Download or read book An Analysis of the Coherence based Genealogical Method Using Phylogenetics written by Andrew Charles Edmondson and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Novum Testamentum Graecum: Editio Critica Maior is the first major critical edition of the New Testament for a century, aiming to document the New Testament's textual history through its first millennium. To date, two of the six volumes have been published. As part of this project the Institut für neutestamentliche Textforschung in Münster has developed the Coherence-Based Genealogical Method (CBGM), a computer-aided method designed to handle complete sets of textual evidence and to identify their initial text and textual history. The CBGM is widely held to be difficult to understand and its results are treated with scepticism. Phylogenetics is the study of relationships between groups of organisms and their evolutionary history. Phylogenetics and the CBGM (and wider textual criticism) have many commonalities. This thesis provides a thorough examination of the CBGM using phylogenetics. Part One documents the literature surrounding the CBGM and includes a worked example of the process. Part Two explores the ECM data for John's Gospel and identifies appropriate methods for applying phylogenetics to it. Part Three compares the results of phylogenetics and the CBGM. It concludes that the CBGM is producing valid results from the data, but could be improved in a number of ways.

Download or read book A Critical Examination of the Coherence Based Genealogical Method in New Testament Textual Criticism written by Peter J. Gurry and published by BRILL. This book was released on 2017-09-18 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: This study offers the first sustained examination of the Coherence-Based Genealogical Method (CBGM), a computerized method being used to edit the most widely-used editions of the Greek New Testament. Part one addresses the CBGM’s history and reception before providing a fresh statement of its principles and procedures. Parts two and three consider the method’s ability to recover the initial text and to delineate its history. A new portion of the global stemma is presented for the first time and important conclusions are drawn about the nature of the initial text, scribal habits, and the origins of the Byzantine text. A final chapter suggests improvements and highlights limitations. Overall, the CBGM is positively assessed but not without important criticisms and cautions.

Download or read book The Comparative Textual Criticism of Religious Scriptures written by and published by BRILL. This book was released on 2024-05-30 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of articles uniquely brings into scholarly dialogue the textual history and criticism of authoritative literatures from diverse cultures: they study Mesopotamian literature, the Hebrew Bible, the New Testament, the Homeric epics, the Quran, and Hindu and Buddhist literatures with an interest in all matters of their textual transmission. Contributors address questions such as: What role does textual criticism play in the study of authoritative texts in these fields? How much variation exists in these textual traditions? Can you observe processes of textual standardization? What role does the oral transmission play? How are critical editions prepared? While these questions have produced a wealth of scholarly literature for each individual field, this volume is the first to study them from a comparative perspective.

Download or read book The New Testament in Antiquity and Byzantium written by H.A.G. Houghton and published by Walter de Gruyter GmbH & Co KG. This book was released on 2019-12-02 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: Klaus Wachtel has pioneered the creation of major editions of the Greek New Testament through a blend of traditional philological approaches and innovative digital tools. In this volume, an international range of New Testament scholars and editors honour his achievements with thirty-one original studies. Many of the themes mirror Wachtel's own publications on the history of the Byzantine text, the identification of manuscript families and groups, detailed analysis of individual witnesses and the development of software and databases to support the editorial process. Other contributions draw on the production of the Editio Critica Maior, with reference to the Gospels of Mark and John, the Acts of the Apostles, the Pauline Epistles and the Apocalypse. Several chapters consider the application of the Coherence-Based Genealogical Method. A wide selection of material is considered, from papyri to printed editions. The Greek text is analysed from multiple perspectives, including exegesis, grammar and orthography, alongside evidence from versions in Latin, Syriac, Coptic and Gothic. This collection provides new insights into the history of the biblical text and the creation, development, analysis and application of modern editions.

Download or read book The Phylogenetic Handbook written by Philippe Lemey and published by Cambridge University Press. This book was released on 2009-03-26 with total page 763 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.

