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Sample records for ancient dna resolves

  1. 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...

  2. 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 ...

  3. Ancient and modern environmental DNA

    DEFF Research Database (Denmark)

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

    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 woo...

  4. 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...

  5. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L.A.; Gilbert, M Thomas P; Hofreiter, Michael

    2013-01-01

    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...... (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well....... To date, at least 124 partially or fully assembled mitogenomes from more than 20 species have been obtained, and, given the rapid progress in sequencing technology, this number is likely to dramatically increase in the future. The increased information content offered by analysing full mitogenomes has...

  6. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth;

    2013-01-01

    In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages...

  7. gargammel: a sequence simulator for ancient DNA.

    Science.gov (United States)

    Renaud, Gabriel; Hanghøj, Kristian; Willerslev, Eske; Orlando, Ludovic

    2016-10-29

    Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.

  8. Detecting hybridization using ancient DNA.

    Science.gov (United States)

    Schaefer, Nathan K; Shapiro, Beth; Green, Richard E

    2016-06-01

    It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.

  9. The biochemistry of ancient DNA in bone.

    Science.gov (United States)

    Tuross, N

    1994-06-15

    The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and 'Magic' preparations yielded DNA that spanned from 3.4 micrograms/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts.

  10. 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...

  11. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    , 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......Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA...... 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...

  12. 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.

  13. 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...... of the sampling methods and strategies (taphonomic processes), the more fundamental molecular methodologies (e.g. extraction and sequencing) and eventually the bioinformatic processing. In the enclosed studies we have tried to take some principal steps towards improving this, firstly by reviewing previous...

  14. Ancient bacteria show evidence of DNA repair

    DEFF Research Database (Denmark)

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

    2007-01-01

    Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over......-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...... 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....

  15. Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. 14C analysis showed that this cemetery was used from 217 B.C. to 283 A.D.Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region Ⅰ (mtDNA HVR-Ⅰ), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.

  16. 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...... damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from...

  17. 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...... damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from...... 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...

  18. 2000 Year-old ancient equids: an ancient-DNA lesson from pompeii remains.

    Science.gov (United States)

    Di Bernardo, Giovanni; Del Gaudio, Stefania; Galderisi, Umberto; Cipollaro, Marilena

    2004-11-15

    Ancient DNA extracted from 2000 year-old equine bones was examined in order to amplify mitochondrial and nuclear DNA fragments. A specific equine satellite-type sequence representing 3.7%-11% of the entire equine genome, proved to be a suitable target to address the question of the presence of aDNA in ancient bones. The PCR strategy designed to investigate this specific target also allowed us to calculate the molecular weight of amplifiable DNA fragments. Sequencing of a 370 bp DNA fragment of mitochondrial control region allowed the comparison of ancient DNA sequences with those of modern horses to assess their genetic relationship. The 16S rRNA mitochondrial gene was also examined to unravel the post-mortem base modification feature and to test the status of Pompeian equids taxon on the basis of a Mae III restriction site polymorphism.

  19. 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.

  20. Ancestry of modern Europeans: contributions of ancient DNA.

    Science.gov (United States)

    Lacan, Marie; Keyser, Christine; Crubézy, Eric; Ludes, Bertrand

    2013-07-01

    Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.

  1. Pitfalls in the analysis of ancient human mtDNA

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

  2. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ss......DNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  3. A blind testing design for authenticating ancient DNA sequences.

    Science.gov (United States)

    Yang, H; Golenberg, E M; Shoshani, J

    1997-04-01

    Reproducibility is a serious concern among researchers of ancient DNA. We designed a blind testing procedure to evaluate laboratory accuracy and authenticity of ancient DNA obtained from closely related extant and extinct species. Soft tissue and bones of fossil and contemporary museum proboscideans were collected and identified based on morphology by one researcher, and other researchers carried out DNA testing on the samples, which were assigned anonymous numbers. DNA extracted using three principal isolation methods served as template in PCR amplifications of a segment of the cytochrome b gene (mitochondrial genome), and the PCR product was directly sequenced and analyzed. The results show that such a blind testing design performed in one laboratory, when coupled with phylogenetic analysis, can nonarbitrarily test the consistency and reliability of ancient DNA results. Such reproducible results obtained from the blind testing can increase confidence in the authenticity of ancient sequences obtained from postmortem specimens and avoid bias in phylogenetic analysis. A blind testing design may be applicable as an alternative to confirm ancient DNA results in one laboratory when independent testing by two laboratories is not available.

  4. 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

    2011-01-01

    . 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......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...

  5. Analysis of Mitochondrial DNA from the Ancient Tombs of Turfan

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    MtDNA was successfully extracted from ten individual bones (femurs) in the tombs of ancient Jushi in Turfan basin, dated back to the year about 3 000-2 500 years ago. By means of four overlapping primers, we got nucleotide sequence of the 218bp length. Ancient mtDNA was analyzed by the sequencing of hypervariable region Ⅰ of the mtDNA control region. The result shows that 9 haplotypes with 24 polymorphic sites were obtained. The phylogenetic analysis indicated that Mongolians and Altai are the population genetically closest to the Jushi groups and Jushi mtDNA pool being an admixture of eastern Asian and European lineages. So our preliminary data imply that an ancient mingling of Euro-Asian population had existed in Turfan basin prior to the early Iron Age.

  6. Preservation potential of ancient plankton DNA in Pleistocene marine sediments

    NARCIS (Netherlands)

    Boere, A.C.; Rijpstra, W.I.C.; de Lange, G.J.; Sinninghe Damsté, J.S.; Coolen, M.J.L.

    2011-01-01

    Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach fo

  7. 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 ...

  8. Proboscidean DNA from museum and fossil specimens: an assessment of ancient DNA extraction and amplification techniques.

    Science.gov (United States)

    Yang, H; Golenberg, E M; Shoshani, J

    1997-06-01

    Applications of reliable DNA extraction and amplification techniques to postmortem samples are critical to ancient DNA research. Commonly used methods for isolating DNA from ancient material were tested and compared using both soft tissue and bones from fossil and contemporary museum proboscideans. DNAs isolated using three principal methods served as templates in subsequent PCR amplifications, and the PCR products were directly sequenced. Authentication of the ancient origin of obtained nucleotide sequences was established by demonstrating reproducibility under a blind testing system and by phylogenetic analysis. Our results indicate that ancient samples may respond differently to extraction buffers or purification procedures, and no single method was universally successful. A CTAB buffer method, modified from plant DNA extraction protocols, was found to have the highest success rate. Nested PCR was shown to be a reliable approach to amplify ancient DNA templates that failed in primary amplification.

  9. The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).

    Science.gov (United States)

    Mikić, Aleksandar M

    2015-01-01

    Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350-1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl(-1) of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.

  10. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.

    Science.gov (United States)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  11. Preservation of ancient DNA in thermally damaged archaeological bone

    Science.gov (United States)

    Ottoni, Claudio; Koon, Hannah E. C.; Collins, Matthew J.; Penkman, Kirsty E. H.; Rickards, Olga; Craig, Oliver E.

    2009-02-01

    Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.

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

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2006-01-01

    -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......) report that direct sequencing of ancient microbial DNA produced a sequence resembling (for example) Treponerma pallidum (the causative agent of venereal syphilis) even in the absence of real T. pallidum, simply due to the presence of diverse bacterial DNA in the experiment. In addition, the limited...... knowledge of current microbial diversity (only 1-5% of extant microbial diversity is believed to be known) makes it very difficult to use short aDNA sequences to establish unequivocally the presence of a given pathogen, as even supposed ‘obligate' species of humans or plants may possess currently undetected...

  13. Ancient DNA: genomic amplification of Roman and medieval bovine bones

    Directory of Open Access Journals (Sweden)

    A. Valentini

    2010-04-01

    Full Text Available Cattle remains (bones and teeth of both roman and medieval age were collected in the archaeological site of Ferento (Viterbo, Italy with the aim of extracting and characterising nucleic acids. Procedures to minimize contamination with modern DNA and to help ancient DNA (aDNA preservation of the archaeological remains were adopted. Different techniques to extract aDNA (like Phenol/chloroform extraction from bovine bones were tested to identify the method that applies to the peculiar characteristics of the study site. Currently, aDNA investigation is mainly based on mtDNA, due to the ease of amplification of the small and high-copied genome and to its usefulness in evolutionary studies. Preliminary amplification of both mitochondrial and nuclear aDNA fragments from samples of Roman and medieval animals were performed and partial specific sequences of mitochondrial D-loop as well as of nuclear genes were obtained. The innovative amplification of nuclear aDNA could enable the analysis of genes involved in specific animal traits, giving insights of ancient economic and cultural uses, as well as providing information on the origin of modern livestock population.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon; Gilbert, M Thomas P;

    2012-01-01

    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...... 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...... post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our...

  15. An ancient protein-DNA interaction underlying metazoan sex determination.

    Science.gov (United States)

    Murphy, Mark W; Lee, John K; Rojo, Sandra; Gearhart, Micah D; Kurahashi, Kayo; Banerjee, Surajit; Loeuille, Guy-André; Bashamboo, Anu; McElreavey, Kenneth; Zarkower, David; Aihara, Hideki; Bardwell, Vivian J

    2015-06-01

    DMRT transcription factors are deeply conserved regulators of metazoan sexual development. They share the DM DNA-binding domain, a unique intertwined double zinc-binding module followed by a C-terminal recognition helix, which binds a pseudopalindromic target DNA. Here we show that DMRT proteins use a unique binding interaction, inserting two adjacent antiparallel recognition helices into a widened DNA major groove to make base-specific contacts. Versatility in how specific base contacts are made allows human DMRT1 to use multiple DNA binding modes (tetramer, trimer and dimer). Chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) indicates that multiple DNA binding modes also are used in vivo. We show that mutations affecting residues crucial for DNA recognition are associated with an intersex phenotype in flies and with male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction underlying much of metazoan sexual development.

  16. 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 ph...

  17. The first attested extraction of ancient DNA in legumes (Fabaceae

    Directory of Open Access Journals (Sweden)

    Aleksandar M. Mikić

    2015-11-01

    Full Text Available Ancient DNA (aDNA is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analysing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum and bitter vetch (Vicia ervilia from Hissar, southeast Serbia, dated to 1,350 - 1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl-1 of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK and rbcL among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighbouring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.

  18. Ancient DNA perspectives on American colonization and population history.

    Science.gov (United States)

    Raff, Jennifer A; Bolnick, Deborah A; Tackney, Justin; O'Rourke, Dennis H

    2011-12-01

    Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.

  19. Highly informative ancient DNA 'snippets' for New Zealand moa.

    Directory of Open Access Journals (Sweden)

    Jonathan McCallum

    Full Text Available BACKGROUND: Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. METHODOLOGY/PRINCIPAL FINDINGS: By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. CONCLUSIONS/SIGNIFICANCE: Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.

  20. 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...

  1. No ancient DNA damage in Actinobacteria from the Neanderthal bone.

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    Katarzyna Zaremba-Niedźwiedzka

    Full Text Available BACKGROUND: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized. PRINCIPAL FINDINGS: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences. CONCLUSIONS/SIGNIFICANCE: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the

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

    Science.gov (United States)

    Margaryan, Ashot; Stenderup, Jesper; Lynnerup, Niels; Willerslev, Eske; Allentoft, Morten E.

    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 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 (pros and cons of sampling the different elements. PMID:28129388

  3. Case study: ancient sloth DNA recovered from hairs preserved in paleofeces.

    Science.gov (United States)

    Clack, Andrew A; Macphee, Ross D E; Poinar, Hendrik N

    2012-01-01

    Ancient hair, which has proved to be an excellent source of well-preserved ancient DNA, is often preserved in paleofeces. Here, we separate and wash hair shafts preserved in a paleofecal specimen believed to be from a Darwin's ground sloth, Mylodon darwinii. After extracting DNA from the recovered and cleaned hair using a protocol optimized for DNA extraction from keratinous substrates, we amplify 12S and 16S rDNA sequences from the DNA extract. As expected, the recovered sequences most closely match previously published sequences of M. darwinii. Our results demonstrate that hair preserved in paleofeces, even from temperate cave environments, is an effective source of ancient DNA.

  4. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies.

    Science.gov (United States)

    Richart, Casey H; Hayashi, Cheryl Y; Hedin, Marshal

    2016-02-01

    Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.

  5. Short sequence effect of ancient DNA on mammoth phylogenetic analyses

    Institute of Scientific and Technical Information of China (English)

    Guilian SHENG; Lianjuan WU; Xindong HOU; Junxia YUAN; Shenghong CHENG; Bojian ZHONG; Xulong LAI

    2009-01-01

    The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.

  6. Ancient DNA reveals past existence of Eurasian lynx in Spain

    DEFF Research Database (Denmark)

    Rodríguez-Varela, R.; García, N.; Nores, C.

    2016-01-01

    The known distribution of the Iberian lynx Lynx pardinus within the Iberian Peninsula since the Middle Pleistocene and the lack of reliable records of Eurasian lynx Lynx lynx in this region have led to the assumption that the Iberian lynx was the sole inhabitant of Iberia. In this study, we...... identified ancient mitochondrial DNA (a total of 337 base pairs from the control region and cytochrome b) from eight northern Iberian lynx remains as Eurasian lynx. These results confirm the presence of Eurasian lynx in northern Iberia from the Pleistocene/Holocene boundary until just a few centuries ago....... The paleontological record and our data indicate a population replacement of the Iberian lynx by the Eurasian lynx during the Pleistocene/Holocene transition in the Cantabrian cornice of Spain. Phylogeographic patterns of Late Pleistocene and Holocene Eurasian lynx from Iberia, France, Italy and Denmark show...

  7. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route.

    Science.gov (United States)

    Lacan, Marie; Keyser, Christine; Ricaut, François-Xavier; Brucato, Nicolas; Duranthon, Francis; Guilaine, Jean; Crubézy, Eric; Ludes, Bertrand

    2011-06-14

    The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

  8. 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.

  9. Ancient DNA analysis of human remains from the Upper Capital City of Kublai Khan.

    Science.gov (United States)

    Fu, Yuqin; Xie, Chengzhi; Xu, Xuelian; Li, Chunxiang; Zhang, Quanchao; Zhou, Hui; Zhu, Hong

    2009-01-01

    Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons.

  10. mapDamage: testing for damage patterns in ancient DNA sequences

    DEFF Research Database (Denmark)

    Ginolhac, Aurelien; Rasmussen, Morten; Gilbert, M Thomas P;

    2011-01-01

    Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequenci...... of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems....

  11. 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.

  12. 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.

  13. Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA.

    Science.gov (United States)

    Yao, Yong-Gang; Kong, Qing-Peng; Man, Xiao-Yong; Bandelt, Hans-Jürgen; Zhang, Ya-Ping

    2003-02-01

    The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

  14. 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

    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 contai...

  15. 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...

  16. 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. PMID:26442080

  17. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.

    Science.gov (United States)

    Welker, Frido; Collins, Matthew J; Thomas, Jessica A; Wadsley, Marc; Brace, Selina; Cappellini, Enrico; Turvey, Samuel T; Reguero, Marcelo; Gelfo, Javier N; Kramarz, Alejandro; Burger, Joachim; Thomas-Oates, Jane; Ashford, David A; Ashton, Peter D; Rowsell, Keri; Porter, Duncan M; Kessler, Benedikt; Fischer, Roman; Baessmann, Carsten; Kaspar, Stephanie; Olsen, Jesper V; Kiley, Patrick; Elliott, James A; Kelstrup, Christian D; Mullin, Victoria; Hofreiter, Michael; Willerslev, Eske; Hublin, Jean-Jacques; Orlando, Ludovic; Barnes, Ian; MacPhee, Ross D E

    2015-06-04

    No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing

  18. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

    DEFF Research Database (Denmark)

    Gamba, Cristina; Hanghøj, Kristian Ebbesen; Gaunitz, Charleen

    2016-01-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs...... of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning...... a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules...

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

    Science.gov (United States)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic

    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, 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.

  20. 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.

  1. 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.

  2. 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.

  3. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

    Science.gov (United States)

    Brotherton, Paul; Endicott, Phillip; Sanchez, Juan J.; Beaumont, Mark; Barnett, Ross; Austin, Jeremy; Cooper, Alan

    2007-01-01

    Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy. PMID:17715147

  4. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions.

    Science.gov (United States)

    Brotherton, Paul; Endicott, Phillip; Sanchez, Juan J; Beaumont, Mark; Barnett, Ross; Austin, Jeremy; Cooper, Alan

    2007-01-01

    Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

  5. 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.

  6. Ancient DNA, climatic change, and loss of genetic diversity in an endemic Patagonian mammal

    Science.gov (United States)

    Chan, Y.; Lacey, E.; Ramakrishnan, U.; Pearson, O.; Hadly, E.

    2004-12-01

    Understanding the response of animal populations to climatic change is essential for the future maintenance of biodiversity. One question that remains difficult to answer, and is particularly important to conservation, is how animals respond over time scales relevant to evolutionary change. Ancient DNA provides a unique opportunity to track animal response to Holocene climate change and to study species replacement patterns and genetic diversity over time. We used ancient DNA to compare response to climatic change in two species, C. sociabilis and C. haigi, over the last 8,000 years. Our study site, Cueva Traful, is a late-Holocene raptor roost in Parque Nacional Nahuel Huapi, Argentina. A lack of genetic diversity in modern C. sociabilis populations is indicative of past bottleneck events and a previous ancient DNA study found that it had remained genetically identical for at least 1000 years in the face of climatic change and human disturbance. Since Cueva Traful goes back further in time, our first goal was to examine genetic diversity in order to place a longer term historical perspective on the modern bottleneck. The second goal was to compare changes in genetic diversity in C. sociabilis to C. haigi a closely related species that may respond differently to climatic change. The use of ancient DNA presents unique challenges due to low copy number, environmental damage to template, and high contamination risk. Despite these challenges, ancient DNA provides a unique perspective on evolutionary history.

  7. Optimization of the Phenol -Chloroform Silica DNA Extraction Method in Ancient Bones DNA Extraction

    Directory of Open Access Journals (Sweden)

    Morteza Sadeghi

    2014-04-01

    Full Text Available Introduction: DNA extraction from the ancient bones tissues is currently very difficult. Phenol chloroform silica method is one of the methods currently used for this aim. The purpose of this study was to optimize the assessment method. Methods: DNA of 62 bone tissues (average 3-11 years was first extracted with phenol chloroform silica methods and then with changing of some parameters of the methods the extracted DNA was amplified in eight polymorphisms area including FES, F13, D13S317, D16, D5S818, vWA and CD4. Results from samples gained by two methods were compared in acrylamide gel. Results: The average of PCR yield for new method and common method in eight polymorphism regions was 75%, 78%, 81%, 76%, 85%, 71%, 89%, 86% and 64%, 39%, 70%, 49%, 68%, 76%, 71% and 28% respectively. The average of DNA in optimized (in 35l silica density and common method were 267.5 µg/ml with 1.12 purity and 192.76 g/ml with 0.84 purity respectively. Conclusions: According to the findings of this study, it is estimated that longer EDTA attendance is an efficient agent in removing calcium and also adequate density of silica particles can be efficient in removal of PCR inhibitors.

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

    Science.gov (United States)

    Ávila-Arcos, María C.; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno-Mayar, J. Víctor; Rasmussen, Morten; Fordyce, Sarah L.; Montiel, Rafael; Vielle-Calzada, Jean-Philippe; Willerslev, Eske; Gilbert, M. Thomas P.

    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. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA. PMID:22355593

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

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    Organisms release DNA both when they live and die. Eventually the DNA disintegrates entirely or it is re-metabolized. There is a constant deposition and decomposition that maintains an environmental pool with large quantities of extracellular DNA, some of which can be thousands of years old...... it by damaged short DNA with abasic sites, crosslinks, and miscoding lesions, which are the most common damages in environmental DNA. This is emphasized by successful natural transformation by 43,000-year-old DNA. We find that the process is a simple variant of natural transformation. On top, we illustrate...... acquire functional genetic signatures of the deeper past. Moreover, not only can old DNA revert microbes to past genotypes, but damaged DNA can also produce new variants of already functional sequences. Besides, DNA fragments carry potential to combine functional domains in new ways. The identified novel...

  10. 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

    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...

  11. 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.

  12. Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

    Science.gov (United States)

    Juras, Anna; Chyleński, Maciej; Krenz-Niedbała, Marta; Malmström, Helena; Ehler, Edvard; Pospieszny, Łukasz; Łukasik, Sylwia; Bednarczyk, Józef; Piontek, Janusz; Jakobsson, Mattias; Dabert, Miroslawa

    2017-01-01

    We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS (14)C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct

  13. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.

    Science.gov (United States)

    Gamba, Cristina; Hanghøj, Kristian; Gaunitz, Charleen; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Bradley, Daniel G; Orlando, Ludovic

    2016-03-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.

  14. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb;

    2007-01-01

    , and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved...

  15. 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 tha...

  16. 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

    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...

  17. DNA extraction of ancient animal hard tissue samples via adsorption to silica particles.

    Science.gov (United States)

    Rohland, Nadin

    2012-01-01

    A large number of subfossil and more recent skeletal remains, many of which are stored in museums and private collections, are potentially accessible for DNA sequence analysis. In order to extract the small amount of DNA preserved in these specimens, an efficient DNA release and purification method is required. In this chapter, I describe an efficient and straightforward purification and concentration method that uses DNA adsorption to a solid surface of silica particles. Comparative analysis of extraction methods has shown that this method works reliably for ancient as well as younger, museum-preserved specimens.

  18. Technical note: improved DNA extraction from ancient bones using silica-based spin columns.

    Science.gov (United States)

    Yang, D Y; Eng, B; Waye, J S; Dudar, J C; Saunders, S R

    1998-04-01

    We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick3, QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old.

  19. Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits.

    Science.gov (United States)

    Gold, David A; Robinson, Jacqueline; Farrell, Aisling B; Harris, John M; Thalmann, Olaf; Jacobs, David K

    2014-02-01

    Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.

  20. High-Resolution Analysis of Cytosine Methylation in Ancient DNA

    OpenAIRE

    Llamas, Bastien; Holland, Michelle L.; Chen, Kefei; Jennifer E Cropley; Cooper, Alan; Suter, Catherine M

    2012-01-01

    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 parti...

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

    Science.gov (United States)

    Hansen, Anders J; Mitchell, David L; Wiuf, Carsten; Paniker, Lakshmi; Brand, Tina B; Binladen, Jonas; Gilichinsky, David A; Rønn, Regin; Willerslev, Eske

    2006-06-01

    Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks; single- and double-stranded breaks; and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate approximately 100 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 sediments is to be significantly increased. Using the obtained rate constant for interstrand crosslinks the maximal survival time of amplifiable 120-bp fragments of bacterial 16S ribosomal DNA was estimated to be approximately 400,000 years. Additionally, a clear relationship was found between DNA damage and sample age, contradicting previously raised concerns about the possible leaching of free DNA molecules between permafrost layers.

  2. Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus).

    Science.gov (United States)

    Perry, Tahlia; van Loenen, Ayla L; Heiniger, Holly; Lee, Carol; Gongora, Jaime; Cooper, Alan; Mitchell, Kieren J

    2017-03-28

    The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    We extracted DNA from 39 Danish aurochs specimens and successfully amplified and sequenced a 252 base pair long fragment of the multivariable region I of the mitochondrial control region from 11 specimens. The sequences from these specimens dated back to 9830-2865 14C yr BP and represent the first...... 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...

  4. Ancient DNA in human bone remains from Pompeii archaeological site.

    Science.gov (United States)

    Cipollaro, M; Di Bernardo, G; Galano, G; Galderisi, U; Guarino, F; Angelini, F; Cascino, A

    1998-06-29

    aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing.

  5. 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...

  6. 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...

  7. 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

    We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes......, and that their water sources were pooled or stored water. Both mtDNA sequence data and Y SNP data hint at possible gene flow or a common ancestral population for both the Beothuk and the current day Mikmaq, but more importantly the data do not lend credence to the proposed idea that the Beothuk (specifically......, 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...

  8. Analyses of DNA from ancient bones of a pre-Columbian Cuban woman and a child

    Directory of Open Access Journals (Sweden)

    Ricardo Lleonart

    1999-09-01

    Full Text Available Molecular anthropology has brought new possibilities into the study of ancient human populations. Amplification of chromosomal short tandem repeat (STR loci and mitochondrial DNA (mtDNA has been successfully employed in analyses of ancient bone material. Although several studies have reported on continental Amerindian populations, none have addressed the ancient populations inhabiting the Caribbean islands. We used STR and mtDNA analyses to study the skeletal remains of a Cuban Ciboney female adult holding an infant. Results showed that for the STR analyzed the skeletal remains shared common alleles, suggesting a relationship. Mitochondrial DNA analysis showed sequence identity, thus corroborating a possible mother-child relationship. The mtDNA sequence grouped these remains into haplogroup A, commonly found in Amerindian populations. Based on these results, we speculated on a South American origin of pre-Columbian Antilles populations and possible infanticide practices in these populations. This constitutes the first report on DNA analysis of ancient pre-Columbian Cuban populations.A antropologia molecular trouxe novas possibilidades para o estudo de populações humanas antigas. A amplificação de loci em pequenos segmentos cromossômicos repetidos (short tandem repeat, STR e de DNA mitocondrial (mtDNA tem sido empregada com sucesso em análises de material ósseo antigo. Embora vários estudos tenham sido publicados a respeito de populações ameríndias continentais, nenhum estudou as populações antigas que habitavam as ilhas do Caribe. Nós usamos análise de STR e mtDNA para estudar os restos de ossos de uma mulher adulta da tribo Ciboney cubana carregando uma criança. Os resultados mostraram que para o STR analisado os restos ósseos compartilhavam alelos comuns, sugerindo um parentesco. A análise de mtDNA mostrou identidade de seqüência, corroborando assim uma possível relação mãe-filho. A seqüência de mtDNA alocou esses

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

    DEFF Research Database (Denmark)

    Sandoval Velasco, Marcela

    these limitations. Rigorous laboratory procedures, optimized capture enrichment methods coupled to high-throughput sequencing platforms, and expanding modern reference datasets have enabled the generation of complete ancient genomes from numerous extinct and extant species, including humans and hominins...... suboptimal conditions. However, experimental and analytical methods have been developed to overcome these limitations. Rigorous laboratory procedures, optimized capture enrichment methods coupled to high-throughput sequencing platforms, and expanding modern reference datasets have enabled the generation...... of complete ancient genomes from numerous extinct and extant species, including humans and hominins. In addition, the field has gradually opened the opportunity to study human populations through history. In this thesis I have applied, tested and investigated the performance of different ancient DNA...

  10. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.

    Science.gov (United States)

    Thomson, Vicki A; Lebrasseur, Ophélie; Austin, Jeremy J; Hunt, Terry L; Burney, David A; Denham, Tim; Rawlence, Nicolas J; Wood, Jamie R; Gongora, Jaime; Girdland Flink, Linus; Linderholm, Anna; Dobney, Keith; Larson, Greger; Cooper, Alan

    2014-04-01

    The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.

  11. 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

    2007-07-01

    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.

  12. Ancient DNA from 8400 Year-Old Catalhoyuk Wheat: Implications for the Origin of Neolithic Agriculture.

    Directory of Open Access Journals (Sweden)

    Hatice Bilgic

    Full Text Available Human history was transformed with the advent of agriculture in the Fertile Crescent with wheat as one of the founding crops. Although the Fertile Crescent is renowned as the center of wheat domestication, archaeological studies have shown the crucial involvement of Çatalhöyük in this process. This site first gained attention during the 1961-65 excavations due to the recovery of primitive hexaploid wheat. However, despite the seeds being well preserved, a detailed archaeobotanical description of the samples is missing. In this article, we report on the DNA isolation, amplification and sequencing of ancient DNA of charred wheat grains from Çatalhöyük and other Turkish archaeological sites and the comparison of these wheat grains with contemporary wheat species including T. monococcum, T. dicoccum, T. dicoccoides, T. durum and T. aestivum at HMW glutenin protein loci. These ancient samples represent the oldest wheat sample sequenced to date and the first ancient wheat sample from the Middle East. Remarkably, the sequence analysis of the short DNA fragments preserved in seeds that are approximately 8400 years old showed that the Çatalhöyük wheat stock contained hexaploid wheat, which is similar to contemporary hexaploid wheat species including both naked (T. aestivum and hulled (T. spelta wheat. This suggests an early transitory state of hexaploid wheat agriculture from the Fertile Crescent towards Europe spanning present-day Turkey.

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

    Directory of Open Access Journals (Sweden)

    Fernando Racimo

    2016-04-01

    Full Text Available 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%.

  14. Using ancient DNA and coalescent-based methods to infer extinction.

    Science.gov (United States)

    Chang, Dan; Shapiro, Beth

    2016-02-01

    DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction.

  15. Taming the Past: Ancient DNA and the Study of Animal Domestication.

    Science.gov (United States)

    MacHugh, David E; Larson, Greger; Orlando, Ludovic

    2017-02-08

    During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.

  16. Recent advances in ancient DNA research and their implications for archaeobotany

    DEFF Research Database (Denmark)

    Brown, Terence A.; Cappellini, Enrico; Kistler, Logan

    2015-01-01

    The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material...... but their utility has been demonstrated with desiccated, waterlogged and charred remains. The future use of NGS is likely to open up new areas of investigation that have been difficult or impossible with the traditional approach to aDNA sequencing. Species identification should become more routine...

  17. Insights into early pig domestication provided by ancient DNA analysis

    Science.gov (United States)

    Caliebe, Amke; Nebel, Almut; Makarewicz, Cheryl; Krawczak, Michael; Krause-Kyora, Ben

    2017-01-01

    Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens. We developed a quantitative mathematical model tracing the haplotypes of the domestic pigs back to their most likely geographic origin. Our modelling results suggest that, between 5000 and 4000 BC, almost all matrilines in the north originated from domesticated animals from the south of central Europe. In the following period (4000–3000 BC), an estimated 78–100% of domesticates in the north were of northern matrilineal origin, largely from local wild boars. These findings point towards a dramatic change in suid management strategies taking place throughout south-central and northern Europe after 4000 BC. PMID:28300151

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

    Science.gov (United States)

    Cruz-Dávalos, Diana I; Llamas, Bastien; Gaunitz, Charleen; Fages, Antoine; Gamba, Cristina; Soubrier, Julien; Librado, Pablo; Seguin-Orlando, Andaine; Pruvost, Mélanie; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Scheu, Amelie; Beneke, Norbert; Ludwig, Arne; Cooper, Alan; Willerslev, Eske; Orlando, Ludovic

    2016-08-27

    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 represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.

  19. 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; Burger, Pamela A

    2016-06-14

    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.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Treena Swanston

    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.

  2. 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

    Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern...... 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....... Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other...

  3. Phylogenetic Analysis of mtDNA from the Ancient Human of Yuan Dynasty in Inner Mongolia in China

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A study of the genetic structure of an ancient human excavated from the Yikeshu site of Yuanshangdu ancient city in Inner Mongolia and the relationships between the ancient population and the extant populations was carried out.Sequences of the control region and coding region of mtDNA from the ancient human were analyzed by using direct sequencing and restriction-fragment length polymorphism (RFLP) methods. Phylogenetic analysis and multidimensional scaling analysis were also performed on the mtDNA data of the ancient population and 12 extant populations. These results show that the ancient individuals of Yikeshu site can be assigned to D, G, B and Z haplogroups that are prevalent in Duars and Mongolians from Inner Mongolia. The ancient population is also closer to Duar and Mongolian populations in genetic distance than other compared populations. This study reveals that the ancient population from Yikeshu site in the Yuan Dynasty shares a common ancestor with Mongolic-speaking Daur and Mongolian tribes.

