39 research outputs found
The Animal Turn, Archaeozoology, aDNA: Revealing past entanglements
No full textBorn out of the Modernist Project, archaeology has been deeply rooted in anthropocentric ontologies ever since its beginnings. It was about humans in the past, as understood by humans in the present. And yet, through archaeological research, multiple other-than-human pasts emerge. They tell stories of coexistence, predation, extinction, commensalism, partnership, companionship, mutual becomings – i.e. the shifting webs of relations with a myriad of different creatures humans entangled themselves in. As articulated by Donna Haraway, rather than a single species, it is the assemblages of organic beings and abiotic actors which make history. In the age which came to be known as the Anthropocene, many of these webs have been impaired or broken. With the devastating rate of human-induced mass extinctions, it is estimated that the majority of species and associated ecological assemblages will be lost by the end of the 21st century. In their recent book Arts of Living on a Damaged Planet, Tsing et al. have referred to the vestiges of past lifeways and lifeforms as ̔ghosts’ or ̔haunted landscapes’. Ultimately, the material traces of a number of non-human animals which once roamed the Earth are and will be preserved in the archaeological record only. As a discipline dedicated to the study of animal remains from archaeological sites, archaeozology provides unique opportunities to explore past entanglements of humans and non-humans, some of which have been long gone. Ancient DNA analysis offers further insights into their presence and dispersal. In this paper, I discuss a particular case study from the Mesolithic Danube Gorges, related to the discovery of Rutilus frisii, a fish species previously unknown in the region. Archaeozoological and aDNA analysis have have shown that it was once ubiquitous in the Danube at least up to the Middle Holocene. Moreover, with its perpetual, seasonal return, and specific pearl-like tubercles occurring in breeding males in spring, this species ocuppied an important place in the ontology of Mesolithic hunter-gatherer-fisher communities. The ornamental practice involving R. frisii pharyngeal teeth worn as garment appliqués suggests that human bodies could have been perceived as fluid, becoming parts of new assemblages by incorporating non-human elements. Ultimately, archaeozoological and aDNA analyses are not only vital to the reconstruction of former biodiversity, but, along with recent paradigmatic shifts to decenter the human, offer unique possibilities of thinking about multispecies pasts and histories of entanglement.The author acknowledges the financial support of the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grant No. 451-03-9/2021-14/200358
The necessity for authentication of ancient DNA from archaeological artefacts
Full text linkThe study of ancient DNA (aDNA) has revolutionised the fields of archaeology, human evolution and paleoecology, offering new insights into the past. In particular, aDNA can be used to study the origin of unique archaeological artefacts and adds an exciting line of evidence to the multifaceted research of these artefacts. However, aDNA methodology requires thorough consideration due to the inherent risks of modern DNA contamination, misinterpretation of results, and the irreversible destruction of culturally significant materials. This article revisits the importance of adhering to standardised aDNA protocols and established criteria for aDNA authentication. Through the discussion of several peer-reviewed studies from recent literature, we illustrate the benefits and challenges of integrating aDNA into archaeological research. Ultimately, we advocate for consultation and collaboration between archaeologists and aDNA specialists and present a study design schematic that integrates the roles of archaeologists, paleogeneticists and other stakeholders to ensure appropriate protocol selection, and accurate interpretation of aDNA data for the study of archaeological artefacts. © 2025 The Author
Toward high-resolution population genomics using archaeological samples
No full textThe term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleoepidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research. © The Author 2016
Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics
Full text linkDegraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields. © 2023 The Author(s
Computational methods of variant calling and their applications
