During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.
An Introduction to Molecular Evolution and Phylogenetics presents the fundamental concepts and intellectual tools you need to understand how the genome records information about evolutionary past and processes, how that information can be "read", and what kinds of questions we can use that information to answer. Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to anunderstanding of the way molecular data is used in modern biology.
The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
The use of DNA and other biological macromolecules has revolutionized systematic studies of evolutionary history. Methods that use sequences of nucleotides and amino acids are now routinely used as data for addressing evolutionary questions that, although not new questions, have defied description and analysis. The world-renowned contributors use these new methods to unravel particular aspects of the evolutionary history of birds. Avian Molecular Evolution and Systematics presents an overview of the theory and application of molecular systematics, focusing on the phylogeny and evolutionary biology of birds. New, developing areas in the phylogeny of birds at multiple taxonomic areas are covered, as well as methods of analysis for molecular data, evolutionary genetics within and between bird populations, and the application of molecular-based phylogenies to broader questions of evolution. Contains authoritative contributions from leading researchers Discusses the utility of different molecular markers for questions of avian evolution, involving populations and higher-level taxa Applies molecular-based phylogenies of birds and molecular population genetics data to broad questions of organismal and molecular evolution. Compares and contrasts molecular and morphological data sets
Molecular evolution, phylogenetics, genomics, and other related topics are all critical to understanding evolutionary processes. All too frequently, however, they are treated separately in textbooks and courses, such that students fail to connect all of the concepts, principles, and nuances of the evolutionary processes. Integrated Molecular Evolution brings these related areas together in one volume, facilitating student comprehension of often difficult concepts. Incorporating the emerging fields of genomics and bioinformatics with traditional fields such as evolution, genetics, and molecular biology, this volume explores a myriad of topics, including Life on Earth and the possible origins of life The evolution of organisms on Earth and the history of the study of evolution Basic structures of DNA, RNA, proteins, and other biological molecules, and the synthesis of each Molecular biology and the evolution, structure, and function of ribosomes DNA replication and the various ways in which chromosomes are separated Ways in which DNA can be changed to produce mutations, infectious causes of mutation, and repair of DNA Definitions, evolution, and the importance of multigene families Phylogenetic analysis and how researchers use the raw sequence data to reconstruct portions of evolutionary processes Details of the genomes of a variety of organisms, from RNA viruses to eukaryotes, presented in order of complexity Each chapter ends with a summary of key points, forming an effective review and enabling students to isolate critical material. The series of topics and the masterful integration of these topics lead students to a full understanding of evolution and the component processes that have led to biological evolution on Earth.
This volume surveys advances in the study of adaptive radiation showing how molecular characters can be used to analyze the origin and pattern of diversification within a lineage in a non-circular fashion.
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.
This dissertation, "Molecular Evolution and Phylogeny of Methanogenic Archael Genomes" by Jun, Li, 李俊, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Methane (CH4) is the major chemical component of natural gas, as well as a particularly potent greenhouse gas. Methanogens are the archaeal organisms that produce methane and play a key role in biological methanogenesis. A total of six taxonomic orders of archaeal methanogens have been discovered and almost all previous phylogenetics studies have confirmed that these methanogens are genetically diversified and do not belong to a phylogenetically monophyletic group. To date, the relationships between methanogens and closely related non-methanogen species at the taxonomic order level remain unresolved and different studies have often produced contradictory results based on different gene markers. These studies suggest the complicated and distinct evolutionary histories between different genes in these genomes. In this thesis, 74 fully sequenced archaeal genomes, including 41 methanogens, were collected and used in a comprehensive comparative genomics and evolutionary analysis. First, numerous phylogenomic trees were reconstructed based on various datasets using several methods and the results show that Methanopyrales is close to Methanobacteriales (or Methanopyrales) in the statistically best species tree. In addition, Methnocellales and Methanosarcinales, and as well as Methanomicrobiales and Halobacteriales are sister clades in the best species tree, but the confidence level is low. Further incongruence tests among the phylogenetic forest, which is composed of 3,694 ortholog gene families, reveal that the archaeal core genes have much stronger consistent vertical evolutionary signals than other genes, but these core genes are not topologically fully congruent with each other. Secondly, a series of weighted network analyses were implemented to decompose the hierarchical structure and to reveal the co-evolved gene modules, global and local features in the archaeal methanogen phylogenetic forest. The results show that this co-evolution network contains 7 statistical robust modules, and the module with the highest average node strength includes the majority of the core genes located in the central position of the network. Further in-depth evolutionary analysis reveals that the modularized evolution in the archaeal phylogenetic forest is closely related to the time of origin, HGT rate and ubiquitous vertical inheritance in gene families. Lastly, to investigate the causes for and factors related to the pervasive topology incongruence in the phylogenetic forest, in-depth clanistics analysis and HGT detection were carried out. These results show that (1) about 63% of gene families experienced at least 1 HGT event in their whole history; (2) core genes are not immune to HGT but they do have much lower HGT rates than other genes; (3) methanogens have distinct trends of HGTs from non-methanogen species; and (4) highly frequent inter-order HGTs, even for core genes, in methanogen genomes lead to their scrambled phylogenetic relationships. Further clanistics analysis screened out 119 candidate genes related to methanogenic pathways adaptation and most of these gene families have experienced at least one HGT. In conclusion, a complex evolutionary scenario for methanogenic archaeal species was described in this thesis as a combination of complicated vertical and non-vertical evolutionary processes in a modularized phylogenetic forest. DOI: 10.5353/th_b5185916 Subjects: Methan
