five cryptic species within the formerly monotypic Rhynchoedura points to ancient divergences within the arid zone that likely were driven by wet phases as well as dry ones. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Patterns of DNA Methylation in Development, Division of Labor and Hybridization in an Ant with Genetic Caste Determination

    OpenAIRE

    Smith, Chris R.; Mutti, Navdeep S.; Jasper, W. Cameron; Naidu, Agni; Smith, Christopher D.; Gadau, Jürgen

    2012-01-01

    BACKGROUND: DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events. METHODOLOGY/PRINCIPAL FINDINGS: Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucle...

  3. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

    DEFF Research Database (Denmark)

    Campos, Paula; Kristensen, Tommy; Orlando, Ludovic Antoine Alexandre

    2010-01-01

    of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two...... well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals...... and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate...

  4. Sex and Gender Related Health Status Differences in Ancient and Contemporary Skeletal Populations

    Directory of Open Access Journals (Sweden)

    Velissaria Vanna

    2007-11-01

    Full Text Available Human skeletal and dental remains are an invaluable source of information for interpreting the way of life of past people and also provide the only direct evidence of non-living populations’ health status. This research paper discusses the sex-related health differences observed in two skeletal populations from Greece, an ancient and a modern, by employing multiple health indicators, and aims at determining the biological and possible social factors that contribute to this variation. Particular emphasis is given to the importance of hypotheses-driven, population-based studies of human remains as the most effective means of reconstructing life in the past. The results showed that fracture ('ancient': females 0.08%, males 0.12%; 'modern': females 0.38%, males 0.19% and osteoarthritis ('ancient': females 0.7%, males: 3.0%; 'modern': females 4.4%, males 3.2% frequencies were higher for male individuals than females in the ancient population, which can be explained by greater engagement in strenuous and risky activity. Dental caries ('ancient': females 1.2%, males 1.8%; 'modern': females 23.6%, males 17.4% and ante-mortem tooth loss ('ancient': females 12.3%, males 7.7%; 'modern': females 69.5%, males 49.5% rates were higher for females than males (with the exception of the almost equal caries rates for the ancient population, most likely due to hormonal fluctuations, saliva content and flow, because female teeth erupt earlier and also perhaps as a result of differences in dietary habits. Periodontitis levels were more elevated in males ('ancient': females 9.6%, males 30.1%; 'modern': females 29.1%, males 38.3%, possibly due to poor oral hygiene practices and excessive masticatory loading. Dental enamel defects rates showed that in the ancient population, males had more chances of surviving childhood stress than females (females 19.5%, males 20.0%, whereas, in the modern population, the exact opposite was the case (females 6.1%, males 22.7%.

  5. Neutron activation analysis of some ancient and modern Chinese Jun Porcelain samples

    International Nuclear Information System (INIS)

    Gao Zhengyao; Wang Jie; Chen Songhua; Huang Zhongxiang; Han Song; Jia Xiuqin

    1997-01-01

    Up to 43 glaze and body samples of ancient and modern Chinese Jun Porcelain and other porcelain are chosen and contents of 36 elements for each sample are determined by NAA. The NAA data are then analysed by the fuzzy cluster method. The result shows that although the ancient Jun Porcelain samples span leaped 600 years and are from different kilns and their glaze colors are utterly different, they have a long-term, stable and mainly the same supply of raw material. The relation between ancient Jun Porcelain and ancient Ru Porcelain is also preliminarily analysed. It is found that only few modern Jun Porcelain samples are similar to ancient Jun Porcelain but the majority of them are different from ancient ones

  6. Uxoricide in pregnancy: ancient Greek domestic violence in evolutionary perspective.

    Science.gov (United States)

    Deacy, Susan; McHardy, Fiona

    2013-10-24

    Previous studies of ancient Greek examples of uxoricide in pregnancy have concluded that the theme is used to suggest tyrannical abuse of power and that the violence is a product of the patriarchal nature of ancient society. This article uses evolutionary analyses of violence during pregnancy to argue that the themes of sexual jealousy and uncertainty over paternity are as crucial as the theme of power to an understanding of these examples and that the examples can be seen as typical instances of spousal abuse as it occurs in all types of society.

  7. Reconstructing an Ancient Wonder.

    Science.gov (United States)

    Imhof, Christopher J.

    2001-01-01

    Describes a Montessori class project involving the building of a model of the ancient Briton monument, Stonehenge. Illustrates how the flexibility of the Montessori elementary curriculum encourages children to make their own toys and learn from the process. (JPB)

  8. The Challenges of Qualitatively Coding Ancient Texts

    Science.gov (United States)

    Slingerland, Edward; Chudek, Maciej

    2012-01-01

    We respond to several important and valid concerns about our study ("The Prevalence of Folk Dualism in Early China," "Cognitive Science" 35: 997-1007) by Klein and Klein, defending our interpretation of our data. We also argue that, despite the undeniable challenges involved in qualitatively coding texts from ancient cultures,…

  9. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C.; Welch, Andreanna J.; Ratan, Aakrosh; Bedoya-Reina, Oscar C.; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C.; Drautz, Daniela I.; Wittekindt, Nicola E.; Tomsho, Lynn P.; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K.; Rode, Karyn D.; Obbard, Martyn E.; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Ólafur; Aars, Jon; Mailund, Thomas; Wiig, Øystein; Talbot, Sandra L.; Lindqvist, Charlotte

    2012-01-01

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  10. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

    Science.gov (United States)

    Miller, Webb; Schuster, Stephan C; Welch, Andreanna J; Ratan, Aakrosh; Bedoya-Reina, Oscar C; Zhao, Fangqing; Kim, Hie Lim; Burhans, Richard C; Drautz, Daniela I; Wittekindt, Nicola E; Tomsho, Lynn P; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis; Peacock, Elizabeth; Farley, Sean; Sage, George K; Rode, Karyn; Obbard, Martyn; Montiel, Rafael; Bachmann, Lutz; Ingólfsson, Olafur; Aars, Jon; Mailund, Thomas; Wiig, Oystein; Talbot, Sandra L; Lindqvist, Charlotte

    2012-09-04

    Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

  11. DNA identification of a 10th century female skeleton from the Prague Castle belonging to a member of the Przemyslids Dynasty

    Czech Academy of Sciences Publication Activity Database

    Votrubová, J.; Sasková, L.; Frolík, Jan; Vaněk, D.

