Search results for: molecular-evolution-and-phylogenetics

Molecular Evolution and Phylogenetics

Author : Masatoshi Nei
File Size : 34.87 MB
Format : PDF
Download : 499
Read : 750
Download »
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

Author : Lindell Bromham
File Size : 46.25 MB
Format : PDF
Download : 235
Read : 708
Download »
DNA can be extracted and sequenced from a diverse range of biological samples, providing a vast amount of information about evolution and ecology. The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untanglingfamily relationships.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 thatinformation to answer. Starting with evolutionary principles, and illustrated throughout with biological examples, it is the perfect starting point on the journey to an understanding of the way molecular data is used in modern biology.Online Resource CentreThe Online Resource Centre features:For registered adopters of the book:- Class plans for one-hour hands-on sessions associated with each chapter- Figures from the textbook to view and download

Molecular Evolution

Author : Roderick D.M. Page
File Size : 89.4 MB
Format : PDF, Docs
Download : 327
Read : 592
Download »
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.

Molecular Evolution and Phylogenetics

Author : Masatoshi Nei
File Size : 62.62 MB
Format : PDF, Kindle
Download : 557
Read : 499
Download »
Molecular basis of evolution; Evolutionary change of amino acid sequences; Evolutionary change of DNA sequences; Synonymous and nonsynonymous nucleotide substitutions; Phylogenetic trees; Phyologenetic inference: distance methods; Phyologenetic inference:maximum parsimony methods; Phyologenetic inference: maximum likelihood methods; Accuracies and statistical tests of phylogenetic trees; Molecular clocks and linearized trees; Ancestral nucleotide and amino acid sequences; Genetic polymorphism and evolution; Population trees from genetic markers; Perspectives.

Molecular Evolution and Phylogenetics

Author : M. Nei
File Size : 84.95 MB
Format : PDF, Kindle
Download : 619
Read : 718
Download »
Molecular basis of evolution; Evolutionary change of amino acid sequences; Evolutionary change of DNA sequences; Synonymous and nonsynonymous nucleotide substitutions; Phylogenetic trees; Phyologenetic inference: distance methods; Phyologenetic inference:maximum parsimony methods; Phyologenetic inference: maximum likelihood methods; Accuracies and statistical tests of phylogenetic trees; Molecular clocks and linearized trees; Ancestral nucleotide and amino acid sequences; Genetic polymorphism and evolution; Population trees from genetic markers; Perspectives.

Analysis of Phylogenetics and Evolution with R

Author : Emmanuel Paradis
File Size : 68.10 MB
Format : PDF, Kindle
Download : 309
Read : 594
Download »
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.

Molecular Evolution

Author : Ziheng Yang
File Size : 27.39 MB
Format : PDF
Download : 435
Read : 1327
Download »
"Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology."--back cover.

Morphology Molecules Evolution and Phylogeny in Polychaeta and Related Taxa

Author : Universität Osnabrück
File Size : 67.66 MB
Format : PDF, ePub, Docs
Download : 126
Read : 1150
Download »
Recently, evidence has been accumulated which shows that some of the groups formerly regarded as independent "phyla" such as Pogonophora (now recognized as Siboglinidae), Echiura, Myzostomida and perhaps Sipuncula, are most probably nothing else than greatly modified Annelida. The extreme morphological diversity found especially in Polychaeta displays the plasticity of a simple segmented organisation that basically is nothing else but a serial repetition of identical units. Thus, annelids are highly important to our understanding of fundamental questions about morphological and adaptive diversity, as well as clarifying evolutionary changes and phylogenetic relationships. The book aims to summarize our knowledge on Polychaetes polychaetes and their allies and gives an overview of recent advances gained by studies that employed conventional and modern methods plus, increasingly and importantly, the use of molecular markers and computer-assisted kinship analyses. It also reflects the state of art in polychaete sciences and presents new questions and controversies. As such it will significantly influence the direction of research on Polychaeta and their related taxa.

Bioinformatics and Molecular Evolution

Author : Paul G. Higgs
File Size : 81.69 MB
Format : PDF, ePub
Download : 430
Read : 1026
Download »
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.

Molecular Evolution and Phylogenetics

Author : Masatoshi Nei
File Size : 71.29 MB
Format : PDF, ePub, Mobi
Download : 168
Read : 701
Download »
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.