  4. Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data.

    Science.gov (United States)

    Weiß, Clemens L; Dannemann, Michael; Prüfer, Kay; Burbano, Hernán A

    2015-11-03

    Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

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

    Directory of Open Access Journals (Sweden)

    Alice A Storey

    Full Text Available 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.

  6. 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.

  7. 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. PMID:22848352

  8. 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

  9. Ancient DNA Study: A Powerful Molecular Biology Tool for Tracing the Past

    Institute of Scientific and Technical Information of China (English)

    Wang Li

    2001-01-01

    In the present study, the author has completed an analysis of the DNA sequence of the human bones unearthed from ancient tombs in the vicinity of Linzi City, in the central part of Shandong Province,making clear the distribution and genetic types of human populations on the Shandong Peninsula during different historical periods and their affinity with modern man. The author also introduces an on-going project to examine the bones of Shang Dynasty (1600-1046 BC) people excavated from Yinxu, located in today′s Anyang City, in northern Henan Province, which will reconstruct the population structure,migration patterns and cultural features of the dynasty.

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

    Science.gov (United States)

    Lira, Jaime; Linderholm, Anna; Olaria, Carmen; Brandström Durling, Mikael; Gilbert, M Thomas P; Ellegren, Hans; Willerslev, Eske; Lidén, Kerstin; Arsuaga, Juan Luis; Götherström, Anders

    2010-01-01

    Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern 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. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.

  11. 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.

  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

    Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or...

  13. 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.

  14. Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA.

    Science.gov (United States)

    Zeyland, J; Wolko, L; Bocianowski, J; Szalata, M; Słomski, R; Dzieduszycki, A M; Ryba, M; Przystałowska, H; Lipiński, D

    2013-01-01

    Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon-dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

  15. 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.

  16. 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

    2017-03-08

    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.

  17. 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.

  18. Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy.

    Science.gov (United States)

    Donoghue, Helen D; Spigelman, Mark; O'Grady, Justin; Szikossy, Ildikó; Pap, Ildikó; Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Minnikin, David E

    2015-06-01

    Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago.

  19. DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories.

    Science.gov (United States)

    Witt, Kelsey E; Judd, Kathleen; Kitchen, Andrew; Grier, Colin; Kohler, Timothy A; Ortman, Scott G; Kemp, Brian M; Malhi, Ripan S

    2015-02-01

    As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.

  20. 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.

  1. New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius )

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments ( 109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.

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

    Science.gov (United States)

    Bellemain, Eva; Davey, Marie L; Kauserud, Håvard; Epp, Laura S; Boessenkool, Sanne; Coissac, Eric; Geml, Jozsef; Edwards, Mary; Willerslev, Eske; Gussarova, Galina; Taberlet, Pierre; Haile, James; Brochmann, Christian

    2013-04-01

    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 16 000-32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000-32 000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.

  3. 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

  4. Application of DNA Profiling in Resolving Aviation Forensic Toxicology Issues

    Science.gov (United States)

    2009-10-01

    Pilot: Bone ,.muscle,.skin,.and.lung Toxicological Findings Pilot: Propoxyphene.0 .308.µg/g.in.muscle.and.0 .341. µg/g.in.skin Norpropoxyphene.0 .671...Female Passenger: Negative Male Passenger: Diazepam ,.nordiazepam,.and.zolpi- dem.present.in.body.tissue Reason for DNA Profiling

  5. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

    DEFF Research Database (Denmark)

    Jørgensen, Tina; Haile, James Seymour; Möller, Per

    2012-01-01

    Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistoce...

  6. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA.

    Science.gov (United States)

    Larson, Greger; Liu, Ranran; Zhao, Xingbo; Yuan, Jing; Fuller, Dorian; Barton, Loukas; Dobney, Keith; Fan, Qipeng; Gu, Zhiliang; Liu, Xiao-Hui; Luo, Yunbing; Lv, Peng; Andersson, Leif; Li, Ning

    2010-04-27

    The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

  7. A conditional likelihood is required to estimate the selection coefficient in ancient DNA

    CERN Document Server

    Valleriani, Angelo

    2016-01-01

    Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to end anywhere. Based on the Moran model of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation ...

  8. Radiocarbon-dating and ancient DNA reveal rapid replacement of extinct prehistoric penguins

    Science.gov (United States)

    Rawlence, Nicolas J.; Perry, George L. W.; Smith, Ian W. G.; Scofield, R. Paul; Tennyson, Alan J. D.; Matisoo-Smith, Elizabeth A.; Boessenkool, Sanne; Austin, Jeremy J.; Waters, Jonathan M.

    2015-03-01

    Prehistoric faunal extinctions dramatically reshaped biological assemblages around the world. However, the timing of such biotic shifts is often obscured by the fragmentary nature and limited temporal resolution of fossil records. We use radiocarbon-dating and ancient-DNA analysis of prehistoric (ca A.D. 1450-1834) Megadyptes penguin specimens to assess the time-frame of biological turnover in coastal New Zealand following human settlement. These data suggest that the final extirpation of the endemic Megadyptes waitaha, and subsequent replacement by the previously sub-Antarctic-limited Megadyptes antipodes, likely occurred within a narrow temporal window (e.g. a century or less). This transition represents one of the most rapid prehistoric faunal turnover events documented, and is likely linked to human demographic and cultural transitions during the 15th Century. Our results suggest that anthropogenic forces can trigger rapid biogeographic shifts.

  9. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing.

    Science.gov (United States)

    Teasdale, M D; van Doorn, N L; Fiddyment, S; Webb, C C; O'Connor, T; Hofreiter, M; Collins, M J; Bradley, D G

    2015-01-19

    Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

  10. Joseon funerary texts tested using ancient DNA analysis of a Korean mummy.

    Science.gov (United States)

    Oh, Chang Seok; Koh, Bou-Ja; Yoo, Dong Soo; Park, Jun Bum; Min, So Ri; Kim, Yi-Suk; Lee, Sang Sup; Ge, Jianye; Seo, Seung Bum; Shin, Dong Hoon

    2015-06-01

    In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites.

  11. Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

    Directory of Open Access Journals (Sweden)

    Braun Mihály

    2011-03-01

    Full Text Available Abstract Background Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR record for spruce that helped us to infer changes in population size at this site. Results We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP and three bottlenecks (around 9180, 7200 and 2200 cal yr BP, likely triggered by climatic change and human impact. Conclusion Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher

  12. Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism

    Science.gov (United States)

    Zhang, Xuezhi; Soldati, Thierry

    2016-01-01

    Since the discovery of the formation of DNA-based extracellular traps (ETs) by neutrophils as an innate immune defense mechanism (1), hundreds of articles describe the involvement of ETs in physiological and pathological human and animal conditions [reviewed in Ref. (2), and the previous Frontiers Research Topic on NETosis: http://www.frontiersin.org/books/NETosis_At_the_Intersection_of_Cell_Biology_Microbiology_and_Immunology/195]. Interestingly, a few reports reveal that ETs can be formed by immune cells of more ancient organisms, as far back as the common ancestor of vertebrates and invertebrates (3). Recently, we reported that the Sentinel cells of the multicellular slug of the social amoeba Dictyostelium discoideum also produce ETs to trap and kill slug-invading bacteria [see Box 1; and Figure 1 Ref. (4)]. This is a strong evidence that DNA-based cell-intrinsic defense mechanisms emerged much earlier than thought, about 1.3 billion years ago. Amazingly, using extrusion of DNA as a weapon to capture and kill uningestable microbes has its rationale. During the emergence of multicellularity, a primitive innate immune system developed in the form of a dedicated set of specialized phagocytic cells. This professionalization of immunity allowed the evolution of sophisticated defense mechanisms including the sacrifice of a small set of cells by a mechanism related to NETosis. This altruistic behavior likely emerged in steps, starting from the release of “dispensable” mitochondrial DNA by D. discoideum Sentinel cells. Grounded in this realization, one can anticipate that in the near future, many more examples of the invention and fine-tuning of ETs by early metazoan ancestors will be identified. Consequently, it can be expected that this more complete picture of the evolution of ETs will impact our views of the involvement and pathologies linked to ETs in human and animals. PMID:27458458

  13. The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico.

    Science.gov (United States)

    Mata-Míguez, Jaime; Overholtzer, Lisa; Rodríguez-Alegría, Enrique; Kemp, Brian M; Bolnick, Deborah A

    2012-12-01

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

  14. Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age.

    Science.gov (United States)

    Gao, Shi-Zhu; Zhang, Ye; Wei, Dong; Li, Hong-Jie; Zhao, Yong-Bin; Cui, Yin-Qiu; Zhou, Hui

    2015-05-01

    Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

  15. 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.

  16. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.

    Science.gov (United States)

    Carpenter, Meredith L; Buenrostro, Jason D; Valdiosera, Cristina; Schroeder, Hannes; Allentoft, Morten E; Sikora, Martin; Rasmussen, Morten; Gravel, Simon; Guillén, Sonia; Nekhrizov, Georgi; Leshtakov, Krasimir; Dimitrova, Diana; Theodossiev, Nikola; Pettener, Davide; Luiselli, Donata; Sandoval, Karla; Moreno-Estrada, Andrés; Li, Yingrui; Wang, Jun; Gilbert, M Thomas P; Willerslev, Eske; Greenleaf, William J; Bustamante, Carlos D

    2013-11-07

    Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

  17. A conditional likelihood is required to estimate the selection coefficient in ancient DNA.

    Science.gov (United States)

    Valleriani, Angelo

    2016-08-16

    Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.

  18. A conditional likelihood is required to estimate the selection coefficient in ancient DNA

    Science.gov (United States)

    Valleriani, Angelo

    2016-08-01

    Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.

  19. Use of pollen and ancient DNA as conservation baselines for offshore islands in New Zealand.

    Science.gov (United States)

    Wilmshurst, Janet M; Moar, Neville T; Wood, Jamie R; Bellingham, Peter J; Findlater, Amy M; Robinson, James J; Stone, Clive

    2014-02-01

    Islands play a key role globally in the conservation of endemic species. Many island reserves have been highly modified since human colonization, and their restoration and management usually occur without knowledge of their prehuman state. However, conservation paleoecology is increasingly being recognized as a tool that can help to inform both restoration and conservation of island reserves by providing prehuman vegetation baselines. Many of New Zealand's mammal-free offshore islands are foci for biological diversity conservation and, like many islands in the Polynesian region, were deforested following initial human settlement. Therefore, their current restoration, replanting, and management are guided either by historic vegetation descriptions or the occurrence of species on forested islands. We analyzed pollen and ancient DNA in soil cores from an offshore island in northern New Zealand. The result was a 2000-year record of vegetation change that began >1200 years before human settlement and spanned 550 years of human occupation and 180 years of forest succession since human occupation ceased. Between prehuman and contemporary forests there was nearly a complete species turnover including the extirpation of a dominant conifer and a palm tree. The podocarp-dominated forests were replaced by a native but novel angiosperm-dominated forest. There is no modern analog of the prehuman forests on any northern New Zealand island, and those islands that are forested are dominated by angiosperms which are assumed to be climax forests. The pollen and DNA evidence for conifer- and palm-rich forests in the prehuman era challenge this climax forest assumption. Prehuman vegetation records can thus help to inform future restoration of degraded offshore islands by informing the likely rate and direction of successional change; helping to determine whether natural rates of succession are preferable to more costly replanting programs; and providing past species lists if

  20. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    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......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  1. Geochemical Analyses of Macrophytes (Potamogeton sp.) and ancient DNA from Lake Karakul, Tajikistan

    Science.gov (United States)

    Heinecke, Liv; Epp, Laura S.; Mischke, Steffen; Reschke, Maria; Stoof-Leichsenring, Kathleen; Rajabov, Ilhomjon; Herzschuh, Ulrike

    2016-04-01

    Mountain ecosystems are very sensitive towards changes in moisture and temperature and therefore most likely to be affected by climate change. To be able to get a closer insight into the alpine system of the Pamir Mountains, a 11.25 m long core was retrieved from the eastern basin of Lake Karakul (3,929 m asl), Tajikistan, in 2012. In order to gain insights into changes in the paleo-productivity of Lake Karakul over the last 29 cal kyrs BP, we investigate temporal gradients of elemental content (TOC, TN) and stable isotopes (δ13C, δ15N) of macrophyte remains (Potamogeton sp.) and plant communities obtained from ancient sedimentary DNA along the core. For the geochemical analyses we make use of the ability of submerged macrophytes, such as Potamogeton, to use HCO3- for photosynthesis in times of CO2 shortage and implement our results in a transfer function for paleo-productivity inferences. No data are available from 20 to 7 cal kyrs BP as no macrophyte remains are preserved, indicating unfavourable conditions for plant growth at the coring site or poor preservation conditions during this time. Biogeochemical analyses show significant variations from core base until approx. 20 cal kyrs BP with TOCPotamogeton 25-45 %, TNPotamogeton 0.5 % - 1.5 %, δ13CPotamogeton below -9 ‰ and δ15NPotamogeton of below 3.5 ‰ suggesting a cooler climate and reflecting the last glacial maximum. Sediments in the upper 4.5 m (approx. 6.7 cal kyrs BP) are rich in macrophyte remains. TOCPotamogeton and TNPotamogeton values from this part of the core are higher, and an enrichment of heavier isotopes with δ13CPotamogeton up to -7 ‰ and δ15NPotamogeton up to 6 ‰ indicating a higher productivity within the lake due to more favourable conditions for macrophyte growths on the lake floor. We assume shifts towards a warmer climate and changes in lake level as the dominating causes. Ancient sedimentary DNA was extracted from selected sediment slices and a metabarcoding approach (using

  2. Topoisomerase IB of Deinococcus radiodurans resolves guanine quadruplex DNA structures in vitro

    Indian Academy of Sciences (India)

    Swathi Kota; Hari S Misra

    2015-12-01

    Deinococcus radiodurans genome contains a large number of guanine repeats interrupted by a few non-guanine bases, termed G motifs. Some of these G motifs were shown forming guanine quadruplex (G4) DNA structure in vitro. How is the formation and relaxation of G4 DNA regulated in the genome of D. radiodurans is not known and is worth investigating. Here, we showed that the topoisomerase lb of D. radiodurans (DraTopolB) could change the electrophoretic mobility of fast migrating intramolecular rec-G4 DNA into the slow migrating species. DraTopolB also reduced the positive ellipticity in circular diachroism (CD) spectra of intramolecular rec-G4 DNA structures stabilized by K+. On the contrary, when DraTopolB is incubated with G-motifs annealed without K+, it showed neither any change in electrophoretic mobility nor was ellipticity of the CD spectra affected. DNA synthesis by Taq DNA polymerase through G4 DNA structure was attenuated in the presence of G4 DNA binding drugs, which was abrogated by DraTopolB. This implies that DraTopolB could destabilize the G4 DNA structure, which is required for G4 drugs binding and stabilization. Camptothecin treatment inhibited DraTopolB activity on intramolecular G4 DNA structures. These results suggested that DraTopolB can relax intramolecular G4 DNA structure in vitro and it may be one such protein that could resolve G4 DNA under normal growth conditions in D. radiodurans.

  3. 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

    . 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...... 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...

  4. Novel DNA Extraction Method Unveiled the Ancient Hot Deep Biosphere Concealed in Terrestrial Sedimentary Rocks

    Science.gov (United States)

    Kouduka, M.; Suko, T.; Okuzawa, K.; Fukuda, A.; Nanba, K.; Yamamoto, M.; Sakata, S.; Ito, K.; Suzuki, Y.

    2009-12-01

    thermophilic bacteria and the transformation of silica minerals in the deep subsurface. As intensive erosion is unlikely around the drilling site, a short period of hydrothermal activities rather than long-term burial at great depth caused high temperature conditions, which might explain the lack of maturity in hydrocarbon. A novel DNA-based approach coupled mineralogical and organic geochemical analyses has the potential to reconstruct ancient biogeochemical processes mediated in the deep subsurface as well as geothermal history. This study was supported by grants from the Nuclear and Industrial Safety Agency (NISA) and Japan Nuclear Energy Safety Organization (JNES).

  5. Detection of the A189G mtDNA heteroplasmic mutation in relation to age in modern and ancient bones.

    Science.gov (United States)

    Lacan, Marie; Thèves, Catherine; Amory, Sylvain; Keyser, Christine; Crubézy, Eric; Salles, Jean-Pierre; Ludes, Bertrand; Telmon, Norbert

    2009-03-01

    The aim of this study was to demonstrate the presence of the A189G age-related point mutation on DNA extracted from bone. For this, a peptide nucleic acid (PNA)/DNA sequencing method which can determine an age threshold for the appearance of the mutation was used. Initially, work was done in muscle tissue in order to evaluate the sensitivity of the technique and afterwards in bone samples from the same individuals. This method was also applied to ancient bones from six well-preserved skeletal remains. The mutation was invariably found in muscle, and at a rate of up to 20% in individuals over 60 years old. In modern bones, the mutation was detected in individuals aged 38 years old or more, at a rate of up to 1%, but its occurrence was not systematic (only four out of ten of the individuals over 50 years old carried the heteroplasmy). For ancient bones, the mutation was also found in the oldest individuals according to osteologic markers. The study of this type of age-related mutation and a more complete understanding of its manifestation has potentially useful applications. Combined with traditional age markers, it could improve identification accuracy in forensic cases or in anthropological studies of ancient populations.

  6. 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

  7. 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.

  8. 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

    2015-01-19

    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.

  9. Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii.

    Science.gov (United States)

    Cipollaro, M; Di Bernado, G; Forte, A; Galano, G; De Masi, L; Galderisi, U; Guarino, F M; Angelini, F; Cascino, A

    1999-09-01

    Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption.

  10. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  11. Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

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    Alcover Josep Antoni

    2005-12-01

    Full Text Available Abstract Background Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs, plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

  12. 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.

  13. Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

    Science.gov (United States)

    Ottoni, Claudio; Girdland Flink, Linus; Evin, Allowen; Geörg, Christina; De Cupere, Bea; Van Neer, Wim; Bartosiewicz, László; Linderholm, Anna; Barnett, Ross; Peters, Joris; Decorte, Ronny; Waelkens, Marc; Vanderheyden, Nancy; Ricaut, François-Xavier; Çakırlar, Canan; Çevik, Özlem; Hoelzel, A. Rus; Mashkour, Marjan; Mohaseb Karimlu, Azadeh Fatemeh; Sheikhi Seno, Shiva; Daujat, Julie; Brock, Fiona; Pinhasi, Ron; Hongo, Hitomi; Perez-Enciso, Miguel; Rasmussen, Morten; Frantz, Laurent; Megens, Hendrik-Jan; Crooijmans, Richard; Groenen, Martien; Arbuckle, Benjamin; Benecke, Nobert; Strand Vidarsdottir, Una; Burger, Joachim; Cucchi, Thomas; Dobney, Keith; Larson, Greger

    2013-01-01

    Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages. PMID:23180578

  14. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.

    Science.gov (United States)

    Ottoni, Claudio; Flink, Linus Girdland; Evin, Allowen; Geörg, Christina; De Cupere, Bea; Van Neer, Wim; Bartosiewicz, László; Linderholm, Anna; Barnett, Ross; Peters, Joris; Decorte, Ronny; Waelkens, Marc; Vanderheyden, Nancy; Ricaut, François-Xavier; Cakirlar, Canan; Cevik, Ozlem; Hoelzel, A Rus; Mashkour, Marjan; Karimlu, Azadeh Fatemeh Mohaseb; Seno, Shiva Sheikhi; Daujat, Julie; Brock, Fiona; Pinhasi, Ron; Hongo, Hitomi; Perez-Enciso, Miguel; Rasmussen, Morten; Frantz, Laurent; Megens, Hendrik-Jan; Crooijmans, Richard; Groenen, Martien; Arbuckle, Benjamin; Benecke, Nobert; Vidarsdottir, Una Strand; Burger, Joachim; Cucchi, Thomas; Dobney, Keith; Larson, Greger

    2013-04-01

    Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.

  15. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Science.gov (United States)

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

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

  16. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Directory of Open Access Journals (Sweden)

    Clio Der Sarkissian

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

  17. Mitochondrial haplogroup C in ancient mitochondrial DNA from Ukraine extends the presence of East Eurasian genetic lineages in Neolithic Central and Eastern Europe.

    Science.gov (United States)

    Nikitin, Alexey G; Newton, Jeremy R; Potekhina, Inna D

    2012-09-01

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

  18. CMOS Time-Resolved, Contact, and Multispectral Fluorescence Imaging for DNA Molecular Diagnostics

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    Nan Guo

    2014-10-01

    Full Text Available Instrumental limitations such as bulkiness and high cost prevent the fluorescence technique from becoming ubiquitous for point-of-care deoxyribonucleic acid (DNA detection and other in-field molecular diagnostics applications. The complimentary metal-oxide-semiconductor (CMOS technology, as benefited from process scaling, provides several advanced capabilities such as high integration density, high-resolution signal processing, and low power consumption, enabling sensitive, integrated, and low-cost fluorescence analytical platforms. In this paper, CMOS time-resolved, contact, and multispectral imaging are reviewed. Recently reported CMOS fluorescence analysis microsystem prototypes are surveyed to highlight the present state of the art.

  19. CMOS time-resolved, contact, and multispectral fluorescence imaging for DNA molecular diagnostics.

    Science.gov (United States)

    Guo, Nan; Cheung, Kawai; Wong, Hiu Tong; Ho, Derek

    2014-10-31

    Instrumental limitations such as bulkiness and high cost prevent the fluorescence technique from becoming ubiquitous for point-of-care deoxyribonucleic acid (DNA) detection and other in-field molecular diagnostics applications. The complimentary metal-oxide-semiconductor (CMOS) technology, as benefited from process scaling, provides several advanced capabilities such as high integration density, high-resolution signal processing, and low power consumption, enabling sensitive, integrated, and low-cost fluorescence analytical platforms. In this paper, CMOS time-resolved, contact, and multispectral imaging are reviewed. Recently reported CMOS fluorescence analysis microsystem prototypes are surveyed to highlight the present state of the art.

  20. Evidence Supporting the Uptake and Genomic Incorporation of Environmental DNA in the “Ancient Asexual” Bdelloid Rotifer Philodina roseola

    Directory of Open Access Journals (Sweden)

    Olaf R. P. Bininda-Emonds

    2016-09-01

    Full Text Available Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens, which, like other monogononts, is facultative sexual and cannot withstand desiccation. In addition, environmental DNA that was more similar to the host DNA was retained more often and for a longer period of time. Indirect evidence (increased variance in the reproductive output of the untreated F1 generation suggests that environmental DNA can be incorporated into the genome during desiccation and is thus heritable. Our observed fitness effects agree with sexual theory and also occurred when the animals were desiccated in groups (thereby acting as DNA donors, but not individually, indicating the mechanism could occur in nature. Thus, although DNA uptake and its genomic incorporation appears proximally related to anhydrobiosis in bdelloids, it might also facilitate accidental genetic exchange with closely related taxa, thereby maintaining higher levels of genetic diversity than is otherwise expected for this group of “ancient asexuals”.

  1. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

    Science.gov (United States)

    Pacioni, Carlo; Hunt, Helen; Allentoft, Morten E; Vaughan, Timothy G; Wayne, Adrian F; Baynes, Alexander; Haouchar, Dalal; Dortch, Joe; Bunce, Michael

    2015-12-01

    The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000-4000 years in association with a dramatic population decline. In addition, we obtained near-complete 11-loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of 'new' microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current-day conservation strategies.

  2. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

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    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  3. 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.

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

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    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.

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

    Science.gov (United States)

    Shepherd, Lara D; Worthy, Trevor H; Tennyson, Alan J D; Scofield, R Paul; Ramstad, Kristina M; Lambert, David M

    2012-01-01

    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.

  6. The examination of ancient DNA: guidelines on precautions, controls, and sample processing

    Directory of Open Access Journals (Sweden)

    Scholz, M.

    2000-06-01

    Full Text Available The young discipline of palaeogenetics has developed into a successful and expectant field of archaeobiological research within the last decade. Palaeogenetic investigation (e.g. PCR, DNA sequencing of ancient specimens is, however, susceptible to falsification by the presence of contamination from more recent times. Contamination which can lead to amplification of non-authentic sequences is known to stem from several sources: (i human biomolecules derived from the persons performing the genetic experiments, perhaps also from the archeologists and other persons who have previously handled the specimens or (ii edaphic DNA sequences derived primarily from bacterial or fungal growth upon the specimen. A third source of contamination can arise from (iii substances used for conservation of specimens. Here we give advice on the correct processing of prehistoric bone samples when further molecular biological examination is required. Along with the demonstration of necessary precautions and working conditions, we further explain how an unequivocal DNA contamination monitoring is performed.

    La paleogenética se ha convertido en los últimos años en una disciplina coronada de éxito que ofrece grandes expectativas para el desarrollo de la investigación arqueobiológica. No obstante, la investigación paleogenética (p. ej: PCR, secuenciación del ADN de especímenes antiguos es susceptible de ser falsificada por la presencia de una contaminación más reciente. Actualmente sabemos que la contaminación que provoca la amplificación de secuencias ''no auténticas" procede de las siguientes fuentes: (i las biomoléculas humanas provienen de la persona que realiza el experimento genético o incluso también del arqueólogo u otras personas que previamente hayan tenido contacto con el espécimen; (ii de secuencias de ADN edáficas derivadas básicamente del crecimiento bacterial o fúngico en el seno del espécimen. La tercera fuente de contaminaci

  7. 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

    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....... Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination...

  8. 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.

  9. Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.

    Directory of Open Access Journals (Sweden)

    Marc García-Garcerà

    Full Text Available BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus that was treated with a depurinating agent (bleach, an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain, and a Neandertal sample from the El Sidrón site (Asturias, Spain. The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively, that we positively know are contaminants. CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.

  10. 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.

  11. 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.

  12. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family

    Directory of Open Access Journals (Sweden)

    Rothblatt Jonathan

    2008-07-01

    transcriptional induction of BH3 domain proteins is likely to be an ancient DNA damage response function of the p53 family. Interestingly, although the apoptotic response to DNA damage is regulated through the transcriptional activity of CEP-1, other DNA damage responses do not appear to be regulated on the transcriptional level and do not require the p53 like gene cep-1.

  13. Ancient DNA assessment of tiger salamander population in Yellowstone National Park.

    Science.gov (United States)

    McMenamin, Sarah K; Hadly, Elizabeth A

    2012-01-01

    Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum) in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological time and to assess past responses to climatic changes in the region. Using subfossils collected from a cave in northern Yellowstone, we analyzed >700 base pairs of mitochondrial sequence from 16 samples ranging in age from 100 to 3300 years old and found that all shared an identical haplotype. Although mitochondrial diversity was extremely low within the living population, we still were able to detect geographic subdivision within the local area. Using serial coalescent modelling with Bayesian priors from both modern and ancient genetic data we simulated a range of probable population sizes and mutation rates through time. Our simulations suggest that regional mitochondrial diversity has remained relatively constant even through climatic fluctuations of recent millennia.

  14. Ancient DNA assessment of tiger salamander population in Yellowstone National Park.

    Directory of Open Access Journals (Sweden)

    Sarah K McMenamin

    Full Text Available Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological time and to assess past responses to climatic changes in the region. Using subfossils collected from a cave in northern Yellowstone, we analyzed >700 base pairs of mitochondrial sequence from 16 samples ranging in age from 100 to 3300 years old and found that all shared an identical haplotype. Although mitochondrial diversity was extremely low within the living population, we still were able to detect geographic subdivision within the local area. Using serial coalescent modelling with Bayesian priors from both modern and ancient genetic data we simulated a range of probable population sizes and mutation rates through time. Our simulations suggest that regional mitochondrial diversity has remained relatively constant even through climatic fluctuations of recent millennia.

  15. 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

    Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10 to 400 thousand years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks, single and double stranded breaks, and f...

  16. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile.

    Science.gov (United States)

    Hekkala, Evon; Shirley, Matthew H; Amato, George; Austin, James D; Charter, Suellen; Thorbjarnarson, John; Vliet, Kent A; Houck, Marlys L; Desalle, Rob; Blum, Michael J

    2011-10-01

    The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.

  17. Mitochondrial DNA Reveals the Trace of the Ancient Settlers of a Violently Devastated Late Bronze and Iron Ages Village.

    Science.gov (United States)

    Núñez, Carolina; Baeta, Miriam; Cardoso, Sergio; Palencia-Madrid, Leire; García-Romero, Noemí; Llanos, Armando; M de Pancorbo, Marian

    2016-01-01

    La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups.

  18. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process.

    Science.gov (United States)

    Tiengwe, Calvin; Marques, Catarina A; McCulloch, Richard

    2014-01-01

    Nuclear DNA replication is, arguably, the central cellular process in eukaryotes, because it drives propagation of life and intersects with many other genome reactions. Perhaps surprisingly, our understanding of nuclear DNA replication in kinetoplastids was limited until a clutch of studies emerged recently, revealing new insight into both the machinery and genome-wide coordination of the reaction. Here, we discuss how these studies suggest that the earliest acting components of the kinetoplastid nuclear DNA replication machinery - the factors that demarcate sites of the replication initiation, termed origins - are diverged from model eukaryotes. In addition, we discuss how origin usage and replication dynamics relate to the highly unusual organisation of transcription in the genome of Trypanosoma brucei.

  19. 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...... (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....

  20. 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, M.W.; Ginolhac, A.; Orlando, L.

    2013-01-01

    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...... 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...

  1. Novel contribution on the diagenetic physicochemical features of bone and teeth minerals, as substrates for ancient DNA typing.

    Science.gov (United States)

    Grunenwald, A; Keyser, C; Sautereau, A M; Crubézy, E; Ludes, B; Drouet, C

    2014-07-01

    The extraction of DNA from skeletal remains is a major step in archeological or forensic contexts. However, diagenesis of mineralized tissues often compromises this task although bones and teeth may represent preservation niches allowing DNA to persist over a wide timescale. This exceptional persistence is not only explained on the basis of complex organo-mineral interactions through DNA adsorption on apatite crystals composing the mineral part of bones and teeth but is also linked to environmental factors such as low temperatures and/or a dry environment. The preservation of the apatite phase itself, as an adsorption substrate, is another crucial factor susceptible to significantly impact the retrieval of DNA. With the view to bring physicochemical evidence of the preservation or alteration of diagenetic biominerals, we developed here an analytical approach on various skeletal specimens (ranging from ancient archeological samples to recent forensic specimens), allowing us to highlight several diagenetic indices so as to better apprehend the complexity of bone diagenesis. Based on complementary techniques (X-ray diffraction (XRD), Fourier transform infrared (FTIR), calcium and phosphate titrations, SEM-EDX, and gravimetry), we have identified specific indices that allow differentiating 11 biological samples, primarily according to the crystallinity and maturation state of the apatite phase. A good correlation was found between FTIR results from the analysis of the v3(PO4) and v4(PO4) vibrational domains and XRD-based crystallinity features. A maximal amount of information has been sought from this analytical approach, by way of optimized posttreatment of the data (spectral subtraction and enhancement of curve-fitting parameters). The good overall agreement found between all techniques leads to a rather complete picture of the diagenetic changes undergone by these 11 skeletal specimens. Although the heterogeneity and scarcity of the studied samples did not allow us

  2. Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization.

