Molecular Markers, Natural History, and Evolution, Second Edition

John C. Avise

2004
541 pages, 137 illustrations
paper

About This Title

Molecular markers have opened exciting new windows through which to view the natural biological world. This treatment addresses the many applications for genetic markers (from polymorphic proteins and DNA) from the perspectives of population biology, behavioral ecology, organismal evolution, and phylogeny. Opening chapters review the history and purview of molecular approaches, and compare and contrast various laboratory techniques for revealing molecular markers. Subsequent chapters review the extensive scientific literature of molecular ecology and evolution, and describe a cornucopia of captivating discoveries about nature's workings, past and present.

The book is taxonomically balanced with numerous examples from plants, animals, and microbes. It is also temporally balanced with examples ranging from assessments of genetic parentage and kinship in the most recent generations to phylogenetic assessments deep in the Tree of Life (and nearly everything in-between). This Second Edition of a seminal work (first published in 1994) brings the reader up-to-date on the many dramatic advances and insights made over the last decade. Furthermore, by retaining descriptions of many pioneering works, this book also traces the empirical and conceptual roots of each subject, and thereby provides a rich sense of the field's history.

Appropriate for advanced undergraduates, graduate students, and scientists in such disciplines as ecology, genetics, population biology, ethology, molecular biology, systematics, and conservation biology, this new edition is for anyone interested in the application of molecular markers to organisms in the wild.

About the Author(s)

John C. Avise is Professor of Genetics at the University of Georgia. His educational background includes a B.S. in Natural Resources from the University of Michigan, an M.A. in Zoology from the University of Texas, and a Ph.D. from the University of California at Davis. His research centers on natural history, ecology, genetics, and the evolution of animals in nature, primarily as revealed by molecular markers. Topics studied range from micro-evolutionary to macro-evolutionary, and include analyses of genetic parentage, mating patterns, geographic population structure, gene flow, hybridization, introgression, phylogeography, speciation, systematics, and phylogenetics. Dr. Avise's interests also include the relevance of evolutionary biology and genetics to human affairs. He is currently President of the Society for Molecular Biology and Evolution, and he has also served as President of the Society for the Study of Evolution, and the American Genetic Association. He is an elected member of both the National Academy of Sciences and the American Academy of Arts and Sciences.

Reviews and Commentary

“This book will continue to be the reference for graduate students and experienced researchers in the field of molecular evolutionary biology for years to come. With admirable clarity and astonishing breadth and depth, Avise authoritatively reviews the seemingly exponentially increasing literature in fields ranging from molecular phylogenetics and phylogeography to conservation biology and population genetics, some of which the author has shaped and even invented himself.”
—Axel Meyer, The Quarterly Review of Biology

“[This book's] achievements are considerable, both in explanatory power and conceptual depth. . . . It is a major task to master and distill the enormous literature that has resulted from [the PCR explosion], and we are fortunate to have John Avise to do this in such a balanced and scholarly manner. . . . For me, one of the best features of this book is its simple yet learned writing, which effortlessly takes one from raw data to an understanding of fundamental evolutionary processes, and this clarity promotes one's own thoughts and ideas. . . . This matured treatise marks a milestone in our path of evolutionary enlightenment.”
—GM Hewitt, Heredity

“This excellent book is suitable to incite the interest of undergraduate and graduate students for the use of molecular markers. It is also highly useful for experienced researchers to broaden their knowledge and gather ideas beyond their immediate area of expertise, and it is definitely a treasure chest for university teaching.”
—Dirk Redecker, Écoscience

“This is an impressive reworking of a book that was certainly worth updating. This volume is not a detailed review of a particular topic or theory or a thorough users' guide to a set of techniques, but rather an unusual combination of the two with substantial hybrid vigor. At heart, Avise's book is an inspiring reminder of how field and laboratory perspectives can be combined to answer profound biological questions, and of how fun it is to become immersed in these explorations of molecular natural history.”
—Irby J. Lovette, The Auk