    2017-01-01

    Roč. 6, December (2017), „e135”-„e136” ISSN 1875-1768 R&D Projects: GA ČR GB14-36938G Institutional support: RVO:67985912 Keywords : mitochondrial DNA * ancient bones * Przemyslid dynasty * haplogroup * haplotype * mtDNA databases Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology http://www.fsigeneticssup.com/article/S1875-1768(17)30159-2/pdf

  12. Studies on sildenafil citrate (Viagra) interaction with DNA using electrochemical DNA biosensor.

    Science.gov (United States)

    Rauf, Sakandar; Nawaz, Haq; Akhtar, Kalsoom; Ghauri, Muhammad A; Khalid, Ahmad M

    2007-05-15

    The interaction of sildenafil citrate (Viagra) with DNA was studied by using an electrochemical DNA biosensor. The binding mechanism of sildenafil citrate was elucidated by using constant current potentiometry and differential pulse voltammetry at DNA-modified glassy carbon electrode. The decrease in the guanine oxidation peak area or peak current was used as an indicator for the interaction in 0.2M acetate buffer (pH 5). The binding constant (K) values obtained were 2.01+/-0.05 x 10(5) and 1.97+/-0.01 x 10(5)M(-1) with constant current potentiometry and differential pulse voltammetry, respectively. A linear dependence of the guanine peak area or peak current was observed within the range of 1-40 microM sildenafil citrate with slope=-2.74 x 10(-4)s/microM, r=0.989 and slope=-2.78 x 10(-3)microA/microM, r=0.995 by using constant current potentiometry and differential pulse voltammetry, respectively. Additionally, binding constant values for sildenafil citrate-DNA interaction were determined for the pH range of 4-8 and in biological fluids (serum and urine) at pH 5. The influence of sodium and calcium ions was also studied to elucidate the mechanism of sildenafil citrate-DNA interaction under different solution conditions. The present study may prove to be helpful in extending our understanding of the anticancer activity of sildenafil citrate from cellular to DNA level.

  13. Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

    Directory of Open Access Journals (Sweden)

    Parker Hugo J

    2011-12-01

    Full Text Available Abstract Background Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. Results Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. Conclusions These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs, which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.

  14. Study of provenance properties on ancient celadon of different kilns with NAA

    International Nuclear Information System (INIS)

    Feng Songlin; Fan Dongyu; Feng Xiangqian; Xu Qing; Cheng Lin; Lei Yong; Shen Yueming; Zhang Wenjiang; Zhua Zhenxi

    2005-01-01

    Provenance characteristic is an important scientific parameter to identify ancient porcelain wares unearthed from sites and graves. The porcelain samples of Si-Long-Kou Yue kiln of Zhejiang Province, Hong-Zhou kiln of Jiangxi Province and Yao-Zhou kiln of Shanxi Province have been analyzed with neutron activation analysis (NAA). The experimental data were studied with statistic methods. The results show that the chemical compositions of porcelain body samples for three kilns were different. The difference was able to be identified. The body materials of both Si-Long-Kou Yue kiln and Hong-Zhou kiln of Jiangxi were similar. The samples of Yao-Zhou kiln in north of China existed obvious difference. (authors)

  15. Applied investigation of Moessbauer effect for the famous ancient chinese porcelains

    International Nuclear Information System (INIS)

    Gao Zhengyao; Chen Songhua; Shen Zuocheng

    1996-10-01

    The famous Ru porcelain, Jun porcelain and Guan porcelain of Song Dynasty and Yuan Dynasty are analyzed. The Moessbauer parameters of the ancient porcelains and the imitative ancient porcelains are compared. The firing techniques, coloring mechanism and microstructures of the ancient Chinese porcelains have been discussed. (7 figs., 4 tabs.)

  16. Notions of "Rhetoric as Epistemic" in Ancient Greece.

    Science.gov (United States)

    Benoit, William L.

    The notion that rhetoric (and to a lesser extent, argument) is epistemic is an increasingly popular one today, although it can be traced to ancient Greece. The notion holds that rhetoric, or the art of persuasion, creates and shapes knowledge. Two ancient authors--Aristophanes and Plato--provide evidence that others had notions of rhetoric as…

  17. Lipid biomarkers for bacterial ecosystems: studies of cultured organisms, hydrothermal environments and ancient sediments

    Science.gov (United States)

    Summons, R. E.; Jahnke, L. L.; Simoneit, B. R.

    1996-01-01

    This paper forms part of our long-term goal of using molecular structure and carbon isotopic signals preserved as hydrocarbons in ancient sediments to improve understanding of the early evolution of Earth's surface environment. We are particularly concerned with biomarkers which are informative about aerobiosis. Here, we combine bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems to construct models for the nature, behaviour and preservation potential of primitive microbial communities. We use a combined molecular and isotopic approach to characterize lipids produced by cultured bacteria and test a variety of culture conditions which affect their biosynthesis. This information is then compared with lipid mixtures isolated from contemporary hot springs and evaluated for the kinds of chemical change that would accompany burial and incorporation into the sedimentary record. In this study we have shown that growth temperature does not appear to alter isotopic fractionation within the lipid classes produced by a methanotropic bacterium. We also found that cultured cyanobacteria biosynthesize diagnostic methylalkanes and dimethylalkanes with the latter only made when growing under low pCO2. In an examination of a microbial mat sample from Octopus Spring, Yellowstone National Park (USA), we could readily identify chemical structures with 13C contents which were diagnostic for the phototrophic organisms such as cyanobacteria and Chloroflexus. We could not, however, find molecular evidence for operation of a methane cycle in the particular mat samples we studied.