    Science.gov (United States)

    García-Bour, Jaume; Pérez-Pérez, Alejandro; Alvarez, Sara; Fernández, Eva; López-Parra, Ana María; Arroyo-Pardo, Eduardo; Turbón, Daniel

    2004-04-01

    Ancient mtDNA was successfully recovered from 24 skeletal samples of a total of 60 ancient individuals from Patagonia-Tierra del Fuego, dated to 100-400 years BP, for which consistent amplifications and two-strand sequences were obtained. Y-chromosome STRs (DYS434, DYS437, DYS439, DYS393, DYS391, DYS390, DYS19, DYS389I, DYS389II, and DYS388) and the biallelic system DYS199 were also amplified, Y-STR alleles could be characterized in nine cases, with an average of 4.1 loci per sample correctly typed. In two samples of the same ethnic group (Aonikenk), an identical and complete eight-loci haplotype was recovered. The DYS199 biallelic system was used as a control of contamination by modern DNA and, along with DYS19, as a marker of American origin. The analysis of both mtDNA and Y-STRs revealed DNA from Amerindian ancestry. The observed polymorphisms are consistent with the hypothesis that the ancient Fuegians are close to populations from south-central Chile and Argentina, but their high nucleotide diversity and the frequency of single lineages strongly support early genetic differentiation of the Fuegians through combined processes of population bottleneck, isolation, and/or migration, followed by strong genetic drift. This suggests an early genetic diversification of the Fuegians right after their arrival at the southernmost extreme of South America.

  3. Ancient DNA reveals that the genetic structure of the northern Han Chinese was shaped prior to 3,000 years ago.

    Science.gov (United States)

    Zhao, Yong-Bin; Zhang, Ye; 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.

  4. Ancient DNA suggests the leading role played by men in the Neolithic dissemination.

    Science.gov (United States)

    Lacan, Marie; Keyser, Christine; Ricaut, François-Xavier; Brucato, Nicolas; Tarrús, Josep; Bosch, Angel; Guilaine, Jean; Crubézy, Eric; Ludes, Bertrand

    2011-11-08

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

  5. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

    Science.gov (United States)

    Larson, Greger; Cucchi, Thomas; Fujita, Masakatsu; Matisoo-Smith, Elizabeth; Robins, Judith; Anderson, Atholl; Rolett, Barry; Spriggs, Matthew; Dolman, Gaynor; Kim, Tae-Hun; Thuy, Nguyen Thi Dieu; Randi, Ettore; Doherty, Moira; Due, Rokus Awe; Bollt, Robert; Djubiantono, Tony; Griffin, Bion; Intoh, Michiko; Keane, Emile; Kirch, Patrick; Li, Kuang-Ti; Morwood, Michael; Pedriña, Lolita M.; Piper, Philip J.; Rabett, Ryan J.; Shooter, Peter; Van den Bergh, Gert; West, Eric; Wickler, Stephen; Yuan, Jing; Cooper, Alan; Dobney, Keith

    2007-01-01

    Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called “wild” pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region. PMID:17360400

  6. 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

  7. 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

  8. Ancient DNA from 8400 Year-Old Çatalhöyük Wheat: Implications for the Origin of Neolithic Agriculture.

    Science.gov (United States)

    Bilgic, Hatice; Hakki, Erdogan E; Pandey, Anamika; Khan, Mohd Kamran; Akkaya, Mahinur S

    2016-01-01

    Human history was transformed with the advent of agriculture in the Fertile Crescent with wheat as one of the founding crops. Although the Fertile Crescent is renowned as the center of wheat domestication, archaeological studies have shown the crucial involvement of Çatalhöyük in this process. This site first gained attention during the 1961-65 excavations due to the recovery of primitive hexaploid wheat. However, despite the seeds being well preserved, a detailed archaeobotanical description of the samples is missing. In this article, we report on the DNA isolation, amplification and sequencing of ancient DNA of charred wheat grains from Çatalhöyük and other Turkish archaeological sites and the comparison of these wheat grains with contemporary wheat species including T. monococcum, T. dicoccum, T. dicoccoides, T. durum and T. aestivum at HMW glutenin protein loci. These ancient samples represent the oldest wheat sample sequenced to date and the first ancient wheat sample from the Middle East. Remarkably, the sequence analysis of the short DNA fragments preserved in seeds that are approximately 8400 years old showed that the Çatalhöyük wheat stock contained hexaploid wheat, which is similar to contemporary hexaploid wheat species including both naked (T. aestivum) and hulled (T. spelta) wheat. This suggests an early transitory state of hexaploid wheat agriculture from the Fertile Crescent towards Europe spanning present-day Turkey.

  9. Aprataxin resolves adenylated RNA–DNA junctions to maintain genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Tumbale, Percy [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States). Lab. of Structural Biology; Williams, Jessica S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States). Lab. of Structural Biology; Schellenberg, Matthew J. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States). Lab. of Structural Biology; Kunkel, Thomas A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States). Lab. of Structural Biology and Lab. of Molecular Genetics; Williams, R. Scott [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States). Lab. of Structural Biology and Lab. Molecular Genetics

    2013-12-22

    Faithful maintenance and propagation of eukaryotic genomes is ensured by three-step DNA ligation reactions used by ATP-dependent DNA ligases. Paradoxically, when DNA ligases encounter nicked DNA structures with abnormal DNA termini, DNA ligase catalytic activity can generate and/or exacerbate DNA damage through abortive ligation that produces chemically adducted, toxic 5'-adenylated (5'-AMP) DNA lesions. Aprataxin (APTX) reverses DNA adenylation but the context for deadenylation repair is unclear. Here we examine the importance of APTX to RNase-H2-dependent excision repair (RER) of a lesion that is very frequently introduced into DNA, a ribonucleotide. We show that ligases generate adenylated 5' ends containing a ribose characteristic of RNase H2 incision. APTX efficiently repairs adenylated RNA–DNA, and acting in an RNA–DNA damage response (RDDR), promotes cellular survival and prevents S-phase checkpoint activation in budding yeast undergoing RER. Structure–function studies of human APTX–RNA–DNA–AMP–Zn complexes define a mechanism for detecting and reversing adenylation at RNA–DNA junctions. This involves A-form RNA binding, proper protein folding and conformational changes, all of which are affected by heritable APTX mutations in ataxia with oculomotor apraxia 1. Together, these results indicate that accumulation of adenylated RNA–DNA may contribute to neurological disease.

  10. Assessment of the extirpated Maritimes walrus using morphological and ancient DNA analysis.

    Directory of Open Access Journals (Sweden)

    Brenna A McLeod

    Full Text Available Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory. The walrus (Odobenus rosmarus has a discontinuous circumpolar distribution in the arctic and subarctic that once included the southeastern Canadian Maritimes region. However, exploitation of the Maritimes population during the 16th-18th centuries led to extirpation, and the species has not inhabited areas south of 55°N for ∼250 years. We examined genetic and morphological characteristics of specimens from the Maritimes, Atlantic (O. r. rosmarus and Pacific (O. r. divergens populations to test the hypothesis that the first group was distinctive. Analysis of Atlantic and Maritimes specimens indicated that most skull and mandibular measurements were significantly different between the Maritimes and Atlantic groups and discriminant analysis of principal components confirmed them as distinctive groups, with complete isolation of skull features. The Maritimes walrus appear to have been larger animals, with larger and more robust tusks, skulls and mandibles. The mtDNA control region haplotypes identified in Maritimes specimens were unique to the region and a greater average number of nucleotide differences were found between the regions (Atlantic and Maritimes than within either group. Levels of diversity (h and π were lower in the Maritimes, consistent with other studies of species at range margins. Our data suggest that the Maritimes walrus was a morphologically and genetically distinctive group that was on a different evolutionary path from other walrus found in the north Atlantic.

  11. Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

    Science.gov (United States)

    Fernández, Eva; Pérez-Pérez, Alejandro; Gamba, Cristina; Prats, Eva; Cuesta, Pedro; Anfruns, Josep; Molist, Miquel; Arroyo-Pardo, Eduardo; Turbón, Daniel

    2014-01-01

    The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and

  12. Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)

    Science.gov (United States)

    Hildegard Zimmermann, Heike; Raschke, Elena; Saskia Epp, Laura; Rosmarie Stoof-Leichsenring, Kathleen; Schwamborn, Georg; Schirrmeister, Lutz; Overduin, Pier Paul; Herzschuh, Ulrike

    2017-02-01

    Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4-11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.

  13. DNA analysis of a 30,000-year-old Urocitellus glacialis from northeastern Siberia reveals phylogenetic relationships between ancient and present-day arctic ground squirrels

    Science.gov (United States)

    Faerman, Marina; Bar-Gal, Gila Kahila; Boaretto, Elisabetta; Boeskorov, Gennady G.; Dokuchaev, Nikolai E.; Ermakov, Oleg A.; Golenishchev, Fedor N.; Gubin, Stanislav V.; Mintz, Eugenia; Simonov, Evgeniy; Surin, Vadim L.; Titov, Sergei V.; Zanina, Oksana G.; Formozov, Nikolai A.

    2017-01-01

    In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El’ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed 14C dating and ancient DNA analyses of one of the El’ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia. Phylogenetic reconstructions, based on complete cytochrome b gene sequences of five Late Pleistocene arctic ground squirrels and those of modern U. parryii from 21 locations across western Beringia, provided no support for earlier proposals that ancient arctic ground squirrels from Siberia constitute a distinct species. In fact, we observed genetic continuity of the glacialis mitochondrial DNA lineage in modern U. parryii of the Kamchatka peninsula. When viewed in a broader geographic perspective, our findings provide new insights into the genetic history of U. parryii in Late Pleistocene Beringia. PMID:28205612

  14. A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

    Directory of Open Access Journals (Sweden)

    Robert Muscarella

    Full Text Available The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i low terminal phylogenetic resolution and (ii arbitrarily defined species pools.We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%. We used a maximum likelihood (ML approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%. We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types changed some of our results depending on which phylogeny (ML vs. Phylomatic was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny.With the DNA barcode phylogeny presented here (based on an island-wide species pool, we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii provide insight into

  15. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.

    Directory of Open Access Journals (Sweden)

    Stefan Prost

    Full Text Available BACKGROUND: Global temperature increased by approximately half a degree (Celsius within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus, which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød warming phase at 14.5 kyrs BP. CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population

  16. Analysis of the Intrinsically Disordered N-Terminus of the DNA Junction-Resolving Enzyme T7 Endonuclease I: Identification of Structure Formed upon DNA Binding.

    Science.gov (United States)

    Freeman, Alasdair D J; Stevens, Michael; Declais, Anne-Cecile; Leahy, Adam; Mackay, Katherine; El Mkami, Hassane; Lilley, David M J; Norman, David G

    2016-08-01

    The four-way (Holliday) DNA junction of homologous recombination is processed by the symmetrical cleavage of two strands by a nuclease. These junction-resolving enzymes bind to four-way junctions in dimeric form, distorting the structure of the junction in the process. Crystal structures of T7 endonuclease I have been determined as free protein, and the complex with a DNA junction. In neither crystal structure was the N-terminal 16-amino acid peptide visible, yet deletion of this peptide has a marked effect on the resolution process. Here we have investigated the N-terminal peptide by inclusion of spin-label probes at unique sites within this region, studied by electron paramagnetic resonance. Continuous wave experiments show that these labels are mobile in the free protein but become constrained on binding a DNA junction, with the main interaction occurring for residues 7-10 and 12. Distance measurements between equivalent positions within the two peptides of a dimer using PELDOR showed that the intermonomeric distances for residues 2-12 are long and broadly distributed in the free protein but are significantly shortened and become more defined on binding to DNA. These results suggest that the N-terminal peptides become more organized on binding to the DNA junction and nestle into the minor grooves at the branchpoint, consistent with the biochemical data indicating an important role in the resolution process. This study demonstrates the presence of structure within a protein region that cannot be viewed by crystallography.

  17. 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...

  18. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA.

    Science.gov (United States)

    Vergnaud, Gilles; Li, Yanjun; Gorgé, Olivier; Cui, Yujun; Song, Yajun; Zhou, Dongsheng; Grissa, Ibtissem; Dentovskaya, Svetlana V; Platonov, Mikhail E; Rakin, Alexander; Balakhonov, Sergey V; Neubauer, Heinrich; Pourcel, Christine; Anisimov, Andrey P; Yang, Ruifu

    2007-01-01

    The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR

  19. Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing

    DEFF Research Database (Denmark)

    Børglum, Anders; Nyegaard, Mette; Kvistgaard, AB;

    1997-01-01

    hundred loci as spots in a 2-D pattern. The majority of the loci resolved are polymorphic. Using linkage analysis in a large CEPH family, this study reports the mapping of 34 loci detected by the minisatellite core probe 33.6. By multipoint linkage analysis, regional chromosome positions of the 33.6 loci...... in genome scanning, not only in theoretical but also in practical terms. Moreover, it can be anticipated that this method will have a specific advantage in studies that scan for trinucleotide repeat expansions and somatic instability, where the repeat sequences detected by appropriate core probes...

  20. DNA Barcoding in a Crop Genebank: Resolving the Capsicum annuum Species Complex.

    Science.gov (United States)

    Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnC-rpoB, rps16, and matK, and the nuclear waxy intron was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense, and C. rhomboide...

  1. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.

    Science.gov (United States)

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1,040,000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43,000 RNA-mediated interactions, and ∼12,000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network

  2. 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.

  3. Tamil merchant in ancient Mesopotamia.

    Science.gov (United States)

    Palanichamy, Malliya Gounder; Mitra, Bikash; Debnath, Monojit; Agrawal, Suraksha; Chaudhuri, Tapas Kumar; Zhang, Ya-Ping

    2014-01-01

    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.

  4. Ancient Egypt.

    Science.gov (United States)

    Evers, Virginia

    This four-week fourth grade social studies unit dealing with religious dimensions in ancient Egyptian culture was developed by the Public Education Religion Studies Center at Wright State University. It seeks to help students understand ancient Egypt by looking at the people, the culture, and the people's world view. The unit begins with outlines…

  5. 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.

  6. Ancient DNA analyses of early archaeological sites in New Zealand reveal extreme exploitation of moa (Aves: Dinornithiformes) at all life stages

    Science.gov (United States)

    Oskam, Charlotte L.; Allentoft, Morten E.; Walter, Richard; Scofield, R. Paul; Haile, James; Holdaway, Richard N.; Bunce, Michael; Jacomb, Chris

    2012-10-01

    The human colonisation of New Zealand in the late thirteenth century AD led to catastrophic impacts on the local biota and is among the most compelling examples of human over-exploitation of native fauna, including megafauna. Nearly half of the species in New Zealand' s pre-human avifauna are now extinct, including all nine species of large, flightless moa (Aves: Dinornithiformes). The abundance of moa in early archaeological sites demonstrates the significance of these megaherbivores in the diet of the first New Zealanders. Combining moa assemblage data, based on DNA identification of eggshell and bone, with morphological identification of bone (literature and museum catalogued specimens), we present the most comprehensive audit of moa to date from several significant 13th-15th century AD archaeological deposits across the east coast of the South Island. Mitochondrial DNA (mtDNA) was amplified from 251 of 323 (78%) eggshell fragments and 22 of 27 (88%) bone samples, and the analyses revealed the presence of four moa species: Anomalopteryx didiformis; Dinornis robustus; Emeus crassus and Euryapteryx curtus. The mtDNA, along with polymorphic microsatellite markers, enabled an estimate of the minimum number of individual eggs consumed at each site. Remarkably, in one deposit over 50 individual eggs were identified - a number that likely represents a considerable proportion of the total reproductive output of moa in the area and emphasises that human predation of all life stages of moa was intense. Molecular sexing was conducted on bones (n = 11). Contrary to previous ancient DNA studies from natural sites that consistently report an excess of female moa, we observed an excess of males (2.7:1), suggestive that males were preferential targets. This could be related to different behaviour between the two highly size-dimorphic sexes in moa. Lastly, we investigated the moa species from recovered skeletal and eggshell remains from seven Wairau Bar burials, and identified

  7. Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand.

    Science.gov (United States)

    Allentoft, Morten E; Rawlence, Nicolas J

    2012-01-20

    The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.

  8. Time-Resolved Fluorescence Anisotropy Study of the Interaction Between DNA and a Peptide Truncated from the p53 Protein Core Domain.

    Science.gov (United States)

    Liu, Chengxuan; Liang, Gaiting; Liu, Zhen; Zu, Lily

    2014-03-01

    Time-resolved fluorescence anisotropy spectroscopy was applied to study the interaction between a peptide truncated from the binding site of tumor suppressor p53 protein and the DNAs covalently labeled with 6-carboxyfluorescein (FAM) dye. Fluorescence intensity quenching and changes of anisotropy decay lifetime were monitored when FAM labeled DNA formed complex with the peptide. The results demonstrated that the sequence of DNA could not define the binding specificity between the peptide and DNA. But the anisotropy decay of FAM can be used to examine the binding affinity of the peptide to DNA. The fluorescent dynamics of FAM can also be used to represent the rigidity of the complex formed between the peptide and DNA.

  9. Identification of Photosynthetic Plankton Communities Using Sedimentary Ancient DNA and Their Response to late-Holocene Climate Change on the Tibetan Plateau

    Science.gov (United States)

    Hou, Weiguo; Dong, Hailiang; Li, Gaoyuan; Yang, Jian; Coolen, Marco J. L.; Liu, Xingqi; Wang, Shang; Jiang, Hongchen; Wu, Xia; Xiao, Haiyi; Lian, Bin; Wan, Yunyang

    2014-10-01

    Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

  10. Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau.

    Science.gov (United States)

    Hou, Weiguo; Dong, Hailiang; Li, Gaoyuan; Yang, Jian; Coolen, Marco J L; Liu, Xingqi; Wang, Shang; Jiang, Hongchen; Wu, Xia; Xiao, Haiyi; Lian, Bin; Wan, Yunyang

    2014-10-17

    Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

  11. 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; Fredensborg, Brian Lund; Nejsum, Peter;

    parasite eggs from environmental samples collected at a Viking-age settlement (1018-1030 A.D.) are DNA typed to the species level. The human whipworm (Trichuris trichiura) and the human roundworm (Ascaris lumbricoides) are identified indicating that these parasites were endemic in Denmark in the Viking...

  12. Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (Apteryx spp.) and a Recently Extinct Lineage of Spotted Kiwi

    OpenAIRE

    Shepherd, Lara D; Worthy, Trevor H.; Tennyson, Alan J. D.; R Paul Scofield; Ramstad, Kristina M.; Lambert, David M.

    2012-01-01

    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 littl...

  13. Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock

    OpenAIRE

    Daniela Piras; Maria Grazia Doro; Giuseppina Casu; Paola Maria Melis; Simona Vaccargiu; Ignazio Piras; Debora Parracciani; Roberta Stradoni; Bruno Frongia; Graziano Lai; Salvatore Sale; Walter Cattari; Roberto Piras; Ombretta Querci; Piergiorgio Demuro

    2012-01-01

    Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection oper...

  14. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.

    Science.gov (United States)

    Jørgensen, Tina; Kjaer, Kurt H; Haile, James; Rasmussen, Morten; Boessenkool, Sanne; Andersen, Kenneth; Coissac, Eric; Taberlet, Pierre; Brochmann, Christian; Orlando, Ludovic; Gilbert, M Thomas P; Willerslev, Eske

    2012-04-01

    Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.

  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. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

    Directory of Open Access Journals (Sweden)

    Dirk-Martin Scheel

    2014-05-01

    Full Text Available Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M.tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.

  17. On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations.

    Science.gov (United States)

    Kefi, Rym; Hechmi, Meriem; Naouali, Chokri; Jmel, Haifa; Hsouna, Sana; Bouzaid, Eric; Abdelhak, Sonia; Beraud-Colomb, Eliane; Stevanovitch, Alain

    2016-12-30

    The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

  18. 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.

  19. Haplotype affinities resolve a major component of goat (Capra hircus MtDNA D-loop diversity and reveal specific features of the Sardinian stock.

    Directory of Open Access Journals (Sweden)

    Daniela Piras

    Full Text Available Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1 to provide an operational definition of meaningful mtDNA units within haplogroup A, 2 to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3 to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591 which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

  20. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock.

    Science.gov (United States)

    Piras, Daniela; Doro, Maria Grazia; Casu, Giuseppina; Melis, Paola Maria; Vaccargiu, Simona; Piras, Ignazio; Parracciani, Debora; Stradoni, Roberta; Frongia, Bruno; Lai, Graziano; Sale, Salvatore; Cattari, Walter; Piras, Roberto; Querci, Ombretta; Demuro, Piergiorgio; Cui, Sandro; Atzori, Franco; Mancosu, Marco; Marchiori, Francesca; Cammelli, Rossana; Spiga, Alessandra; Loddo, Pier Paolo; Pili, Gianfranco; Boi, Roberto; Argiolas, Giuseppe; Mereu, Paolo; Leoni, Giovanni Giuseppe; Naitana, Salvatore; Pirastu, Mario; Novelletto, Andrea

    2012-01-01

    Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.

  1. Angle-resolved XPS analysis and characterization of monolayer and multilayer silane films for DNA coupling to silica.

    Science.gov (United States)

    Shircliff, Rebecca A; Stradins, Paul; Moutinho, Helio; Fennell, John; Ghirardi, Maria L; Cowley, Scott W; Branz, Howard M; Martin, Ina T

    2013-03-26

    We measure silane density and Sulfo-EMCS cross-linker coupling efficiency on aminosilane films by high-resolution X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) measurements. We then characterize DNA immobilization and hybridization on these films by (32)P-radiometry. We find that the silane film structure controls the efficiency of the subsequent steps toward DNA hybridization. A self-limited silane monolayer produced from 3-aminopropyldimethylethoxysilane (APDMES) provides a silane surface density of ~3 nm(-2). Thin (1 h deposition) and thick (19 h deposition) multilayer films are generated from 3-aminopropyltriethoxysilane (APTES), resulting in surfaces with increased roughness compared to the APDMES monolayer. Increased silane surface density is estimated for the 19 h APTES film, due to a ∼32% increase in surface area compared to the APDMES monolayer. High cross-linker coupling efficiencies are measured for all three silane films. DNA immobilization densities are similar for the APDMES monolayer and 1 h APTES. However, the DNA immobilization density is double for the 19 h APTES, suggesting that increased surface area allows for a higher probe attachment. The APDMES monolayer has the lowest DNA target density and hybridization efficiency. This is attributed to the steric hindrance as the random packing limit is approached for DNA double helices (dsDNA, diameter ≥ 2 nm) on a plane. The heterogeneity and roughness of the APTES films reduce this steric hindrance and allow for tighter packing of DNA double helices, resulting in higher hybridization densities and efficiencies. The low steric hindrance of the thin, one to two layer APTES film provides the highest hybridization efficiency of nearly 88%, with 0.21 dsDNA/nm(2). The XPS data also reveal water on the cross-linker-treated surface that is implicated in device aging.

  2. The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny.

    Science.gov (United States)

    Williams, S T; Foster, P G; Littlewood, D T J

    2014-01-01

    A need to increase sampling of mitochondrial genomes for Vetigastropoda has been identified as an important step towards resolving relationships within the Gastropoda. We used shotgun sequencing of genomic DNA, using an Illumina MiSeq, to obtain the first mitochondrial genome for the vetigastropod family Turbinidae, doubling the number of genomes for the species-rich superfamily Trochoidea. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, resulting in a timely and cost-effective method for obtaining whole mitochondrial genomes from ethanol-preserved tissue samples. Bayesian analysis of amino acid variation for all available gastropod genomes including the new turbinid mtgenome produced a well resolved tree with high nodal support for most nodes. Major clades within Gastropoda were recovered with strong support, with the exception of Littorinimorpha, which was polyphyletic. We confirm here that mitogenomics is a useful tool for molluscan phylogenetics, especially when using powerful new models of amino acid evolution, but recognise that increased taxon sampling is still required to resolve existing differences between nuclear and mitochondrial gene trees.

  3. Time-resolved luminescence biosensor for continuous activity detection of protein acetylation-related enzymes based on DNA-sensitized terbium(III) probes.

    Science.gov (United States)

    Han, Yitao; Li, Hao; Hu, Yufang; Li, Pei; Wang, Huixia; Nie, Zhou; Yao, Shouzhuo

    2015-09-15

    Protein acetylation of histone is an essential post-translational modification (PTM) mechanism in epigenetic gene regulation, and its status is reversibly controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Herein, we have developed a sensitive and label-free time-resolved luminescence (TRL) biosensor for continuous detection of enzymatic activity of HATs and HDACs, respectively, based on acetylation-mediated peptide/DNA interaction and Tb(3+)/DNA luminescent probes. Using guanine (G)-rich DNA-sensitized Tb(3+) luminescence as the output signal, the polycationic substrate peptides interact with DNA with high affinity and subsequently replace Tb(3+), eliminating the luminescent signal. HAT-catalyzed acetylation remarkably reduces the positive charge of the peptides and diminishes the peptide/DNA interaction, resulting in the signal on detection via recovery of DNA-sensitized Tb(3+) luminescence. With this TRL sensor, HAT (p300) can be sensitively detected with a wide linear range from 0.2 to 100 nM and a low detection limit of 0.05 nM. The proposed sensor was further used to continuously monitor the HAT activity in real time. Additionally, the TRL biosensor was successfully applied to evaluating HAT inhibition by two specific inhibitors, anacardic acid and C464, and satisfactory Z'-factors above 0.73 were obtained. Moreover, this sensor is feasible to continuously monitor the HDAC (Sirt1)-catalyzed deacetylation with a linear range from 0.5 to 500 nM and a detection limit of 0.5 nM. The proposed sensor is a convenient, sensitive, and mix-and-read assay, presenting a promising platform for protein acetylation-targeted epigenetic research and drug discovery.

  4. A Novel Mechanism for Activator-Controlled Initiation of DNA Replication that Resolves the Auto-regulation Sequestration Paradox

    Science.gov (United States)

    Nilsson, K.; Ehrenberg, M.

    For bacterial genes to be inherited to the next bacterial generation, the gene containing DNA sequences must be duplicated before cell division so that each daughter cell contains a complete set of genes. The duplication process is called DNA replication and it starts at one defined site on the DNA molecule called the origin of replication (oriC) [1]. In addition to chromosomal DNA, bacteria often also contain plasmid DNA. Plasmids are extra-chromosomal DNA molecules carrying genes that increase the fitness of their host in certain environments, with genes encoding antibiotic resistance as a notorious example [2]. The chromosome is found at a low per cell copy number and initiation of replication takes place synchronously once every cell generation [3,4], while many plasmids exist at a high copy number and replication initiates asynchronously, throughout the cell generation [5]. In this chapter we present a novel mechanism for the control of initiation of replication, where one type of molecule may activate a round of replication by binding to the origin of replication and also regulate its own synthesis accurately. This mechanism of regulating the initiation of replication also offers a novel solution to the so-called auto-regulation sequestration paradox, i.e. how a molecule sequestered by binding to DNA may at the same time accurately regulate its own synthesis [6]. The novel regulatory mechanism is inspired by the molecular set-up of the replication control of the chromosome in the bacterium Escherichia coli and is here transferred into a plasmid model. This allows us to illustrate principles of replication control in a simple way and to put the novel mechanism into the context of a previous analysis of plasmids regulated by inhibitor-dilution copy number control [7]. We analyze factors important for a sensitive response of the replication initiation rate to changes in plasmid concentration in an asynchronous model and discover a novel mechanism for creating a

  5. Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding

    DEFF Research Database (Denmark)

    Riemann, L.; Alfredsson, H.; Hansen, Michael Møller

    2010-01-01

    that even the smallest larvae feed on a striking variety of plankton organisms, and that gelatinous zooplankton is of fundamental dietary importance. Hence, the specific plankton composition seems essential for eel larval feeding and growth, suggesting a linkage between eel survival and regional plankton......, the Sargasso Sea is oligotrophic, with generally low plankton biomass, and the feeding biology of eel larvae has so far remained a mystery, hampering understanding of this peculiar life history. DNA barcoding of gut contents of 61 genetically identified A. anguilla larvae caught in the Sargasso Sea showed...

  6. Qualitative assessment of the diet of European eel larvae in the Sargasso Sea resolved by DNA barcoding.

    Science.gov (United States)

    Riemann, Lasse; Alfredsson, Hanna; Hansen, Michael M; Als, Thomas D; Nielsen, Torkel G; Munk, Peter; Aarestrup, Kim; Maes, Gregory E; Sparholt, Henrik; Petersen, Michael I; Bachler, Mirjam; Castonguay, Martin

    2010-12-23

    European eels (Anguilla anguilla) undertake spawning migrations of more than 5000 km from continental Europe and North Africa to frontal zones in the Sargasso Sea. Subsequently, the larval offspring are advected by large-scale eastward ocean currents towards continental waters. However, the Sargasso Sea is oligotrophic, with generally low plankton biomass, and the feeding biology of eel larvae has so far remained a mystery, hampering understanding of this peculiar life history. DNA barcoding of gut contents of 61 genetically identified A. anguilla larvae caught in the Sargasso Sea showed that even the smallest larvae feed on a striking variety of plankton organisms, and that gelatinous zooplankton is of fundamental dietary importance. Hence, the specific plankton composition seems essential for eel larval feeding and growth, suggesting a linkage between eel survival and regional plankton productivity. These novel insights into the prey of Atlantic eels may furthermore facilitate eel larval rearing in aquaculture, which ultimately may replace the unsustainable use of wild-caught glass eels.

  7. Genetic diversity among ancient Nordic populations.

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, 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 locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  8. A 150-year record of ancient DNA, lipid biomarkers and hydrogen isotopes, tracing the microbial-planktonic community succession controlled by (hydro)climatic variability in a tropical lake

    Science.gov (United States)

    Smittenberg, Rienk; Yamoah, Kweku; Callac, Nolwenn; Fru, Ernest Chi; Chabangborn, Akkaneewut; Rattray, Jayne; Wohlfarth, Barbara

    2016-04-01

    We investigated the decadal variations in phytoplankton communities, and their response to environmental and climatic conditions, from a ˜150 year long sedimentary archive of Lake Nong Thale Prong (NTP), southern Thailand. We applied a combination of analyses: lipid biomarkers, compound-specific hydrogen isotopes, bulk carbon and nitrogen concentrations and isotopes, environmental SEM, and fossil DNA using qPCR targeted to specific taxa. Past hydrological conditions were reconstructed using the hydrogen isotopic composition of leaf wax n-alkanes. Temperatures were reconstructed using the tetraether-based MBT/CBT index, measured using a new and efficient reverse-phase HPLC-MS method. The climatological data compared well with meteorological data from the last decades. Reconstructed drier and warmer conditions from ˜1857-1916 Common Era (CE) coincided with oligotrophic lake water conditions and dominance of the green algae Botryococcus braunii - evidenced by a combination of both fossil DNA and the occurrence of characteristic botryococcene lipids. A change to higher silica (Si) input ˜1916 CE was related to increased rainfall and lower temperatures concurring with an abrupt takeover by diatom blooms lasting for 50 years - as evidenced by ancient DNA, characteristic highly branched isoprenoid lipids, and SEM. From the 1970s onwards, more eutrophic conditions prevailed, and these were likely caused by increased levels of anthropogenic phosphate (P), aided by stronger lake stratification caused by dryer and warmer conditions. The eutrophic conditions led to increased primary productivity in the lake, consisting again of a Botryococcus sp., although this time not producing botryococcene lipids. Moreover, Cyanobacteria became dominant - again evidenced by ancient DNA and the characteristic C19 alkane. Throughout the record, stratification and primary production could be linked to the intensity of methane cycling, by targeting and quantifying the mcrA gene that is used

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

    DEFF Research Database (Denmark)

    Mouatt, Julia Thidamarth Vilstrup

    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...

