Molecular Markers, Natural History, and Evolution

667 Pages·2004·29.596 MB·English

by  John C. Avise

Molecular Markers,
Natural History,
and Evolution
Second Edition
JOHN C. AVISE
iS'
University of Georgia
Uppsala Umversitetsbibliotek
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About the Cover
Clockwise from the top: Autoradiograph of an electrophoretic gel showing microsatel­
lite DNA bands from a wild population of Peromyscus mice. (From the Avise lab) •
Quaking aspens, Populus tremuloides, in the Rocky Mountains of Colorado. (Copy­
right © Bob Thompson/In Image Photography) • An evolutionary tree. • Shoal of
juvenile striped catfish, Piotosus lineatus, photographed in the tropical ocean off
Mabul, Malaysia. (Copyright © Matthew Oldfield/SPL/Photo Researchers, Inc.).
Cpver design by John C. Avise.
Molecular Markers, Natural History, and Evolution Second Edition
Copyright © 2004 by Sinauer Associates, Inc. All rights reserved. This book may not
be reproduced in whole or in part, by any means, without permission. For informa­
tion address:
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Library of Congress Cataloging-in-Publication Data
Avise, John C.
Molecular markers, natural history, and evolution / John C. Avise.— 2nd ed.
p.; cm.
Includes bibliographical references and index.
ISBN 0-87893-041-8 (pbk.)
1. Biochemical markers. 2. Molecular evolution.
[DNLM: 1. Genetic Markers. 2. Evolution, Molecular.
QH 438.4.B55 A958m 2004J I. Title.
QH438.4.B55A95 2004
572.8'6—dc22 2004003130
Printed in U.S.A.
5 4 3 2 1
Contents
PARTI The Classical-Balance Debate 24
Background Classical versus balance views of genome
structure 24
Molecular input to the debate 26
CHAPTER 1: Introduction 1 Questions of empirical refinement 29
Why Employ Molecular Genetic Markers ? 5 The Neutralist-Selectionist Debate 30
Molecular data are genetic 6 Multi-locus allozyme heterozygosity and
organismal fitness 36
Molecular methods open the entire
biological world for genetic scrutiny 6 Single-locus allozyme variation and the
vertical approach 40
Molecular methods access a nearly unlimit­
ed pool of genetic variability 7 Selection at the level of DNA 41
Molecular data can distinguish homology The unresolved status of the controversy 44
from analogy 8 Must Molecular Markers Be Neutral To Be
Molecular data provide common yardsticks Informative? 47
for measuring divergence 9
The Molecule-Morphology Debate 48
Molecular approaches facilitate mechanistic
appraisals of evolution 14 Molecular Phylogenetics 49
Molecular approaches are challenging and
exciting 17 - CHAPTER 3: Molecular
Why Not Employ Molecular Genetic Techniques 55
Markers? 20
Protein Immunology 55
Protein Electrophoresis 57
CHAPTER 2: The History of
Mendelian markers 59
Interest in Genetic Variation
Idiosyncratic protein features 61
23
DNA-DNA Hybridization 63
Restriction Analyses 67 PART II
Animal mitochondrial DNA 70 Applications
Plant organelle DNA 78
Single-copy nuclear DNA 79
Moderately repetitive gene families 83 > CHAPTER FIVE: Individuality
Minisatellites and DNA fingerprinting 84 and Parentage 161
Polymerase Chain Reaction 87 Human Forensics 161
RAPDs 91 History of laboratory approaches 162
STRs (microsatellites) 92 History of controversies 165
AFLPs 94 Empirical examples 167
SINEs 95 Ramets and Genets 169
SSCPs 97 Background '169
SNPs 97 Spatial Distributions of Clones 172
HAPSTRs and SNPSTRs 98 Ages of clones 179
DNA sequencing 98 Clonal reproduction in microorganisms
Categorical Breakdowns of Molecular 183
Methods 101 Genetic chimeras 192
Protein versus DNA information 104 Gender Ascertainment 194
Discrete versus distance data 105 Genetic Parentage 196
Detached versus connectable information Behavioral and evolutionary contexts 202
110
Selected empirical examples by taxa 204
Single-locus versus multi-locus data 111
Selected empirical examples by topic 221
Utility of data along the phylogenetic
hierarchy 111
- CHAPTER SIX: Kinship and
CHAPTER FOUR: Philosophies Intraspecific Genealogy 231
and Methods of Molecular Close Kinship and Family Structure 231
Data Analysis 115 Eusocial colonies 235
Non-eusocial groups 241
Cladistics versus Phenetics 115
Kin recognition 244
Molecular Clocks 120
Genetic relationships of specific individuals
History of clock calibrations and
245
controversies 123
Geographic Population Structure and
Absolute and relative rate comparisons 128
Gene Flow 248
Closing thoughts on clocks 131
Autogamous mating systems 249
Phylogenetic Reconstruction 132
Gametic and zygotic dispersal 257
Distance-based approaches 134
Direct estimates of dispersal distances 266
Character-state approaches 139
Vagility, philopatry, and dispersal scale 267