  18. Surgical history of ancient China: Part 2.

    Science.gov (United States)

    Fu, Louis

    2010-03-01

    In this second part of ancient Chinese surgical history, the practice of bone setting in China began around 3000 years ago. Throughout this period, significant progress was made, some highlights of which are cited. These methods, comparable with Western orthopaedic technique, are still being practised today. In conclusion, the possible reasons for the lack of advancement in operative surgery are discussed, within context of the cultural, social and religious background of ancient China.

  19. Social Norms in the Ancient Athenian Courts

    OpenAIRE

    Lanni, Adriaan M.

    2013-01-01

    Ancient Athens was a remarkably peaceful and well-ordered society by both ancient and contemporary standards. Scholars typically attribute Athens’ success to internalized norms and purely informal enforcement mechanisms. This article argues that the formal Athenian court system played a vital role in maintaining order by enforcing informal norms. This peculiar approach to norm enforcement compensated for apparent weaknesses in the state system of coercion. It mitigated the effects of under-e...

  20. Musical ensembles in Ancient Mesapotamia

    NARCIS (Netherlands)

    Krispijn, T.J.H.; Dumbrill, R.; Finkel, I.

    2010-01-01

    Identification of musical instruments from ancient Mesopotamia by comparing musical ensembles attested in Sumerian and Akkadian texts with depicted ensembles. Lexicographical contributions to the Sumerian and Akkadian lexicon.

  1. history repeats itself : saddam and the ancient mesopotamian royal

    African Journals Online (AJOL)

    harkhu

    ancient Mesopotamia (present day Iraq)2, from the fourth millennium3 until its incorporation into the ..... aspects of Mesopotamian culture that could not be separated from the other. Saddam, on the ..... site of ancient Babylon. Large parts of the ...

  2. A model system for DNA repair studies

    International Nuclear Information System (INIS)

    Lange, C.S.; Perlmutter, E.

    1984-01-01

    The search for the ''lethal lesion:'' which would yield a molecular explanation of biological survival curves led to attempts to correlate unrepaired DNA lesions with loss of reproductive integrity. Such studies have shown the crucial importance of DNA repair systems. The unrepaired DSB has been sought for such correlation, but in such study the DNA was too large, polydisperse, and/or structurally complex to permit precise measurement of break induction and repair. Therefore, an analog of higher order systems but with a genome of readily measurable size, is needed. Bacteriophage T4 is such an analog. Both its biological (PFU) and molecular (DNA) survival curves are exponentials. Its aerobic /sub PFU/D/sub 37///sub DNA/D/sub 37/ ratio, (410 +- 4.5Gy/540 +- 25 Gy) indicates that 76 +- 4% of lethality at low multiplicity infection (moi 1) the survival is greater than can be explained if the assumption of no parental DSB repair were valid. Both T4 and its host have DSB repair systems which can be studied by the infectious center method. Results of such studies are discussed

  3. The history of parkinsonism: descriptions in ancient Indian medical literature.

    Science.gov (United States)

    Ovallath, Sujith; Deepa, P

    2013-05-01

    The clinical syndrome of parkinsonism was identified in ancient India even before the period of Christ and was treated methodically. The earliest reference to bradykinesia dates to 600 bc. Evidences prove that as early as 300 bc, Charaka proposed a coherent picture of parkinsonism by describing tremor, rigidity, bradykinesia, and gait disturbances as its components. The scenario was further developed by Madhava, Vagbhata, and Dalhana all through history. The 15th-century classic "Bhasava rajyam" introduced the term kampavata, which may be regarded as an ayurvedic analogue of parkinsonism. The pathogenesis of kampavata centered on the concept of imbalance in the vata factor, which controls psychomotor activities. The essential element in therapy was the administration of powdered seed of Mucuna pruriens, or atmagupta, which as per reports, contains 4%-6% of levodopa. In addition to proving the existence and identification of parkinsonism in ancient India, the study points to the significance of ancient Indian Sanskrit works in medical history. Copyright © 2013 Movement Disorder Society.

  4. Migration of vascular plant species to a recent wood adjoining ancient woodland

    Directory of Open Access Journals (Sweden)

    Zbigniew Dzwonko

    2014-01-01

    Full Text Available Woodland communities can be restored by natural succession in sites adjoining ancient woodlands which can act as seed sources for trees, shrubs and woodland herbs. The influence of dominant tree species and the distance from an adjacent ancient oak-hornbeam woodland upon the floristic composition of species in a recent pine wood planted on dry rendzina soil were studied. It was found that, in spite of a 52-year long succession, the border between woods was sharp and the composition of species in the recent wood were significantly different than in the adjacent ancient woodland. Canonical correspondence analysis (CCA showed that the distance to the ancient woodland had a significant influence on species distributions in the recent wood. The numbers of species from the Querco-Fagetea class, vegetatively reproducing species and myrmecochores decreased with this distance, whereas the numbers of anemochores increased. The migration rate of many woodland species, calculated on occurrence of the farthest individuals was very slow, varying from 0.0 m year-1 to 0.38 m year-1. The restoration of the field layer vegetation in the studied pine wood was much slower than in recent deciduous woods on rich and moist soils where the migration rate of some species exceeded 1.50 m year-1. Recent woods adjacent to ancient woodlands can be more effectively colonised by woodland species only when they are dominated by broad-leaved trees with quickly decomposing litter, and the spatial continuity of these woods persists for a long period.