  10. [The Dynamics of the Composition of mtDNA Haplotypes of the Ancient Population of the Altai Mountains from the Early Bronze Age (3rd Millennium BC) to the Iron Age (2nd-1st Centuries BC)].

    Science.gov (United States)

    Gubina, M A; Kulikov, I V; Babenko, V N; Chikisheva, T A; Romaschenko, A G; Voevoda, M I; Molodin, V I

    2016-01-01

    The mtDNA polymorphism in representatives of various archaeological cultures of the Developed Bronze Age, Early Scythian, and Hunnish-Sarmatian periods was analyzed (N = 34). It detected the dominance of Western-Eurasian haplotypes (70.6%) in mtDNA samples from the representatives of the ancient population of the Early Bronze Age--Iron Age on the territory of Altai Mountains. Since the 8th to the 7th centuries BC, a sharp increase was revealed in the Eastern-Eurasian haplogroups A, D, C, andZ (43.75%) as compared to previous cultures (16.7%). The presence of haplotype 223-242-290-319 of haplogroup A8 in Dolgans, Itelmens, Evens, Koryaks, and Yakuts indicates the possible long-term presence of its carriers in areas inhabited by these populations. The prevalence of Western-Eurasian haplotypes is observed not only in the Altai Mountains but also in Central Asia (Kazakhstan) and the South of the Krasnoyarsk Krai. All of the three studied samples from the Western-Eurasian haplogroups were revealed to contain U, H, T, and HV. The ubiquitous presence of haplotypes of haplogroup H and some haplogroups of cluster U (U5al, U4, U2e, and K) in the vast territory from the Yenisei River basin to the Atlantic Ocean may indicate the direction of human settlement, which most likely occurred in the Paleolithic Period from Central Asia.

  11. Co-located 18S/5S rDNA arrays: an ancient and unusual chromosomal trait in Julidini species (Labridae, Perciformes)

    Science.gov (United States)

    Amorim, Karlla Danielle Jorge; Cioffi, Marcelo de Bello; Bertollo, Luiz Antonio Carlos; Soares, Rodrigo Xavier; de Souza, Allyson Santos; da Costa, Gideão Wagner Werneck Felix; Molina, Wagner Franco

    2016-01-01

    Abstract Wrasses (Labridae) are extremely diversified marine fishes, whose species exhibit complex interactions with the reef environment. They are widely distributed in the Indian, Pacific and Atlantic oceans. Their species have displayed a number of karyotypic divergent processes, including chromosomal regions with complex structural organization. Current cytogenetic information for this family is phylogenetically and geographically limited and mainly based on conventional cytogenetic techniques. Here, the distribution patterns of heterochromatin, GC-specific chromosome regions and Ag-NORs, and the organization of 18S and 5S rDNA sites of the Atlantic species Thalassoma noronhanum (Boulenger, 1890), Halichoeres poeyi (Steindachner, 1867), Halichoeres radiatus (Linnaeus, 1758), Halichoeres brasiliensis (Bloch, 1791) and Halichoeres penrosei Starks, 1913, belonging to the tribe Julidini were analyzed. All the species exhibited 2n=48 chromosomes with variation in the number of chromosome arms among genera. Thalassoma noronhanum has 2m+46a, while species of the genus Halichoeres Rüppell, 1835 share karyotypes with 48 acrocentric chromosomes. The Halichoeres species exhibit differences in the heterochromatin distribution patterns and in the number and distribution of 18S and 5S rDNA sites. The occurrence of 18S/5S rDNA syntenic arrangements in all the species indicates a functionally stable and adaptive genomic organization. The phylogenetic sharing of this rDNA organization highlights a marked and unusual chromosomal singularity inside the family Labridae. PMID:28123678

  12. Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: the bison was a horse, and the muskox and beats were goats

    DEFF Research Database (Denmark)

    Sinding, Mikkel-Holger; Arneborg, Jette; Nyegaard, Georg

    2015-01-01

    mitochondrial 16S DNA analysis. The results revealed that the putative bison was, in fact horse, while the bears and muskox were goat. The results demonstrate the importance of using genetic analyses to validate results derived from morphological analyses on hair, in particular where such studies lead...

  13. Ancient DNA of the extinct lava shearwater (Puffinus olsoni from the Canary Islands reveals incipient differentiation within the P. puffinus complex.

    Directory of Open Access Journals (Sweden)

    Oscar Ramirez

    Full Text Available BACKGROUND: The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands. METHODOLOGY/PRINCIPAL FINDINGS: We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni from Fuerteventura (Canary Islands, the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species. CONCLUSIONS: The phylogenetic analyses based on the DNA data reveal that: (i the "Puffinus puffinus complex", an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae, shows unresolved phylogenetic relationships; (ii despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus.

  14. Ancient Astronomy in Armenia

    Science.gov (United States)

    Parsamian, Elma S.

    2007-08-01

    The most important discovery, which enriched our knowledge of ancient astronomy in Armenia, was the complex of platforms for astronomical observations on the Small Hill of Metzamor, which may be called an ancient “observatory”. Investigations on that Hill show that the ancient inhabitants of the Armenian Highlands have left us not only pictures of celestial bodies, but a very ancient complex of platforms for observing the sky. Among the ancient monuments in Armenia there is a megalithic monument, probably, being connected with astronomy. 250km South-East of Yerevan there is a structure Zorats Kar (Karahunge) dating back to II millennium B.C. Vertical megaliths many of which are more than two meters high form stone rings resembling ancient stone monuments - henges in Great Britain and Brittany. Medieval observations of comets and novas by data in ancient Armenian manuscripts are found. In the collection of ancient Armenian manuscripts (Matenadaran) in Yerevan there are many manuscripts with information about observations of astronomical events as: solar and lunar eclipses, comets and novas, bolides and meteorites etc. in medieval Armenia.

  15. Haplotype affinities resolve a major component of goat (Capra hircus) MtDNA D-loop diversity and reveal specific features of the Sardinian stock

    OpenAIRE

    Piras, Daniela; Doro, Maria Grazia; Casu, Giuseppina; Melis, Paola Maria; Vaccargiu, Simona; Piras, Ignazio; Parracciani, Debora; Stradoni, Roberta; Frongia, Bruno; Lai, Graziano; Sale, Salvatore; Cattari, Walter; Piras, Roberto; Querci, Ombretta; Demuro, Piergiorgio

    2012-01-01

    Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection oper...

  16. Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes.

    Directory of Open Access Journals (Sweden)

    Yinqiu Cui

    Full Text Available To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor-descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

  17. Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe.

    Directory of Open Access Journals (Sweden)

    Montserrat Hervella

    Full Text Available BACKGROUND/PRINCIPAL FINDINGS: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. METHODOLOGY/SIGNIFICANCE: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria. In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples and replication of the results (43% of the samples by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe. CONCLUSION: The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different

  18. Human evolution: a tale from ancient genomes.

    Science.gov (United States)

    Llamas, Bastien; Willerslev, Eske; Orlando, Ludovic

    2017-02-05

    The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

  19. Putative ancient microorganisms from amber nuggets.

    Science.gov (United States)

    Veiga-Crespo, Patricia; Blasco, Lucía; Poza, Margarita; Villa, Tomás G

    2007-06-01

    Evolutionary microbiology studies based on the isolation of ancient DNA and/or microbial samples are scarce due to the difficulty of finding well preserved biological specimens. However, amber is a fossil resin with natural preserving properties for microbial cells and DNA. The visualization by transmission electron microscopy of different microorganism-like specimens found in amber nuggets from both the Miocene and the Cretaceous periods was accompanied by studies of ancient DNA obtained from the nuggets. After the design of specific primers based on the present sequences of both genes in Saccharomyces cerevisiae, the ancestral AGP2 sequence from the Miocene, as well as the 18S rRNA from the Cretaceous, were amplified.

  20. [Anomalous pregnancies in ancient medicine].

    Science.gov (United States)

    Gazzaniga, Valentina

    2010-01-01

    In ancient Greek medicine female physiology is determined by a particular state of non-steady equilibrium, largely based on pregnancy and lactation, presented as the only balanced and healthy periods in women's life. Nonetheless, pregnancy can be also a pathological moment, in particular referring to specific alterations of its 'normal time' ('seven-months', 'eight-months' and 'ten-months' children). The article analyzes the well-known case of myle, an abnormal pregnancy developing in three and sometimes four years, non resolving in a normal delivery, but often in a dramatic haemorrhagic flux. The author compares Hippocratic and Aristotelic testimonies about myle and abnormal pregnancies with the evidence fournished by the historical-religious recent studies about Hera and her parthenogenetic, monstrous children.

  1. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, 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 locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  2. An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genus Zamia.

    Science.gov (United States)

    Cafasso, Donata; Chinali, Gianni

    2014-03-01

    ZpS1 satellite DNA is specific to the genus Zamia and presents repetitive units organized as long arrays and also as very short arrays dispersed in the genome. We have characterized the structure of the ZpS1 repeats in 12 species representative of the whole geographic distribution of the genus. In most species, the clone most common sequences (cMCS) were so similar that a general most common sequence (GMCS) of the ZpS1 repetitive unit in the genus could be obtained. The few partial variations from the GMCS found in cMCS of some species correspond to variable positions present in most other species, as indicated by the clone consensus sequences (cCS). Two species have an additional species-specific variety of ZpS1 satellite. The dispersed repeats were found to contain more mutations than repeats from long arrays. Our results indicate that all or most species of Zamia inherited the ZpS1 satellite from a common ancestor in Miocene and have maintained repetitive units of the original structure till present. The features of ZpS1 satellite in the genus Zamia are poorly compatible with the model of concerted evolution, but they are perfectly consistent with a new model of satellite evolution based on experimental evidences indicating that a specific amplification-substitution repair mechanism maintains the homogeneity and stability of the repeats structure in each satellite DNA originally present in a species as long as the species exists.

  3. Ancient Marital Rites

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    Clearly defined rites governing speech and actions dominated both the social and domestic activities of ancient Chinese people. Rites not only dominated the lives of men, but were also prominent in the lives of women.

  4. Ancient Chinese Architecture

    Institute of Scientific and Technical Information of China (English)

    1993-01-01

    CHINESE people have accu-mulated a great deal ofexperience in architecture,constantly improving building ma-terials and thus creating uniquebuilding styles.The history of ancient Chinesearchitechtural development can be

  5. Dentistry in ancient mesopotamia.

    Science.gov (United States)

    Neiburger, E J

    2000-01-01

    Sumer, an empire in ancient Mesopotamia (southern Iraq), is well known as the cradle of our modern civilization and the home of biblical Abraham. An analysis of skeletal remains from cemeteries at the ancient cities of Ur and Kish (circa 2000 B.C.), show a genetically homogeneous, diseased, and short-lived population. These ancient Mesopotamians suffered severe dental attrition (95 percent), periodontal disease (42 percent), and caries (2 percent). Many oral congenital and neoplastic lesions were noted. During this period, the "local dentists" knew only a few modern dental techniques. Skeletal (dental) evidence indicates that the population suffered from chronic malnutrition. Malnutrition was probably caused by famine, which is substantiated in historic cuneiform and biblical writings, geologic strata samples, and analysis of skeletal and forensic dental pathology. These people had modern dentition but relatively poor dental health. The population's lack of malocclusions, caries, and TMJ problems appear to be due to flat plane occlusion.

  6. 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.

  7. 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…

  8. Ancient Egypt: Personal Perspectives.

    Science.gov (United States)

    Wolinski, Arelene

    This teacher resource book provides information on ancient Egypt via short essays, photographs, maps, charts, and drawings. Egyptian social and religious life, including writing, art, architecture, and even the practice of mummification, is conveniently summarized for the teacher or other practitioner in a series of one to three page articles with…

  9. Cloning Ancient Trees

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    west of Tiananmen Square in Beijing, in Zhongshan Park, there stand several ancient cypress trees, each more than 1,000 years old. Their leafy crowns are all more than 20 meters high, while four have trunks that are 6 meters in circumference. The most unique of these

  10. Ancient ports of Kalinga

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    The ancient Kingdom of Kalinga mentioned in the Hathigumpha inscription of Kharavela (1st century B.C.) extended from the mouths of the Ganges to the estuary of Godavari river on the East Coast. Ptolemy (100 A.D.) mentions that Paluru (District...

  11. Ancient deforestation revisited.

    Science.gov (United States)

    Hughes, J Donald

    2011-01-01

    The image of the classical Mediterranean environment of the Greeks and Romans had a formative influence on the art, literature, and historical perception of modern Europe and America. How closely does is this image congruent with the ancient environment as it in reality existed? In particular, how forested was the ancient Mediterranean world, was there deforestation, and if so, what were its effects? The consensus of historians, geographers, and other scholars from the mid-nineteenth century through the first three quarters of the twentieth century was that human activities had depleted the forests to a major extent and caused severe erosion. My research confirmed this general picture. Since then, revisionist historians have questioned these conclusions, maintaining instead that little environmental damage was done to forests and soils in ancient Greco-Roman times. In a reconsideration of the question, this paper looks at recent scientific work providing proxy evidence for the condition of forests at various times in ancient history. I look at three scientific methodologies, namely anthracology, palynology, and computer modeling. Each of these avenues of research offers support for the concept of forest change, both in abundance and species composition, and episodes of deforestation and erosion, and confirms my earlier work.

  12. Printing Ancient Terracotta Warriors

    Science.gov (United States)

    Gadecki, Victoria L.

    2010-01-01

    Standing in awe in Xian, China, at the Terra Cotta warrior archaeological site, the author thought of sharing this experience and excitement with her sixth-grade students. She decided to let her students carve patterns of the ancient soldiers to understand their place in Chinese history. They would make block prints and print multiple soldiers on…

  13. Ancient human microbiomes.

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J; Lewis, Cecil M

    2015-02-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

  14. Comets in ancient India

    CERN Document Server

    Gupta, Patrick Das

    2014-01-01

    The Indo-aryans of ancient India observed stars and constellations for ascertaining auspicious times for sacrificial rites ordained by vedas. It is but natural that they would have recounted in the vedic texts about comets. In Rigveda ($\\sim $ 1700 - 1500 BC) and Atharvaveda ($\\sim $ 1150 BC), there are references to dhumaketus and ketus, which stand for comets in Sanskrit. Varahamihira in 550 AD and Ballala Sena ($\\sim $ 1100 - 1200 AD) have described a large number of comets recorded by ancient seers such as Parashara, Vriddha Garga, Narada, Garga, etc. In this article, I conjecture that an episode narrated in Mahabharata of a radiant king, Nahusha, ruling the heavens, and later turning into a serpent after he had kicked the seer Agastya (also the star Canopus), is a mythological retelling of a cometary event.

  15. Deep sequencing of RNA from ancient maize kernels.

    Directory of Open Access Journals (Sweden)

    Sarah L Fordyce

    Full Text Available 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 hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication.

  16. Deep Sequencing of RNA from Ancient Maize Kernels

    Science.gov (United States)

    Rasmussen, Morten; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Alquezar-Planas, David E.; Penfield, Steven; Brown, Terence A.; Vielle-Calzada, Jean-Philippe; Montiel, Rafael; Jørgensen, Tina; Odegaard, Nancy; Jacobs, Michael; Arriaza, Bernardo; Higham, Thomas F. G.; Ramsey, Christopher Bronk; Willerslev, Eske; Gilbert, M. Thomas P.

    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 hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication. PMID:23326310

  17. Ambrosia of Ancients

    Institute of Scientific and Technical Information of China (English)

    HUOJIANYING

    2004-01-01

    IN 196 B.C. a Chinese philosopher observedto his ruler: "A lord's to ppriority is the welfare of his subjects; to the peopie, eating is foremost." Chinese ancients perceived clearly the essentiality of grain cultivation to the survival of the population and country as a whole. This is apparent in the premillennial term for "country" -sheji literally translated as god of land and grain.

  18. Population structure of plaice ( Pleuronectes platessa L.) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data

    Science.gov (United States)

    Hoarau, G.; Piquet, A. M.-T.; van der Veer, H. W.; Rijnsdorp, A. D.; Stam, W. T.; Olsen, J. L.

    2004-05-01

    We used Single Strand Conformation Polymorphism (SSCP) of mtDNA control region to assess the population structure of the flatfish Pleuronectes platessa (plaice), to compare these data with a previous study based on microsatellite loci, and to test for possible sex-biased dispersal. From 461 individuals, 163 haplotypes were identified across 11 locations. Diversity was higher with mtDNA ( h =0.776 to 0.981; π = 0.0178 to 0.0298) as compared to microsatellite loci using the same samples ( He = 0.721 to 0.77). Genetic diversity was lower in samples from Iceland and Faroe, as compared to the continental shelf samples. Although both classes of markers revealed a relatively strong differentiation between shelf and off-shelf populations ( θ = 0.1015 and θ = 0.0351, respectively), only the mtDNA data were able to detect differentiation within the continental shelf, i.e., a North Sea-Irish Sea group which was weakly distinguishable from Norway ( θ = 0.0046), the Baltic ( θ = 0.0136) and the Bay of Biscay ( θ = 0.0162). No evidence was obtained for isolation by distance, nor for sex-biased dispersal. This study demonstrates the importance of using more than one class of markers, especially for species such as plaice, with large populations, high dispersal and recent colonisation histories.

  19. Time-resolved fluorescence of 2-aminopurine in DNA duplexes in the presence of the EcoP15I Type III restriction-modification enzyme.

    Science.gov (United States)

    Ma, Long; Wu, Xiaohua; Wilson, Geoffrey G; Jones, Anita C; Dryden, David T F

    2014-06-20

    EcoP15I is a Type III DNA restriction and modification enzyme of Escherichia coli. We show that it contains two modification (Mod) subunits for sequence-specific methylation of DNA and one copy of a restriction endonuclease (Res) subunit for cleavage of DNA containing unmethylated target sequences. Previously the Mod2 dimer in the presence of cofactors was shown to use nucleotide flipping to gain access to the adenine base targeted for methylation (Reddy and Rao, J. Mol. Biol. 298 (2000) 597-610.). Surprisingly the Mod2 enzyme also appeared to flip a second adenine in the target sequence, one which was not subject to methylation. We show using fluorescence lifetime measurements of the adenine analogue, 2-aminopurine, that only the methylatable adenine undergoes flipping by the complete Res1Mod2 enzyme and that this occurs even in the absence of cofactors. We suggest that this is due to activation of the Mod2 core by the Res subunit.

  20. 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

  1. The structure-specific endonuclease Ercc1-Xpf is required to resolve DNA interstrand cross-link-induced double-strand breaks.

    Science.gov (United States)

    Niedernhofer, Laura J; Odijk, Hanny; Budzowska, Magda; van Drunen, Ellen; Maas, Alex; Theil, Arjan F; de Wit, Jan; Jaspers, N G J; Beverloo, H Berna; Hoeijmakers, Jan H J; Kanaar, Roland

    2004-07-01

    Interstrand cross-links (ICLs) are an extremely toxic class of DNA damage incurred during normal metabolism or cancer chemotherapy. ICLs covalently tether both strands of duplex DNA, preventing the strand unwinding that is essential for polymerase access. The mechanism of ICL repair in mammalian cells is poorly understood. However, genetic data implicate the Ercc1-Xpf endonuclease and proteins required for homologous recombination-mediated double-strand break (DSB) repair. To examine the role of Ercc1-Xpf in ICL repair, we monitored the phosphorylation of histone variant H2AX (gamma-H2AX). The phosphoprotein accumulates at DSBs, forming foci that can be detected by immunostaining. Treatment of wild-type cells with mitomycin C (MMC) induced gamma-H2AX foci and increased the amount of DSBs detected by pulsed-field gel electrophoresis. Surprisingly, gamma-H2AX foci were also induced in Ercc1(-/-) cells by MMC treatment. Thus, DSBs occur after cross-link damage via an Ercc1-independent mechanism. Instead, ICL-induced DSB formation required cell cycle progression into S phase, suggesting that DSBs are an intermediate of ICL repair that form during DNA replication. In Ercc1(-/-) cells, MMC-induced gamma-H2AX foci persisted at least 48 h longer than in wild-type cells, demonstrating that Ercc1 is required for the resolution of cross-link-induced DSBs. MMC triggered sister chromatid exchanges in wild-type cells but chromatid fusions in Ercc1(-/-) and Xpf mutant cells, indicating that in their absence, repair of DSBs is prevented. Collectively, these data support a role for Ercc1-Xpf in processing ICL-induced DSBs so that these cytotoxic intermediates can be repaired by homologous recombination.

  2. Dance in Ancient Greek Culture

    OpenAIRE

    Spalva, Rita

    2015-01-01

    The greatness and harmony of ancient Greece has had an impact upon the development of the Western European culture to this day. The ancient Greek culture has influenced contemporary literature genres and systems of philosophy, principles of architecture, sculpture and drama and has formed basis for such sciences as astronomy and mathematics. The art of ancient Greece with its penchant for beauty and clarity has been the example of the humanity’s search for an aesthetic ideal. Despite only bei...

  3. Mathematics in ancient Greece

    CERN Document Server

    Dantzig, Tobias

    2006-01-01

    More than a history of mathematics, this lively book traces mathematical ideas and processes to their sources, stressing the methods used by the masters of the ancient world. Author Tobias Dantzig portrays the human story behind mathematics, showing how flashes of insight in the minds of certain gifted individuals helped mathematics take enormous forward strides. Dantzig demonstrates how the Greeks organized their precursors' melange of geometric maxims into an elegantly abstract deductive system. He also explains the ways in which some of the famous mathematical brainteasers of antiquity led

  4. Ancient concrete works

    CERN Document Server

    Sparavigna, Amelia Carolina

    2011-01-01

    It is commonly believed that the ancient Romans were the first to create and use concrete. This is not true, as we can easily learn from the Latin literature itself. For sure, Romans were able to prepare high-quality hydraulic cements, comparable with the modern Portland cements. In this paper, we will see that the use of concrete is quite older, ranging back to the Homeric times. For instance, it was used for the floors of some courts and galleries of the Mycenaean palace at Tiryns

  5. Climate and Ancient Societies

    DEFF Research Database (Denmark)

    Climate, and human responses to it, have a strongly interconnected relationship. This when climate change occurs, the result of either natural or human causes, societies should react and adapt to these. But do they? If so, what is the nature of that change, and are the responses positive...... or negative for the long-term survival of social groups? In this volume, scholars from diverse disciplines including archaeology, geology and climate sciences explore scientific and material evidence for climate changes in the past, their causes, their effects on ancient societies and how those societies...

  6. 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...

  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. Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The mtDNA hypervariable region I (HVR-I) of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure. The relationships between the ancient population and related extant populations, as well as its possible origin at the molecular level, were also studied. Moreover, phylogenetic analysis and multi-dimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population. The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage. Combining the research results of archaeology and anthropology as well as molecular biology, we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia, China.

  9. Characterization of Ancient Tripitaka

    Science.gov (United States)

    Gong, Y. X.; Geng, L.; Gong, D. C.

    2015-08-01

    Tripitaka is the world's most comprehensive version of Buddhist sutra. There are limited numbers of Tripitaka currently preserved, most of them present various patterns of degradation. As little is known about the materials and crafts used in Tripitaka, it appeared necessary to identify them, and to further define adapted conservation treatment. In this work, a study concerning the paper source and dyestuff of the Tripitaka from approximate 16th century was carried out using fiber analysis and thin-layer chromatography (TLC). The results proved that the papers were mainly made from hemp or bark of mulberry tree, and indigo was used for colorizing the paper. At the end, we provide with suggestions for protecting and restoring the ancient Tripitaka.

  10. Genome-wide patterns of selection in 230 ancient Eurasians

    Science.gov (United States)

    Mathieson, Iain; Lazaridis, Iosif; Rohland, Nadin; Mallick, Swapan; Patterson, Nick; Roodenberg, Songül Alpaslan; Harney, Eadaoin; Stewardson, Kristin; Fernandes, Daniel; Novak, Mario; Sirak, Kendra; Gamba, Cristina; Jones, Eppie R.; Llamas, Bastien; Dryomov, Stanislav; Pickrel, Joseph; Arsuaga, Juan Luís; de Castro, José María Bermúdez; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Rojo Guerra, Manuel A.; Roodenberg, Jacob; Vergès, Josep Maria; Krause, Johannes; Cooper, Alan; Alt, Kurt W.; Brown, Dorcas; Anthony, David; Lalueza-Fox, Carles; Haak, Wolfgang; Pinhasi, Ron; Reich, David

    2016-01-01

    Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture whose genetic material we extracted from the DNA-rich petrous bone and who we show were members of the population that was the source of Europe’s first farmers. We also report a complete transect of the steppe region in Samara between 5500 and 1200 BCE that allows us to recognize admixture from at least two external sources into steppe populations during this period. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. PMID:26595274

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

    DEFF Research Database (Denmark)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak

    2014-01-01

    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) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction......Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral...... 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...

  12. Time-resolved EPR studies with DNA photolyase: excited-state FADH0 abstracts an electron from Trp-306 to generate FADH-, the catalytically active form of the cofactor.

    Science.gov (United States)

    Kim, S T; Sancar, A; Essenmacher, C; Babcock, G T

    1993-09-01

    Photolyase repairs UV-induced cyclobutane-pyrimidine dimers in DNA by photoinduced electron transfer. The enzyme isolated from Escherichia coli contains 5,10-methenyltetrahydrofolate, which functions as the light-harvesting chromophore, and fully reduced flavin adenine dinucleotide (FAD), which functions as the redox catalyst. During enzyme preparation, the flavin is oxidized to FADH0, which is catalytically inert. Illumination of the enzyme with 300- to 600-nm light converts the flavin to the fully reduced form in a reaction that involves photooxidation of an amino acid in the apoenzyme. The results of earlier optical studies had indicated that the redox-active amino acid in this photoactivation process was tryptophan. We have now used time-resolved electron paramagnetic resonance (EPR) spectroscopy to investigate the photoactivation reaction. Excitation of the flavin-radical-containing inactive enzyme produces a spin-polarized radical that we identify by 2H and 15N labeling as originating from a tryptophan residue, confirming the inferences from the optical work. These results and Trp-->Phe replacement by site-directed mutagenesis reveal that flavin radical photoreduction is achieved by electron abstraction from Trp-306 by the excited-state FADH0. Analysis of the hyperfine couplings and spin density distribution deduced from the isotopic-labeling results shows that the product of the light-driven redox chemistry is the Trp-306 cation radical. The results strongly suggest that the active form of photolyase contains FADH- and not FADH2.

  13. Layout of Ancient Maya Cities

    Science.gov (United States)

    Aylesworth, Grant R.

    Although there is little doubt that the ancient Maya of Mesoamerica laid their cities out based, in part, on astronomical considerations, the proliferation of "cosmograms" in contemporary scholarly discourse has complicated matters for the acceptance of rigorous archaeoastronomical research.

  14. Astronomical Significance of Ancient Monuments

    Science.gov (United States)

    Simonia, I.

    2011-06-01

    Astronomical significance of Gokhnari megalithic monument (eastern Georgia) is considered. Possible connection of Amirani ancient legend with Gokhnari monument is discussed. Concepts of starry practicality and solar stations are proposed.

  15. Hunting for Ancient Rocky Shores.

    Science.gov (United States)

    Johnson, Markes E.

    1988-01-01

    Promotes the study of ancient rocky shores by showing how they can be recognized and what directions future research may follow. A bibliography of previous research articles, arranged by geologic period, is provided in the appendix to this paper. (CW)

  16. 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...... cores as well. Here, we present some future perspectives for DNA studies on polar ice cores in regard to molecular ecology, DNA damage and degradation, anabiosis and antibiotic resistance genes. Finally, we address some of the methodological problems connected to ancient DNA research....

  17. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes).

    Science.gov (United States)

    Wood, Jamie R; Wilmshurst, Janet M; Richardson, Sarah J; Rawlence, Nicolas J; Wagstaff, Steven J; Worthy, Trevor H; Cooper, Alan

    2013-10-15

    Knowledge of extinct herbivore community structuring is essential for assessing the wider ecological impacts of Quaternary extinctions and determining appropriate taxon substitutes for rewilding. Here, we demonstrate the potential for coprolite studies to progress beyond single-species diet reconstructions to resolving community-level detail. The moa (Aves: Dinornithiformes) of New Zealand are an intensively studied group of nine extinct herbivore species, yet many details of their diets and community structuring remain unresolved. We provide unique insights into these aspects of moa biology through analyses of a multispecies coprolite assemblage from a rock overhang in a montane river valley in southern New Zealand. Using ancient DNA (aDNA), we identified 51 coprolites, which included specimens from four sympatric moa species. Pollen, plant macrofossils, and plant aDNA from the coprolites chronicle the diets and habitat preferences of these large avian herbivores during the 400 y before their extinction (∼1450 AD). We use the coprolite data to develop a paleoecological niche model in which moa species were partitioned based on both habitat (forest and valley-floor herbfield) and dietary preferences, the latter reflecting allometric relationships between body size, digestive efficiency, and nutritional requirements. Broad ecological niches occupied by South Island giant moa (Dinornis robustus) and upland moa (Megalapteryx didinus) may reflect sexual segregation and seasonal variation in habitat use, respectively. Our results show that moa lack extant ecological analogs, and their extinction represents an irreplaceable loss of function from New Zealand's terrestrial ecosystems.

  18. 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.

  19. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.

    Directory of Open Access Journals (Sweden)

    Jan Janouškovec

    Full Text Available Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase - a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.

  20. The Ancient Evolutionary History of Polyomaviruses.

    Directory of Open Access Journals (Sweden)

    Christopher B Buck

    2016-04-01

    Full Text Available Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

  1. 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.

  2. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

    Science.gov (United States)

    Hanghøj, Kristian; Seguin-Orlando, Andaine; Schubert, Mikkel; Madsen, Tobias; Pedersen, Jakob Skou; Willerslev, Eske; Orlando, Ludovic

    2016-12-01

    The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.

  3. Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

    OpenAIRE

    Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; Turroni, Francesca; Ferrario, Chiara; Duranti, Sabrina; Van Sinderen, Douwe; Ventura, Marco

    2017-01-01

    Background Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. Results Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean...

  4. Neonatal medicine in ancient art.

    Science.gov (United States)

    Yurdakök, Murat

    2010-01-01

    There are a limited number of artistic objects from ancient times with particular importance in neonatal medicine. The best examples are figurines from ancient Egypt of Isis nursing Horus, showing the importance of breastfeeding. The earliest images of the human fetus were made by the Olmecs in Mexico around 1200- 400 BCE. One of the earliest representations of congenital anomalies is a figurine of diencephalic twins thought to be the goddess of Anatolia, dated to around 6500 BCE. In addition to these figurines, three sets of twins in the ancient world have medical importance, and Renaissance artists often used them as a subject for their paintings: "direct suckling animals" (Romulus and Remus), "heteropaternal superfecundation" (mother: Leda, fathers: Zeus, the king of the Olympian gods, and Leda's husband, Tyndareus), and "twin-to-twin transfusion" in monozygotic twins (Jacob and Esau).

  5. Ancient "Observatories" - A Relevant Concept?

    Science.gov (United States)

    Belmonte, Juan Antonio

    It is quite common, when reading popular books on astronomy, to see a place referred to as "the oldest observatory in the world". In addition, numerous books on archaeoastronomy, of various levels of quality, frequently refer to the existence of "prehistoric" or "ancient" observatories when describing or citing monuments that were certainly not built with the primary purpose of observing the skies. Internet sources are also guilty of this practice. In this chapter, the different meanings of the word observatory will be analyzed, looking at how their significances can be easily confused or even interchanged. The proclaimed "ancient observatories" are a typical result of this situation. Finally, the relevance of the concept of the ancient observatory will be evaluated.