No full textGenome sequencing is becoming an indispensable part of biological research. Mutations identified in genomic sequence contribute to explanations of disease, phenotypic variation, and evolutionary adaptation. Increasing reliance on next generation sequencing (NGS) data necessitates efficient and accurate means of genome analysis. We developed two algorithms, GROM-RD and GROM, to address current issues of mutation calling in NGS data. GROM-RD analyzes multiple biases in read coverage to improve copy number variation (CNV) detection in NGS data. GROM-RD takes a two-tiered approach to complex and repetitive segments, while incorporating excessive coverage masking, GC weighting, GS bias normalization, dinucleotide repeat bias normalization, and a sliding-window break-point calculator. Current NGS projects produce massive amounts of data, often on multiple samples; with several approaches designed specifically for each variant, use of multiple algorithms is necessary. GROM provides comprehensive genome analysis into a single algorithm, identifying single nucleotide polymorphisms (SNPs), indels, CNVs, and structural variants (SV), with superior sensitivity and precision while reducing the time cost up to 72 fold. Comparative genomics studies typically limit their focus to SNVs, such as in previous comparisons of woolly mammoth and another comparison of eastern gorilla. We extended these analyses to identify SVs and indels. Our analysis found mammoth-specific variants suggesting adaptations to Arctic conditions, including variants associated with metabolism, immunity, circadian rhythms, and structural features. In gorilla populations, variants were identified that associate with physical features used to distinguish between the two subspecies. Within the gorilla subspecies was also found unique genetic evidence related to disease and abnormality, evidence of dwindling populations. Untested and ad hoc methods of mutation calling are often used in ancient DNA (aDNA) studies. While aDNA NGS analysis is highly susceptible to aDNA degradation, many studies utilize standard mutation calling algorithms, not taking into account unique aDNA challenges of excessive contamination, degradation, or environmental damage. We present ARIADNA, a novel approach based on machine learning techniques, using specific aDNA characteristics as features, to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality variants, while reducing the false positive rate compared to other approaches.Ph.D.Includes bibliographical referencesby Joseph Kenneth Kawas
EFEKTIVITAS PERMAINAN TRADISIONAL ULAR NAGA DALAM MENINGKATKAN KETERAMPILAN BERBICARA SISWA
Full text linkPenelitian ini membahas penggunaan permainan tradisional Ular Naga dalam meningkatkan keterampilan berbicara bahasa Perancis oleh para siswa SMA. Penelitian ini bertujuan untuk (1) mendeskripsikan hasil pembelajaran berbicara bahasa Perancis siswa sebelum dan sesudah menggunakan permainan tradisional Ular Naga, (2) mendeskripsikan tingkat efektivitas permainan tradisional Ular Naga dalam pembelajaran bahasa Perancis, (3) mendeskripsikan pendapat siswa terhadap penggunaan permainan tradisional Ular Naga dalam pembelajaran keterampilan berbicara bahasa Perancis. Metode yang digunakan dalam penelitian ini adalah metode pra-eksperimen dengan desain One Group Pretest-Posttest dan instrumen yang digunakan adalah tes dan angket. Sampel dari penelitian ini adalah karakteristik keterampilan berbicara bahasa Perancis dari 33 siswa kelas XI IPS 6 SMAN 6 Cimahi Tahun Ajaran 2016/2017. Berdasarkan hasil analisis data diperoleh nilai rata-rata prates siswa sebesar 10,5 dan nilai rata-rata pascates siswa sebesar 12,5, artinya terdapat peningkatan sebesar 2. Dengan demikian, peneliti mengambil kesimpulan bahwa terdapat peningkatan hasil belajar siswa sebelum dan sesudah menggunakan permainan tradisional Ular Naga. Berdasarkan perhitungan statistik, diperoleh nilai thitung sebesar 7,4. Taraf signifikansi ( ) yang digunakan dalam penelitian ini adalah 1%, sehingga diperoleh nilai ttabel sebesar 2,73 yang berarti thitung > ttabel. Berdasarkan data tersebut, maka dapat disimpulkan bahwa hipotesis dalam penelitian ini dapat diterima. Artinya, permainan tradisional Ular Naga efektif digunakan dalam meningkatkan keterampilan berbicara bahasa Perancis pada siswa kelas XI IPS 6 SMAN 6 Cimahi. Berdasarkan hasil analisis angket, peneliti dapat menyimpulkan bahwa seluruh siswa tertarik dan termotivasi ketika belajar berbicara dalam bahasa Perancis dengan menggunakan permainan tradisional Ular Naga, sehingga permainan tersebut berkontribusi dalam meningkatkan keterampilan berbicara mereka. Dengan demikian, permainan tradisional Ular Naga dapat dijadikan salah satu teknik pembelajaran alternatif dalam pembelajaran bahasa.----