  5. Ancient genomes document multiple waves of migration in Southeast Asian prehistory.

    Science.gov (United States)

    Lipson, Mark; Cheronet, Olivia; Mallick, Swapan; Rohland, Nadin; Oxenham, Marc; Pietrusewsky, Michael; Pryce, Thomas Oliver; Willis, Anna; Matsumura, Hirofumi; Buckley, Hallie; Domett, Kate; Hai, Nguyen Giang; Hiep, Trinh Hoang; Kyaw, Aung Aung; Win, Tin Tin; Pradier, Baptiste; Broomandkhoshbacht, Nasreen; Candilio, Francesca; Changmai, Piya; Fernandes, Daniel; Ferry, Matthew; Gamarra, Beatriz; Harney, Eadaoin; Kampuansai, Jatupol; Kutanan, Wibhu; Michel, Megan; Novak, Mario; Oppenheimer, Jonas; Sirak, Kendra; Stewardson, Kristin; Zhang, Zhao; Flegontov, Pavel; Pinhasi, Ron; Reich, David

    2018-05-17

    Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from eighteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants. Copyright © 2018, American Association for the Advancement of Science.

  6. SOCIOLOGIC EXAMINATION OF HELLENISTIC ART IN THE LIGHT OF ANCIENT ERA

    Directory of Open Access Journals (Sweden)

    Z. Aslıhan OZTURK

    2016-10-01

    Full Text Available In this study, the emergence of Hellenistic Art, historical and social background that constitutive it, important features that put it forward and important artworks in the light of Ancient Era Society and Art general framework will be examined. Hellenistic Art as an Ancient Era Art was existed blending Greek culture and art which are dominant elements of the empire and cultures of conquered lands, progressed as a mixed culture. On the wide geography that Alexander the Great conquered, in time differences showed up in the direction of the beliefs, social structure and sense of art of this region and powerful and effective artworks were revealed taking form of this differences with a common understanding. In this reseach, Hellenistic Art that showed a common understanding belongs to almost whole known World in Ancient Era and its sociologic Fundamentals will be analyzed.

  7. Dating ancient Chinese celadon porcelain by neutron activation analysis and bayesian classification

    International Nuclear Information System (INIS)

    Xie Guoxi; Feng Songlin; Feng Xiangqian; Zhu Jihao; Yan Lingtong; Li Li

    2009-01-01

    Dating ancient Chinese porcelain is one of the most important and difficult problems in porcelain archaeological field. Eighteen elements in bodies of ancient celadon porcelains fired in Southern Song to Yuan period (AD 1127-1368) and Ming dynasty (AD 1368-1644), including La, Sm, U, Ce, etc., were determined by neutron activation analysis (NAA). After the outliers of experimental data were excluded and multivariate normal distribution was tested, and Bayesian classification was used for dating of 165 ancient celadon porcelain samples. The results show that 98.2% of total ancient celadon porcelain samples are classified correctly. It means that NAA and Bayesian classification are very useful for dating ancient porcelain. (authors)

  8. ANCIENT BREAD STAMPS FROM JORDAN

    OpenAIRE

    Kakish, Randa

    2014-01-01

    Marking bread was an old practice performed in different parts of the old world. It was done for religious, magical, economic and identification purposes. Bread stamps differ from other groups of stamps. Accordingly, the aim of this article is to identify such stamps, displayed or stored, in a number of Jordanian Archaeological Museums. A col-lection of twelve ancient bread stamps were identified and studied. Two of the stamps were of unknown provenance while the others came from al-Shuneh, D...

  9. Ancient ports of Kalinga

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    which plied between Kalinga and south east Asian countries. Nanda Raja, is said to have attacked Kalinga with the intention of getting access to the sea for the landlocked Kingdom of Magadha (Bihar). The ancient texa Artha Sastra (3rd-4th century B...

  10. Ancient Greek in modern language of medicine

    OpenAIRE

    Marković Vera

    2007-01-01

    In order to standardize language of medicine, it is essential to have a good command of ancient Greek and Latin. We cannot deny a huge impact of ancient Greek medicine on medical terminology. Compounds of Greek origin related to terms for organs, illnesses, inflammations, surgical procedures etc. have been listed as examples. They contain Greek prefixes and suffixes transcribed into Latin and they have been analyzed. It may be concluded that the modern language of medicine basically represent...

  11. From ancient Greek Logos to European rationality

    OpenAIRE

    APOSTOLOPOULOU GEORGIA

    2016-01-01

    Because of history, culture, and politics, European identity has its archetypical elements in ancient Greek culture. Ancient Greek philosophy brought Logos to fore and defined it as the crucial problem and the postulate of the human. We translate the Greek term Logos in English as reason or rationality. These terms, however, do not cover the semantic field of Logos since this includes, among other things, order of being, ground, language, argument etc. The juxtaposition of Logos (reason) to m...

  12. Living with the world heritage. An ethnographic study of the ancient city of Nessebar, Bulgaria

    Directory of Open Access Journals (Sweden)

    Luleva Ana

    2015-01-01

    Full Text Available Since the mid-1950s the Ancient city of Nessebar has had the status of national cultural heritage; in 1983 it was inscribed in the World heritage list of UNESCO. The article makes an attempt to study the regimes of using of and living in the city - world cultural heritage in two different political and economic contexts. The pressure of the tourism industry on the value, which was visible even in the years of the late state socialism, became irresistible after 1989 in the context of the liberalised market economy, the interests of the private investors and the accepted as part of the "normal" market order corrupt practices of the institutions that are responsible for the safeguarding and management of the cultural heritage. The ethnographic study argues that intertwined in a Gordian knot around the central question for the residents of the ancient city of Nessebar, viz. the occupation of the city, which has been declared a world heritage site, are issues like trust and distrust in the institutions, the experience of abiding by formal and informal rules for operation with private property, the notions of social justice, local identity, the use of the cultural heritage as symbolic capital by different social actors and its transformation into economic one, with the conflicting interconnection between tourist industry and cultural heritage.

  13. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  14. Single Molecule Study of DNA Organization and Recombination

    Science.gov (United States)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force

  15. Duplex Alu Screening for Degraded DNA of Skeletal Human Remains

    Directory of Open Access Journals (Sweden)

    Fabian Haß

    2017-10-01

    Full Text Available The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs, have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.

