Rogers - Integrated molecular evolution

INTEGRATED MOLECULAR EVOLUTION

SECOND EDITION

INTEGRATED MOLECULAR EVOLUTION

SECOND EDITION

SCOTT ORLAND ROGERS

CRC Press

Taylor & Francis Group

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2017 by Taylor & Francis Group, LLC

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Version Date: 20160204

International Standard Book Number-13: 978-1-4822-3089-5 (Hardback)

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Library of Congress Cataloging-in-Publication Data

Names: Rogers, Scott O., 1953- , author.

Title: Integrated molecular evolution / Scott Orland Rogers.

Description: Second edition. | Boca Raton : Taylor & Francis, 2016. |

Includes bibliographical references and index.

Identifiers: LCCN 2015045976 | ISBN 9781482230895 (alk. paper)

Subjects: | MESH: Evolution, Molecular | Molecular Biology | Genetic Phenomena

Classification: LCC QH325 | NLM QU 475 | DDC 572.8/38--dc23

LC record available at http://lccn.loc.gov/2015045976

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Contents

As with the first edition of this book, it was written with students in mind. It is meant to introduce the major topics of molecular evolution in a way that will encourage students to delve deeper into each of the topics. The book started as a series of notes, overheads, and digital slides that comprised a course in molecular evolution. The course was designed as an integrated approach to this field, for which there was no single textbook available. It draws from concepts in evolution, geology, chemistry, biochemistry, molecular biology, genetics, taxonomy, bioinformatics, various OMICS fields, and, of course, molecular evolution. Because it discusses aspects of each of these disciplines, students with broad backgrounds (as well as those with very focused backgrounds) should be able to grasp the concepts, principles, and details of this book. It presents some of the usual information regarding various aspects of cell function, but also details the variety of mechanisms that have evolved. This has been done to present a broader view of evolution that is meant to show that some processes have been approached in very different ways by the diversity of species during their evolution on Earth.

Although the first edition was organized into 18 chapters, including 197 figures, the second edition has been substantially expanded into 34 chapters, with 413 figures, essentially doubling the size of the first edition. It has been divided into six sections. , Genomes, is a survey of a set of genomes that represents a compendium of some of the important aspects of the evolution of genomes, in general.

presents the common, as well as many of the uncommon, modes of separating chromosomes, from separation of chromosomes in bacteria to mitosis and meiosis in a variety of eukaryotes.

in the first edition.

is focused on the genetic changes and mechanisms in carcinogenesis. Some of the same mechanisms that cause evolutionary changes are the same mechanisms that cause cancer.

, Phylogenomics and Comparative Genomics, explains some of the processes and challenges in using genomic data in genomic studies of evolutionary processes.

The final section, . Part of the additions to this chapter includes details about how the human genome has led to some practical applications of the information.

Scott Orland Rogers
Bowling Green State University, Ohio

I thank my wife Mary, daughter Liz, and son Ben for providing moral support. I could not have written this without their support. I also thank my mother, father, sister, and brother for their support throughout the years. I thank all of my students who always brought up new ideas, questions, papers, and insights, all of which made me think and rethink the ideas presented in this book. Also, thanks to Professor Arnie Bendich (my PhD Major Professor) who provided ideas, papers, enthusiasm, and critical questions about parts of this book. He taught me to think and read critically, deeply, and broadly. Special thanks to Zeynep Koer, Lorena Harris, Amal Abu Almakarem, and Maitreyee Mukerjee for providing useful feedback on several parts of this book. Also, I want to thank the many people who provided feedback on the first edition of this book. The comments were very helpful to formulate and write the second edition. Special thanks to Chuck Crumly at Taylor & Francis Group for the time and energy that he spent assuring that this second edition would be published, and for providing comments, suggestions, and critiques. The book would not have been possible without him. Thanks also to Barbara Norwitz (also at Taylor & Francis Group) for helping to make the first edition of this book a success. Finally, I thank colleagues and students at BGSU for having patience with my frequent and lengthy absences from my office and lab while I was diligently working on this book at home.

Scott Orland Rogers is a professor of molecular biology and evolution at Bowling Green State University, Bowling Green, Ohio. He received his BS (1976) and MS (1980) degrees in biology from the University of Oregon, Eugene; and PhD (1987) in plant molecular biology from the University of Washington, Seattle. He was an assistant professor and associate professor at the State University of New York College of Environmental Science and Forestry, Syracuse, NY, from 1989 through 2001, before moving to BGSU. He has taught courses in biology, botany, cell physiology, molecular biology, molecular genetics, bioinformatics, and molecular evolution. Research in his lab includes studies of microbes and nucleic acids preserved in ice, life in extreme environments, group I introns, molecular microbial phylogenetics, microbial metagenomics/metatranscriptomics, ancient DNA, and plant development.