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This book focuses on bioinformatics, the study of the management and analysis of information used in biological systems. Particular emphasis explains to the reader how to study and extract useful information, such as relatedness of species, function of specific sequences, and genome organization from genomic sequences. This book focuses on the algorithmic aspects of bioinformatics and not on databases and software packages. There are two important discriminating characteristics that sets the book apart. It connects the algorithmic aspects and approaches to bioinformatics with the biological context while maintaining a user friendly and accessible description of the algorithms. The authors have curated the content for use a stand alone reference or the book will fit a one semester course on the subject.

Phylogenomics is a rapidly growing field of study concerned with using genome-wide data—usually in the form of DNA sequence loci—to infer the evolution of genes, genomes, and the Tree of Life. Accordingly, this discipline connects many areas in biology including molecular and genomic evolution, systems biology, molecular systematics, phylogeography, conservation genetics, DNA barcoding, and others. With the advent of Next Generation Sequencing in addition to advances in computer hardware and software over the past decade, researchers can now generate unparalleled phylogenomic datasets that are helping to illuminate many areas in the life sciences. This book is an introduction to the principles and practices of gathering these data. Phylogenomic Data Acquisition: Principles and Practice is intended for a broad cross-section of biologists and anyone else interested in learning how to obtain phylogenomic data using the latest methods.

Animal phylogeny is undergoing a major revolution due to the availability of an exponentially increasing amount of molecular data and the application of novel methods of phylogenetic reconstruction, as well as the many spectacular advances in palaeontology and molecular developmental biology. Traditional views of the relationships among major phyla have been shaken and new, often unexpected, relationships are now being considered. At the same time, the emerging discipline of evolutionary developmental biology, or'evo-devo', has offered new insights into the origin and evolvability of major traits of animal architecture and life cycle. All these developments call for a revised interpretation of the pathways along which animal structure and development has evolved since the origin of the Metazoa. Perspectives in Animal Phylogeny and Evolution takes on this challenge, successfully integrating morphological, fossil and molecular evidence to produce a novel reinterpretation of animal evolution. Central to the book's approach is an'evo-devo'perspective on animal evolution (with all the fresh insights this has given into the origin of animal organization and life cycles), complementary to the more traditional perspectives of pattern (cladistics, comparative anatomy and embryology), mechanisms (developmental biology) and adaptation (evolutionary biology). The author advocates the need to approach the study of animal evolution with a critical attitude towards many key concepts of comparative morphology and developmental biology. Particular attention in the book is paid to the evolution of life cycles and larval forms.

During the last decade a wealth of new data has arisen from the use of new fluorescent labelling techniques and the sequencing of whole microbial genomes. One important conclusion from these data is that bacterial cells are much more structured than previously thought. The wall and the outer membrane contain topological domains, some proteins localize or move in specific patterns inside the cells, and some genes appear clustered in the chromosome and form conserved evolutionary units. Many of these structures are related to the cell cycle and to the process of cell morphogenesis, two processes that are themselves related to each other. From these observations the dcw gene cluster appears as a phylogenetic trait that is mainly conserved in bacilli. Molecules in Time and Space reviews the data on the formation of subcellular patterns or structures in bacteria, presents observations and hypotheses on the establishment and the maintenance of cell shape, and on the organization of genetic information in the chromosome.

Homology Effects offers contributions from an international panel of researchers whose aim has been both to introduce newcomers to the field of homology effects, and to bring colleagues up to date. Topic coverage includes dosage compensation, X-inactivation, imprinting, paramutation, homology-dependent gene silencing, transvection, pairing-sensitive silencing, nuclear organization of chromosomes, DNA repair, quelling, RIP, RNAi and antisense biology, homology effects in ciliates, prion biology, and a discourse on the evolution of gene duplications. Advances in Genetics presents an eclectic mix of articles of use to all human and molecular geneticists. They are written and edited by recognized leaders in the field and make this an essential series of books for anyone in the genetics field. - Homology, the examination of similarity due to shared common ancestry, encompasses a fascinating class of phenomena in mammals, plants, insects, ciliates, nematodes, fungi, and bacteria. Homology effects concern processes that recognize homology at the level of DNA and/or RNA, as well as at the level of protein. Their collective history begins at the turn of the century and includes some of the most puzzling and extraordinary observations in biology. The volume covers phenomena that have often been considered unusual, exceptional to the rule, and'out of the ordinary'and, therefore, not for general study. However, it is now becoming clear that taken together, these phenomena represent a class of regulatory mechanisms that are widespread, as well as exceptionally powerful.

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.