Download or read book A New Approach to Textual Criticism written by Tommy Wasserman and published by SBL Press. This book was released on 2017-11-17 with total page 164 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential introduction for scholars and students of New Testament Greek With the publication of the widely used 28th edition of Nestle-Aland’s Novum Testamentum Graece and the 5th edition of the United Bible Society Greek New Testament, a computer-assisted method known as the Coherence-Based Genealogical Method (CBGM) was used for the first time to determine the most valuable witnesses and establish the initial text. This book offers the first full-length, student-friendly introduction to this important new method. After setting out the method’s history, separate chapters clarify its key concepts, including genealogical coherence, textual flow diagrams, and the global stemma. Examples from across the New Testament are used to show how the method works in practice. The result is an essential introduction that will be of interest to students, translators, commentators, and anyone else who studies the Greek New Testament. Features A clear explanation of how and why the text of the Greek New Testament is changing Step-by-step guidance on how to use the CBGM in textual criticism Diagrams, illustrations, and glossary of key terms

Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2011-11-06 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Download or read book A Cooperative Method of Learning Logic and Analysis in Genealogy written by William M. Litchman and published by . This book was released on 2018-10-22 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: While you may not have had the advantage of scientific training in your life, the skills of logical and analytical thinking so basic to science and to genealogy can be yours. In a lifetime of teaching, the author has found ways to help others build the skills needed to provide believable proof for conclusions based only on indirect and limited evidence. These skills are accessible to you and to all who have the desire, dedication, and persistence to learn to think rationally, using logic and analysis to work through proofs where evidence is fragmentary and piece-meal. Follow the learning path outlined in Chapter 1, and use real-life examples of how logic and rational thinking leads to solving tricky family-history problems. Use the method outlined there to develop your abilities and skills for finding solutions in genealogical research. Chapters include: Learning Observation, Analysis, and Logic; The Case of the Missing Grandma; Using Passenger Lists to Find a Maiden Name; The Birth Family of Amelia (Alpiger) Lentz; Widows, Stepkin and Support Networks; A Census Consensus, 1840, Warren County, Missouri; A Leap of Faith: The Dunlap-Pattison Family of Maghera; Scattered Pieces: Assembling a Family from Scanty Records; Using Cluster Methodology to Backtrack an Ancestor; Explaining the Sudden Disappearance of Mitch Evins; Descendants of Job Timberley and Rachel Melbourne; and, Shaving with Occam's Razor.

Download or read book Family 13 in St John s Gospel written by Jac Perrin and published by BRILL. This book was released on 2018-10-08 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Family 13 in Saint John’s Gospel, Jac Perrin innovatively applies phylogenetic software to shed new light on Family 13 membership. To date, the relocation of the Pericope Adulterae from its traditional location in John 7:53 has been the sole criterion of Family 13 filiality. This book demonstrates the inadequacy of this criterion, and proposes new criteria in its stead. Nineteen potential Family 13 witnesses are analyzed by means of a sampling process developed by David Parker, identifying eight witnesses inappropriately nominated as Family 13 members. This analysis is corroborated by a complete computer assisted collation of all variant readings in all known Family 13 witnesses. Lastly, the volume offers a comprehensive stemma representing the entire Johannine corpus of ten confirmed Family witnesses in constellation.

Download or read book Kinship and Beyond written by Sandra Bamford and published by Berghahn Books. This book was released on 2012 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genealogical model has a long-standing history in Western thought. The contributors to this volume consider the ways in which assumptions about the genealogical model--in particular, ideas concerning sequence, essence, and transmission--structure other modes of practice and knowledge-making in domains well beyond what is normally labeled "kinship." The detailed ethnographic work and analysis included in this text explores how these assumptions have been built into our understandings of race, personhood, ethnicity, property relations, and the relationship between human beings and non-human species. The authors explore the influences of the genealogical model of kinship in wider social theory and examine anthropology's ability to provide a unique framework capable of bridging the "social" and "natural" sciences. In doing so, this volume brings fresh new perspectives to bear on contemporary theories concerning biotechnology and its effect upon social life.