This study investigated the used of traditional game Ular Naga in learning speaking skill in French. This study is aimed to explain (1) the result of French speaking skill learning before and after using a traditional game of Ular Naga, (2) the effectivity of traditional game Ular Naga in learning French, (3) the student’s opinions toward the use of the traditional game of Ular Naga in learning French language speaking skills. The methods used in this research is a method of design experiments with One Group Pretest-Posttest. The instruments used in this study are test and questionnaire. The sample of this study is the characteristic of French speaking skill of 33 students of XI IPS 6 class of SMAN 6 Cimahi 2016/2017. Based on the data analysis, the average of students pre-test score 10,5 and post-test 12,5. The data shows that there is 2 increase in students speaking skill score. Hence, the author concludes that there is an improvement toward students speaking skill after aplication of the traditional games. According to the statistic calculation, the value of Tcalc acquired is 7,4. With significance level ( ) used is 1%, the value Ttab is 2,73 which means Tcalc > Ttab. Thus, the calculation shows that the hypothesis of this study is accepted, meaning the traditional game of Ular Naga is effective in improving the students French speaking skill. Based on the results of the analysis of the question form, all students are interested and motivated in learning to speak in French after using the traditional game of Ular Naga. Thus, the traditional game of Ular Naga can be one alternative learning techniques in language learning
Extensive human DNA contamination in extracts from ancient dog bones and teeth
No full textAncient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used. © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.</p
The ancient DNA and archaeobotanical analysis suggest cultivation of Triticum aestivum subsp. spelta at Yumuktepe and Yenikapı Pottery Neolithic sites in Turkey
Full text linkArchaeobotanical materials subject to aDNA analysis were recovered from Yumuktepe and Yenikapı, two important archaeological sites in Anatolia and date back to the Pottery Neolithic Period i.e., 7th millennium BC. Many charred ancient seeds representing various cereal species including a great number of wheat grains were documented in mentioned sites. Among the cereal seeds, charred wheat samples were tentatively identified as Triticum aestivum subsp. spelta L. or Triticum new glume wheat (NGW) or atypical emmer or naked wheat in Yumuktepe and Yenikapı showed similarities with the morphological characteristics of T. aestivum subsp. spelta wheat, but it was difficult to reach a firm conclusion. This study aimed to provide genetic data to enable more precise identification of charred wheat seeds using an ancient DNA (aDNA) approach. aDNAs were successfully extracted from the representative charred seeds of T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat. The PCR amplification of 26SrDNA and IGS gene regions with aDNA was carried out and sequenced. The expected product sizes of IGS 158 bp for the D genome and 87 bp for the A or B genomes and DNA sequence comparisons with other wheat species revealed that T. aestivum subsp. spelta or NGW or atypical emmer or naked wheat samples included the D genome from Aegilops tauschii and is more likely to be T. aestivum subsp. spelta. The discovery of T. aestivum subsp. spelta grains in the Yenikapı and Yumuktepe suggest that the cultivation of hexaploid wheat was widespread. Further, spelta hulled wheat, which is the progenitor of the hexaploid wheat, might have been cultivated in these settlements. © 2022, The Author(s), under exclusive licence to Springer Nature B.V
O PROCESSO CRIATIVO DE ALEILTON FONSECA EM NHÔ GUIMARÃES: EDIÇÃO GENÉTICA E ESTUDO CRÍTICO
No full textO processo criativo do escritor baiano Aleilton Fonseca em Nhô Guimarães: edição genética e estudo crítico. Trata-se do primeiro trabalho de tese de doutorado sobre o escritor e sua obra. Buscou-se, através deste, fazer uma proposta de edição genética horizontal do processo de criação de Nhô Guimarães: romance-homenagem a Guimarães Rosa, a fim de projetar uma visão mais ampla sobre o perfil do escritor quanto à percepção do labor da sua escritura, bem como das múltiplas possibilidades e movimentos que um texto pode apresentar, mostrando assim toda sua mobilidade e dinâmica. Apresenta-se o autor, através de sua obra, sua vida acadêmica, e como suas vivências interferiram na construção das obras que escreveu, sua recepção crítica e as relações existentes entre autor, escritor e leitor, objetivando assim, fomentar a representatividade dos escritores