Avian Molecular Evolution and Systematics

Author : David P. Mindell
File Size : 86.23 MB
Format : PDF, Docs
Download : 305
Read : 976
Download »
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

Phylogenetics

Author : E. O. Wiley
File Size : 58.9 MB
Format : PDF, Docs
Download : 903
Read : 813
Download »
The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Molecular Evolution Phylogenetics and Parasitism in Antarctic Cidaroid Echinoids

Author : Susanne J. Lockhart
File Size : 58.80 MB
Format : PDF, Kindle
Download : 388
Read : 902
Download »

Molecular and Genome Evolution EBook

Author : Dan Graur
File Size : 85.91 MB
Format : PDF
Download : 378
Read : 519
Download »

Molecular Evolution and Phylogeny of Methanogenic Archael Genomes

Author : Professor Jun Li
File Size : 51.62 MB
Format : PDF, Kindle
Download : 402
Read : 861
Download »
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

Molecular Evolution and Phylogenetics of Circular Single stranded DNA Viruses

Author : Yee Mey Seah
File Size : 28.14 MB
Format : PDF, ePub, Mobi
Download : 212
Read : 252
Download »
Viruses infect a wide variety of hosts across all domains of life. Despite their ubiquity, and a long history of virus research, fundamental questions such as what constitutes a virus species, and how viruses evolve and are modeled, have yet to be adequately answered. We compared viral sequences across five genomic architectures (single- and double-stranded DNA and RNA) and demonstrate the presence of substitution bias, especially in single-stranded viruses. Most striking is a consistent pattern of over-represented cytosine-to- thymine substitutions in single-stranded DNA (ssDNA) viruses. This led us to question the validity of using time-reversible nucleotide substitution models in viral phylogenetic inference, as these models assume equal rates of forward and reverse substitutions. We found that an unrestricted substitution model fit the data better for most single- and double-stranded viral datasets, as measured by corrected Akaike Information Criterion, and hierarchical likelihood ratio test scores. We also approached the question of virus species identification by examining members of the most species-rich viral genus Begomovirus (Family Geminiviridae), which are circular single-stranded DNA (ssDNA) viral crop pathogens transmitted by whitefly vectors. We used novel sweet potato-infecting begomoviruses (sweepoviruses) collected during a recent vector-enabled metagenomic survey to evaluate the concept of pairwise percent nucleotide identity threshold as a criterion for species demarcation. We demonstrate that species demarcation based on pairwise percent nucleotide identities group divergent sweepovirus clusters together, and is highly influenced by when, and how much sampling occurs.

Computational Molecular Evolution

Author : Ziheng Yang
File Size : 48.18 MB
Format : PDF, Kindle
Download : 353
Read : 1195
Download »
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.

Evolution

Author : Mark Ridley
File Size : 42.97 MB
Format : PDF, Mobi
Download : 959
Read : 488
Download »
Mark Ridley's Evolution has become the premier undergraduate text in the study of evolution. Readable and stimulating, yet well-balanced and in-depth, this text tells the story of evolution, from the history of the study to the most revent developments in evolutionary theory. The third edition of this successful textbook features updates and extensive new coverage. The sections on adaptation and diversity have been reorganized for improved clarity and flow, and a completely updated section on the evolution of sex and the inclusion of more plant examples have all helped to shape this new edition. Evolution also features strong, balanced coverage of population genetics, and scores of new applied plant and animal examples make this edition even more accessible and engaging. Dedicated website – provides an interactive experience of the book, with illustrations downloadable to PowerPoint, and a full supplemental package complementing the book – www.blackwellpublishing.com/ridley. Margin icons – indicate where there is relevant information included in the dedicated website. Two new chapters – one on evolutionary genomics and one on evolution and development bring state-of-the-art information to the coverage of evolutionary study. Two kinds of boxes – one featuring practical applications and the other related information, supply added depth without interrupting the flow of the text. Margin comments – paraphrase and highlight key concepts. Study and review questions – help students review their understanding at the end of each chapter, while new challenge questions prompt students to synthesize the chapter concepts to reinforce the learning at a deeper level.

Phylogeny and Classification of Birds

Author : Charles Gald Sibley
File Size : 45.3 MB
Format : PDF
Download : 709
Read : 667
Download »
This book presents the results of a study of the evolutionary history and classification of living birds based on comparisons of the DNAs (genetic material) of about 1700 species. Sibley and Ahlquist's DNA-DNA hybridization technqiue is a biochemical method that measures the degree of genetic similarity between the DNAs of different species of other groups of organisms, but this book includes the largest set of DNA comparisons for any group.

Plant Molecular Evolution

Author : J.J. Doyle
File Size : 69.91 MB
Format : PDF, ePub
Download : 137
Read : 913
Download »
Plant molecular biology has produced an ever-increasing flood of data about genes and genomes. Evolutionary biology and systematics provides the context for synthesizing this information. This book brings together contributions from evolutionary biologists, systematists, developmental geneticists, biochemists, and others working on diverse aspects of plant biology whose work touches to varying degrees on plant molecular evolution. The book is organized in three parts, the first of which introduces broad topics in evolutionary biology and summarizes advances in plant molecular phylogenetics, with emphasis on model plant systems. The second segment presents a series of case studies of gene family evolution, while the third gives overviews of the evolution of important plant processes such as disease resistance, nodulation, hybridization, transposable elements and genome evolution, and polyploidy.