  6. Ultrahigh spatiotemporal resolved spectroscopy

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ We review the technique and research of the ultrahigh spatiotemporal resolved spectroscopy and its applications in the field of the ultrafast dynamics of mesoscopic systems and nanomaterials. Combining femtosecond time-resolved spectroscopy and scanning near-field optical microscopy (SNOM), we can obtain the spectra with ultrahigh temporal and spatial resolutions simultaneously. Some problems in doing so are discussed. Then we show the important applications of the ultrahigh spatiotemporal resolved spectroscopy with a few typical examples.

  7. Ultrahigh spatiotemporal resolved spectroscopy

    Institute of Scientific and Technical Information of China (English)

    LI; Zhi

    2007-01-01

    We review the technique and research of the ultrahigh spatiotemporal resolved spectroscopy and its applications in the field of the ultrafast dynamics of mesoscopic systems and nanomaterials. Combining femtosecond time-resolved spectroscopy and scanning near-field optical microscopy (SNOM), we can obtain the spectra with ultrahigh temporal and spatial resolutions simultaneously. Some problems in doing so are discussed. Then we show the important applications of the ultrahigh spatiotemporal resolved spectroscopy with a few typical examples.……

  8. Skeletal dysplasia in ancient Egypt.

    Science.gov (United States)

    Kozma, Chahira

    2008-12-01

    The ancient Egyptian civilization lasted for over 3000 years and ended in 30 BCE. Many aspects of ancient Egyptian culture, including the existence of skeletal dysplasias, and in particular achondroplasia, are well known through the monuments and records that survived until modern times. The hot and dry climate in Egypt allowed for the preservation of bodies and skeletal anomalies. The oldest dwarf skeleton, the Badarian skeleton (4500 BCE), possibly represents an epiphyseal disorder. Among the remains of dwarfs with achondroplasia from ancient Egypt (2686-2190 BCE), exists a skeleton of a pregnant female, believed to have died during delivery with a baby's remains in situ. British museums have partial skeletons of dwarfs with achondroplasia, humeri probably affected with mucopolysaccharidoses, and a skeleton of a child with osteogenesis imperfecta. Skeletal dysplasia is also found among royal remains. The mummy of the pharaoh Siptah (1342-1197 BCE) shows a deformity of the left leg and foot. A mummified fetus, believed to be the daughter of king Tutankhamun, has scoliosis, spina bifida, and Sprengel deformity. In 2006 I reviewed the previously existing knowledge of dwarfism in ancient Egypt. The purpose of this second historical review is to add to that knowledge with an expanded contribution. The artistic documentation of people with skeletal dysplasia from ancient Egypt is plentiful including hundreds of amulets, statues, and drawing on tomb and temple walls. Examination of artistic reliefs provides a glance of the role of people with skeletal dysplasia and the societal attitudes toward them. Both artistic evidence and moral teachings in ancient Egypt reveal wide integration of individuals with disabilities into the society.

  9. Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

    Science.gov (United States)

    Montiel, Rafael; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A.; González-Ruiz, Mercedes; Cañadas, Mari Pau; Simões, Nelson; Isidro, Albert; Malgosa, Assumpció

    2012-01-01

    Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of “La Ermita de la Soledad” (XVI–XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals. PMID:22567153

  10. Night blindness and ancient remedy

    Directory of Open Access Journals (Sweden)

    H.A. Hajar Al Binali

    2014-01-01

    Full Text Available The aim of this article is to briefly review the history of night blindness and its treatment from ancient times until the present. The old Egyptians, the Babylonians, the Greeks and the Arabs used animal liver for treatment and successfully cured the disease. The author had the opportunity to observe the application of the old remedy to a patient. Now we know what the ancients did not know, that night blindness is caused by Vitamin A deficiency and the animal liver is the store house for Vitamin A.

  11. Tuberculosis in ancient times

    Directory of Open Access Journals (Sweden)

    Louise Cilliers

    2008-09-01

    Full Text Available In spite of an array of effective antibiotics, tuberculosis is still very common in developing countries where overcrowding, malnutrition and poor hygienic conditions prevail. Over the past 30 years associated HIV infection has worsened the situation by increasing the infection rate and mortality of tuberculosis. Of those diseases caused by a single organism only HIV causes more deaths internationally than tuberculosis. The tubercle bacillus probably first infected man in Neolithic times, and then via infected cattle, but the causative Mycobacteriacea have been in existence for 300 million years. Droplet infection is the most common way of acquiring tuberculosis, although ingestion (e.g. of infected cows’ milk may occur. Tuberculosis probably originated in Africa. The earliest path gnomonic evidence of human tuberculosis in man was found in osteo-archaeological findings of bone tuberculosis (Pott’s disease of the spine in the skeleton of anEgyptian priest from the 21st Dynasty (approximately 1 000 BC. Suggestive but not conclusiveevidence of tuberculotic lesions had been found in even earlier skeletons from Egypt and Europe. Medical hieroglyphics from ancient Egypt are silent on the disease, which could be tuberculosis,as do early Indian and Chinese writings. The Old Testament refers to the disease schachapeth, translated as phthisis in the Greek Septuagint. Although the Bible is not specific about this condition, tuberculosis is still called schachapeth in modern Hebrew. In pre-Hippocratic Greece Homer did not mention phthisis, a word meaning non-specific wasting of the body. However. Alexander of Tralles (6th century BC seemed to narrow the concept down to a specific disease, and in the Hippocratic Corpus (5th-4th centuries BC phthisis can be recognised as tuberculosis. It was predominantly a respiratory disease commonly seen and considered to be caused by an imbalance of bodily humours. It was commonest in autumn, winter and spring

  12. 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,...

  13. 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 r...

  14. 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...

  15. The ancient art of memory.

    Science.gov (United States)

    Hobson, Allan

    2013-12-01

    Revision of Freud's theory requires a new way of seeking dream meaning. With the idea of elaborative encoding, Sue Llewellyn has provided a method of dream interpretation that takes into account both modern sleep science and the ancient art of memory. Her synthesis is elegant and compelling. But is her hypothesis testable?

  16. Ancient medicine--a review.

    Science.gov (United States)

    Zuskin, Eugenija; Lipozencić, Jasna; Pucarin-Cvetković, Jasna; Mustajbegović, Jadranka; Schachter, Neil; Mucić-Pucić, Branka; Neralić-Meniga, Inja

    2008-01-01

    Different aspects of medicine and/or healing in several societies are presented. In the ancient times as well as today medicine has been closely related to magic, science and religion. Various ancient societies and cultures had developed different views of medicine. It was believed that a human being has two bodies: a visible body that belongs to the earth and an invisible body of heaven. In the earliest prehistoric days, a different kind of medicine was practiced in countries such as Egypt, Greece, Rome, Mesopotamia, India, Tibet, China, and others. In those countries, "medicine people" practiced medicine from the magic to modern physical practices. Medicine was magical and mythological, and diseases were attributed mostly to the supernatural forces. The foundation of modern medicine can be traced back to ancient Greeks. Tibetan culture, for instance, even today, combines spiritual and practical medicine. Chinese medicine developed as a concept of yin and yang, acupuncture and acupressure, and it has even been used in the modern medicine. During medieval Europe, major universities and medical schools were established. In the ancient time, before hospitals had developed, patients were treated mostly in temples.

  17. Molecular analysis of skeletal tuberculosis in an ancient Egyptian population.

    Science.gov (United States)

    Zink, A; Haas, C J; Reischl, U; Szeimies, U; Nerlich, A G

    2001-04-01

    A paleomicrobiological study was performed on 37 skeletal tissue specimens from cadavers in the necropolis of Thebes-West, Upper Egypt, (2120-500 BC) and four from the necropolis of Abydos (3000 BC). The subjects had typical macromorphological evidence of osseous tuberculosis (n = 3), morphological alterations that were not specific, but probably resulted from tuberculosis (n = 17), or were without morphological osseous changes (n = 21). DNA was extracted from these bone samples and amplified by PCR with a primer pair that recognised the Mycobacterium tuberculosis complex insertion sequence IS6110. To confirm specificity of the analysis, the amplification products of several samples were subjected to restriction enzyme digestion, or direct sequencing, or both. In 30 of the 41 cases analysed, ancient DNA was demonstrated by amplification by the presence of the human beta-actin or the amelogenin gene and nine of these cases were positive for M. tuberculosis DNA. The results were confirmed by restriction endonuclease digestion and sequencing. A positive result for M. tuberculosis DNA was seen in two of the three cases with typical morphological signs of tuberculosis and amplifiable DNA, in five of 13 non-specific, but probable cases (including two cases from c. 3000 BC), but also in two of 14 cases without pathological bone changes. These observations confirm that tuberculosis may be diagnosed unequivocally in skeletal material from ancient Egypt, even dating back to c. 3000 BC. As a positive molecular reaction was observed in most of the typical cases of skeletal tuberculosis, in about one-third of non-specific, but probable tuberculous osseous changes and, surprisingly, in about one-seventh of unremarkable samples, this suggests that infection with M. tuberculosis was relatively frequent in ancient Egypt.

  18. A Huge Ancient Schwannoma of the Epiglottis.

    Science.gov (United States)

    Lee, Dong Hoon; Kim, Jo Heon; Yoon, Tae Mi; Lee, Joon Kyoo; Lim, Sang Chul

    2016-03-01

    Ancient schwannoma of the epiglottis is extremely rare. The authors report the first case of a patient with a huge ancient schwannoma of the epiglottis. Clinicians should consider the possibility that ancient schwannoma may originate in the epiglottis mimicking the other more frequently observed lesions.

  19. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    Lianwen Zhang; Lianwen Zhang

    2005-12-01

    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, mainly represented by temperature and heating time, affects the DNA degradation via DNA depurination followed by cleavage of nearby phosphodiesters. The heating time influence is temperature-dependent. By reactive oxygen species (ROS) scavenging and 1,3-diphenyl-isobenzofuran (DPBF) bleaching experiments the influence of oxygen on DNA thermal degradation was shown to occur via a singlet oxygen pathway. A comparative study of the thermal degradation of cellular DNA and isolated DNA showed that cellular lipids can aggravate DNA thermal degradation. These results confirm the possibility of gene amplification from thermally degraded DNA. They can be used to evaluate the feasibility of the retrieval of single gene from ancient remains.

  20. LUCApedia: a database for the study of ancient life.

    Science.gov (United States)

    Goldman, Aaron David; Bernhard, Tess M; Dolzhenko, Egor; Landweber, Laura F

    2013-01-01

    Organisms represented by the root of the universal evolutionary tree were most likely complex cells with a sophisticated protein translation system and a DNA genome encoding hundreds of genes. The growth of bioinformatics data from taxonomically diverse organisms has made it possible to infer the likely properties of early life in greater detail. Here we present LUCApedia, (http://eeb.princeton.edu/lucapedia), a unified framework for simultaneously evaluating multiple data sets related to the Last Universal Common Ancestor (LUCA) and its predecessors. This unification is achieved by mapping eleven such data sets onto UniProt, KEGG and BioCyc IDs. LUCApedia may be used to rapidly acquire evidence that a certain gene or set of genes is ancient, to examine the early evolution of metabolic pathways, or to test specific hypotheses related to ancient life by corroborating them against the rest of the database.

  1. 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

    2014-09-01

    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.

  2. Models of ancient sound vases

    Science.gov (United States)

    Bruel, Per V.

    2002-11-01

    Models were made of vases described by Vitruvius in Rome in about the year 70 A.D. and of sound vases (lydpotter) placed in Danish churches from 1100-1300 A.D. Measurements of vase's resonant frequencies and damping (reradiation) verified that the model vases obeyed expected physical rules. It was concluded that the excellent acoustical quality of many ancient Greek and Roman theaters cannot be ascribed to the vases placed under their seats. This study also found that sound vases placed in Nordic churches could not have shortened the reverberation time because there are far too few of them. Moreover, they could not have covered a broad frequency range. It remains a mystery why vases were installed under the seats of ancient Greek theaters and why, 1000 years later, Danes placed vases in their churches.

  3. Identifications of ancient Egyptian royal mummies from the 18th Dynasty reconsidered.

    Science.gov (United States)

    Habicht, M E; Bouwman, A S; Rühli, F J

    2016-01-01

    For centuries, ancient Egyptian Royal mummies have drawn the attention both of the general public and scientists. Many royal mummies from the New Kingdom have survived. The discoveries of the bodies of these ancient rulers have always sparked much attention, yet not all identifications are clear even nowadays. This study presents a meta-analysis to demonstrate the difficulties in identifying ancient Egyptian royal mummies. Various methods and pitfalls in the identification of the Pharaohs are reassessed since new scientific methods can be used, such as ancient DNA-profiling and CT-scanning. While the ancestors of Tutankhamun have been identified, some identities are still highly controversial (e.g., the mystery of the KV-55 skeleton, recently most likely identified as the genetic father of Tutankhamun). The meta-analysis confirms the suggested identity of some mummies (e.g., Amenhotep III, Thutmosis IV, and Queen Tjye).

  4. Splendid Arts Fram Ancient Capitals

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    IT was in the golden autumn in Beijing, when the sky was high and the air clear, that I hurried to Zhongshan Park to witness the display of the songs and dances of the seven Chinese ancient capitals. The flower beds arranged for the celebration of National Day were still there and the colorful blooms looked especially bright in the sunshine. The seven cities which have served as capitals in Chinese history are Beijing,

  5. Psychiatric Thoughts in Ancient India

    Directory of Open Access Journals (Sweden)

    Ravi Abhyankar

    2015-01-01

    Full Text Available A review of the literature regarding psychiatric thoughts in ancient India is attempted. Besides interesting reading, many of the concepts are still relevant and can be used in day-to-day practice especially towards healthy and happy living. Certain concepts are surprisingly contemporary and valid today. They can be used in psychotherapy and counselling and for promoting mental health. However, the description and classification of mental illness is not in tune with modern psychiatry.

  6. Nanoscience of an ancient pigment.

    Science.gov (United States)

    Johnson-McDaniel, Darrah; Barrett, Christopher A; Sharafi, Asma; Salguero, Tina T

    2013-02-06

    We describe monolayer nanosheets of calcium copper tetrasilicate, CaCuSi(4)O(10), which have strong near-IR luminescence and are amenable to solution processing methods. The facile exfoliation of bulk CaCuSi(4)O(10) into nanosheets is especially surprising in view of the long history of this material as the colored component of Egyptian blue, a well-known pigment from ancient times.

  7. 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.

  8. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.

    Directory of Open Access Journals (Sweden)

    Catherine Thèves

    Full Text Available Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th to the 19(th century, we propose a methodology that includes the: 1 amplification of all 16S rDNA gene sequences present in each sample; 2 identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3 identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4 establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1 the correct identification of bacterial molecular sequence signatures by quality criteria; 2 the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3 the distribution of bacterial species for each subject and for each burial; and 4 the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th century to the early 18(th century.

  9. From Here I Walked into Ancient China

    Institute of Scientific and Technical Information of China (English)

    Yan Manman

    2011-01-01

    @@ When I was a little girl, I had heard about the eighth world wonder - terra cotta warriors in Qin Emperor Mausoleum.I have been wishing to visit there to see those magnificent scene which were created thousands of years ago.While with my age added, I gradually learned the terra cotta warriors were lust only one of many ancient marks of Xi'an, which once was capital of 13 dynasties in ancient China.Xi'an actually is a carrier of ancient China culture, where I walked from the modern world to the ancient China.

  10. 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...

  11. 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 ...

  12. Ancient Indian Leaps into Mathematics

    CERN Document Server

    Yadav, B S

    2011-01-01

    This book presents contributions of mathematicians covering topics from ancient India, placing them in the broader context of the history of mathematics. Although the translations of some Sanskrit mathematical texts are available in the literature, Indian contributions are rarely presented in major Western historical works. Yet some of the well-known and universally-accepted discoveries from India, including the concept of zero and the decimal representation of numbers, have made lasting contributions to the foundation of modern mathematics. Through a systematic approach, this book examines th

  13. Chinese Ancient Football with Romanticism

    Institute of Scientific and Technical Information of China (English)

    江凌; 李晓勤

    2004-01-01

    Like other traditional Chinese sports, the ancient Chinese football, which used to be called “cuju”, has some differences from several sports in western countries concerning cultural and hamanist purport as well as metal aspiration, although it was similar with modern football to some extent, such as a leather-made ball with a bladder, rectangle sports ground, referee, goal and certain competitiveness. The author tries to talk about such difference in cultural and humanist purport as well as mental aspiration by making a comparison between “cuju” and modern football.

  14. Interpersonal Forgiveness within the Helping Professions: An Attempt to Resolve Differences of Opinion.

    Science.gov (United States)

    Enright, Robert D.; And Others

    1992-01-01

    Uses Lakatos's philosophy of science as guide for resolving published authors' differences of opinion about interpersonal forgiveness. Reviews ancient writings and current philosophical writings on interpersonal forgiveness. Critiques papers on forgiveness which have counseling implications. Describes process model of interpersonal forgiveness.…

  15. Resolving Disputes in Education.

    Science.gov (United States)

    Seeley, Kenneth R.; Schrant, Nancy E.

    Because of the increasing incidence of disputes in schools, educators need more knowledge about methods of dispute resolution. The adversary system of resolving disputes, on which the U.S. judicial system is founded, assumes that truth is best found through a struggle between two opposing parties. In the adversary system, due process plays a…

  16. Resolved SZE Cluster Count

    Institute of Scientific and Technical Information of China (English)

    Jia-Yu Tang; Zu-Hui Fan

    2003-01-01

    We study the counts of resolved SZE (Sunyaev-Zel'dovich effect) clus-ters expected from an interferometric survey in different cosmological models underdifferent conditions. The self-similar universal gas model and Press-Schechter massfunction are used. We take the observing frequency to be 90 GHz, and consider twodish diameters, 1.2 m and 2.5 m. We calculate the number density of the galaxyclusters dN/(dΩdz) at a high flux limit Slimv = 100mJy and at a relative lowSlimv = 10 mJy. The total numbers of SZE clusters N in two low-Ω0 models arecompared. The results show that the influence of the resolved effect depends notonly on D, but also on Slimv: at a given D, the effect is more significant for a highthan for a low Slim Also, the resolved effect for a flat universe is more impressivethan that for an open universe. For D = 1.2m and Slimv= 10mJy, the resolvedeffect is very weak. Considering the designed interferometers which will be used tosurvey SZE clusters, we find that the resolved effect is insignificant when estimatingthe expected yield of the SZE cluster surveys.

  17. Resolving-Power Quantization

    CERN Document Server

    Neuberger, Herbert

    2016-01-01

    Starting with a general discussion, a program is sketched for a quantization based on dilations. This resolving-power quantization is simplest for scalar field theories. The hope is to find a way to relax the requirement of locality so that the necessity to fine tune mass parameters is eliminated while universality is still preserved.

  18. Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon

    Directory of Open Access Journals (Sweden)

    Paganelli Arturo

    2007-08-01

    Full Text Available Abstract Background 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. Results 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

  19. Foreign Guests in Ancient Greece

    Directory of Open Access Journals (Sweden)

    Zora Žbontar

    2013-12-01

    Full Text Available Xenía was a special relationship between a foreign guest and his host in Ancient Greece. The ritual of hosting a foreigner included an exchange of objects, feasting, and the establishment of friendship between people from different social backgrounds. This relationship implied trust, loyalty, friendship, and mutual aid between the people involved. Goods and services were also exchanged without any form of payment. There were no formal laws governing xenía – it was based entirely on a moral appeal. Mutual appreciation between the host and the guest was established during the ritual, but the host did retain a certain level of superiority over the guest. Xenía was one of the most important institutions in Ancient Greece. It had a lot of features and obligations similar to kinship and marriage. In literary sources the word xénos varies in meaning from “enemy stranger”, “friendly stranger”, “foreigner”, “guest”, “host” to “ritual friend”, and it is often hard to tell which usage is appropriate in a given passage. The paper describes the emphasis on hospitality towards foreigners. It presents an example of a depiction indicating xenía is presented, as well as several objects which were traded during the ritual. The paper also addresses the importance of hospitality in Greek drama in general, especially with examples of violations of the hospitality code.

  20. [Ancient history of Indian pharmacy].

    Science.gov (United States)

    Okuda, Jun; Natsume, Yohko

    2010-01-01

    The study of the ancient history of Indian medicine has recently been revived due to the publication of polyglot translations. However, little is known of ancient Indian pharmacy. Archaeological evidence suggests the Indus people lived a settled life approximately in 2500 B.C. Their cities were enjoying the cleanest and most hygienic daily life with elaborate civic sanitation systems. The whole conception shows a remarkable concern for health. Then, the early Aryans invaded India about 1500 B.C. and the Vedic age started. The Rgveda texts contain the hymns for Soma and those for herbs. The term Ayurveda (i.e., science of life) is found in some old versions of both Ramāyana and Mahābhārata and in the Atharvaveda. Suśruta had the credit of making a breakthrough in the field of surgery. The Ayurveda, a work on internal medicine, gives the following transmission of sages: Brahmā-->Daksa-->Prajāpati-->Aśivinau-->Indra-->Caraka. On the other hand, the Suśruta-samhitā, which deals mainly with surgical medicine, explains it as follows; Indra-->Dhanvantari-->Suśruta Both Caraka and Suśruta were medical doctors as well as pharmacists, so they studied more than 1000 herbs thoroughly. The Ayurveda had been used by his devotees for medical purposes. It eventually spread over Asia with the advanced evolution of Buddhism.

  1. 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.

  2. Attitudes Toward Deviant Sex in Ancient Mesopotamia

    Science.gov (United States)

    Bullough, Vern L.

    1971-01-01

    The article concludes that the whole question of sexual life in ancient Mesopotamia is difficult to reconstruct and fraught with many uncertainties. Nevertheless, it seems certain that the ancient Mesopotamians had fewer prohibitions against sex than our own civilization, and regarded as acceptable many practices which later societies condemned.…

  3. Women--Sex Objects in Ancient Egypt.

    Science.gov (United States)

    Mutimer, Brian T. P.

    Although it has been said that the women in Ancient Egypt enjoyed a reasonable state of social and professional equality with men, this paper presents an alternate theory--that women were second-class citizens whose physical prowess was secondary to their role as sex objects. It appears that men and women in Ancient Egypt often participated in the…

  4. The Idea of Ancient Greek Philosophy

    Institute of Scientific and Technical Information of China (English)

    苏雪

    2016-01-01

    As the source of western philosophy, ancient Greek philosophy had a profound influence on western philosophy. Ancient philosophers were hard to reach a consensus on the existence of all the things in the world. They tried to grasp the profound understanding of the world, which is the clue of the history of philosophy.

  5. 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...

  6. Structural recognition of ancient Chinese ideographic characters

    Institute of Scientific and Technical Information of China (English)

    Li Ning; Chen Dan

    2014-01-01

    Ancient Chinese characters, typically the ideographic characters on bones and bronze before Shang Dynasty (16th—11th century B.C.), are valuable culture legacy of history. However the recognition of Ancient Chinese characters has been the task of paleography experts for long. With the help of modern computer technique, everyone can expect to be able to recognize the characters and understand the ancient inscriptions. This research is aimed to help people recognize and understand those ancient Chinese characters by combining Chinese paleography theory and computer information processing technology. Based on the analysis of ancient character features, a method for structural character recognition is proposed. The important characteristics of strokes and basic components or radicals used in recognition are introduced in detail. A system was implemented based on above method to show the effectiveness of the method.

  7. 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.

  8. [Being old in ancient Hellas].

    Science.gov (United States)

    van Hooff, A J

    1983-08-01

    There is room for a more balanced view of old age among the ancient Greeks than is furnished by De Beauvoir's la Vieillesse and other more or less one-sided publications. The old body was despised by the Greeks of classical times; especially walking with three legs (tripous) was stressed as a mark of old age. The Hippocratic writings show some interest in the infirmities of elderly people. Specific psychic and intellectual qualities were not attributed to senescence: old age brought out good and bad qualities of a person more sharply than before. The share of old people in the population cannot be established with any certainty, but there was always a group of men in their sixties who had specific tasks in society. Old age was not an autonomous theme in art, it was solely accidental. The position of the elderly was challenged occasionally in democratic Athens, but it was never undermined. Old people were never marginated in classical Greece.

  9. Ancient Acupuncture Literature on Apoplexy

    Institute of Scientific and Technical Information of China (English)

    XU Yi-zeng; BI Zhen; Xiao Yuan-chun

    2003-01-01

    This paper reviews twenty-eight Chinese medicine books with complete prescriptions prior to the Qing Dynasty, and analyzes the characteristics of acupoint selection and needling manipulations from the perspective of apoplectic symptoms. It is concluded that,in ancient times, apoplexy is often treated on the basis of its symptoms and a great number of acupoints are employed; hemiplegia is mainly treated by the acupoints of the Large Intestine Meridian and Gallbladder Meridian,with two key acupoints; coma is mainly treated by first-aid acupoints and qi-supplementing acupoints, with seven key acupoints; wry mouth and convulsion are mainly treated by the local acupoints; as for needling manipulations, moxibustion with moxa cones is principally used, while needling is less used.

  10. First complete mitochondrial genome data from ancient South American camelids - The mystery of the chilihueques from Isla Mocha (Chile).

    Science.gov (United States)

    Westbury, Michael; Prost, Stefan; Seelenfreund, Andrea; Ramírez, José-Miguel; Matisoo-Smith, Elizabeth A; Knapp, Michael

    2016-12-08

    In South American societies, domesticated camelids were of great cultural importance and subject to trade and translocation. South American camelids were even found on remote and hard to reach islands, emphasizing their importance to historic and pre-historic South American populations. Isla Mocha, a volcanic island 35 km offshore of Central-South Chile, is an example of such an island. When Dutch and Spanish explorers reached the island in the early 17th century, they found that domesticated camelids called "chilihueque" played a major role in the island's society. The origin and taxonomy of these enigmatic camelids is unclear and controversial. This study aims to resolve this controversy through genetic analyses of Isla Mocha camelid remains dating from pre-Columbian to early historic times. A recent archaeological excavation of site P21-3 on Isla Mocha yielded a number of camelid remains. Three complete mitochondrial genomes were successfully recovered and analysed. Phylogenetic analyses suggest that "chilihueque" was a local term for a domesticated guanaco. Results from phylogeographic analyses are consistent with Isla Mocha camelids being sourced from Southern Chilean guanaco populations. Our data highlights the capability of ancient DNA to answer questions about extinct populations which includes species identity, potential translocation events and origins of founding individuals.

  11. 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

    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...... of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues...

  12. Resolvability in Circulant Graphs

    Institute of Scientific and Technical Information of China (English)

    Muhammad SALMAN; Imran JAVAID; Muhammad Anwar CHAUDHRY

    2012-01-01

    A set W of the vertices of a connected graph G is called a resolving set for G if for every two distinct vertices u,v ∈ V(G) there is a vertex w ∈ W such that d(u,w) ≠ d(v,w).A resolving set of minimum cardinality is called a metric basis for G and the number of vertices in a metric basis is called the metric dimension of G,denoted by dim(G).For a vertex u of G and a subset S of V(G),the distance between u and S is the number mins∈s d(u,s).A k-partition H ={S1,S2,...,Sk} of V(G) is called a resolving partition if for every two distinct vertices u,v ∈ V(G) there is a set Si in Π such that d(u,Si) ≠ d(v,Si).The minimum k for which there is a resolving k-partition of V(G) is called the partition dimension of G,denoted by pd(G).The circulant graph is a graph with vertex set Zn,an additive group ofintegers modulo n,and two vertices labeled i and j adjacent if and only if i - j (mod n) ∈ C,where C C Zn has the property that C =-C and 0(∈) C.The circulant graph is denoted by Xn,△ where A =|C|.In this paper,we study the metric dimension of a family of circulant graphs Xn,3 with connection set C ={1,-n/2,n - 1} and prove that dim(Xn,3) is independent of choice of n by showing that 3 for all n =0 (mod 4),dim(X,n,3) ={ 4 for all n =2 (mod 4).We also study the partition dimension of a family of circulant graphs Xn,4 with connection set C ={±1,±2} and prove that pd(Xn,4) is independent of choice of n and show that pd(X5,4) =5 and 3 forall odd n≥9,pd(Xn,4) ={ 4 for all even n ≥ 6 and n =7.

  13. Brief resolved unexplained event

    Science.gov (United States)

    Arane, Karen; Claudius, Ilene; Goldman, Ran D.

    2017-01-01

    Abstract Question For many years, the term apparent life-threatening event (ALTE) was associated with sudden infant death syndrome, and parents who described an acute event in their infants were sent to the hospital for admission. I understand that for infants new terminology is recommended. What is the current approach to a near-death experience of an infant? Answer A recent clinical practice guideline revised the name and definition of an ALTE to a brief resolved unexplained event (BRUE). The diagnosis of BRUE in infants younger than 1 year of age is made when infants experience 1 of the following BRUE symptoms: a brief episode (ie, less than 1 minute and usually less than 20 to 30 seconds) that is entirely resolved (infant is at baseline), which remains unexplained after the history and physical examination are completed, and includes an event characterized by cyanosis or pallor; absent, decreased, or irregular breathing; hypertonia or hypotonia; or altered responsiveness. Low-risk infants should not be admitted to the hospital and overtesting is discouraged. PMID:28115439

  14. Time-resolved EPR studies with DNA photolyase: excited-state FADH0 abstracts an electron from Trp-306 to generate FADH-, the catalytically active form of the cofactor.

    OpenAIRE

    1993-01-01

    Photolyase repairs UV-induced cyclobutane-pyrimidine dimers in DNA by photoinduced electron transfer. The enzyme isolated from Escherichia coli contains 5,10-methenyltetrahydrofolate, which functions as the light-harvesting chromophore, and fully reduced flavin adenine dinucleotide (FAD), which functions as the redox catalyst. During enzyme preparation, the flavin is oxidized to FADH0, which is catalytically inert. Illumination of the enzyme with 300- to 600-nm light converts the flavin to th...

  15. Historias en código genético: Los aportes de los estudios de ADN antiguo en antropología y sus implicancias éticas Historias em código genético: As contribuições dos estudos de ADN antigo em antropologia e suas implicâncias éticas 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 Desde hace varias décadas, la antropología biológica comenzó a utilizar marcadores moleculares en estudios poblacionales. A partir de la década de 1990 se desarrollaron diferentes técnicas en biología molecular que permitieron extraer y tipificar ADN conservado en diferentes restos provenientes de museos y sitios arqueológicos. Los estudios de ADN antiguo relacionados con problemáticas arqueológicas conforman hoy un campo de estudio denominado Arqueogenética. Se presentan en este trabajo algunas de las aplicaciones del ADN antiguo. Se discuten las ventajas y limitaciones de estos estudios y su relación con temas éticos y legales.Faz já varias décadas que à antropologia biológica tem começado a usar marcadores moleculares em estudos de população. Ao começo da década de 1990, se desenvolveram técnicas diferentes em biologia molecular que permitiram obter e tipificar o ADN conservado em restos diferentes vindos de museus e sítios arqueológicos. Os estudos de ADN antigo relacionados a problemáticas arqueológicas são hoje um campo de estudo chamado de Arqueogenética. Se apresentam neste trabalho algumas das aplicações do ADN antigo. Também se discutem as vantagens e limitações desses estudos e a sua relação com assuntos éticos e legais.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.