  16. Paleogenetic investigations of hominin diversity and dispersals in Eurasian prehistory

    OpenAIRE

    Posth, Cosimo

    2017-01-01

    Ancient DNA (aDNA) is able to provide genetic snapshots into the human past that can be linked together to study evolutionary processes and demographic patterns impossible to uncover with the study of modern-day DNA alone. In this thesis I make use of major methodological “game changers” in the field of aDNA in order to reconstruct complete mitochondrial DNA (mtDNA), as well as genome-wide nuclear data (nDNA) from ancient human specimens. The combination of next generation sequencing (NGS) te...

  17. Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies

    Science.gov (United States)

    El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

    2014-01-01

    Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at −20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

  18. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies.

    Science.gov (United States)

    El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H C; De Keersmaecker, Sigrid C J

    2014-12-01

    Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.

  19. Evolutionary history of continental southeast Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data.

    Science.gov (United States)

    Jinam, Timothy A; Hong, Lih-Chun; Phipps, Maude E; Stoneking, Mark; Ameen, Mahmood; Edo, Juli; Saitou, Naruya

    2012-11-01

    The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two major migrations: the ancient "Out of Africa" migration ∼50,000 years before present (YBP) and the relatively recent "Out of Taiwan" expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated from the ancient migration, whereas the majority of island Southeast Asians are associated with the Austronesian expansion. We determined 86 mitochondrial DNA (mtDNA) complete genome sequences in four indigenous Malaysian populations, together with a reanalysis of published autosomal single-nucleotide polymorphism (SNP) data of Southeast Asians to test the plausibility and impact of those migration models. The three Austronesian groups (Bidayuh, Selatar, and Temuan) showed high frequencies of mtDNA haplogroups, which originated from the Asian mainland ∼30,000-10,000 YBP, but low frequencies of "Out of Taiwan" markers. Principal component analysis and phylogenetic analysis using autosomal SNP data indicate a dichotomy between continental and island Austronesian groups. We argue that both the mtDNA and autosomal data suggest an "Early Train" migration originating from Indochina or South China around the late-Pleistocene to early-Holocene period, which predates, but may not necessarily exclude, the Austronesian expansion.

  20. Archaeological and taxonomic significance of ancient wood samples ...

    African Journals Online (AJOL)

    Ancient wood samples from an archaeological excavation, Test Pit II, in Ahanve, near Badagry were analysed to ascertain their identity. Anatomical study of the wood samples revealed oval-circular xylem pores, diffuse apotracheal axial parenchyma, procumbent and homogeneous ray and non-septate fibres, all consistent ...

  1. X-ray analysis of pigments on ancient Egyptian monuments

    International Nuclear Information System (INIS)

    Uda, M.; Sassa, S.; Yoshioka, T.

    1999-01-01

    Ancient pigments were analyzed using PIXE and XRD methods in the laboratory, which were painted on ancient Egyptian monuments. On the other hand, those on monuments remaining with entire shape were investigated using the hand-held type of an XRF spectrometer and an X-ray diffractometer in the field. For the laboratory experiment, several wall fragments of the Malqata palace in ancient Egypt (18th Dynasty, ca. 1390 B.C.) were investigated. In the field experiment, the block of Ramesses II (19th Dynasty, ca. 1270 B.C.), the Wooden Coffin of Neb-sny (18th Dynasty, ca. 1400 B.C.), the Funerary Stele of Amenemhat (11th Dynasty, ca. 2000 B.C.), and the painted walls of the Tomb of Userhat (18th Dynasty, ca. 1400 B.C.) were investigated. From white and blue colored parts, huntite and Egyptian blue were found, respectively, which are a very rare mineral and an artificial pigment prepared only in ancient Egypt, respectively. (author)

  2. X-ray analysis of pigments on ancient Egyptian monuments

    Energy Technology Data Exchange (ETDEWEB)

    Uda, M.; Sassa, S.; Yoshioka, T. [Waseda Univ., Department of Materials Science and Engineering, Tokyo (JP)] [and others

    1999-07-01

    Ancient pigments were analyzed using PIXE and XRD methods in the laboratory, which were painted on ancient Egyptian monuments. On the other hand, those on monuments remaining with entire shape were investigated using the hand-held type of an XRF spectrometer and an X-ray diffractometer in the field. For the laboratory experiment, several wall fragments of the Malqata palace in ancient Egypt (18th Dynasty, ca. 1390 B.C.) were investigated. In the field experiment, the block of Ramesses II (19th Dynasty, ca. 1270 B.C.), the Wooden Coffin of Neb-sny (18th Dynasty, ca. 1400 B.C.), the Funerary Stele of Amenemhat (11th Dynasty, ca. 2000 B.C.), and the painted walls of the Tomb of Userhat (18th Dynasty, ca. 1400 B.C.) were investigated. From white and blue colored parts, huntite and Egyptian blue were found, respectively, which are a very rare mineral and an artificial pigment prepared only in ancient Egypt, respectively. (author)

  3. Historical overview of spinal deformities in ancient Greece

    Science.gov (United States)

    Vasiliadis, Elias S; Grivas, Theodoros B; Kaspiris, Angelos

    2009-01-01

    Little is known about the history of spinal deformities in ancient Greece. The present study summarizes what we know today for diagnosis and management of spinal deformities in ancient Greece, mainly from the medical treatises of Hippocrates and Galen. Hippocrates, through accurate observation and logical reasoning was led to accurate conclusions firstly for the structure of the spine and secondly for its diseases. He introduced the terms kyphosis and scoliosis and wrote in depth about diagnosis and treatment of kyphosis and less about scoliosis. The innovation of the board, the application of axial traction and even the principle of trans-abdominal correction for correction of spinal deformities have their origin in Hippocrates. Galen, who lived nearly five centuries later impressively described scoliosis, lordosis and kyphosis, provided aetiologic implications and used the same principles with Hippocrates for their management, while his studies influenced medical practice on spinal deformities for more than 1500 years. PMID:19243609

