The Changing Text of Acts : A Phylogenetic Approach

Peer reviewe

Handbook of Stemmatology

Stemmatology studies aspects of textual criticism that use genealogical methods. This handbook is the first to cover the entire field, encompassing both theoretical and practical aspects, ranging from traditional to digital methods. Authors from all the disciplines involved examine topics such as the material aspects of text traditions, methods of traditional textual criticism and their genesis, and modern digital approaches used in the field

An analysis of the coherence-based genealogical method using phylogenetics

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

Towards a Model of (Variant) Readings

In scholarly editing, more particularly in the context of collating various versions of a text, the definition of a variant reading is crucial. Yet, despite its importance, the meaning of a variant reading is often reduced to a “difference.” The reason for such a vague definition is that what makes a variant can largely depend on the field of study: scholars of the Homeric oral tradition will consider different variants from scholars of medieval traditions or early printed texts, or from genetic critics. This contribution will focus on the modelling of a reading, arguing that formalizing this concept is necessary in order to define, and thus model, a variant. This article will also address digital representation of a reading by focusing on one implementation: the JSON data format used in conjunction with collation programs such as CollateX

AN EVOLUTIONARY APPROACH TO BIBLIOGRAPHIC CLASSIFICATION

This dissertation is research in the domain of information science and specifically, the organization and representation of information. The research has implications for classification of scientific books, especially as dissemination of information becomes more rapid and science becomes more diverse due to increases in multi-, inter-, trans-disciplinary research, which focus on phenomena, in contrast to traditional library classification schemes based on disciplines.The literature review indicates 1) human socio-cultural groups have many of the same properties as biological species, 2) output from human socio-cultural groups can be and has been the subject of evolutionary relationship analyses (i.e., phylogenetics), 3) library and information science theorists believe the most favorable and scientific classification for information packages is one based on common origin, but 4) library and information science classification researchers have not demonstrated a book classification based on evolutionary relationships of common origin.The research project supports the assertion that a sensible book classification method can be developed using a contemporary biological classification approach based on common origin, which has not been applied to a collection of books until now. Using a sample from a collection of earth-science digitized books, the method developed includes a text-mining step to extract important terms, which were converted into a dataset for input into the second step—the phylogenetic analysis. Three classification trees were produced and are discussed. Parsimony analysis, in contrast to distance and likelihood analyses, produced a sensible book classification tree. Also included is a comparison with a classification tree based on a well-known contemporary library classification scheme (the Library of Congress Classification).Final discussions connect this research with knowledge organization and information retrieval, information needs beyond science, and this type of research in context of a unified science of cultural evolution

Studying Evolutionary Change: Transdisciplinary Advances in Understanding and Measuring Evolution

Evolutionary processes can be found in almost any historical, i.e. evolving, system that erroneously copies from the past. Well studied examples do not only originate in evolutionary biology but also in historical linguistics. Yet an approach that would bind together studies of such evolving systems is still elusive. This thesis is an attempt to narrowing down this gap to some extend. An evolving system can be described using characters that identify their changing features. While the problem of a proper choice of characters is beyond the scope of this thesis and remains in the hands of experts we concern ourselves with some theoretical as well data driven approaches. Having a well chosen set of characters describing a system of different entities such as homologous genes, i.e. genes of same origin in different species, we can build a phylogenetic tree. Consider the special case of gene clusters containing paralogous genes, i.e. genes of same origin within a species usually located closely, such as the well known HOX cluster. These are formed by step- wise duplication of its members, often involving unequal crossing over forming hybrid genes. Gene conversion and possibly other mechanisms of concerted evolution further obfuscate phylogenetic relationships. Hence, it is very difficult or even impossible to disentangle the detailed history of gene duplications in gene clusters. Expanding gene clusters that use unequal crossing over as proposed by Walter Gehring leads to distinctive patterns of genetic distances. We show that this special class of distances helps in extracting phylogenetic information from the data still. Disregarding genome rearrangements, we find that the shortest Hamiltonian path then coincides with the ordering of paralogous genes in a cluster. This observation can be used to detect ancient genomic rearrangements of gene clus- ters and to distinguish gene clusters whose evolution was dominated by unequal crossing over within genes from those that expanded through other mechanisms. While the evolution of DNA or protein sequences is well studied and can be formally described, we find that this does not hold for other systems such as language evolution. This is due to a lack of detectable mechanisms that drive the evolutionary processes in other fields. Hence, it is hard to quantify distances between entities, e.g. languages, and therefore the characters describing them. Starting out with distortions of distances, we first see that poor choices of the distance measure can lead to incorrect phylogenies. Given that phylogenetic inference requires additive metrics we can infer the correct phylogeny from a distance matrix D if there is a monotonic, subadditive function ζ such that ζ^−1(D) is additive. We compute the metric-preserving transformation ζ as the solution of an optimization problem. This result shows that the problem of phylogeny reconstruction is well defined even if a detailed mechanistic model of the evolutionary process is missing. Yet, this does not hinder studies of language evolution using automated tools. As the amount of available and large digital corpora increased so did the possibilities to study them automatically. The obvious parallels between historical linguistics and phylogenetics lead to many studies adapting bioinformatics tools to fit linguistics means. Here, we use jAlign to calculate bigram alignments, i.e. an alignment algorithm that operates with regard to adjacency of letters. Its performance is tested in different cognate recognition tasks. Using pairwise alignments one major obstacle is the systematic errors they make such as underestimation of gaps and their misplacement. Applying multiple sequence alignments instead of a pairwise algorithm implicitly includes more evolutionary information and thus can overcome the problem of correct gap placement. They can be seen as a generalization of the string-to-string edit problem to more than two strings. With the steady increase in computational power, exact, dynamic programming solutions have become feasible in practice also for 3- and 4-way alignments. For the pairwise (2-way) case, there is a clear distinction between local and global alignments. As more sequences are consid- ered, this distinction, which can in fact be made independently for both ends of each sequence, gives rise to a rich set of partially local alignment problems. So far these have remained largely unexplored. Thus, a general formal frame- work that gives raise to a classification of partially local alignment problems is introduced. It leads to a generic scheme that guides the principled design of exact dynamic programming solutions for particular partially local alignment problems