This book presents coverage of the principles and practice of molecular clocks, which have provided fascinating and unprecedented insights into the evolutionary timescale of life on earth. It begins by following the early development of the molecular evolutionary clock in the 1960s, and leads to the complex statistical approaches that are now used to analyse genome sequences. The chapters of this book have been contributed by leading experts in the field and address the important issues of evolutionary rates, molecular dating, and phylogenomic analysis. This is the first time that these different aspects of the molecular clock have been brought together in a single, comprehensive volume. It is an invaluable reference for students and researchers interested in evolutionary biology, genetic analysis, and genomic evolution.

Determining the precise timing for the evolutionary origin of groups of organisms has become increasingly important as scientists from diverse disciplines attempt to examine rates of anatomical or molecular evolution and correlate intrinsic biological events to extrinsic environmental events. Molecular clock analyses indicate that many major groups

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. Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative. 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.

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.

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.

This work provides a unified theory that addresses the important problem of the origin and maintenance of genetic variation in natural populations. With modern molecular techniques, variation is found in all species, sometimes at astonishingly high levels. Yet, despite these observations, the forces that maintain variation within and between species have been difficult subjects of study. Because they act very weakly and operate over vast time scales, scientists must rely on indirect inferences and speculative mathematical models. However, despite these obstacles, many advances have been made. The author's research in molecular genetics, evolution, and bio-mathematics has enabled him to draw on this work, and present a coherent and valuable view of the field. The book is divided into three parts. The first consists of three chapters on protein evolution, DNA evolution, and molecular mechanisms. This section reviews the experimental observations on genetic variation. The second part gives a unified treatment of the mathematical theory of selection in a fluctuating environment. The final two chapters combine the earlier assessments in a treatment of the scientific status of two competing theories for the maintenance of genetic variation. Steeped in the enormous advances population genetics has made over the past 25 years, this book has proven highly popular among human geneticists, biologists, evolutionary theorists, and bio-mathematicians.

The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data.

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.

This volume provides an overview of (1) the physical and chemical foundations of dating methods and (2) the applications of dating methods in the geological sciences, biology, and archaeology, in almost 200 articles from over 200 international authors. It will serve as the most comprehensive treatise on widely accepted dating methods in the earth sciences and related fields. No other volume has a similar scope, in terms of methods and applications and particularly time range. Dating methods are used to determine the timing and rate of various processes, such as sedimentation (terrestrial and marine), tectonics, volcanism, geomorphological change, cooling rates, crystallization, fluid flow, glaciation, climate change and evolution. The volume includes applications in terrestrial and extraterrestrial settings, the burgeoning field of molecular-clock dating and topics in the intersection of earth sciences with forensics. The content covers a broad range of techniques and applications. All major accepted dating techniques are included, as well as all major datable materials.