  4. Historical overview of spinal deformities in ancient Greece

    Directory of Open Access Journals (Sweden)

    Kaspiris Angelos

    2009-02-01

    Full Text Available Abstract Little is known about the history of spinal deformities in ancient Greece. The present study summarizes what we know today for diagnosis and management of spinal deformities in ancient Greece, mainly from the medical treatises of Hippocrates and Galen. Hippocrates, through accurate observation and logical reasoning was led to accurate conclusions firstly for the structure of the spine and secondly for its diseases. He introduced the terms kyphosis and scoliosis and wrote in depth about diagnosis and treatment of kyphosis and less about scoliosis. The innovation of the board, the application of axial traction and even the principle of trans-abdominal correction for correction of spinal deformities have their origin in Hippocrates. Galen, who lived nearly five centuries later impressively described scoliosis, lordosis and kyphosis, provided aetiologic implications and used the same principles with Hippocrates for their management, while his studies influenced medical practice on spinal deformities for more than 1500 years.

  5. An investigation into the ancient Egyptian cultural influences on the Yorubas of Nigeria

    Directory of Open Access Journals (Sweden)

    Jock M. Agai

    2013-07-01

    Full Text Available There are many cultural practices that connect ancient Egyptians to the Yorubas and the new interpretation of the Oduduwa legend suggests that the Yorubas have originated or are influenced mainly by the Egyptians. The attestation of Egypt as the main influencer of the Yoruba culture made Egypt significant in the study of the history of the Yoruba people. Some writers are beginning to think that the ancient Egyptians were responsible for introducing and spreading many cultures amongst the Yorubas. As more Yorubas are tracing their origins and the origins of their culture to ancient Egypt, this research investigates whether the Egyptians were the originators and the main spreaders of the afterlife culture in Yorubaland.

  6. Analysis of DNA damage in sea lamprey (Petromyzon marinus) spermatozoa by UV, hydrogen peroxide, and the toxicant bisazir

    International Nuclear Information System (INIS)

    Ciereszko, Andrzej; Wolfe, Tobie D.; Dabrowski, Konrad

    2005-01-01

    In this study we sought to demonstrate that Comet assay can be applied to sea lamprey sperm DNA fragmentation and used to describe the relationship between sperm DNA damage and sperm fertilizing ability. We show that the assay can be used reliably and accurately, and unlike in the case of mammals, there is no need for additional steps related to improvement of efficacy of lysis and DNA decondensation. This agrees with the presence of histone proteins in lamprey sperm. An increase in DNA fragmentation was noted during short-term storage of milt on ice (0-4 days). We demonstrated genotoxic effects of UV radiation and oxidative stress (exposure to hydrogen peroxide) and found that oxidative damage to sperm DNA was likely repaired after fertilization in the embryo. Repairing capacity of the oocyte toward sperm DNA lesions caused by UV was restricted. Toxic effect of p,p-bis-(1-aziridinyl)-N-methylphosphinothioic acid (p,p-bis(1-aziridinyl)-N-methylphosphinothioic amide), a sea lamprey chemosterilant, could not be linked to DNA fragmentation in the in vitro tests. Its genotoxicity in vivo may possibly be associated with other mechanisms of DNA degradation (oxidation or DNA-protein and DNA-DNA cross-linking). In conclusion, this study demonstrates that Comet assay can be successfully applied to monitor effects of environmental disturbances and imposed injuries in sea lamprey spermatozoa and possibly other species of ancient fish with acrosomal sperm

  7. Analysis of DNA damage in sea lamprey (Petromyzon marinus) spermatozoa by UV, hydrogen peroxide, and the toxicant bisazir

    Energy Technology Data Exchange (ETDEWEB)

    Ciereszko, Andrzej [School of Natural Resources, Ohio State University, 210 Kottman Hall, 2021 Coffey Rd., Columbus, OH 434210 (United States); Semen Biology Group, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-747 Olsztyn (Poland); Wolfe, Tobie D. [School of Natural Resources, Ohio State University, 210 Kottman Hall, 2021 Coffey Rd., Columbus, OH 434210 (United States); Dabrowski, Konrad [School of Natural Resources, Ohio State University, 210 Kottman Hall, 2021 Coffey Rd., Columbus, OH 434210 (United States)]. E-mail: dabrowski.1@osu.edu

    2005-06-15

    In this study we sought to demonstrate that Comet assay can be applied to sea lamprey sperm DNA fragmentation and used to describe the relationship between sperm DNA damage and sperm fertilizing ability. We show that the assay can be used reliably and accurately, and unlike in the case of mammals, there is no need for additional steps related to improvement of efficacy of lysis and DNA decondensation. This agrees with the presence of histone proteins in lamprey sperm. An increase in DNA fragmentation was noted during short-term storage of milt on ice (0-4 days). We demonstrated genotoxic effects of UV radiation and oxidative stress (exposure to hydrogen peroxide) and found that oxidative damage to sperm DNA was likely repaired after fertilization in the embryo. Repairing capacity of the oocyte toward sperm DNA lesions caused by UV was restricted. Toxic effect of p,p-bis-(1-aziridinyl)-N-methylphosphinothioic acid (p,p-bis(1-aziridinyl)-N-methylphosphinothioic amide), a sea lamprey chemosterilant, could not be linked to DNA fragmentation in the in vitro tests. Its genotoxicity in vivo may possibly be associated with other mechanisms of DNA degradation (oxidation or DNA-protein and DNA-DNA cross-linking). In conclusion, this study demonstrates that Comet assay can be successfully applied to monitor effects of environmental disturbances and imposed injuries in sea lamprey spermatozoa and possibly other species of ancient fish with acrosomal sperm.