  16. 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...... and Latin texts and the term ‘scholars’ is used to describe readers of these documents (e.g. papyrologists, epigraphers, palaeographers). However, the results from this research can be applicable to many other texts ranging from Nordic runes to 18th Century love letters. In order to develop an appropriate...... 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...

  17. 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

  18. Ancient Magnetic Reversals: Clues to the Geodynamo.

    Science.gov (United States)

    Hoffman, Kenneth A.

    1988-01-01

    Discusses the question posed by some that the earth's magnetic field may reverse. States that rocks magnetized by ancient fields may offer clues to the underlying reversal mechanism in the earth's core. (TW)

  19. 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...

  20. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla Friis; Olsen, Maia E.; Brandt, Luise Ørsted

    2012-01-01

    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...

  1. Monitoring Biodiversity using Environmental DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis

    was less successful than acoustic detections. However, at one site, long-finned pilot whale – a species rarely sighted in the target area – was detected. Another study examines DNA extracted from leeches to account for biodiversity of terrestrial mammals, on which they have been feeding. The persistence......, a study tests the applicability of non-destructive DNA extraction from old and ancient insect remains. DNA is successfully retrieved, amplified and equenced from dried museum beetle specimens up to 188 years old, ermafrost-preserved macrofossils up to 26.000 years old and directly from 1800-3000 years old......As any species interacts with its environment, most of them will at some point expel DNA to their surroundings. Such DNA can be picked up in environmental samples, isolated and analysed. Within the last decade, this has become a multidisciplinary research field known as Environmental DNA (eDNA...

  2. 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.

  3. 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.

  4. 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.

  5. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.

    Science.gov (United States)

    Zink, A R; Grabner, W; Reischl, U; Wolf, H; Nerlich, A G

    2003-04-01

    We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450-500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66.7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20.8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14.0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis.

  6. Radiocarbon dating of ancient Japanese documents

    Energy Technology Data Exchange (ETDEWEB)

    Oda, H. [Nagoya Univ., Center for Chronological Research, Nagoya, Aichi (Japan)

    2001-06-01

    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)

  7. Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda.

    Directory of Open Access Journals (Sweden)

    Isa Schön

    Full Text Available BACKGROUND: Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied. METHODOLOGY/PRINCIPAL FINDINGS: We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC. We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis, five to six (D. stevensoni and two (P. aotearoa, respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies. CONCLUSIONS/SIGNIFICANCE: Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

  8. A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes.

    Directory of Open Access Journals (Sweden)

    Joel O Wertheim

    2007-07-01

    Full Text Available While the circumstances surrounding the origin and spread of HIV are becoming clearer, the particulars of the origin of simian immunodeficiency virus (SIV are still unknown. Specifically, the age of SIV, whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of SIV have been documented, the similarity between the African green monkey (AGM and SIVagm phylogenies has long been held as suggestive of ancient codivergence between SIVs and their primate hosts. Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology. Furthermore, we demonstrate that the SIVagm topology can be explained by a pattern of west-to-east transmission of the virus across existing AGM geographic ranges. Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago. This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.

  9. Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Cristina Olivieri

    Full Text Available BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions" has been the object of extensive investigations. METHODOLOGY/PRINCIPAL FINDINGS: To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp mitochondrial (mt DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85% of the observed nucleotide misincorporations in ancient sequences. CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine

  10. The Kalash genetic isolate: ancient divergence, drift, and selection.

    Science.gov (United States)

    Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

    2015-05-01

    The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319-2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600-12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.

  11. Livistona palms in Australia: ancient relics or opportunistic immigrants?

    Science.gov (United States)

    Crisp, Michael D; Isagi, Yuji; Kato, Yohei; Cook, Lyn G; Bowman, David M J S

    2010-02-01

    Eighteen of the 34 species of the fan palm genus Livistona (Arecaceae) are restricted to Australia and southern New Guinea, east of Wallace's Line, an ancient biogeographic boundary between the former supercontinents Laurasia and Gondwana. The remaining species extend from SE Asia to Africa, west of Wallace's Line. Competing hypotheses contend that Livistona is (a) ancient, its current distribution a relict of the supercontinents, or (b) a Miocene immigrant from the north into Australia as it drifted towards Asia. We have tested these hypotheses using Bayesian and penalized likelihood molecular dating based on 4Kb of nuclear and chloroplast DNA sequences with multiple fossil calibration points. Ancestral areas and biomes were reconstructed using parsimony and maximum likelihood. We found strong support for the second hypothesis, that a single Livistona ancestor colonized Australia from the north about 10-17Ma. Spread and diversification of the genus within Australia was likely favoured by a transition from the aseasonal wet to monsoonal biome, to which it could have been preadapted by fire-tolerance.

  12. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates

    DEFF Research Database (Denmark)

    Welker, Frido; Collins, Matthew J.; Thomas, Jessica A.

    2015-01-01

    like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies....... The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses...

  13. Discovery of a new family of amphibians from northeast India with ancient links to Africa

    OpenAIRE

    2012-01-01

    The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group rela...

  14. Evidence for Ancient Mesoamerican Earthquakes

    Science.gov (United States)

    Kovach, R. L.; Garcia, B.

    2001-12-01

    Evidence for past earthquake damage at Mesoamerican ruins is often overlooked because of the invasive effects of tropical vegetation and is usually not considered as a casual factor when restoration and reconstruction of many archaeological sites are undertaken. Yet the proximity of many ruins to zones of seismic activity would argue otherwise. Clues as to the types of damage which should be soughtwere offered in September 1999 when the M = 7.5 Oaxaca earthquake struck the ruins of Monte Alban, Mexico, where archaeological renovations were underway. More than 20 structures were damaged, 5 of them seriously. Damage features noted were walls out of plumb, fractures in walls, floors, basal platforms and tableros, toppling of columns, and deformation, settling and tumbling of walls. A Modified Mercalli Intensity of VII (ground accelerations 18-34 %b) occurred at the site. Within the diffuse landward extension of the Caribbean plate boundary zone M = 7+ earthquakes occur with repeat times of hundreds of years arguing that many Maya sites were subjected to earthquakes. Damage to re-erected and reinforced stelae, walls, and buildings were witnessed at Quirigua, Guatemala, during an expedition underway when then 1976 M = 7.5 Guatemala earthquake on the Motagua fault struck. Excavations also revealed evidence (domestic pttery vessels and skeleton of a child crushed under fallen walls) of an ancient earthquake occurring about the teim of the demise and abandonment of Quirigua in the late 9th century. Striking evidence for sudden earthquake building collapse at the end of the Mayan Classic Period ~A.D. 889 was found at Benque Viejo (Xunantunich), Belize, located 210 north of Quirigua. It is argued that a M = 7.5 to 7.9 earthquake at the end of the Maya Classic period centered in the vicinity of the Chixoy-Polochic and Motagua fault zones cound have produced the contemporaneous earthquake damage to the above sites. As a consequences this earthquake may have accelerated the

  15. 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.

  16. 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.

  17. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...... for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture....

  18. The Vindolanda Tablets and the Ancient Economy

    DEFF Research Database (Denmark)

    Evers, Kasper Grønlund

    , a model is outlined which takes into account the different economic behaviours revealed by the tablets and attempts to fit them together into one coherent, economic system, whilst also relating the activities to questions of scale in the ancient economy; moreover, the conclusions drawn in the study......, the aim is to investigate how best to comprehend the economic system attested at Vindolanda and to consider the wider implications for studies of the ancient economy in general. This is accomplished by a three-step approach: first, the nature of the Vindolandan evidence is assessed, and the state...... of research on both studies of the ancient economy and the economy of early Roman Britain is accounted for, so as to highlight the value of the Vindolanda Tablets and lay the ground for the interpretations which follow. Secondly, the economic activities attested by the tablets are analysed in terms of market...

  19. Palaeoparasitology - Human Parasites in Ancient Material.

    Science.gov (United States)

    Araújo, Adauto; Reinhard, Karl; Ferreira, Luiz Fernando

    2015-01-01

    Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.

  20. Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae).

    Science.gov (United States)

    Percy, Diana M; Garver, Adam M; Wagner, Warren L; James, Helen F; Cunningham, Clifford W; Miller, Scott E; Fleischer, Robert C

    2008-07-07

    Knowledge of the evolutionary history of plants that are ecologically dominant in modern ecosystems is critical to understanding the historical development of those ecosystems. Metrosideros is a plant genus found in many ecological and altitudinal zones throughout the Pacific. In the Hawaiian Islands, Metrosideros polymorpha is an ecologically dominant species and is also highly polymorphic in both growth form and ecology. Using 10 non-coding chloroplast regions, we investigated haplotype diversity in the five currently recognized Hawaiian Metrosideros species and an established out-group, Metrosideros collina, from French Polynesia. Multiple haplotype groups were found, but these did not match morphological delimitations. Alternative morphologies sharing the same haplotype, as well as similar morphologies occurring within several distinct island clades, could be the result of developmental plasticity, parallel evolution or chloroplast capture. The geographical structure of the data is consistent with a pattern of age progressive island colonizations and suggests de novo intra-island diversification. If single colonization events resulted in a similar array of morphologies on each island, this would represent parallel radiations within a single, highly polymorphic species. However, we were unable to resolve whether the pattern is instead explained by ancient introgression and incomplete lineage sorting resulting in repeated chloroplast capture. Using several calibration methods, we estimate the colonization of the Hawaiian Islands to be potentially as old as 3.9 (-6.3) Myr with an ancestral position for Kaua'i in the colonization and evolution of Metrosideros in the Hawaiian Islands. This would represent a more ancient arrival of Metrosideros to this region than previous studies have suggested.

  1. 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, 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...

  2. Pectus excavatum in mummies from ancient Egypt.

    Science.gov (United States)

    Kwiecinski, Jakub

    2016-12-01

    Pectus excavatum is one of the common congenital anomalies, yet there seems to be a suspicious absence of any cases or descriptions of this deformity from antiquity. This could represent a real change in disease prevalence but is more likely just due to an inadequate reporting in medico-historical literature. The current study reviews reports of computed tomography (CT) scans of 217 ancient Egyptian mummies, revealing 3 presumed cases of this deformity. Therefore, pectus excavatum was in fact present already in ancient times, with prevalence roughly similar to the modern one.

  3. Symmetries in Images on Ancient Seals

    CERN Document Server

    Sparavigna, Amelia

    2008-01-01

    In this paper, we discuss the presence of symmetries in images engraved on ancient seals, in particular on stamp seals. Mainly used to secure the containers from tampering and for owner's identification, these objects appeared during the 5th millennium BC in Mesopotamia. Usually the seals were engraved with simple images, suitable to communicate an immediate information. Rotational symmetries are already displayed by the most ancient stamp seals, whose images reach a quasi-perfect symmetry in their small circular or ovoid spaces. Bilateral symmetries are quite common in Egyptian scarab seals.

  4. Automatic indexing and reformulation of ancient dictionaries

    OpenAIRE

    Belaïd, Abdel; Turcan, Isabelle; Pierrel, Jean-Marie; Belaïd, Yolande; Rangoni, Yves; Hadjamar, Hassen

    2004-01-01

    International audience; This paper is related to automatic indexing and reformu-lation of ancient dictionaries. The objective is to make easy the access to ancient printed documents from XVI to XIX century for a diversified public (historians, scien-tists, librarians, etc.). Since the facsimile mode is insuffi-cient, the aim is to look further for the use of the index-ing based on the formal structure representative of some contents in order to optimize their exploration. Starting from a firs...

  5. Mythological Emblem Glyphs of Ancient Maya Kings

    DEFF Research Database (Denmark)

    Helmke, Christophe

    2012-01-01

    Heinrich Berlin’s identification of Emblem Glyphs in 1958 has rightly been hailed as one of the major breakthroughs in the decipherment of ancient Maya writing. Although their exact function and meaning was unclear at the time, these are now recognized to serve as exalted regal titles that incorp......Heinrich Berlin’s identification of Emblem Glyphs in 1958 has rightly been hailed as one of the major breakthroughs in the decipherment of ancient Maya writing. Although their exact function and meaning was unclear at the time, these are now recognized to serve as exalted regal titles...

  6. A Modern Take on an Ancient Master

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    A new English translation of The Analects gives a fresh perspective on Confucius and his philosophy by Zan Jifang Confucius(551-491 B.C.) is generally viewed as ancient China’s foremost thinker.His philosophy is probably best catalogued in The Analects,a record of the sage’s wisdom compiled after his death.This Confucian classic provides a shortcut to understanding Chinese culture. A new English edition of the ancient classic(published by the Foreign Languages Press)

  7. Evolution of medical education in ancient Greece

    Institute of Scientific and Technical Information of China (English)

    Emmanouil Pikoulis; Pavlos Msaouel; Efthimios D Avgerinos; Sofia Anagnostopoulou; Christos Tsigris

    2008-01-01

    @@ The study of ancient Greece is essential for the proper understanding of the evolution of modem Western medicine.An important innovation of classical Greek medicine was the development of a body of medical theory associated with natural philosophy,i.e.a strong secular tradition of free enquiry,or what would now be called "science" (Επιστημη).Medical education rests upon the ancient Greek foundations and its history remains a fascinating topic for modem physicians and medical teachers.

  8. Records of solar eclipse observations in ancient China

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Like ancient people at other places of the world, the ancient Chinese lived in awe of the Sun. As they felt solar eclipses extremely significant events, they closely observed the occurrence of solar eclipse. Ancient astronomers further realized very early that solar eclipses were one of the important astronomical phenomena to revise and improve the ancient calendar. Interestingly, ancient emperors regarded solar eclipses as warnings from heaven that might affect the stability of their throne. Consequently, observing and recording solar eclipses became official, which dated far back to ancient China when numerous relevant descriptions were recorded in historical books. These records contribute substantially to China as an ancient civilization, as well as to the research of the long-term variation of the rotation rate of the Earth during >2000 years before the 17th century. This paper briefly reviews the perception, observations and recording of solar eclipses by ancient Chinese astronomers.

  9. Records of solar eclipse observations in ancient China

    Institute of Scientific and Technical Information of China (English)

    HAN YanBen; QIAO OiYuan

    2009-01-01

    Like ancient people at other places of the world, the ancient Chinese lived in awe of the Sun. As they felt solar eclipses extremely significant events, they closely observed the occurrence of solar eclipse. Ancient astronomers further realized very early that solar eclipses were one of the important astro-nomical phenomena to revise and improve the ancient calendar. Interestingly, ancient emperors re-garded solar eclipses as warnings from heaven that might affect the stability of their throne. Conse-quently, observing and recording solar eclipses became official, which dated far back to ancient China when numerous relevant descriptions were recorded in historical books. These records contribute substantially to China as an ancient civilization, as well as to the research of the long-term variation of the rotation rate of the Earth during >2000 years before the 17th century. This paper briefly reviews the perception, observations and recording of solar eclipses by ancient Chinese astronomers.

  10. Resolving the tips of the tree of life: How much mitochondrialdata doe we need?

    Energy Technology Data Exchange (ETDEWEB)

    Bonett, Ronald M.; Macey, J. Robert; Boore, Jeffrey L.; Chippindale, Paul T.

    2005-04-29

    Mitochondrial (mt) DNA sequences are used extensively to reconstruct evolutionary relationships among recently diverged animals,and have constituted the most widely used markers for species- and generic-level relationships for the last decade or more. However, most studies to date have employed relatively small portions of the mt-genome. In contrast, complete mt-genomes primarily have been used to investigate deep divergences, including several studies of the amount of mt sequence necessary to recover ancient relationships. We sequenced and analyzed 24 complete mt-genomes from a group of salamander species exhibiting divergences typical of those in many species-level studies. We present the first comprehensive investigation of the amount of mt sequence data necessary to consistently recover the mt-genome tree at this level, using parsimony and Bayesian methods. Both methods of phylogenetic analysis revealed extremely similar results. A surprising number of well supported, yet conflicting, relationships were found in trees based on fragments less than {approx}2000 nucleotides (nt), typical of the vast majority of the thousands of mt-based studies published to date. Large amounts of data (11,500+ nt) were necessary to consistently recover the whole mt-genome tree. Some relationships consistently were recovered with fragments of all sizes, but many nodes required the majority of the mt-genome to stabilize, particularly those associated with short internal branches. Although moderate amounts of data (2000-3000 nt) were adequate to recover mt-based relationships for which most nodes were congruent with the whole mt-genome tree, many thousands of nucleotides were necessary to resolve rapid bursts of evolution. Recent advances in genomics are making collection of large amounts of sequence data highly feasible, and our results provide the basis for comparative studies of other closely related groups to optimize mt sequence sampling and phylogenetic resolution at the &apos

  11. Dialogue Genre Texts in Ancient Greek Prose: Linguostylistic Aspect

    OpenAIRE

    Gita Bērziņa

    2011-01-01

    Dialogue Genre Texts in Ancient Greek Prose: Linguostylistic Aspect Doctoral thesis deals with the study of essential linguistic features of the Ancient Greek dialogue as an important ancient prose genre. The goal of the thesis is to disclose the specific linguistic characteristics of the genre of Ancient Greek dialogue on the basis of comparative analysis of the linguistic structure (on all levels as well as in style) of the texts of three most prominent authors (Plato, Xenoph...

  12. Fire usage and ancient hominin detoxification genes

    NARCIS (Netherlands)

    Aarts, Jac M.M.J.G.; Alink, Gerrit M.; Scherjon, Fulco; MacDonald, Katharine; Smith, Alison C.; Nijveen, Harm; Roebroeks, Wil

    2016-01-01

    Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general heal

  13. Discovering the Ancient Maya from Space

    Science.gov (United States)

    Sever, T. L.

    2008-01-01

    The Pet6n region of northern Guatemala contains some of the most significant Mayan archeological sites in Latin America. It was in this region that the Maya civilization began, flourished, and abruptly disappeared. Remote sensing technology is helping to locate and map ancient Maya sites that are threatened today by accelerating deforestation and looting. Thematic Mapper, IKONOS, and QuickBird satellite, and airborne STAR-3i and AIRSAR radar data, combined with Global Positioning System (GPS) technology, are successfully detecting ancient Maya features such as sites, roadways, canals, and water reservoirs. Satellite imagery is also being used to map the bajos, which are seasonally flooded swamps that cover over 40% of the land surface. Through the use of various airborne and satellite sensor systems we have been able to detect and map ancient causeways, temples, reservoirs, and land forms, and locate these features on the ground through GPS technology. Recently, we have discovered that there is a strong relationship between a tropical forest vegetation signature in satellite imagery and the location of archeological sites. We believe that the use of limestone and lime plasters in ancient Maya construction affects the moisture, nutrition, and plant species of the surface vegetation. We have mapped these vegetation signatures in the imagery and verified through field survey that they are indicative of archeological sites. Through the use of remote sensing and GIS technology it is possible to identify unrecorded archeological features in a dense tropical forest environment and monitor these cultural features for their protection.

  14. Ancient Human Parasites in Ethnic Chinese Populations

    Science.gov (United States)

    Yeh, Hui-Yuan; Mitchell, Piers D.

    2016-01-01

    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. PMID:27853113

  15. Ancient bronze disks, decorations and calendars

    CERN Document Server

    Sparavigna, Amelia Carolina

    2012-01-01

    Recently, it was published that some ancient bronze disks could had been calendars, that is, that their decorations had this function. Here I am discussing an example, the disk of the Trundholm Sun Chariot, proposing a new interpretation of it, giving a calendar of 360 days. Some geometric diagrams concerning the decoration layout are also proposed.

  16. Tapping Ancient Roots: Plaited Paper Baskets

    Science.gov (United States)

    Patrick, Jane

    2011-01-01

    With ancient roots, basket making has been practiced since the earliest civilizations, and according to textile experts, probably pre-dates pottery. This is partly conjecture since few baskets remain. It is through evidence found in clay impressions that the earliest baskets reveal themselves. Basically, basketry construction is like flat weaving.…

  17. Ancient Pyramids Help Students Learn Math Concepts

    Science.gov (United States)

    Smith, Courtney D.; Stump, Amanda M.; Lazaros, Edward J.

    2010-01-01

    This article presents an activity that allows students to use mathematics and critical-thinking skills to emulate processes used by the ancient Egyptians to prepare the site for the Pyramids of Giza. To accomplish this, they use three different methods. First, they create a square using only simple technological tools that were available to the…

  18. 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.

  19. Ancient whole grain gluten-free flatbreads

    Science.gov (United States)

    The USDA food guide recommends that at least ½ of all the grains eaten should be whole grains. The FDA allows food Health Claim labels for food containing 51% whole gains and 11 g of dietary fiber. This is the only report demonstrating innovative ancient whole grain gluten-free (no yeast or chemical...

  20. An ancient musical instrument returns home

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    After 300 years abroad, an ancient Chinese musical instrument returned home with its face lifted and a Japanese name. Originally a one-stringed plucker, the Daisho Modo now features a whole family of electric high-, medium-pitched and bass instruments. With crisp tone and wide range, the Daisho Modo is

  1. The Study of Women in Ancient Society.

    Science.gov (United States)

    Moscovich, M. James

    1982-01-01

    Presents ideas for teaching about the roles of women in ancient Greek and Roman societies for undergraduate history and sociology classes. The discussion covers the roots of misogyny in Western culture, parallels between mythologies and sociocultural patterns, and the legal status of women in antiquity. (AM)

  2. [Ancient tattooing from today's point of view].

    Science.gov (United States)

    Zimmermann, R; Zimmermann, K

    1981-06-01

    Both literary and arachaeological evidence indicates that, up to now, ancient tattoos can be traced with certainty in painting only among Thracians. A comparison with modern tattoos reveals differences of motivation and motifs, whereas localization, technique, and removal show similarities. The illustrations demonstrate some tattoos typical for Thracians on Greek vases.

  3. Case report 872. "Ancient" schwannoma (degenerated neurilemoma).

    Science.gov (United States)

    Schultz, E; Sapan, M R; McHeffey-Atkinson, B; Naidich, J B; Arlen, M

    1994-10-01

    A case of an ancient schwannoma was presented. The rare occurrence of this tumor has resulted in only a few reported cases with descriptions of its features on imaging. Our patient's tumor, like one previously reported case, demonstrated calcification on the plain film - a finding not associated with other histologic types of schwannomas. Angiography revealed the tumor to be hypervascular. Evaluation by MRI demonstrated a lobulated, encapsulated soft tissue mass containing several cystic areas that corresponded histologically to areas of necrosis. Hypertrophied blood vessels were seen in the periphery of the tumoral mass. Too few ancient schwannomas have been reported to conclude whether or not radiographic evidence of soft tissue calcification is characteristic of this histologically distinctive subtype of schwannoma. However, since calcification is seen histologically as part of the degenerating process, its presence on plain films could be a feature of this tumor. Furthermore, the presence of cystic areas on MRI is not surprising given the pathological changes that occur in this tumor. We suggest that a diagnosis of ancient schwannoma be considered when a patient presents with a hypervascular soft tissue mass containing amorphous calcification on plain films and cystic areas on MRI. Despite the nonspecificity of these imaging findings, this point is relevant because each of these features suggests the presence of a malignant mass. Awareness of the possibility of a benign ancient schwannoma could obviate unnecessary radical surgery.

  4. Communication Arts in the Ancient World.

    Science.gov (United States)

    Havelock, Eric A., Ed.; Hershbell, Jackson P., Ed.

    Intended for both classicists and nonclassicists, this volume explores the beginnings of literacy in ancient Greece and Rome and examines the effects of written communication on these cultures. The nine articles, written by classical scholars and educators in the field of communication, discuss the following: the superiority of the alphabet over…

  5. Paragons of Education in Ancient Times

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    MOTHERS contributed greatly to children’s education in ancient China long before schools took shape. Behind many prominent figures lay greatmothers whose personal example and verbal instruction benefited their children throughout life. There is an old sayingabout the "stern father and compassionate mother."However, you will always

  6. The Roots of Science in Ancient China.

    Science.gov (United States)

    Fisher, Arthur

    1982-01-01

    A 45-year-old research project (culminating in the multivolume "Science and Civilization in China") is examining major scientific innovations in ancient China and attempting to explain why, although the Chinese gained a technological edge in the past, they did not make the forward leap into modern science. (JN)

  7. 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, the standard tools…

  8. Mitochondrial phylogenomics of modern and ancient equids

    DEFF Research Database (Denmark)

    Vilstrup, Julia T; Seguin-Orlando, Andaine; Stiller, Mathias;

    2013-01-01

    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...

  9. Genomic correlates of atherosclerosis in ancient humans.

    Science.gov (United States)

    Zink, Albert; Wann, L Samuel; Thompson, Randall C; Keller, Andreas; Maixner, Frank; Allam, Adel H; Finch, Caleb E; Frohlich, Bruno; Kaplan, Hillard; Lombardi, Guido P; Sutherland, M Linda; Sutherland, James D; Watson, Lucia; Cox, Samantha L; Miyamoto, Michael I; Narula, Jagat; Stewart, Alexandre F R; Thomas, Gregory S; Krause, Johannes

    2014-06-01

    Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.

  10. The Ancient stellar population of Leo A.

    NARCIS (Netherlands)

    Saha, Abhijit; Fiorentino, Giuliana; Tolstoy, Eline; Cole, Andrew

    2010-01-01

    The primary goal of our proposal is the characterisation of the oldest stellar populations in Leo A using the properties of ancient RR Lyrae variable stars as tracers. Well known and long established correlations exist between the periods and luminosities of RR Lyrae variable stars and their ages an

  11. 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

  12. Angle resolved photoemission in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Petroff, Y.

    1983-02-01

    Bases of angular resolved photoemission: determination of the electronic band structure of solids (bulk), measurements of life-time and mean free path, determination of surfaces states (valence and core) and their relationship with surface reconstruction are described.

  13. 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…

  14. 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...... maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication....

  15. 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

  16. 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

  17. Ancient and Medieval Cosmology in Armenian Highland

    Science.gov (United States)

    Farmanyan, Sona V.; Mickaelian, Areg M.

    2016-12-01

    Humankind has always sought to recognize the nature of various sky related phenomena and tried to give them explanations. It is especially vivid in ancient cultures, many of which are related to the Middle East. The purpose of this study is to identify ancient Armenian's pantheistic and cosmological perceptions, world view, notions and beliefs. By this study we answer the question "How did the Universe work in Ancient Armenian Highland?" The paper focuses on the structure of the Universe and many phenomena of nature that have always had major influence on ancient Armenians thinking. Here we weave together astronomy, anthropology and mythology of Armenia, and scientific thinking revealed in local astronomy traditions. The initial review of the study covers Moses of Khoren, Yeznik of Koghb, Anania Shirakatsi and other 5th-7th centuries historians' and scientists' records about the Universe related superstitious beliefs and cosmological understanding. By discussing and comparing Universe structure in various regional traditions, myths, folk songs and phraseological units we very often came across "seven worlds", "seven earths" and "seven layers" concepts. We draw parallels between scientific and mythological Earth and Heaven and thus find similar number of layers on both of the ancient and modern thinking. In the article we also give some details about the tripartite structure of the Universe and how these parts are connected with axis. This axis is either a column or a Cosmic Tree (Kenatz Tsar). In Armenian culture the preliminary meanings of the Kenatz Tsar are more vivid in folk songs (Jan gyulums), plays, epic, and so on, which was subsequently mixed with religious and spiritual views. We conclude that the perception of the Universe structure and celestial objects had a significant impact on culture and worldview of the people of the Armenian Highland; particularly it was one of the bases of the regional cultural diversity.

  18. RESOLVE and ECO: Survey Design

    Science.gov (United States)

    Kannappan, Sheila; Moffett, Amanda J.; Norris, Mark A.; Eckert, Kathleen D.; Stark, David; Berlind, Andreas A.; Snyder, Elaine M.; Norman, Dara J.; Hoversten, Erik A.; RESOLVE Team

    2016-01-01

    The REsolved Spectroscopy Of a Local VolumE (RESOLVE) survey is a volume-limited census of stellar, gas, and dynamical mass as well as star formation and galaxy interactions within >50,000 cubic Mpc of the nearby cosmic web, reaching down to dwarf galaxies of baryonic mass ~10^9 Msun and spanning multiple large-scale filaments, walls, and voids. RESOLVE is surrounded by the ~10x larger Environmental COntext (ECO) catalog, with matched custom photometry and environment metrics enabling analysis of cosmic variance with greater statistical power. For the ~1500 galaxies in its two equatorial footprints, RESOLVE goes beyond ECO in providing (i) deep 21cm data with adaptive sensitivity ensuring HI mass detections or upper limits designed to complement other radio and optical surveys in providing diverse, contiguous, and uniform local/global environment data as well as unusually high completeness extending into the gas-dominated dwarf galaxy regime. RESOLVE also offers superb reprocessed photometry including full, deep NUV coverage and synergy with other equatorial surveys as well as unique northern and southern facilities such as Arecibo, the GBT, and ALMA. The RESOLVE and ECO surveys have been supported by funding from NSF grants AST-0955368 and OCI-1156614.

  19. 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.

  20. The Origin of Garden Chrysanthemums and Molecular Phylogeny of Dendranthema in China based on Nucleotide Sequences of nrDNA ITS, trnT-trnL and trnL-trnF Intergenic Spacer Regions in cpDNA%基于核糖体DNA的ITS序列和叶绿体trnT-trnL及trnL-trnF基因间区的菊花起源与中国菊属植物分子系统学研究

    Institute of Scientific and Technical Information of China (English)

    赵惠恩; 汪小全; 陈俊愉; 洪德元

    2003-01-01

    Several sequences were applied to resolve phylogenetic relationships within Dendranthema and clarify the origin of garden chrysanthemums including sequences of nrDNA ITS, trnT-trnL and trnL-trnF intergenic spacer regions in cpDNA. The relationships among the species are so close that the three sequences could only provide limited information. From the evidence presented, we suggest that: ① D.rhmobifolium be the chloroplast donor of D.vestitum (HN) with the resembling morphology and the same trnT/L IGS sequence. ② D.vestitum, a putative ancestor, may be not the chloroplast donor of garden chrysanthemums. D.lavand-ulifolium might be the chloroplast donor of the type population of D.indicum (HN) or the direct chloroplast donor of the ancient garden chrysanthemum cultivar. ③ D.zawaskii might be not the ancestor of garden chrysanthemums.

  1. Mitochondrial DNA Variation in Southeastern Pre-Columbian Canids.

    Science.gov (United States)

    Brzeski, Kristin E; DeBiasse, Melissa B; Rabon, David R; Chamberlain, Michael J; Taylor, Sabrina S

    2016-05-01

    The taxonomic status of the red wolf (Canis rufus) is heavily debated, but could be clarified by examining historic specimens from the southeastern United States. We analyzed mitochondrial DNA (mtDNA) from 3 ancient (350-1900 year olds) putative wolf samples excavated from middens and sinkholes within the historic red wolf range. We detected 3 unique mtDNA haplotypes, which grouped with the coyote mtDNA clade, suggesting that the canids inhabiting southeastern North America prior to human colonization from Europe were either coyotes, which would vastly expand historic coyote distributions, an ancient coyote-wolf hybrid, or a North American evolved red wolf lineage related to coyotes. Should the red wolf prove to be a distinct species, our results support the idea of either an ancient hybrid origin for red wolves or a shared common ancestor between coyotes and red wolves.

  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

    -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. Distribution patterns of postmortem damage in human mitochondrial DNA

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Willerslev, Eske; Hansen, Anders J;

    2002-01-01

    The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (rho(v)) was calculated for nucleotide positions within the human hypervariable region...