baianos no cenário da literatura nacional. Segue-se, então, a apresentação do romance e aspectos culturais do texto, como também, um estudo sobre os processos intertextuais presentes em Nhô Guimarães (2006) e Grande Sertão: veredas (1956). Para o tratamento do objeto de estudo, o texto, utilizou-se o olhar a perspectiva da Crítica Genética, propondo-se uma edição genética horizontal, ou seja, de uma parte considerada significativa no processo de criação textual de Nhô Guimarães, analisando-se as interpolações feitas por um revisor-crítico na versão C, do dossiê genético, identificando nas versões D e E, o que foi aceito, rejeitado ou aceito parcialmente pelo autor, fomentando assim a discussão das questões de autoria e das vozes presentes no texto. O dossiê genético da obra é composto de oito versões digitoscritas, com características de manuscritos autógrafos, e um impresso, a única edição publicada em livro.The creative process of the writer from Bahia Aleilton Fonseca in Nhô Guimarães: genetic editing and critical study. This is the first work of doctoral thesis on this writer and his work. Through this, a proposal was made for horizontal genetic editing in the process of creation of Nhô Guimarães, in order to project a broader view of the writer's profile regarding the perception of the work of his writing, as well as the multiple possibilities and movements that a text can present, thus showing all its mobility and dynamics. Through his work, his academic life is presented, and how his experiences interfered in the construction of his works, its critical reception and the relations between author, writer and reader, in order to foster the representativeness of Bahian writers in the scenario of Brazilian literature. It follows, then, the presentation of the novel and cultural aspects of the text, as well as a study on the intertextual processes present in Nhô Guimarães (2006) and Grande Sertão: veredas (1956). For the treatment of the object of study, the text was used to look at the perspective of Genetic Criticism, proposing a horizontal genetic edition, that is, a part considered significant in the process of textual creation of Nhô Guimarães, analyzing the interpolations made by a critic-reviewer in version C of the genetic file, identifying in versions D and E, what was accepted, rejected or partially accepted by the author, thus fomenting the discussion of authorship issues and the voices present in the text .The genetic dossier of the work is composed by eight typed versions, with characteristics of autograph manuscripts, and the only published edition
Ancient DNA techniques : applications for deep-water corals
Full text linkAuthor Posting. © University of Miami - Rosenstiel School of Marine and Atmospheric Science, 2007. This article is posted here by permission of University of Miami - Rosenstiel School of Marine and Atmospheric Science for personal use, not for redistribution. The definitive version was published in Bulletin of Marine Science 81 (2007): 351-359.The potential applications of ancient DNA (aDNA) techniques have been realized relatively recently, and have been revolutionized by the advent of pCR techniques in the mid 1980s. Although these techniques have been proven valuable in ancient specimens of up to 100,000 yrs old, their use in the marine realm has been largely limited to mammals and fish. Using modifications of techniques developed for skeletons of whales and mammals, we have produced a method for extracting and amplifying aDNA from sub-fossil (not embedded in rock) deep-water corals that has been successful in yielding 351 base pairs of the ITS2 region in sub-fossil Desmophyllum dianthus (Esper, 1794) and Lophelia pertusa (Linnaeus, 1758). The comparison of DNA sequences from fossil and live specimens resulted in clustering by species, demonstrating the validity of this new aDNA method. Sub-fossil scler-actinian corals are readily dated using U-series techniques, and so the abundance of directly-dateable skeletons in the world's oceans, provides an extremely useful archive for investigating the interactions of environmental pressures (in particular ocean circulation, climate change) on the past distribution, and the evolution of deep-water corals across the globe.Support for this project was
provided by National Science Foundation grants OCE 0096373 (JFA), OCE 0095331 (Daniel
Scheirer, USGS), OCE 0136871 [D. Yoerger (WH OI) and (TMS)], OCE 0624627 (TMS and
RGW) and NOAA’s Office of Exploration grant NA05OAR4601054 (TMS, RGW, and JFA).
We are also grateful for the enabling support of the Ocean Life Institute and the Ocean and
Climate Change Institute of the Woods Hole Oceanographic Institutio