“The newly released second edition of John Avise's Molecular Markers, Natural History, and Evolution (2004) provides a detailed and comprehensive presentation of the scope of molecular analysis of evolutionary topics, ranging from population-level dynamics to attempts to reconstruct the tree of life. . . . Avise's book is of value for experts in evolutionary biology and genomics alike for the simple reason that it provides such thorough coverage of the kinds of evolutionary questions that could prospectively be addressed by genomic approaches.”
—David L. Remington, BioScience

“ . . . most textbooks devoted to molecular tools are heavy going for the beginner. John Avise's ‘Molecular markers, natural history, and evolution’ is different, focusing on the fascinating results of molecular ecological studies, rather than the fine details of their methods. He conveys the fundamental concepts underpinning molecular techniques using language that is accessible to those of us who wouldn't know a pipette tip from a PCR. At the same time he presents an encyclopedic review of the biologically important questions that have been addressed with molecular markers. The breadth of his review makes this book a valuable resource for novice and expert alike.”
—Tyler Smith, Plant Science Bulletin

“This is a beautifully written book. Avise has a knack for explaining even the most difficult concepts, so that the book will be accessible to anyone with at least some familiarity with biology. Moreover, the book is well organized, superbly illustrated, and the scholarship is amazing! What is perhaps most remarkable is the skill with which hundreds of examples from the literature are seamlessly woven into the narrative, without appearing repetitive or tedious. The author's knowledge and love of natural history pervades the text and leaves the reader with a sense of wonder and awe for the diversity of life that resides on our planet.”
—Loren Rieseberg, Indiana University

Preface to the Second Edition
Preface to the First Edition

PART I. BACKGROUND

Introduction

Why Employ Molecular Genetic Markers?

Molecular Data Are Genetic
Molecular Methods Open the Entire Biological World for Genetic Scrutiny
Molecular Methods Access a Nearly Unlimited Pool of Genetic Variability
Molecular Data Can Distinguish Homology from Analogy
Molecular Data Provide Common Yardsticks for Measuring Divergence
Molecular Approaches Facilitate Mechanistic Appraisals of Evolution
Molecular Approaches Are Challenging and Exciting

Why Not Employ Molecular Genetic Markers?

The History of Interest in Genetic Variation

The Classical-Balance Debate

Classical versus Balance Views of Genome Structure
Molecular Input to the Debate
Questions of Empirical Refinement

The Neutralist-Selectionist Debate

Multi-Locus Allozyme Heterozygosity and Organismal Fitness
Single-Locus Allozyme Variation and the Vertical Approach
Selection at the Level of DNA
The Unresolved Status of the Controversy

Must Molecular Markers be Neutral to Be Informative?
The Molecule-Morphology Debate
Molecular Phylogenetics

Molecular Techniques

Protein Immunology
Protein Electrophoresis

Mendelian Markers
Idiosyncratic Protein Features

DNA-DNA Hybridization
Restriction Analyses

Animal Mitochondrial DNA
Plant Organelle DNA
Single-Copy Nuclear DNA
Moderately Repetitive Gene Families
Minisatellites and DNA Fingerprinting

Polymerase Chain Reaction

RAPDs
STRs
AFLPs
SINEs
SSCPs
SNPs
HAPSTRs and SNPSTRs
DNA Sequencing

Categorical Breakdowns of Molecular Methods

Protein versus DNA Information
Discrete versus Distance Data
Detached versus Connectable Information
Single-Locus versus Multi-Locus Data

Utility of Data along the Phylogenetic Hierarchy

Philosophies and Methods of Data Analysis

Cladistics versus Phenetics
Molecular Clocks

Background
History of Clock Calibrations and Controversies
Absolute and Relative Rate Comparisons
Closing Thoughts on Clocks

Phylogenetic Reconstruction

Distance-Based Approaches
Character-State Approaches
Conclusions about Phylogenetic Procedures

