Anisimova M. (ed.) Evolutionary Genomics. Statistical and Computational Methods

Humana Press, 2012. — 1021 p. — (Methods in Molecular Biology 855).Discovery of genetic material propelled the power of classical evolutionary studies across the diversity of living organisms. Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. The methodology developed focused primarily on inferences from single genes or noncoding DNA segments: mainly on reconstructing the evolutionary relationships between lineages and estimating evolutionary and selective forces. Books offering a comprehensive coverage of such methodologies have already appeared, with Joe Felsenstein’s Inferring Phylogenies and Ziheng Yang’s Computational Molecular Evolution among the favorites.
This volume is intended to review more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. While the first sequenced genome (RNA virus Bacteriophage MS2 in 1976) was not even 4,000 nucleotides long, the sequencing progress culminated with the completion of the human genome of about 3.3 _ 109 base pairs and advanced to sequence many other species genomes, heading ambitiously towards population sequencing projects such as 1,000 genome projects for humans and Drosophila melanogaster. Next-generation sequencing (NGS) technologies sparked the genomics revolution, which triggered a renewed effort towards the development of statistical and computational methods capable of coping with the flood of genomic data and its inherent complexity.
The challenge of analyzing and understanding the dynamics of large-system data can be met only through an integration of organismal, molecular, and mathematical disciplines. This requires commitment to an interdisciplinary approach to science, where both experimental and theoretical scientists from a variety of fields understand each other’s needs and join forces. Evidently, there remains a gap to be breached. This book presents works by top scientists from a variety of disciplines, each of whom embodies the interdisciplinary spirit of evolutionary genomics. The collection includes a wide spectrum of articles—encompassing theoretical works and hands-on tutorials, as well as many reviews with much biological insight.Volume 1
Part I Introduction: Bioinformatician’s Primers
Introduction to Genome Biology: Features, Processes, and Structures
Diversity of Genome Organisation
Probability, Statistics, and Computational Science
The Essentials of Computational Molecular Evolution
Part II Genomic Data Assembly, Alignment, and Homology Inference
Next-Generation Sequencing Technologies and Fragment Assembly Algorithms
Gene Prediction
Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview
Whole-Genome Alignment
Inferring Orthology and Paralogy
Detecting Laterally Transferred Genes
Part III Genome Evolution: Insights from Statistical Analyses
Genome Evolution in Outcrossing Versus Selfing Versus Asexual Species
Transposable Elements and Their Identification
Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans
Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications
Analysis of Gene Order Evolution Beyond Single-Copy Genes
Discovering Patterns in Gene Order
Volume 2
Part I Phylogenomics
Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes
Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life
Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns
Part II Natural Selection, Recombination, and Innovation In Genomic Sequences
Selection on the Protein-Coding Genome
Methods to Detect Selection on Noncoding DNA
The Origin and Evolution of New Genes
Evolution of Protein Domain Architectures
Estimating Recombination Rates from Genetic Variation in Humans
Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
Part III Population Genomics
Association Mapping and Disease: Evolutionary Perspectives
Ancestral Population Genomics
Nonredundant Representation of Ancestral Recombinations Graphs
Part IV The -omics
Using Genomic Tools to Study Regulatory Evolution
Characterization and Evolutionary Analysis of Protein–Protein Interaction Networks
Statistical Methods in Metabolomics
Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases
Genetical Genomics for Evolutionary Studies
Part V Handling Genomic Data: Resources and Computation
Genomics Data Resources: Frameworks and Standards
Sharing Programming Resources Between Bio* Projects Through Remote Procedure Call and Native Call Stack Strategies
Scalable Computing for Evolutionary Genomics