  8. HIGHER SPIRITUAL AND SELF-REGULATIVE CAPACITIES IN ANCIENT KNOWLEDGE SYSTEM - BUDDHISM (APPROACH OF HISTORY OF PSYCHOLOGY

    Directory of Open Access Journals (Sweden)

    G V Ozhiganova

    2015-12-01

    Full Text Available The necessity of research on higher spiritual and self-regulative capacities in the context of ancient oriental system of knowledge is expressed. The historical and psychological methods of studying ancient knowledge are described. The methods of the history of psychology, proposed by the author, are used: such as the method of revealing scientific knowledge reserves, aimed at restoring and practical mastering the psychological heritage of ancient times, as well as the experimental method, involving the verification of psychological facts, phenomena and laws described in ancient texts, with the help of modern scientific research methods (observation, experiment, statistical data. Meditative practices and philosophical concepts of Buddhism are considered from the standpoint of modern psychology. The ancient Buddhist meditative practices “Contemplation of the mind”, linked to the concept of “mindfulness” is described. It is concluded that the concept of the mind is the key in the Buddhist system of knowledge. The understanding of the mind in the ancient Buddhist doctrine is compared with a modern interpretation of the concept of “mind” in psychological science, as well as its content is revealed due to psychological terms “higher self-regulative capacities” and “moral-value aspect of spiritual capacities”. It is revealed that in the Buddhist system of knowledge there can be seen close links between higher self-regulative capacities and moral-value aspect of spiritual capacities. The results of empirical studies of the ancient meditative practices and their positive impact on self-regulation of the modern people are submitted.

  9. Creative Ventures: Ancient Civilizations.

    Science.gov (United States)

    Stark, Rebecca

    The open-ended activities in this book are designed to extend the imagination and creativity of students and encourage students to examine their feelings and values about historic eras. Civilizations addressed include ancient Egypt, Greece, Rome, Mayan, Stonehenge, and Mesopotamia. The activities focus upon the cognitive and affective pupil…

  10. Penile representations in ancient Greek art.

    Science.gov (United States)

    Rempelakos, L; Tsiamis, C; Poulakou-Rebelakou, E

    2013-12-01

    The presentation of the cult of phallus in ancient Greece and the artistic appearance of the phenomenon on vase figures and statues, as indicative of the significant role of the male genitalia in all fertility ceremonies. The examination of a great number of penile representations from the ancient Greek pottery and sculpture and the review of the ancient theater plays (satiric dramas and comedies ). Phallus in artistic representation is connected either with gods of fertility, such as the goat-footed and horned Pan or the ugly dwarf Priapus or the semi-animal nailed figures Satyrs, devotees of the god Dionysus accompanying him in all ritual orgiastic celebrations. Phallus also symbolizes good luck, health and sexuality: people bear or wear artificial phalli exactly like the actors as part of their costume or carry huge penises during the festive ritual processions. On the contrary, the Olympic gods or the ordinary mortals are not imaged ithyphallic; the ideal type of male beauty epitomized in classical sculpture, normally depicts genitals of average or less than average size. It is noteworthy that many of these images belong to athletes during or immediately after hard exercise with the penis shrunk. The normal size genitalia may have been simply a convention to distinguish normal people from the gods of sexuality and fertility, protectors of the reproductive process of Nature. The representation of the over-sized and erected genitalia on vase figures or statues of ancient Greek art is related to fertility gods such as Priapus, Pan and Satyrs and there is strong evidence that imagination and legend were replacing the scientific achievements in the field of erectile function for many centuries.

  11. Medicine and psychiatry in Western culture: Ancient Greek myths and modern prejudices

    Directory of Open Access Journals (Sweden)

    Clementi Nicoletta

    2009-10-01

    Full Text Available Abstract The origins of Western culture extensively relate to Ancient Greek culture. While many ancient cultures have contributed to our current knowledge about medicine and the origins of psychiatry, the Ancient Greeks were among the best observers of feelings and moods patients expressed towards medicine and toward what today is referred to as 'psychopathology'. Myths and religious references were used to explain what was otherwise impossible to understand or be easily communicated. Most ancient myths focus on ambiguous feelings patients may have had towards drugs, especially psychotropic ones. Interestingly, such prejudices are common even today. Recalling ancient findings and descriptions made using myths could represent a valuable knowledge base for modern physicians, especially for psychiatrists and their patients, with the aim of better understanding each other and therefore achieving a better clinical outcome. This paper explores many human aspects and feelings towards doctors and their cures, referring to ancient myths and focusing on the perception of mental illness.

  12. Ancient Egypt

    Science.gov (United States)

    Swamy, Ashwin Balegar

    This thesis involves development of an interactive GIS (Geographic Information System) based application, which gives information about the ancient history of Egypt. The astonishing architecture, the strange burial rituals and their civilization were some of the intriguing questions that motivated me towards developing this application. The application is a historical timeline starting from 3100 BC, leading up to 664 BC, focusing on the evolution of the Egyptian dynasties. The tool holds information regarding some of the famous monuments which were constructed during that era and also about the civilizations that co-existed. It also provides details about the religions followed by their kings. It also includes the languages spoken during those periods. The tool is developed using JAVA, a programing language and MOJO (Map Objects Java Objects) a product of ESRI (Environmental Science Research Institute) to create map objects, to provide geographic information. JAVA Swing is used for designing the user interface. HTML (Hyper Text Markup Language) pages are created to provide the user with more information related to the historic period. CSS (Cascade Style Sheets) and JAVA Scripts are used with HTML5 to achieve creative display of content. The tool is kept simple and easy for the user to interact with. The tool also includes pictures and videos for the user to get a feel of the historic period. The application is built to motivate people to know more about one of the prominent and ancient civilization of the Mediterranean world.

