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Mathematics Of Evolution And Phylogeny

Author: Olivier Gascuel
Publisher: OUP Oxford
ISBN: 9780191513732
Size: 22.94 MB
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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.


Author: Mike Steel
Publisher: SIAM
ISBN: 161197447X
Size: 19.81 MB
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Phylogenetics is a topical and growing area of research. Phylogenies (phylogenetic trees and networks) allow biologists to study and graph evolutionary relationships between different species. These are also used to investigate other evolutionary processes?for example, how languages developed or how different strains of a virus (such as HIV or influenza) are related to each other. This self-contained book addresses the underlying mathematical theory behind the reconstruction and analysis of phylogenies. The theory is grounded in classical concepts from discrete mathematics and probability theory as well as techniques from other branches of mathematics (algebra, topology, differential equations). The biological relevance of the results is highlighted throughout. The author supplies proofs of key classical theorems and includes results not covered in existing books, emphasizes relevant mathematical results derived over the past 20 years, and provides numerous exercises, examples, and figures.


Author: Charles Semple
Publisher: Oxford University Press on Demand
ISBN: 9780198509424
Size: 38.63 MB
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Phylogenetic trees and networks are widely used throughout evolutionary biology, epidemiology, and ecology to infer the historical relationships between species through inherited characteristics. This work discusses the mathematics that underlies the reconstruction and analysis of these phylogenetic trees.

Molecular Evolution And Phylogenetics

Author: Masatoshi Nei
Publisher: Oxford University Press
ISBN: 0199881227
Size: 43.36 MB
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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.

Phylogeny And Evolution Of The Angiosperms

Author: Douglas Soltis
Publisher: University of Chicago Press
ISBN: 022644175X
Size: 61.47 MB
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Although they are relative latecomers on the evolutionary scene, having emerged only 135‒170 million years ago, angiosperms—or flowering plants—are the most diverse and species-rich group of seed-producing land plants, comprising more than 15,000 genera and over 350,000 species. Not only are they a model group for studying the patterns and processes of evolutionary diversification, they also play major roles in our economy, diet, and courtship rituals, producing our fruits, legumes, and grains, not to mention the flowers in our Valentine’s bouquets. They are also crucial ecologically, dominating most terrestrial and some aquatic landscapes. This fully revised edition of Phylogeny and Evolution of the Angiosperms provides an up-to-date, comprehensive overview of the evolution of and relationships among these vital plants. Incorporating molecular phylogenetics with morphological, chemical, developmental, and paleobotanical data, as well as presenting a more detailed account of early angiosperm fossils and important fossil information for each evolutionary branch of the angiosperms, the new edition integrates fossil evidence into a robust phylogenetic framework. Featuring a wealth of new color images, this highly synthetic work further reevaluates long-held evolutionary hypotheses related to flowering plants and will be an essential reference for botanists, plant systematists, and evolutionary biologists alike.

Phylogeny And Evolution Of The Mollusca

Author: W. F. Ponder
Publisher: Univ of California Press
ISBN: 9780520250925
Size: 11.32 MB
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"Ponder and Lindberg provides a breathtaking overview of the evolutionary history of the Mollusca, effectively melding information from anatomy, ecology, genomics, and paleobiology to explore the depths of molluscan phylogeny. Its outstanding success is due to thoughtful planning, focused complementary contributions from 36 expert authors, and careful editing. This volume is a must for malacologists."--Bruce Runnegar, Department of Earth and Space Sciences, University of California, Los Angeles "Our understanding of the phylogeny and evolutionary history of the mollusca has been revolutionized over the past two decades through new molecular data and analysis, and reinvestigation of morphological characters. In this volume Ponder, Lindberg, and their colleagues do a wonderful job of integrating this work to provide new perspectives on the relationships of the major molluscan clades, their evolutionary dynamics, and their history. Particularly timely is the coverage of molluscan evo-devo and genomics."--Douglas H. Erwin, Curator of Paleozoic Invertebrates, National Museum of Natural History

Molecular Evolution

Author: Ziheng Yang
Publisher: Oxford University Press
ISBN: 0199602603
Size: 25.56 MB
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"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.

Human Evolution

Author: Graeme Finlay
Publisher: Cambridge University Press
ISBN: 1107040124
Size: 77.99 MB
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Brings together new research demonstrating how evidence based on genetic phenomena should end any lingering controversy over human evolution.

Phylogenetic Networks

Author: Daniel H. Huson
Publisher: Cambridge University Press
ISBN: 113949287X
Size: 22.75 MB
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The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at

Extinction And Phylogeny

Author: Michael J. Novacek
Publisher: Columbia University Press
ISBN: 9780231074384
Size: 70.51 MB
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More than 99 percent of all life that has ever existed on this planet is extinct. Moreover, human acceleration of the extinction of species has created a crisis in biodiversity. How can the history of past life be retrieved? How does this history bear on our understanding of the organization and evolution of present-day species? These questions are addressed in Extinction and Phylogeny. This book offers new and original research by leading authorities on evolutionary and systematic biology, who rank among the best of the dynamic investigators of botany, zoology, and paleontology. This exciting book includes chapters about the recovery of information from living biota, taking into account the limitations of sampling and the steady rate of contemporary extinction of taxa. Complementary discussions elucidate problems involving the analysis of data sets of variable completeness--for example, partially preserved fossils or patchy samples of extant taxa. Extinction and Phylogeny balances empirical issues with the theoretical and applies cladistic methodology. This detailed text will prove to be a leading-edge book for professional and student biologists alike and for those in related disciplines. The relationship between extinction and phylogenetic theory must be understood if we are to explain existing biological diversity and effectively assess the declining biodiversity of our planet in the decades to come.