  4. Evidence of coat color variation sheds new light on ancient canids.

    Directory of Open Access Journals (Sweden)

    Morgane Ollivier

    Full Text Available We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor and CBD103 (canine-β-defensin, in respectively 15 and 19 ancient canids (dogs and wolf morphotypes from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic to ca. 4000 B.P. (Bronze Age. We provide evidence of a new variant (R301C of the Melanocortin 1 receptor (Mc1r and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant K(B allele (CBD103, which causes melanism, and R301C (Mc1r, the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10,000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process.

  5. Evidence of Coat Color Variation Sheds New Light on Ancient Canids

    Science.gov (United States)

    Ollivier, Morgane; Tresset, Anne; Hitte, Christophe; Petit, Coraline; Hughes, Sandrine; Gillet, Benjamin; Duffraisse, Marilyne; Pionnier-Capitan, Maud; Lagoutte, Laetitia; Arbogast, Rose-Marie; Balasescu, Adrian; Boroneant, Adina; Mashkour, Marjan; Vigne, Jean-Denis; Hänni, Catherine

    2013-01-01

    We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant KB allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10 000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process. PMID:24098367

  6. True single-molecule DNA sequencing of a pleistocene horse bone

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Raghavan, Maanasa

    2011-01-01

    -preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing...... to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates...

  7. 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.

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

    Science.gov (United States)

    Prüfer, Kay; Meyer, Matthias

    2015-02-20

    Chatters et al. (Reports, 16 May 2014, p. 750) reported the retrieval of DNA sequences from a 12,000- to 13,000-year-old human tooth discovered in an underwater cave in Mexico's Yucatan peninsula. They propose that this ancient human individual's mitochondrial DNA (mtDNA) belongs to haplogroup D1. However, our analysis of postmortem damage patterns finds no evidence for an ancient origin of these sequences.

  9. Probiotic Activity of a Bacterial Strain Isolated from Ancient Permafrost Against Salmonella Infection in Mice.

    Science.gov (United States)

    Fursova, O; Potapov, V; Brouchkov, A; Pogorelko, G; Griva, G; Fursova, N; Ignatov, S

    2012-09-01

    Bacillus cereus strain F, collected from relict permafrost located in Siberia, was analyzed for probiotic activity in the mouse Salmonella enterica model. Viable bacterial cells were found in frozen soils taken at Mammoth Mountain in Yakutia from a depth below the level of seasonal thawing. Geological data indicated the absence of a thawing within millions of years of deposited soils, which helped to ensure the ancient origin of our sample. According to DNA analysis, bacterial cells collected from the relict permafrost appeared to be B. cereus strain F. The morphology of these bacteria was analyzed using atomic force microscopy. B. cereus strain F was assessed as a nonpathogenic bacterium by evaluation of its pathogenicity. A S. enterica model is described in mice after per oral inoculation and serves as a model for the human carrier state. Using this model, probiotic activity by the bacterial strain isolated from the ancient permafrost has been shown against Salmonella infection in mice.

  10. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations.

    Science.gov (United States)

    Levin, Liron; Blumberg, Amit; Barshad, Gilad; Mishmar, Dan

    2014-01-01

    Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).

  11. 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'.

  12. 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.

  13. Rangifer and man: An ancient relationship

    Directory of Open Access Journals (Sweden)

    Bryan Gordon

    2003-04-01

    Full Text Available A long-term relationship between Rangifer and humans is documented in three case studies: the Canadian Barrenlands (8000 years ago to Historic period, Ice-Age France (11 000-19 000 years ago and Mesolithic Russia (7000¬10 000 years ago. Ancient human and herd migration occurred in all areas, based upon Rangifer remains and seasonal variations in tools along reconstructed migration routes, with few if any hunting camps outside the routes. An April peak of ancient human births is inferred from the historic record where we see births occurring nine months after peak nutritional states in herds and people. The origin of reindeer domestication and breeding in Eurasia is discussed.

  14. Segmentation of Ancient Telugu Text Documents

    Directory of Open Access Journals (Sweden)

    Srinivasa Rao A.V

    2012-07-01

    Full Text Available OCR of ancient document images remains a challenging task till date. Scanning process itself introduces deformation of document images. Cleaning process of these document images will result in information loss. Segmentation contributes an invariance process in OCR. Complex scripts, like derivatives of Brahmi, encounter many problems in the segmentation process. Segmentation of meaningful units, (instead of isolated patterns, revealed interesting trends. A segmentation technique for the ancient Telugu document image into meaningful units is proposed. The topological features of the meaningful units within the script line are adopted as a basis, while segmenting the text line. Horizontal profile pattern is convolved with Gaussian kernel. The statistical properties of meaningful units are explored by extensively analyzing the geometrical patterns of the meaningful unit. The efficiency of the proposed algorithm involving segmentation process is found to be 73.5% for the case of uncleaned document images.

  15. Resolving Boosted Jets with XCone

    CERN Document Server

    Thaler, Jesse

    2015-01-01

    We show how the recently proposed XCone jet algorithm smoothly interpolates between resolved and boosted kinematics. When using standard jet algorithms to reconstruct the decays of hadronic resonances like top quarks and Higgs bosons, one typically needs separate analysis strategies to handle the resolved regime of well-separated jets and the boosted regime of fat jets with substructure. XCone, by contrast, is an exclusive cone jet algorithm that always returns a fixed number of jets, so jet regions remain resolved even when (sub)jets are overlapping in the boosted regime. In this paper, we perform three LHC case studies---dijet resonances, Higgs decays to bottom quarks, and all-hadronic top pairs---that demonstrate the physics applications of XCone over a wide kinematic range.

  16. The ancient Greeks present: Rational Trigonometry

    CERN Document Server

    Wildberger, N J

    2008-01-01

    Pythagoras' theorem, the area of a triangle as one half the base times the height, and Heron's formula are amongst the most important and useful results of ancient Greek geometry. Here we look at all three in a new and improved light, using quadrance not distance. This leads to a simpler and more elegant trigonometry, in which angle is replaced by spread, and which extends to arbitrary fields and more general quadratic forms.

  17. Computed tomography of ancient Egyptian mummies.

    Science.gov (United States)

    Harwood-Nash, D C

    1979-12-01

    This first report of the application of computed tomography (CT) to the study of ancient mummies, the desiccated brain of a boy and the body of a young woman within her cartonnage, shows that CT is uniquely suitable for the study of such antiquities, a study that does not necessitate destruction of the mummy or its cartonnage. Exquisite images result that are of great paleoanatomical, paleopathological, and archeological significance.

  18. Volatile and Isotopic Imprints of Ancient Mars

    Science.gov (United States)

    Mahaffy, Paul R.; Conrad, Pamela G.

    2015-01-01

    The science investigations enabled by Curiosity rover's instruments focus on identifying and exploring the habitability of the Martian environment. Measurements of noble gases, organic and inorganic compounds, and the isotopes of light elements permit the study of the physical and chemical processes that have transformed Mars throughout its history. Samples of the atmosphere, volatiles released from soils, and rocks from the floor of Gale Crater have provided a wealth of new data and a window into conditions on ancient Mars.

  19. Chemistry Progress and Civilization in Ancient China

    Institute of Scientific and Technical Information of China (English)

    JIANG Yu-Qian; RUAN Shu-Xiang; TANG Shan; SHUAI Zhi-Gang

    2011-01-01

    @@ During the 6,000 years of Chinese civilization, chemistry has played an essential role.The bronzed chime bells of the Warring States Period (475-221 BC) unearthed in Hubei Province shows not only the excellence in musical instruments in ancient China, but also the technological advances in metallurgy.Chinese alchemy was not originated from the quest to turn common metals to gold, instead, it was for searching medicines for longevity of human beings, mostly practised by Taoists.

  20. Ancient News: HMGBs are Universal Sentinels

    Institute of Scientific and Technical Information of China (English)

    Marco E. Bianchi; Barbara Celona

    2010-01-01

    @@ Yanai et al. (2009, Nature 462, 99-103) have shown that high mobility group boxs (HMGBs) are universal sensors of viral nucleic acids, and thus of cell infection. This appears to be an evolutionary ancient mechanism of virus detection, and possibly might be a facet of a more general propensity of HMGBs to act as integrators of signals that pertain to peace and stress, life and death.

  1. 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.

  2. Reconstructing Ancient History-- Historiographical Review of the Ancient History of Korea, 1950s-2000s

    Directory of Open Access Journals (Sweden)

    Stella Xu

    2012-05-01

    Full Text Available The ancient history of Korea has been one of the most controversial and difficult phases to incorporate into an East Asian history survey class, not only because there are indeed quite a number of contested issues, but also because very few updated materials are available in English. This essay aims to provide a comprehensive and critical overview of research on the topic of Korean ancient history in the past six decades (mainly in South Korea, so that the ancient history of Korea can be understood first within the broader frame of East Asian history, and then in relation to the intellectual and ideological evolution which has significantly impacted historical interpretations in South Korea.

  3. Resolving Ethical Issues at School

    Science.gov (United States)

    Benninga, Jacques S.

    2013-01-01

    Although ethical dilemmas are a constant in teachers' lives, the profession has offered little in the way of training to help teachers address such issues. This paper presents a framework, based on developmental theory, for resolving professional ethical dilemmas. The Four-Component Model of Moral Maturity, when used in conjunction with a…

  4. TIME-RESOLVED VIBRATIONAL SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

    Andrei Tokmakoff, MIT (Conference Chair); Paul Champion, Northeastern University; Edwin J. Heilweil, NIST; Keith A. Nelson, MIT; Larry Ziegler, Boston University

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE’s Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all five of DOE’s grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  5. Time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Champion, Paul [Northeastern Univ., Boston, MA (United States); Heilweil, Edwin J. [National Inst. of Standards and Technology (NIST), Boulder, CO (United States); Nelson, Keith A. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Ziegler, Larry [Boston Univ., MA (United States)

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE's Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all fiveof DOE's grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  6. 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.

  7. The Ancient City of Pinqyao:Where the Time Stops

    Institute of Scientific and Technical Information of China (English)

    Lily Wang

    2011-01-01

    @@ It is a common night in May, I found myself wandering in the Ancient City of Pingyao.If not those neon light, I would even doubt that I had gone back to the ancient times.Located on the eastern banks of the Fen River, and in the southwestern edge of the Taiyuan basin, Pingyao Ancient City is the outstanding example of Chinese Han nationality cities during Ming and Qing Dynasties.

  8. Advances in structural mechanics of Chinese ancient architectures

    Institute of Scientific and Technical Information of China (English)

    Maohong YU; Yoshiya ODA; Dongping FANG; Junhai ZHAO

    2008-01-01

    Chinese ancient architectures are valuable heritage of ancient culture of China. Many historical building have been preserved up to now. The researches on the structural mechanics of ancient architectures show the different aspects of structure and mechanics. Systematical studies on the structural mechanics of ancient architectures have been carried out at Xi'an Jiaotong University since 1982. It is related with the need of repair of some national preservation relics in Xi'an. These studies include: 1) Ancient wooden structures including three national preservation relics Arrow Tower at North City Gate, City Tower at East City Gate, and Baogao Temple in Ningbao, Zhejiang province. 2) Ancient tall masonry building, the Big Goose Pagoda and Small Goose Pagoda in Xi'an. 3) Mechanical characteristics of ancient soil under foundation and city wall; the influence of caves in and under the ancient City Wall on the stability of the wall. 4) The typical Chinese ancient building at the center of city: the Bell Tower and Drum tower. 5) The behavior of Dou-Gong and Joggle joint of Chinese ancient wooden structure. 6) The mechanical behavior of ancient soils under complex stress state. A new systematical strength theory, the unified strength theory, is used to analyze the stability of ancient city wall in Xi'an and foundation of tall pagoda built in Tang dynasty. These researches also concern differential settlements of Arrow Tower and resistance to earthquake of these historical architecture heritages. Some other studies are also introduced. This paper gives a summary of these researches. Preservation and research are nowadays an essential requirement for the famous monuments, buildings, towers and others. Our society is more and more conscious of this necessity, which involves increasing activities of restoration, and then sometimes also of repair, mechanical strengthening and seismic retrofitting. Many historical buildings have in fact problems of structural strength and

  9. 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.

  10. Mapping the Ancient Maya Landscape from Space

    Science.gov (United States)

    Sever, Tom

    2003-01-01

    This project uses new satellite and airborne imagery in combination with remote sensing, GIS, and GPS technology to understand the dynamics of how the Maya successfully interacted with their karst topographic landscape for several centuries in the northern Peten region of Guatemala. The ancient Maya attained one of the greatest population densities in human history in the tropical forest of the Peten, Guatemala, and it was in this region that the Maya civilization began, flourished, and abruptly disappeared for unknown reasons around AD 800. How the Maya were able to successfully manage water and feed this dense population is not known at this time. However, a recent NASA-funded project was the first to investigate large seasonal swamps (bajos) that make up 40 percent of the landscape. Through the use of remote sensing, ancient Maya features such as cities, roadways, canals and water reservoirs have been detected and verified through ground reconnaissance. The results of this research cast new light on the adaptation of the ancient Maya to their environment. Micro-environmental variation within the wetlands was elucidated and the different vegetational associations identified in the satellite imagery. More than 70 new archeological sites within and at the edges of the bajo were mapped and tested. Modification of the landscape by the Maya in the form of dams and reservoirs in the Holmul River and its tributaries and possible drainage canals in bajos was demonstrated. The recent acquisition of one-meter IKONOS imagery and high resolution STAR-3i radar imagery (2.5m backscatter/ 10m DEM), opens new possibilities for understanding how a civilization was able to survive for centuries upon a karst topographic landscape and their human-induced effects upon the local climate. This understanding is critical for the current population that is presently experiencing rapid population growth and destroying the landscape through non-traditional farming and grazing techniques

  11. [Bow legged adjectives in ancient literature].

    Science.gov (United States)

    Simon, Frantisek; Steger, Florian

    2011-01-01

    This article addresses the issue of capturing the medical entity called 'curved legs' in a terminologically exact way. In so doing, it refers to the long-lasting process of differentiation of exact nuances of meaning in Ancient Greek and Latin. In the chronological perusal of ancient Greek literature, it becomes evident that the various adjectives employed are often vague when looking at non-medical literature. By contrast, in the Hippocratic corpus these terms are for the first time annotated with explanations intended to lead to a more precise understanding of the described deformity. Further attempts of differentiation can be found in the writings of Galen, who not only distinguishes between outward and inward curvatures, but also between deformities of the thigh and lower leg as well as between pathological and natural curvatures. Latin literature also provides a series of adjectives that were initially often used in the meaning of 'curved' but it was not until Celsus that these were differentiated with respect to the type and direction of the curvature. When comparing Greek and Latin adjectives, it turns out that though the Latin term blaesus can be traced back etymologically to the Greek word beta lambda alpha iota sigma ó zeta, the meaning of beta lambda alpha iota sigma ó zeta does not fully correspond to that of the Latin word. It is not before the later common transliteration of Greek words that this adjective took on the meaning of beta lambda alpha iota sigma ó zeta; however, this was finally lost again. In summary, the article concludes that exact word meanings in ancient literature are often unclear and precise ascriptions of meanings are inconsistent. In the case of "curved legs," this has led to misunderstandings regarding the respective types and directions of the curvature.

  12. Dance Poem presents Ancient Northwestern Settings and Folle Customs

    Institute of Scientific and Technical Information of China (English)

    1995-01-01

    WEST of the Yang Pass, a dance poem created and performed by the Lanzhou Song and Dance Troupe, presents the audience with a picture of ancient times and folk customs on the Loess Plateau in Northwestern China. It depicts our ancestors’ staunch will to live, and their pioneering spirit, as well as the splendid traditional culture. The dance poem includes 11 sections: "Prelude," "Ancient Road," "Desert," "Camel Station," "Crescent Moon Spring," "Ancient Castle," "Temple Oil Lamps," "Mogao Grottoes," "Red Willows," "Market," "Ancient Battle Fields," and "Fields." West of the Yang Pass is a dance without particular characters or coherent plot. A group

  13. The Ancient Maya Landscape from Space

    Science.gov (United States)

    Sever, T.; Arnold, James E. (Technical Monitor)

    1999-01-01

    The Peten, once inhabited by a population of several million before the collapse of the ancient Maya in the 10th and 11th centuries, is being repopulated toward its former demographic peak. Environmental dynamics, however, impose severe constraints to further development. Current practices in subsistence, commercial agriculture, and cattle raising are causing rapid deforestation resulting in the destruction of environmental and archeological resources. The use of remote sensing and Geographic Information Systems (GIS) technology is a cost-effective methodology for addressing issues in Maya archeology as well as monitoring the environmental impacts being experienced by the current population.

  14. Conserved intron positions in ancient protein modules

    Directory of Open Access Journals (Sweden)

    de Roos Albert DG

    2007-02-01

    Full Text Available Abstract Background The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt derived from GenBank. Results A set of conserved intron positions was found by matching identical splice sites sequences from distantly-related eukaryotic kingdoms. Most amino acid sequences with conserved introns were homologous to consensus sequences of functional domains from conserved proteins including kinases, phosphatases, small GTPases, transporters and matrix proteins. These included ancient proteins that originated before the eukaryote-prokaryote split, for instance the catalytic domain of protein phosphatase 2A where a total of eleven conserved introns were found. Using an experimental setup in which the relation between a splice site and the ancientness of its surrounding sequence could be studied, it was found that the presence of an intron was positively correlated to the ancientness of its surrounding sequence. Intron phase conservation was linked to the conservation of the gene sequence and not to the splice site sequence itself. However, no apparent differences in phase distribution were found between introns in conserved versus non-conserved sequences. Conclusion The data confirm an origin of introns deep in the eukaryotic branch and is in concordance with the presence of introns in the first functional protein modules in an 'Exon theory of genes' scenario. A model is proposed in which shuffling of primordial short exonic sequences led to the formation of the first functional protein modules, in line with hypotheses that see the formation of introns integral to the origins of genome evolution

  15. Extinct 244Pu in Ancient Zircons

    Science.gov (United States)

    Turner, Grenville; Harrison, T. Mark; Holland, Greg; Mojzsis, Stephen J.; Gilmour, Jamie

    2004-10-01

    We have found evidence, in the form of fissiogenic xenon isotopes, for in situ decay of 244Pu in individual 4.1- to 4.2-billion-year-old zircons from the Jack Hills region of Western Australia. Because of its short half-life, 82 million years, 244Pu was extinct within 600 million years of Earth's formation. Detrital zircons are the only known relics to have survived from this period, and a study of their Pu geochemistry will allow us to date ancient metamorphic events and determine the terrestrial Pu/U ratio for comparison with the solar ratio.

  16. Archaeological sites as indicators of ancient shorelines

    Digital Repository Service at National Institute of Oceanography (India)

    Vora, K.H.; Gaur, A.S.; Sundaresh; Tripati, S.

    -Type text/plain; charset=ISO-8859-1 Archaeological Sites as Indicators of Ancient Shorelines K H Vora, A. S. Gnur. Sundaresh and S. Tripati National Institute of Oceanogr-aplzy, Dona Paula, Goa Ernail: vora@nio.org Abstract During the late... Coastal areas of the continents have been the focal points of the emergence of the civilization. For in- stance, the Indian Ocean witnessed the rise of 3 major the Bronze Age Civilizations around it during the mid- Holocene period. Ocean has played...

  17. The Charm of An Ancient Southern City

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    AN artistic narrow bridge winds into a place of pavilions, terraces and open halls, all under the pleasant shade of green trees. This is Mist-Water Pavilion Park in Gantang Lake in the city of Jiujiang, Jiangxi Province. When you stand here in the quiet and elegant historic garden and look out over the water on all four sides, you can’t help but think of the ancient war that took place on this very spot 1,700 years ago. During the Three Kingdoms Period (220-280), this was

  18. The astronomical orientation of ancient Greek temples.

    Science.gov (United States)

    Salt, Alun M

    2009-11-19

    Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

  19. Surgical history of ancient China: part 1.

    Science.gov (United States)

    Fu, Louis

    2009-12-01

    Although surgery was an accepted and quite proficient craft very early on in Chinese history, it has deteriorated through the ages. Despite the fact that anaesthetic agents in major surgery were employed during the third century, Chinese surgery is conspicuous by its stagnation. Reverence for the dead, filial piety, abhorrence of shedding blood and other conservative attitudes make it impossible for any accurate knowledge of the human anatomy and physiology, without which surgery cannot progress. This article surveys some highlights in the history of surgery in ancient China and examines the factors responsible for its decline. The second concluding part deals with orthopaedics.

  20. Human Nature Evil in Ancient Western Literature

    Institute of Scientific and Technical Information of China (English)

    张茜

    2015-01-01

    Whether man is good or evil by nature is a constant topic tophilosophers and writers. Is a man born virtuous or evil? What onearth is human nature? Is the origin of human nature kind or wicked?People have been debating over this topic for centuries. Theseseemingly simple questions have perplexed those Great Minds forthousands of years in European countries and are the constant themesof literary works as well. The problem of human nature is the deepestof the issues regarding human beings which have long been underdiscussion since ancient time.

  1. PIXE analysis of ancient Chinese Changsha porcelain

    Energy Technology Data Exchange (ETDEWEB)

    Lin, E.K.; Yu, Y.C.; Wang, C.W.; Liu, T.Y.; Wu, C.M.; Chen, K.M.; Lin, S.S

    1999-04-02

    In this work, proton induced X-ray emission (PIXE) method was applied for the analysis of ancient Chinese Changsha porcelain produced in the Tang dynasty (AD 618-907). A collection of glazed potsherds was obtained in the complex of the famous kiln site at Tongguan, Changsha city, Hunan province. Studies of elemental composition were carried out on ten selected Changsha potsherds. Minor and trace elements such as Ti, Mn, Fe, Co, Cu, Rb, Sr, and Zr in the material of the porcelain glaze were determined. Variation of these elements from sample to sample was investigated. Details of results are presented and discussed.

  2. Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds.

    Science.gov (United States)

    Rollo, F

    1985-12-01

    The analysis of cress seeds from Thebes dated approximately 1400 years B.C. showed that fragments of RNA up to 10 bases in length were still present in the ancient seeds. After having been made radioactive at the 5'OH terminus, the RNA fragments were used as probes in a spot hybridization experiment. They were shown to hybridize to cress DNA and, to a lesser extent, to that of phylogenetically distant species. When fixed onto nitrocellulose and probed with different cloned genes, the RNA fragments were shown to originate from breakage of the 25 and 18s cytoplasmic rRNA.

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

    DEFF Research Database (Denmark)

    Wales, Nathan; Andersen, Kenneth; Cappellini, Enrico;

    2014-01-01

    DNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical...... 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...

  4. Origin of Chinese ancient glasses——study on the earliest Chinese ancient glasses

    Institute of Scientific and Technical Information of China (English)

    GAN Fuxi; CHENG Huansheng; LI Qinghui

    2006-01-01

    The earliest Chinese ancient glasses before the West Han Dynasty (200 BC) from different regions are studied. The glass samples were unearthed from Hunan, Hubei, Yunnan, Sichuan, Guizhou, Guangdong and Xinjiang of China. The chemical composition of these glasses samples is analyzed by proton induced X-ray emission (PIXE) technique, energy dispersive X-ray fluorescence (EDXRF) method and inductively coupled plasma atomic emission spectrometry (ICP-AES). It is shown that the glass chemical compositions belong to barium-lead silicate BaO-PbO-SiO2, potash soda lime silicate K2O (Na2O)-CaO-SiO2 (K2O/Na2O>1), soda potash lime silicate Na2O (K2O)-CaO-SiO2 (K2O/Na2O<1) and potash silicate K2O-SiO2 glass systems, respectively. The origins of the earliest Chinese ancient glasses are discussed from the archaeological and historical points of view. These four types of Chinese ancient glasses were all made in Chinese territory using local raw materials. The glass preparation technology was related to the Chinese ancient bronze metallurgy and proto-porcelain glaze technology. The glass technology relationship between the East and the West is analyzed at the same time.

  5. Time-resolved molecular imaging

    Science.gov (United States)

    Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

    2016-06-01

    Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

  6. Resolved observations of transition disks

    CERN Document Server

    Casassus, Simon

    2016-01-01

    Resolved observations are bringing new constraints on the origin of radial gaps in protoplanetary disks. The kinematics, sampled in detail in one case-study, are indicative of non-Keplerian flows, corresponding to warped structures and accretion which may both play a role in the development of cavities. Disk asymmetries seen in the radio continuum are being interpreted in the context of dust segregation via aerodynamic trapping. We summarise recent observational progress, and also describe prospects for improvements in the near term.

  7. Weak Total Resolvability In Graphs

    Directory of Open Access Journals (Sweden)

    Casel Katrin

    2016-02-01

    Full Text Available A vertex v ∈ V (G is said to distinguish two vertices x, y ∈ V (G of a graph G if the distance from v to x is di erent from the distance from v to y. A set W ⊆ V (G is a total resolving set for a graph G if for every pair of vertices x, y ∈ V (G, there exists some vertex w ∈ W − {x, y} which distinguishes x and y, while W is a weak total resolving set if for every x ∈ V (G−W and y ∈ W, there exists some w ∈ W −{y} which distinguishes x and y. A weak total resolving set of minimum cardinality is called a weak total metric basis of G and its cardinality the weak total metric dimension of G. Our main contributions are the following ones: (a Graphs with small and large weak total metric bases are characterised. (b We explore the (tight relation to independent 2-domination. (c We introduce a new graph parameter, called weak total adjacency dimension and present results that are analogous to those presented for weak total dimension. (d For trees, we derive a characterisation of the weak total (adjacency metric dimension. Also, exact figures for our parameters are presented for (generalised fans and wheels. (e We show that for Cartesian product graphs, the weak total (adjacency metric dimension is usually pretty small. (f The weak total (adjacency dimension is studied for lexicographic products of graphs.

  8. Lifetime Resolved Fluorescence Fluctuation Spectroscopy

    Science.gov (United States)

    Guo, Peng; Berland, Keith

    2009-11-01

    Fluorescence correlation spectroscopy (FCS) has been widely used investigate molecular dynamics and interactions in biological systems. FCS typically resolves the component species of a sample either through differences in diffusion coefficient or molecular brightness. Diffusion based assays currently have a major limitation which requires that the diffusion coefficients of component species in a sample must be substantially different in order to be resolved. This criterion is not met in many important cases, such as when molecules of similar molecular weight bind to each other. This limitation can be overcome, and resolution of FCS measurements enhanced, by combining FCS measurements with measurements of fluorescence lifetimes. By using of global analysis on simultaneously acquired FCS and lifetime data we show that we can dramatically enhance resolution in FCS measurements, and accurately resolve the concentration and diffusion coefficients of multiple sample components even when their diffusion coefficients are identical provided there is a difference in the lifetime of the component species. We show examples of this technique using both simulations and experiments. It is expected that this method will be of significance for binding assays studying molecular interactions.

  9. Antikythera Mechanism and the Ancient World

    Directory of Open Access Journals (Sweden)

    A. N. Safronov

    2016-01-01

    Full Text Available In this historical review, the opinions of Ancient Greece philosophers, astronomers, and poets such as Thales Milesian, Pythagoras, Plato, Eudoxus, Aristotle, Archimedes, Cicero, Diogenes Laertius, Iamblichus, Plutarch, Homer, and Aratus about the planet position calculations and about the possibility of predictions of natural phenomena are analyzed. The planet positions were predicted before Eudoxus (probably before Philolaus by a spindle of Ananke and after Eudoxus by Antikythera mechanism. Following Pythagoras and Plato, it is established that the regular seismoacoustic observations were performed. In the Ancient World in the Mediterranean area, there was an extensive network of acoustic stations (~10 pcs, which were located in close proximity to the geologic faults. Also, it is shown that the ship that was carrying Antikythera mechanism (A-Ship was built in 244 BC in Syracuse with direct participation of Archimedes and Archias from Corinthian. Later, the A-Ship was a part of the Roman Republic safety system. The grain volumes, which were delivered to Rome city by large grain vessels, and the population of Rome city in the period 74–71 BC were estimated. Planetary calculator might be used for the chronology of the historical events as a backward prediction in addition to present Radiocarbon dating and Dendrochronology methods.

  10. Acoustical measurements in ancient Roman theatres

    Science.gov (United States)

    Farnetani, Andrea; Fausti, Patrizio; Pompoli, Roberto; Prodi, Nicola

    2001-05-01

    The Greek and Roman theatres are among the most precious and spectacular items of cultural heritage in the Mediterranean countries. The theatres are famous not only for their impressive architecture, but also for the acoustic qualities. For this reason it is important to consider these theatres as an acoustical heritage and to study their sound field. Within the activities of the ERATO (identification Evaluation and Revival of the Acoustical heritage of ancient Theatres and Odea) project, acoustical measurements were taken in well-preserved ancient Roman theatres at Aspendos (Turkey) and Jerash (Jordan). Roman theatres have an impressive stage building that forms a back wall in the orchestra area, and it was found that, from the analysis of the acoustical parameters, the reverberation time (e.g., 1.7 s at middle frequencies in the theatre of Aspendos) is quite long compared not only with other open-space theatres but also with closed spaces. Contrary to modern halls the clarity is high and this fact, together with a low sound level in most of the seats, gives the sound field a unique character.

  11. Ancient and Medieval Earth in Armenia

    Science.gov (United States)

    Farmanyan, S. V.

    2015-07-01

    Humankind has always sought to recognize the nature of various sky related phenomena and tried to give them explanations. The purpose of this study is to identify ancient Armenians' pantheistic and cosmological perceptions, world view, notions and beliefs related to the Earth. The paper focuses on the structure of the Earth and many other phenomena of nature that have always been on a major influence on ancient Armenians thinking. In this paper we have compared the term Earth in 31 languages. By discussing and comparing Universe structure in various regional traditions, myths, folk songs and phraseological units we very often came across to "Seven Heavens" (Seven heavens is a part of religious cosmology found in many major religions such as Islam, Judaism, Hinduism and Christianity (namely Catholicism) and "Seven Earths". Armenians in their turn divided Earth and Heavens into seven layers. And in science too, both the Earth and the Heavens have 7 layers. The Seven Heavens refer to the layers of our atmosphere. The Seven Earths refer to the layers of the Earth (from core to crust), as well as seven continents. We conclude that the perception of celestial objects varies from culture to culture and preastronomy had a significant impact on humankind, particularly on cultural diversities.

  12. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants.

    Directory of Open Access Journals (Sweden)

    Nadin Rohland

    Full Text Available To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American mastodon, and the woolly mammoth. Our data establish that the Asian elephant is the closest living relative of the extinct mammoth in the nuclear genome, extending previous findings from mitochondrial DNA analyses. We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants. Finally, we document a much larger effective population size in forest elephants compared with the other elephantid taxa, likely reflecting species differences in ancient geographic structure and range and differences in life history traits such as variance in male reproductive success.

  13. Study on the structures and illumination characteristics of Chinese ancient oil lamps

    Science.gov (United States)

    Zhu, Zhiqiang; Zhan, Qingxuan

    2006-01-01

    Chinese ancient firelight lighting had a long history in which developed technologies were applied. The paper concerns itself with a study of Chinese ancient firelight lighting lamps, including the structures and illuminating characteristics of ancient oil lamps.