  13. Plasmodium vivax populations revisited: mitochondrial genomes of temperate strains in Asia suggest ancient population expansion

    Directory of Open Access Journals (Sweden)

    Miao Miao

    2012-02-01

    Full Text Available Abstract Background Plasmodium vivax is the most widely distributed human malaria parasite outside of Africa, and its range extends well into the temperate zones. Previous studies provided evidence for vivax population differentiation, but temperate vivax parasites were not well represented in these analyses. Here we address this deficit by using complete mitochondrial (mt genome sequences to elucidate the broad genetic diversity and population structure of P. vivax from temperate regions in East and Southeast Asia. Results From the complete mtDNA sequences of 99 clinical samples collected in China, Myanmar and Korea, a total of 30 different haplotypes were identified from 26 polymorphic sites. Significant differentiation between different East and Southeast Asian parasite populations was observed except for the comparison between populations from Korea and southern China. Haplotype patterns and structure diversity analysis showed coexistence of two different groups in East Asia, which were genetically related to the Southeast Asian population and Myanmar population, respectively. The demographic history of P. vivax, examined using neutrality tests and mismatch distribution analyses, revealed population expansion events across the entire P. vivax range and the Myanmar population. Bayesian skyline analysis further supported the occurrence of ancient P. vivax population expansion. Conclusions This study provided further resolution of the population structure and evolution of P. vivax, especially in temperate/warm-temperate endemic areas of Asia. The results revealed divergence of the P. vivax populations in temperate regions of China and Korea from other populations. Multiple analyses confirmed ancient population expansion of this parasite. The extensive genetic diversity of the P. vivax populations is consistent with phenotypic plasticity of the parasites, which has implications for malaria control.

  14. Intersegmental interactions in supercoiled DNA: atomic force microscope study

    Energy Technology Data Exchange (ETDEWEB)

    Shlyakhtenko, Luda S.; Miloseska, Lela; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L

    2003-10-15

    Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

  15. Studies of ancient concrete as analogs of cementitious sealing materials for a repository in tuff

    Energy Technology Data Exchange (ETDEWEB)

    Roy, D.M.; Langton, C.A.

    1989-03-01

    The durability of ancient cementitious materials has been investigated to provide data applicable to determining the resistance to weathering of concrete materials for sealing a repository for storage of high-level radioactive waste. Because tuff and volcanic ash are used in the concretes in the vicinity of Rome, the results are especially applicable to a waste repository in tuff. Ancient mortars, plasters, and concretes collected from Rome, Ostia, and Cosa dating to the third century BC show remarkable durability. The aggregates used in the mortars, plasters, and concretes included basic volcanic and pyroclastic rocks (including tuff), terra-cotta, carbonates, sands, and volcanic ash. The matrices of ancient cementitious materials have been characterized and classified into four categories: (1) hydraulic hydrated lime and hydrated lime cements, (2) hydraulic aluminous and ferruginous hydrated lime cements ({plus_minus} siliceous components), (3) pozzolana/hydrated lime cements, and (4) gypsum cements. Most of the materials investigated are in category (3). The materials were characterized to elucidate aspects of the technology that produced them and their response to the environmental exposure throughout their centuries of existence. Their remarkable properties are the result of a combination of chemical, mineralogical, and microstructural factors. Their durability was found to be affected by the matrix mineralogy, particle size, and porosity; aggregate type, grading and proportioning; and the methodology of placement. 30 refs.

  16. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

    Directory of Open Access Journals (Sweden)

    Omer Gokcumen

    2013-04-01

    Full Text Available Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵. Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003 and positive Tajima's D (p = 0.00285 statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European

  17. TREATMENT OF FRACTURES IN ANCIENT EGYPT

    Directory of Open Access Journals (Sweden)

    Z. K. Bashurov

    2012-01-01

    Full Text Available The most complete information about the medicine in Ancient Egypt two papyrus provided: a large medical papyrus of G. Ebers and papyrus about the surgery of E. Smith. Smith’s papyrus is of particular interest as it contains the information on the status of surgery in Ancient Egypt. Papyrus consists of descriptions of the clinical cases. To the present time, 48 cases have survived; it is arranged in order of location - from the head down to the feet. Orthopedic deformities were reflected in the figures on the walls of the pyramids and temples as well as the description of the mummies and archaeological finds.

  18. Issue of Separation of Powers in Ancient Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Javad Javid

    2012-03-01

    Full Text Available Cotemporary public law in Iran cannot ignore the elements of its identity in the past. Although analysis of public law issue in ancient Iran, the most researchers to be considered so it is not easy to speak about separation of powers, the part of the body of public law in the Iran primary governments but this article constants on hypothesis which with think and assimilation in history of ancient Iran which can laying the groundwork of strengthening people rights and limitation of authority's governors with emphasis on three periods of governorship on ancient Iran .for example Hakhamaneshian, Ashkanian and Sasanian. This article intent to clear haw can in these periods, the primary figure and foundation of separation of powers and functions division in body of previous governments of Iran to be observed.

  19. Do ancient types of wheat have health benefits compared with modern bread wheat?

    Science.gov (United States)

    Shewry, Peter R

    2018-01-01

    A number of studies have suggested that ancient wheats have health benefits compared with modern bread wheat. However, the mechanisms are unclear and limited numbers of genotypes have been studied, with a particular focus on Kamut ® (Khorasan wheat). This is important because published analyses have shown wide variation in composition between genotypes, with further effects of growth conditions. The present article therefore critically reviews published comparisons of the health benefits of ancient and modern wheats, in relation to the selection and growth of the lines, including dietary interventions and comparisons of adverse effects (allergy, intolerance, sensitivity). It is concluded that further studies are urgently required, particularly from a wider range of research groups, but also on a wider range of genotypes of ancient and modern wheat species. Furthermore, although most published studies have made efforts to ensure the comparability of material in terms of growth conditions and processing, it is essential that these are standardised in future studies and this should perhaps be a condition of publication.

  20. History through Art and Architecture: Ancient Greek Architecture [and] Ancient Greek Sculpture. Teacher's Manual.

    Science.gov (United States)

    Campbell, Ann

    This document consists of two teaching manuals designed to accompany a commercially-available "multicultural, interdisciplinary video program," consisting of four still videotape programs (72 minutes, 226 frames), one teaching poster, and these two manuals. "Teacher's Manual: Ancient Greek Architecture" covers: "Ancient…