Gene Trees versus Species Trees

PART II. APPLICATIONS

Individuality and Parentage

Human Forensics

History of Laboratory Approaches
History of Controversies
Empirical Examples

Ramets and Genets

Background and Concepts
Spatial Distributions of Clones
Ages of Clones
Clonal Reproduction in Microorganisms
Genetic Chimeras

Gender Ascertainment
Genetic Parentage

Behavioral and Evolutionary Contexts
Selected Empirical Examples by Taxa
Selected Empirical Examples by Topic

Kinship and Intraspecific Genealogy

Close Kinship and Family Structure

Eusocial Colonies
Non-Eusocial Groups
Kin Recognition
Genetic Relationships of Specific Individuals

Geographic Population Structure and Gene Flow

Autogamous Mating Systems
Gametic and Zygotic Dispersal
Direct Estimates of Dispersal Distances
Vagility, Philopatry, and Dispersal Scale
Non-neutrality of Some Molecular Markers
Historical Demographic Events
Population Assignments

Phylogeography

History and Background
Case Studies on Particular Populations or Species
Genealogical Concordance
Genealogical Discordance

Microtemporal Phylogeny
Summary

Speciation and Hybridization

The Speciation Process

How Much Genetic Change Accompanies Speciation?
Do "Population-Bottleneck" Speciations Leave Definitive Genetic Signatures?
What Other Kinds of Phylogenetic Signatures Do Past Speciations Provide?
Are Speciation Rates and Divergence Rates Correlated?
Can Speciation Occur Sympatrically?
What are the Temporal Durations of Speciation Processes?
How Prevalent is Co-speciation?
Can Morphologically Cryptic Species be Diagnosed?
Should a Phylogenetic-Species Concept Replace the BSC?

Hybridization and Introgression

Background
More Hybrid Zone Asymmetries
More Hybrid Zone Phenomena
Speciation by Hybridization

Species Phylogenies and Macroevolution

Rationales for Phylogeny Estimation

Phylogenetic Character Mapping
Biogeographic Assessment
Academic Pursuit of Genealogical Roots

Some Special Topics in Phylogeny Estimation

DNA Hybridization and Avian Systematics
Mitochondrial DNA and the Higher Systematics of Animals
Chloroplast DNA and Higher Systematics of Plants
Ribosomal Gene Sequences and Deep Phylogenies

Genomic Mergers, DNA Transfers, and Life's Early History

From Ancient Endosymbioses to Recent Intergenomic Transfers
Horizontal Gene Transfer
Relationships between Retroviruses and Transposable Elements

Further Topics in Molecular Phylogenetics

Toward a Global Phylogeny and Universal Systematics
Molecular Paleontology

Molecular Markers in Conservation Genetics

Within-Population Heterozygosity Issues

Molecular Variability in Rare and Threatened Species
Does Reduced Molecular Variability Matter?

Intraspecific Genealogy

Tracking Individuals in Wildlife Management
Parentage and Kinship
Gender Identification
Estimating Historical Population Size
Dispersal and Gene Flow

Population Structure and Phylogeography

Genetics-Demography Connections
Inherited versus Acquired Markers
Mixed-Stock Assessment
Shallow versus Deep Population Structures
Conclusions About Intraspecific Phylogeography

Issues at and beyond the Species Level

Speciation and Conservation Biology
Hybridization and Introgression

Species Phylogenies and Macroevolution

Conservation Phylogenetics
Applications
Conclusions

Literature Cited
Index

Pricing and Options

Titles	Product Code	Price (USD)
Molecular Markers, Natural History, and Evolution, Second Edition	0-87893-041-8	$69.95	Purchase	Request Exam Copy
View Cart
Outside the U.S., Canada, or the Caribbean? Check our ordering page for local distributors.

Home || Contact Us || About Ordering || List by Author
List by Subject Area || List by Title || View Shopping Cart

Title Information

Related subject areas

Catalog