Download or read book The Erotic Life of Manuscripts written by Yii-Jan Lin and published by Oxford University Press. This book was released on 2016 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Testament textual critics who used language to group texts into families and genealogies were not pioneering new approaches, but rather borrowing the metaphors and methods of natural scientists. Texts began to be classified into "families, tribes, and nations," and later were racialized as "African" or "Asian," with distinguishable "textual physiognomies" and "textual complexions." These genealogies would later be traced to show the inheritance of "corruptions" and "contamination" through generations, an understanding of textual diversity reflective of eighteenth- and ninteenth-century European anxieties over racial corruption and degeneration. While these biological metaphors have been powerful tools for textual critics, they also produce problematic understandings of textual "purity" and agency, with the use of scientific discourse artificially separating the work of textual criticism from literary interpretation.

Download or read book Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories written by Hussein El Abbass Hejase and published by . This book was released on 2017 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Phylogenetic Analysis of DNA Sequences written by Michael M. Miyamoto and published by Oxford University Press, USA. This book was released on 1991 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. This volume surveys the emerging field of molecular systematics of DNA sequences by focusing on the following topics: DNA sequence data acquisition; phylogenetic inference; congruence and consensus problems; limitations of molecular data; and integration of molecular and morphological data sets. The volume takes its inspiration from a major symposium sponsored by the American Society of Zoologists and the Society of Systematic Zoology in December, 1989.

Download or read book Computational Frameworks for Indel aware Evolutionary Analysis Using Large scale Genomic Sequence Data written by Wei Wang and published by . This book was released on 2021 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies. The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases: multiple sequence alignment and phylogenetic reconstruction from the aligned sequences. As the amount of biomolecular sequence data increases, it has become a major challenge to develop efficient and accurate computational methods for phylogenetic analyses of large-scale sequencing data. Due to the complexity of the phylogenetic reconstruction problem in modern phylogenetic studies, the traditional sequence-based phylogenetic analysis methods involve many over-simplified assumptions. In this thesis, we describe our contribution in relaxing some of these over-simplified assumptions in the phylogenetic analysis.Insertion and deletion events, referred to as indels, carry much phylogenetic information but are often ignored in the reconstruction process of phylogenies. We take into account the indel uncertainties in multiple phylogenetic analyses by applying resampling and re-estimation. Another over-simplified assumption that we contributed to is adopted by many commonly used non-parametric algorithms for the resampling of biomolecular sequences, all sites in an MSA are evolved independently and identically distributed (i.i.d). Many evolution events, such as recombination and hybridization, may produce intra-sequence and functional dependence in biomolecular sequences that violate this assumption. We introduce SERES, a resampling algorithm for biomolecular sequences that can produce resampled replicates that preserve the intra-sequence dependence. We describe the application of the SERES resampling and re-estimation approach to two classical problems: the multiple sequence alignment support estimation and recombination-aware local genealogical inference. We show that these two statistical inference problems greatly benefit from the indel-aware resampling and re-estimation approach and the reservation of intra-sequence dependence.A major drawback of SERES is that it requires parameters to ensure the synchronization of random walks on unaligned sequences. We introduce RAWR, a non-parametric resampling method designed for phylogenetic tree support estimation that does not require extra parameters. We show that the RAWR-based resampling and re-estimation method produces comparable or typically better performance than the traditional bootstrap approach on the phylogenetic tree support estimation problem.We further relax the commonly used assumption of phylogeny. Evolutionary history is usually considered as a tree structure. Evolutionary events that cause reticulated gene flow are ignored. Previous studies show that alignment uncertainty greatly impacts downstream tree inference and learning. However, there is little discussion about the impact of MSA uncertainties on the phylogenetic network reconstruction. We show evidence that the errors introduced in MSA estimation decrease the accuracy of the inferred phylogenetic network, and an indel-aware reconstruction method is needed for phylogenetic network analysis.In this dissertation, we introduce our contribution to phylogenetic estimation using biomolecular sequence data involving complex evolutionary histories, such as sequence insertion and deletion processes and non-tree-like evolution.