  14. Jin Quan Museum Gives New Life to Ancient Coins

    Institute of Scientific and Technical Information of China (English)

    ZhangJing

    2003-01-01

    The saying goes that ""ancient coins are living history"". The rusty ancient coins that appeared in China's 5,000 years of history, such as seashells, Bu Bi (spade-shaped money), Dao Bi (knife-shaped money), Banliang coins from Qin Dynasty and Wuzhu coins from Han Dynasty, are all the reflections of the China's splendid traditions in politics,

  15. 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.

  16. 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...

  17. 古代生物分子与分子考古学%ANCIENT BIOMOLECULES AND MOLECULAR ARCHAEOLOGY—A REVIEW

    Institute of Scientific and Technical Information of China (English)

    赖旭龙

    2001-01-01

    As the development of modern molecular biology, organic geochemistry during past decade,it is possible to use ancient biomolecules includin g ancient DNA, ancient protein,biomarkers and stable isotopes to answer plenty of archaeology-related key problems. This paper mainly reviews ancient biomolec ules and its application to archaeology—the emerging field of molecular archaeo logy. It includes following three main parts:Firstly, ancient DNA preserved in ancient samples younger than 100,000 years can be recovered and amplified by polymerase chain reaction (PCR). It is possible f or us to use ancient DNA for genetic analysis in human origin and migration,pre cise identification of archaeological remains, plant and animal domestication an d development of early agriculture.Secondly, one area of ancient protein research where much greater investment has been made in predictive models of diagenesis, is that of amino-acid racemizati o n. The increase in proportion of the non-biological (D-) isomer of amino-acid relative to L- isomer has been widely used in archaeology as a tool for dating . This new dating approach is of great potential in archaeology and forensic med icine.Thirdly, biomarkers such as lipids and bitumen extracted from archaeological mat erials can reveal secrets of past civilizations. New data also prove that Carbon (C3, C4) and Nitrogen stable isotopes document the diet in ancient human po pulations.Finally, the author also prospect potential fields of molecular archaeology in China.%分别论述了从古DNA、古蛋白质、类脂化合物等古代生物分子的尺度去研究人类的起源和迁移,动、植物的家养和驯化过程及早期农业的发展,考古点动植物残骸的精确鉴定,新的定年技术以及古气候的变化等与考古学相关的许多重要问题。对分子考古学及其应用进行了综述,并就在我国开展分子考古学研究提出了展望。

  18. 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...

  19. [Changes of marriage age in ancient China].

    Science.gov (United States)

    Zhang, D

    1991-04-01

    The changes in age of marriage in ancient China can be classified into 3 periods. Around 680 B.C., the government set the age of marriage at 20 for men and at 15 for women. Even though it was written in the works of the Confucian school that men should marry at 30 and women at 20, it was never really followed. The Wei and Jin dynasties provided the longest periods of war and social instability. Large numbers of population died because of war or famine. Because heavy taxes were collected on each member of family, many families did not report marriage or childbirth. In order to encourage childbirth, the government reduced the age of marriage to 15 for men and 13 for women. Administrative and legislative regulation were introduced to force people to marry early, especially women. Incentives were given to families with more women. These policies was enforced due to the imbalance of the sex ratio and reduction of population size. As female infanticides were prevalent because of differential values placed on male and female children, it was difficult for men to find partners to marry. Shortage of women was also the result of the polygamy of the rich and the aristocracy. The imbalance of the sex ratio forced women to marry early. Nevertheless, women getting married too early were not fertile. Infant or child mortality was high among children of young mothers. From the Song to the Ching dynasties, the age of marriage was set at 16 for men and 14 for women. In the ancient times, the population of China was around 60-70 million before the Ching dynasty. Generally speaking, the population size was small. Early marriage was necessary and feasible. Even though fertility in ancient times was high, mortality has high also. Life expectancy ranged form 22 to 35. People needed to marry early and have children early to replace themselves. On the other hand, large land areas and inefficient production tools required a larger labor force. Large population size also represented

  20. Mapping The Ancient Maya Landscape From Space

    Science.gov (United States)

    Sever, Tom; Arnold, James E. (Technical Monitor)

    2002-01-01

    The Peten region of northern Guatemala is one of the last places on earth where major archeological sites remain to be discovered. It was in this region that the Maya civilization began, flourished, and abruptly disappeared. Remote sensing technology is helping to locate and map ancient Maya sites that are threatened today by accelerating deforestation and looting. Thematic Mapper and IKONOS satellite and airborne Star3-I radar data, combined with Global Positioning System (GPS) technology, are successfully detecting ancient Maya features such as cities, roadways, canals, and water reservoirs. Satellite imagery is also being used to map the bajos, which are seasonally flooded swamps that cover over 40% of the land surface. The use of bajos for farming has been a source of debate within the professional community for many years. But the recent detection and verification of cultural features within the bajo system by our research team are providing conclusive evidence that the ancient Maya had adapted well to wetland environments from the earliest times and utilized them until the time of the Maya collapse. The use of the bajos for farming is also an important resource for the future of the current inhabitants who are experiencing rapid population growth. Remote sensing imagery is also demonstrating that in the Preclassic period (600 BC- AD 250), the Maya had already achieved a high organizational level as evidenced by the construction of massive temples and an elaborate inter-connecting roadway system. Although they experienced several setbacks such as droughts and hurricanes, the Maya nevertheless managed the delicate forest ecosystem successfully for several centuries. However, around AD 800, something happened to the Maya to cause their rapid decline and eventual disappearance from the region. The evidence indicates that at this time there was increased climatic dryness, extensive deforestation, overpopulation, and widespread warfare. This raises a question that

  1. Cosmologies of the ancient Mediterranean world

    Directory of Open Access Journals (Sweden)

    John T. Fitzgerald

    2013-06-01

    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.Kosmologie het te doen met die orde van die heelal en wil rekenskap gee van hierdie orde en ook van die bewussyn daaragter. In die antieke tyd is die kosmos gewoonlik godsdienstig verstaan, met die gevolg dat die kosmologieë van die antieke Mediterreense wêreld óf ’n godsdienstige aard gehad het óf bestaan het uit ’n reaksie op ’n godsdienstig-geskepte begrip van die strukture van die heelal. Mites was die oudste vorm waarin antieke kosmologieë voorkom wat vanweë hulle plooibaarheid dit bewerk het dat hierdie kosmologieë deur verskillende groepe toegeëien, aangepas en gebruik kon word. Hierbenewens het verskillende kosmologieë in die antieke kultuur langs mekaar bestaan – elkeen

  2. Depth-Resolved Cathodoluminescence of Thorium Dioxide

    Science.gov (United States)

    2013-03-01

    DEPTH-RESOLVED CATHODOLUMINESCENCE OF THORIUM DIOXIDE THESIS Michael G. Lee, Major, USA AFIT...RESOLVED CATHODOLUMINESCENCE OF THORIUM DIOXIDE THESIS Presented to the Faculty Department of Engineering Physics Graduate School of Engineering...PUBLIC RELEASE; DISTRIBUTION UNLIMITED AFIT-ENP-13-M-21 DEPTH-RESOLVED CATHODOLUMINESCENCE OF THORIUM DIOXIDE Michael G. Lee, BS Major, USA Approved

  3. Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool

    Science.gov (United States)

    Meylan, S.; Vimont, U.; Incerti, S.; Clairand, I.; Villagrasa, C.

    2016-07-01

    Several DNA representations are used to study radio-induced complex DNA damages depending on the approach and the required level of granularity. Among all approaches, the mechanistic one requires the most resolved DNA models that can go down to atomistic DNA descriptions. The complexity of such DNA models make them hard to modify and adapt in order to take into account different biological conditions. The DnaFabric project was started to provide a tool to generate, visualise and modify such complex DNA models. In the current version of DnaFabric, the models can be exported to the Geant4 code to be used as targets in the Monte Carlo simulation. In this work, the project was used to generate two DNA fibre models corresponding to two DNA compaction levels representing the hetero and the euchromatin. The fibres were imported in a Geant4 application where computations were performed to estimate the influence of the DNA compaction on the amount of calculated DNA damage. The relative difference of the DNA damage computed in the two fibres for the same number of projectiles was found to be constant and equal to 1.3 for the considered primary particles (protons from 300 keV to 50 MeV). However, if only the tracks hitting the DNA target are taken into account, then the relative difference is more important for low energies and decreases to reach zero around 10 MeV. The computations were performed with models that contain up to 18,000 DNA nucleotide pairs. Nevertheless, DnaFabric will be extended to manipulate multi-scale models that go from the molecular to the cellular levels.

  4. The Case of the Missing Ancient Fungal Polyploids.

    Science.gov (United States)

    Campbell, Matthew A; Ganley, Austen R D; Gabaldón, Toni; Cox, Murray P

    2016-12-01

    Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.

  5. Comparison of lactase persistence polymorphism in ancient and present-day Hungarian populations.

    Science.gov (United States)

    Nagy, Dóra; Tömöry, Gyöngyvér; Csányi, Bernadett; Bogácsi-Szabó, Erika; Czibula, Ágnes; Priskin, Katalin; Bede, Olga; Bartosiewicz, László; Downes, C Stephen; Raskó, István

    2011-06-01

    The prevalence of adult-type hypolactasia varies ethnically and geographically among populations. A C/T-13910 single nucleotide polymorphism (SNP) upstream of the lactase gene is known to be associated with lactase non-persistence in Europeans. The aim of this study was to determine the prevalence of lactase persistent and non-persistent genotypes in current Hungarian-speaking populations and in ancient bone samples of classical conquerors and commoners from the 10th-11th centuries from the Carpathian basin; 181 present-day Hungarian, 65 present-day Sekler, and 23 ancient samples were successfully genotyped for the C/T-13910 SNP by the dCAPS PCR-RFLP method. Additional mitochondrial DNA testing was also carried out. In ancient Hungarians, the T-13910 allele was present only in 11% of the population, and exclusively in commoners of European mitochondrial haplogroups who may have been of pre-Hungarian indigenous ancestry. This is despite animal domestication and dairy products having been introduced into the Carpathian basin early in the Neolithic Age. This anomaly may be explained by the Hungarian use of fermented milk products, their greater consumption of ruminant meat than milk, cultural differences, or by their having other lactase-regulating genetic polymorphisms than C/T-13910. The low prevalence of lactase persistence provides additional information on the Asian origin of Hungarians. Present-day Hungarians have been assimilated with the surrounding European populations, since they do not differ significantly from the neighboring populations in their possession of mtDNA and C/T-13910 variants.

  6. 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…

  7. Ancient Forests and the Tree-Ring Reconstruction of Past Climate (Ancient Forests and Dendroclimatology)

    Energy Technology Data Exchange (ETDEWEB)

    Stahle, David (Tree-Ring Laboratory, University of Arkansas)

    2003-02-12

    The original presettlement forests of North America have been dramatically altered, but thousands of unmolested ancient forests survive on remote or noncommercial terrain, including dry-site eastern hardwoods such as chestnut oak and post oak, the pinyon-juniper woodlands of the semiarid West, oak woodlands of California and in northeast Mexico, and the boreal forests of Canada and Alaska. Long tree-ring chronologies derived from these ancient forest remnants provide irreplaceable archives of environmental variability which are crucial for evaluating present and future change. Temperature sensitive tree -ring chronologies from cold treeline environments place 20th century warming into long historical perspective, and moisture sensitive tree-ring chronologies provide analogs to the decadal moisture regimes of the 20th century. These tree-ring data suggests that the 16th century megadrought was the most severe-sustained drought to impact North America in 1500 years, and had huge environmental and social impacts at the dawn of European settlement.

  8. Ancient engineers' inventions precursors of the present

    CERN Document Server

    Rossi, Cesare

    2017-01-01

    This book describes the inventions and designs of ancient engineers who are the precursors of the present. The period ranges mainly from 300 B.C. to 1600 A.D. with several exceptions. Many of the oldest inventions are documented by archaeological finds, often very little known, mainly from Pompeii, Herculaneum and Stabiae and reveal a surprising modernity in their conception. Most of the inventions presented in the first four parts of the book were conceived up to the late Roman Empire and may be considered as milestones, each in their respective field. The fifth part concentrates on more recent centuries. The sixth part deals with some building construction techniques. Generally, for each of the presented inventions, three elements of research and reference are provided: written documents (the classics), iconic references (coins, bas-reliefs, etc.) and archaeological findings. The authors did not write this book for engineers only; hence they describe all the devices without assuming wide technical knowledge...

  9. Were the ancient Romans art forgers?

    Directory of Open Access Journals (Sweden)

    William Casemen

    2016-12-01

    Full Text Available A popularly held tenet in the historical record on art is that the practice of forgery began in ancient Rome, where sculptures made by craftsmen of the day were passed off as classical Greek antiquities. However, revisionist scholars in recent decades have challenged this perspective. One line of criticism denies that forgery was present in Rome, asserting that the evidence for it has been misunderstood. A softer line suggests that while the traditional view overstates the case, there is still reason to accept that the culture of Rome harbored art forgery. This article assesses the competing claims in light of literary references by Roman authors, physical evidence including inscriptions on sculptures, the phenomenon of Corinthian bronze, the nature of Roman copying, social and economic conditions necessary for art forgery to arise, and what art forgery consists of by definition.

  10. Confocal Terahertz Imaging of Ancient Manuscripts

    Science.gov (United States)

    Flammini, Mariano; Bonsi, Claudia; Ciano, Chiara; Giliberti, Valeria; Pontecorvo, Emanuele; Italia, Paola; DelRe, Eugenio; Ortolani, Michele

    2016-11-01

    Terahertz imaging has the potential to identify and decipher portions of ancient manuscripts, which may be unreadable at infrared and visible wavelengths. We use a scanning confocal terahertz microscope to scan a medieval parchment with music notes and pentagrams written with different inks. The microscope is based on a continuous-wave solid-state source at 0.3 THz, emitting in the free space with a horn antenna, and a high numerical-aperture ellipsoidal reflector. We present terahertz images with diffraction-limited lateral resolution of approximately 0.5 mm, where the different inks all give similar high contrast. Symbols written on the "verso" side of the parchment, barely glimpsed in the near-infrared photograph, leave a clear imprint in the terahertz images. Artifacts due to imperfect flatness of the parchment are also briefly discussed.

  11. Optical spectroscopy of ancient paper and textiles

    Science.gov (United States)

    Missori, M.

    2016-03-01

    Ancient paper and textiles represent a striking example of optically inhomogenous materials whose optical responses are strongly governed by scattering effects. In order to recover the absorption coefficient from non-invasive and non-destructive reflectance measurements a specific approach based on Kubelka-Munk two-flux theory must be applied. In this way quantitative chemical information, such as chromophores concentration, can be obtained, as well as quantitative spectra of additional substances such as pigments or dyes. Results on a folio of the Codex on the Flight of Birds by Leonardo da Vinci and a linen cloth dated back to 1653 and called the Shroud of Arquata, a copy of the Shroud of Turin, will be presented.

  12. Ancient Maya astronomical tables from Xultun, Guatemala.

    Science.gov (United States)

    Saturno, William A; Stuart, David; Aveni, Anthony F; Rossi, Franco

    2012-05-11

    Maya astronomical tables are recognized in bark-paper books from the Late Postclassic period (1300 to 1521 C.E.), but Classic period (200 to 900 C.E.) precursors have not been found. In 2011, a small painted room was excavated at the extensive ancient Maya ruins of Xultun, Guatemala, dating to the early 9th century C.E. The walls and ceiling of the room are painted with several human figures. Two walls also display a large number of delicate black, red, and incised hieroglyphs. Many of these hieroglyphs are calendrical in nature and relate astronomical computations, including at least two tables concerning the movement of the Moon, and perhaps Mars and Venus. These apparently represent early astronomical tables and may shed light on the later books.

  13. Coal and cremation in ancient Peru

    Science.gov (United States)

    Brooks, William E.

    2004-01-01

    After my visit to the adobe-walled archaeological site of Chan Chan, near Trujillo in northern Peru in the summer of 2000 (Geotimes, August 2003), my guide asked if I would like to see the metallurgical furnaces used by the Chimú, ancient residents and master metalsmiths of the region. Chan Chan was the capital of the Chimú Empire (A.D. 1100-1400) and the largest pre-Columbian city in the Americas. These furnaces, my guide explained, were where Andean gold, silver and copper ores were smelted and fabricated into jewelry, masks and plates sought by the Spaniards. We left the main part of the complex, followed a dusty trail, and arrived at a site marked by fresh-looking, redbrown, clinker-like debris.

  14. Study of ancient pottery from Slovakia

    Science.gov (United States)

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

    1990-07-01

    Ancient pottery samples collected from south-west Slovakia were studied through subjective observation and by Mössbauer spectroscopy. This method is convenient for determining the provenance and the manufacture of pottery. Transformations, induced by firing the clay and characterized by Mössbauer spectroscopy, give valuable information regarding the manufacture as, for instance, the final temperature of firing in it. The relative abundance of Fe2+ and Fe3+ 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 Mössbauer spectroscopy. An unfired and fired clay was also investigated.

  15. Evidence of Ancient Blisters in Rocks

    Science.gov (United States)

    2004-01-01

    This image from the panoramic camera on the Mars Exploration Rover Spirit shows scoriaceous rocks (rocks containing holes or cavities) on the ground, as well as a transition from rocky terrain (foreground) to smoother terrain (background). Spirit is heading toward the smoother terrain on its way to the 'Columbia Hills.' The holes in some of the rocks may have resulted from 'blisters' formed by water vapor as it escaped lava. This indicates that the rocks were chilled atop an ancient lava flow. Porous rocks such as these, now appearing in abundance, have not been seen since early in the mission. Scientists believe they may have been covered by crater ejecta. This image was taken on sol 110 (April 24, 2004) at a region dubbed 'site 35.'

  16. Recognition of dementia in ancient China.

    Science.gov (United States)

    Liu, Jia; Wang, Lu-Ning; Tian, Jin-Zhou

    2012-12-01

    A search of previous records in the literatures was done to summarize the opinions for dementia in ancient China. The earliest description of dementia was traced in the Yellow emperor's internal classic, a book written 2000 years ago. Hua Tuo (AD 140-208) in Han Dynasty first denominated "dementia" in the book, Hua Tuo Shen Yi Mi Zhuan. The pathogenesis of dementia could be generalized as the insufficiency of Qi, a flowing energy; the stagnation of phlegm, a harmful liquid substance in the body; and the blood stasis, which were also regarded as therapeutic targets. Therefore, we can conclude that dementia has been recognized and investigated in traditional Chinese medicine, which is definitely before the industrial civilization era.

  17. Homosexuality in ancient and modern Korea.

    Science.gov (United States)

    Kim, Young-Gwan; Hahn, Sook-Ja

    2006-01-01

    This paper examines Korean views on the subject of male homosexuality. Using historical and contemporary sources, it seeks to explain elements of new cultural openness towards homosexuality in modern Korea. Korean people's understanding and knowledge of male homosexuality is ambiguous and limited. In the absence of knowledge and open communication, most Korean people imagine that male homosexuality is an abnormal and impure modern phenomenon. Prejudice and confusion lead most Korean male homosexuals to be estranged from their families, religious communities and non-homosexual peers. Moreover, they are often viewed as the 'carriers' of AIDS and Sexually Transmitted Diseases (STDs). The purpose of this paper is to examine current Korean perspectives on male homosexuality by exploring both the ancient history of the practice of male homosexuality and current thinking about homosexual life among Koreans, which has played an important part in the formation of contemporary attitudes toward homosexuality.

  18. [Medicine in ancient Mesopotamia - part 2].

    Science.gov (United States)

    Martins E Silva, J

    2010-01-01

    The second part embraces exclusively the main characteristics of the medicine in Ancient Mesopotamia, in its main facets: concept of disease, healers and practice. The disease was considered a divine punishment or resultant from a malign influence. Insofar, the medicine began by being preventive, by the use of appropriate amulets or by offerings or sacrifices intending to pacify those malign forces. The treatment of the generality of the diseases privileged the expulsion of those spirits and malign influences from the patient body, purifying it, which was done by the specific intervention of a approximately shipu (clergymanexorcist); not having results, the treatment was continued by the asû (practical healer) that appealed to a group of physical manipulations, limited surgical acts and the administration or application of prescriptions, resultants of the mixture of organic and inorganic substances. In case of failing, the patients (as well as common healthy individuals or rule leaders) could fall back upon a priest diviner (bârû) that, by examination of the organs of an animal especially sacrificed for, would give a final decision about the disease or the future. Besides this more occult facet, nourished in religious faiths and in the magic, the medicine of Ancient Mesopotamia included rational knowledge, certainly as the result of systematic patients observation and semiotic interpretation. From those observations and knowledge referred to the Sumerian period, carefully logged, refined and transmitted to the following generations, it was built a valuable group of texts with the description of symptoms, signs, diagnosis and prognostic of the most common diseases, still identifiable in the present.

  19. Biopolymers and the fellowship of DNA rings.

    Science.gov (United States)

    Wang, James C

    2013-12-01

    This article presents a brief account of the historical backdrop of the study of interlocked DNA rings (DNA catenanes), their formation in cells, and the importance of resolving the component rings of an intracellular DNA catenane if they are to be properly partitioned into a pair of progeny cells. In humans, for example, aberrant segregation of intertwined chromosomes is a major cause of birth defects, as well as termination of pregnancy in utero. Some yet unresolved issues of DNA catenation, including plausible structural and/or functional roles of DNA interlacing in chromosomes, are briefly mentioned.

  20. New environmental metabarcodes for analysing soil DNA

    DEFF Research Database (Denmark)

    Epp, Laura S.; Boessenkool, Sanne; Bellemain, Eva P.

    2012-01-01

    was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late......Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized...... in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree...

  1. The ancient Virus World and evolution of cells

    Directory of Open Access Journals (Sweden)

    Dolja Valerian V

    2006-09-01

    Full Text Available Abstract Background Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones. Results Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction

  2. Highly Resolved Paleoclimatic Aerosol Records

    DEFF Research Database (Denmark)

    Kettner, Ernesto

    In ice cores a plethora of proxies for paleoclimatic conditions is archived. Air trapped in the ice during firnification allows for direct measurements of the concentrations and isotope ratios of paleoatmospheric gases while, the isotopic composition of the ice matrix itself is related...... to paleotemperatures. Impurities in the matrix are comprised of particulate and soluble aerosols, each carrying information on its source’s activitiy and|or proximity. Opposed to gases and water isotopes, the seasonality of many aerosols is not smoothed out in the firn column so that large concentration gradients...... with frequently changing signs are preserved. Therefore, these aerosol records can be used for dating by annual layer counting. However, with increasing depth the annual layer thicknesses decreases due to pressure and ice flow and accurate dating is possible only as long as the rapid variations can be resolved...

  3. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  4. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

    Science.gov (United States)

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew

    2016-01-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481784

  5. Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

    Directory of Open Access Journals (Sweden)

    Lunt David H

    2008-07-01

    Full Text Available Abstract Background The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic reproduction including (i large "allelic" sequence divergence (ii lack of phylogenetic clustering of "alleles" within morphological species and (iii decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be hard to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence. Results Here, sequences from nuclear protein-coding genes are used to demonstrate that the first two predictions of ancient asexuality are found within the apomictic root knot nematodes. Alleles are more divergent in the apomictic taxa than in those species exhibiting recombination and do not group phylogenetically according to recognized species. In contrast some nuclear alleles, and mtDNA, are almost identical across species. Sequencing of Major Sperm Protein, a gamete-specific gene, from both meiotic and ameiotic species reveals no increase in evolutionary rate nor change in substitution pattern in the apomictic taxa, indicating that the locus

  6. Retroperitoneal ancient schwannoma: Review of clinico-radiological features

    Energy Technology Data Exchange (ETDEWEB)

    Loke, T.K.L.; Lo, K.K.L.; Lo, J.; Chan, J.C.S. [United Christian Hospital, Kwun Tong, (Hong Kong). Department of Diagnostics Radiology; Yuen, N.W.F. [United Christian Hospital, Kwun Tong, (Hong Kong). Department of Histopathology

    1998-05-01

    A case is reported here of an ancient schwannoma in the retroperitoneum. The findings of abdominal ultrasound and CT in a patient with a retroperitoneal ancient schwannoma are presented, and the clinical and radiological features of this unusual tumour are reviewed. The presence of a large, well-delineated complex cystic mass in the deep soft tissues should raise the possibility of an ancient schwannoma. It is important to recognize these tumours as benign with excellent prognosis so as to avoid unnecessary radical surgery. Copyright (1998) Blackwell Science Pty Ltd 12 refs., 2 figs.

  7. Change of ancient hydrology net in Northeast China Plain

    Institute of Scientific and Technical Information of China (English)

    Hui QU; Yu CHU; Fenglong ZHANG; Fuli QI; Xiangkui YANG

    2006-01-01

    Comparing with lithofacies palaeogeography of several great plains, the authors analyzed four great plains in Quaternary diastrophism, the sedimentary facies, sedimentary environment and their evolution from the independent embryonic and river system of ancient Heilongjiang finally to the Halar highland, Songnen Plain, Sanjiang Plain, the Xingkai Lake Plain and various river systems, collected the unification outside the system of Heilongjiang River to release into the sea, south ancient Xialiao River finally piracy Dongliao River, Xialiao River had released into the sea the ancient water law vicissitude and the evolved rule.

  8. Methods for High-throughput Characterisation of Environmental DNA

    DEFF Research Database (Denmark)

    Andersen, Kenneth

    three, a study is designed to test the performance of alternative DNA extraction protocols, in order to maximise DNA yields from plant macrofossils. Furthermore, the precision and efficiency of PCR amplification of ancient DNA is tested for alternative DNA polymerase enzymes, under influence of PCR...... inhibition. In chapter four, alternative DNA extraction protocols and pipelines for characterising plant eDNA are tested on samples from contrasting environments including modern, Holocene and Pleistocene sediment samples. These results are compared to pollen and macrofossil records described from earlier......This PhD thesis examines the potential of describing biodiversity of green plants (Viridiplantae), birds (Aves) and mammals (Mammalia), in the context of next-generation sequencing, from the DNA that all organisms segregate into the environment (eDNA). The research is based on case studies...

  9. 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

    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......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...... 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...

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

    DEFF Research Database (Denmark)

    Wales, Nathan; Andersen, Kenneth; Cappellini, Enrico

    2014-01-01

    from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical...... resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA...... 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...

  11. True single-molecule DNA sequencing of a pleistocene horse bone

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurélien; Raghavan, Maanasa;

    2011-01-01

    Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect......-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing...... libraries of ancient DNA molecules as required for second-generation sequencing introduce biases into the data, that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications...

  12. [Medicine in ancient Mesopotamia--part 1].

    Science.gov (United States)

    Martins E Silva, J

    2009-01-01

    The present work summarizes the more elucidating aspects on the foundations and the practice of the medicine in Antique Mesopotamia, since the invention of the writing, more than 5000 thousand years ago, and the beginning of our era. The first part of the article includes a brief perspective about the political and social evolution that characterized those archaic civilizations, as well as the inventions and knowledge further used by the following Humanity's generations. Most of what is known on the subject, as well as the history and political-social events that occurred in the region during that remote epoch, resulted of the laborious decoding of about half a million small clay plates or fragments with text engravings in cuneiform characters that were discovered since the middle of the XIX century in the ruins of the main cities of the Babylonian and Assyrian empires. The second part embraces exclusively the main characteristics of the medicine in Ancient Mesopotamia, in its main facets: concept of disease, healers and practice. The disease was considered a divine punishment or resultant from a malign influence. In that base, the medicine began by being preventive, by the use of appropriate amulets, or by offerings or sacrifices intending to pacify those malign forces. The treatment of the generality of the diseases privileged the expulsion of those spirits and malign influences from the patient body, purifying it, which was done by the specific intervention of an ãshipu (clergyman-exorcist); not having results, the treatment was continued by the asû (practical healer) that appealed to a group of physical manipulations, limited surgical acts and the administration or application of prescriptions, resultants of the mixture of organic and inorganic substances. In case of failing, the patients (as well as individuals or rein leaders) could fall back upon a priest diviner (bârû) who, by examination of the organs of an animal especially sacrificed for the effect

  13. Homologous recombination in DNA repair and DNA damage tolerance

    Institute of Scientific and Technical Information of China (English)

    Xuan Li; Wolf-Dietrich Heyer

    2008-01-01

    Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks (DSBs) and interstrand crosslinks (ICLs). In addition, recombination provides critical sup-port for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR: homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modaUties of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.

  14. Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data

    Science.gov (United States)

    Rasteiro, Rita; Chikhi, Lounès

    2013-01-01

    The arrival of agriculture into Europe during the Neolithic transition brought a significant shift in human lifestyle and subsistence. However, the conditions under which the spread of the new culture and technologies occurred are still debated. Similarly, the roles played by women and men during the Neolithic transition are not well understood, probably due to the fact that mitochondrial DNA (mtDNA) and Y chromosome (NRY) data are usually studied independently rather than within the same statistical framework. Here, we applied an integrative approach, using different model-based inferential techniques, to analyse published datasets from contemporary and ancient European populations. By integrating mtDNA and NRY data into the same admixture approach, we show that both males and females underwent the same admixture history and both support the demic diffusion model of Ammerman and Cavalli-Sforza. Similarly, the patterns of genetic diversity found in extant and ancient populations demonstrate that both modern and ancient mtDNA support the demic diffusion model. They also show that population structure and differential growth between farmers and hunter-gatherers are necessary to explain both types of data. However, we also found some differences between male and female markers, suggesting that the female effective population size was larger than that of the males, probably due to different demographic histories. We argue that these differences are most probably related to the various shifts in cultural practices and lifestyles that followed the Neolithic Transition, such as sedentism, the shift from polygyny to monogamy or the increase of patrilocality. PMID:23613761

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

    Directory of Open Access Journals (Sweden)

    Nathan Wales

    Full Text Available 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 aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA 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 decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.

  16. Do All Hemochromatosis Patients Have the Same Origin? A Pilot Study of Mitochondrial DNA and Y-DNA

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    Caitlin J Symonette

    2011-01-01

    Full Text Available BACKGROUND: Mitochondrial DNA (mtDNA and Y-DNA analysis have been widely used to predict ancestral origin. Genetic anthropologists predict that human civilizations may have originated in central Africa one to two million years previously. Primary iron overload is not a common diagnosis among indigenous people of northern Africa, but hereditary hemochromatosis is present in approximately one in 200 people in northern Europe. MtDNA analysis has the potential to determine whether contemporary hemochromatosis patients have an ancient ancestral linkage.

  17. 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.

  18. 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.

  19. 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.

  20. Cases of Trephination in Ancient Greek Skulls

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    Vasiliki Ζafiri

    2012-01-01

    Full Text Available Background: Trephination, or trepanning, is considered to be one of the most ancient surgical operations with an especially extensive geographical incidence, both in the New World and in the Old. In Europe, more than 200 finds of trephination have been found, from Scandinavia to the Balkans. The technique of trephination or trepanning covers overall the last 10,000 years and exhibits great versatility and adjustability in the knowledge, technical means, therapeutic needs, prejudices and social standards of each period and of each population group. Hippocrates was the one to classify for the first time the kinds of cranial fractures and define the conditions and circumstances for carrying out a trepanning.Aim: The present research aims to investigate the Greek cranial trephinations on sculls from the collection of the Anthropological Museum of the Medical School of Athens that come from archaeological excavations.Method: Skulls were examined by macroscopic observation with reflective light. Furthermore, radiographic representation of the skulls was used.Results: The anthropological researches and the studies of anthropological skeleton remains that came out during archaeological excavations from different eras and areas have given information about the medical practices in the very important geographic area of Greece and in particular, we referred to cases of Greek trephinations.