The world is full of DNA. The salad in your sandwich, the pollen in the air, even the dirt on your shoes contains DNA from which a vast amount of information can be gained, including the identification of individuals and species, the structure and distribution of populations, the origins oflineages and the pace and mechanisms of evolutionary change. Reading the story in DNA is a beginner's guide to molecular evolution, and is the perfect companion on the journey to a proper understanding of molecular data. The central theme of the book is that in order to get ecological or evolutionary information out of molecular data, you must understand the way that the molecular data evolves and the influence that the assumptions you make have on the answers you get. The book blends beautifully clear explanations with cutting-edge examples from the research literature, drawing on the fields of biodiversity, conservation biology, epidemiology, phylogeography, evolutionary development and ancient DNA to explore topics such as molecular evolutionary theory,phylogenetics, molecular clocks, detecting selection and recombination, and identifying individuals from molecular data.Technical detail is set apart from the main text, allowing the student to approach the material in different ways: read only the text and skip the finer details, use the text to understand the technical details or vice versa, or identify key case studies and read the concepts and methods particularto that case. The use of "bioinformatic" analyses has revolutionized biology, and there are now few areas of evolution and ecology that remain untouched by molecular data. Today's biology students and researchers need to be familiar with the application of molecular data to answering evolutionary questions. Butthe most pressing question is usually: "Where do I start?!" This book is the answer.Online Resource Centre:The Online Resource Centre features:- Figures from the book in electronic format, ready to download- Discussion questions and tutorial exercisesFor students:- Annotated weblinks- Topical updates: links to relevant journal articles and websites that describe advancements in the field since the book's publication
This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. This book provides an overview of the statistical theory and methods used in studies of molecular evolution. It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. The chapters are written by the leaders of field and they will take the reader from basic introductory material to the state-of-the-art statistical methods. This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. The chapters of the book assume no advanced mathematical skills beyond basic calculus, although familiarity with basic probability theory will help the reader. Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. Rasmus Nielsen received his Ph.D. form the University of California at Berkeley in 1998 and after a postdoc at Harvard University, he assumed a faculty position in Statistical Genomics at Cornell University. He is currently an Ole Rømer Fellow at the University of Copenhagen and holds a Sloan Research Fellowship. His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. From the reviews: "...Overall this is a very useful book in an area of increasing importance." Journal of the Royal Statistical Society "I find Statistical Methods in Molecular Evolution very interesting and useful. It delves into problems that were considered very difficult just several years ago...the book is likely to stimulate the interest of statisticians that are unaware of this exciting field of applications. It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods." Marek Kimmel for the Journal of the American Statistical Association, September 2006 "Who should read this book? We suggest that anyone who deals with molecular data (who does not?) and anyone who asks evolutionary questions (who should not?) ought to consult the relevant chapters in this book." Dan Graur and Dror Berel for Biometrics, September 2006 "Coalescence theory facilitates the merger of population genetics theory with phylogenetic approaches, but still, there are mostly two camps: phylogeneticists and population geneticists. Only a few people are moving freely between them. Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. Although Nielsen did not contribute a chapter to his book, his work permeates all its chapters. This book gives an overview of his interests and current achievements in molecular evolution. In short, this book should be on your bookshelf." Peter Beerli for Evolution, 60(2), 2006
This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.
Wussten Sie, dass Sie mit einem Röhrling näher verwandt sind als mit einem Gänseblümchen oder Vögel den Krokodilen näher sind als Eidechsen? In den letzten 30 Jahren sind die Methoden der Klassifikation des Lebens völlig neu überdacht worden. Das Resultat stellt die bisherige Einteilung der mehr als 2 Millionen bekannten Arten auf den Kopf. Das Buch hilft, die organismische Vielfalt zu bewältigen, indem wesentliche Einteilungs- und Ordnungskriterien vorgestellt und bedeutende stammesgeschichtliche Entwicklungslinien diskutiert werden.
Paul Davies gibt einen genauen und abwägenden Überblick über die vorhandenen Modelle der Entstehung des Lebens und fügt eine weitere, gut belegte Hypothese hinzu, nämlich die der Lebensentstehung fern von der Erde. (Dieser Text bezieht sich auf eine frühere Ausgabe.)