Download or read book Phylogenetic Trees Made Easy written by Barry G. Hall and published by Sinauer Associates Incorporated. This book was released on 2001-01-01 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: A brief overview. Learn more about the principles. Computer programs discussed and where to obtain them. Programs that are not discussed but that might be useful. Download files and utilities from the web site. Some conventions used in this book. Tutorial: create a tree. Why create phylogenetic trees. Otaining related sequences by a BLAST search. Creating the multiple alignment. Phylogenetic analysis. Methods for constructing phylogenies. Using PAUP* to create a tree. Additional methods for creating trees. Presenting and printing your trees. Fine-tuning alignments. Using MrBayes to reconstruct ancestral DNA sequences. Dealing with some common problems. File formats and their interconversion using PAUP*. Printing alignments. Index to major program discussed. Subject index.

Download or read book Statistical Analyses of Genealogical phylogenetic Data written by Tomochika Fujisawa and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Thanks to the recent advancement of the sequence technologies, generating large volumes of DNA sequence data is now becoming more feasible. Sequencing several samples across many species from a range of clades enables us to connect the two fields of study previously separated due to the lack of data: population genetics and phylogenetics. The former has focused on detailed genetic processes in a few species, while the latter has studied large-scale evolutionary relationships across many species. In this thesis, methods to utilize the new type of data, genealogical-phylogenetic data, are explored to tackle the problems lying between the two fields, including how to delimit species with genetic information and how ecological traits affect species genetic properties. First, a method of species delimitation based on single locus gene tree, called the generalized mixed Yule coalescent method (GMYC method), is evaluated. Its statistical properties are assessed on both simulated and real data, and the method is extended to relax some simplifying assumptions and to give a robust confidence measure. The simulation studies showed that the reliability of the delimitation depends on population parameters and patterns of diversification processes. Assessment of the performance on a dataset of 5196 water beetle mitochondrial DNA sequences sampled from across Europe showed that the method accurately delimited half of the studied species. The accuracy was affected by several factors, notably the presence of pseudogenes and potential undersampling of species range. Then, the water beetle data and the GMYC method are used to test the effects of species ecological traits on genetic properties, focusing on species habitat type. Habitat type had significant effects on genetic variation and substitution rate via effects on range size and latitudinal distribution of species. However, direct effects of habitat type on genetic properties were not observed.

Download or read book Phylogenetic Analysis of Multiple Genes Based on Spectral Methods written by Melanie Abeysundera and published by . This book was released on 2011 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here the use of spectral techniques for analyzing multi-gene data sets is explored. The protein sequences are treated as categorical time series and a measure of similarity between a pair of sequences, the spectral covariance, is used to build trees. Unlike other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. We consider two methods with which to combine the dissimilarity or distance matrices of multiple genes. The first method involves properly scaling the dissimilarity measures derived from different genes between a pair of species and using the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. We introduced two criteria for computing scale coefficients which can then be used to combine information across genes, namely the minimum variance (MinVar) criterion and the minimum coefficient of variation squared (MinCV) criterion. The scale coefficients obtained with the MinVar and MinCV criteria can then be used to derive a combined-gene tree from the weighted average of the distance or dissimilarity matrices of multiple genes. The second method is based on the singular value decomposition of a matrix made up of the p-vectors of pairwise distances for k genes. By decomposing such a matrix, we extract the common signal present in multiple genes to obtain a single tree representation of the relationship between a given set of taxa. Influence functions for the components of the singular value decomposition are derived to determine which genes are most influential in determining the combined-gene tree.