Conclusions about phylogenetic procedures Non-neutrality of some molecular markers
142
277
Gene Trees versus Species Trees 143
Historical demographic events 279 Phylogenetic character mapping 402
Population assignments 280 Biogeographic assessment 418
Phylogeography 283 Academic pursuit of genealogical roots 431
History and background 285 Some Special Topics in Phylogeny
Case studies on particular populations or Estimation 433
species 289 DNA hybridization and avian systematics
Genealogical concordance 301 433
Genealogical discordance 314 Mitochondrial DNA and the higher
systematics of animals 434
Microtemporal Phylogeny 316
Chloroplast DNA and the higher
systematics of plants 438
CHAPTER SEVEN: Spéciation Ribosomal gene sequences and
and Hybridization 321 deep phylogenies 443
Genomic Mergers,DNA Transfers,
The Spéciation Process 325
and Life's Early History 444
How much genetic change accompanies
From ancient endosymbioses to
spéciation? 325
recent intergenomic transfers 448
Do founder-induced spéciations leave
Horizontal gene transfer 453
definitive genetic signatures? 338
What other kinds of phylogenetic signa­ Relationships between retroviruses
tures do past spéciations provide? 341 and transposable elements 459
Are spéciation rates and divergence rates Further Topics in Molecular
correlated? 342 Phylogenetics 460
Can spéciation occur sympatrically? 346 Toward a global phylogeny and
What are the temporal durations of universal systematics 460
spéciation processes? 351 Molecular paleontology 466
How prevalent is co-speciation? 353
Can morphologically cryptic species be CHAPTER NINE: Molecular
diagnosed? 356
Markers in Conservation
Should a phylogenetic species concept
replace the BSC? 361 Genetics 475
Hybridization and Introgression 363 Within-Population Heterozygosity Issues
Frequencies and geographic settings of 478
hybridization 363 Molecular variability in rare and threatened
Sexual asymmetries in hybrid zones 367 species 479
More hybrid zone asymmetries 370 Does reduced molecular variability matter?
484
More hybrid zone phenomena 385
Genealogy at the Microevolutionary
Spéciation by hybridization 388
Scale 491
Tracking individuals in wildlife management
CHAPTER EIGHT: Species 491
Phytogenies and Parentage and kinship 492
Macroevolution 401 Gender identification 495
Estimating historical population size 495
Rationales for Phytogeny Estimation 402
Dispersal and gene flow 496
Population Structure and Phylogeography Hybridization and introgression 527
497 Species phylogenies and macroevolution
Genetics-demography connections 497 532
Conclusion 540
Inherited versus acquired markers 500
Mixed-stock assessment 502
Shallow versus deep population structures Literature Cited 543
505
Lessons from intraspecific phylogeography Taxonomic Index 663
510
issues At and Beyond the Species Level
Subject Index 669
515
Speciation and conservation biology 515
Preface to the
Second Edition
This treatment is an updated and expanded version of a book that was first
published in 1994. Much has transpired in the intervening decade: new lab­
oratory methods for uncovering molecular markers have been introduced
and refined, statistical and conceptual approaches for estimating intraspecif­
ic genealogy and interspecific phytogeny have been improved, and a vast
armada of empirical examples has been added to a burgeoning scientific lit­
erature. In some topical areas (e.g., fossil DNA and horizontal genetic trans­
mission), earlier scientific thought has been completely overturned by molec­
ular findings over the past 10 years; and knowledge on numerous other top­
ics (e.g., vertebrate mating systems, ecological speciation, and life's deep
phylogeny) has expanded greatly. On the other hand, the major types of
questions tackled by molecular ecologists, behaviorists, and evolutionists
remain much the same. Researchers still employ molecular markers to esti­
mate and interpret evolutionary relationships of organisms along a temporal
continuum ranging from clonality, genetic parentage and genealogy in the
most recent generations, to phylogenetic affinities in ancient branches of the
Tree of Life. This revised edition will further document how molecular mark­
ers reveal otherwise hidden aspects of behavior, natural history, ecology, and
the evolutionary histories of plants, animals, and microbes in the wild.
Why is a treatment of this topic necessary when several excellent texts
in molecular ecology or evolution already exist? Most of these books have
focused on: proteins and DNA as primary objects of interest in their own
right (e.g., Graur and Li 2000; Li 1997; Li and Graur 1991); broad conceptu­
al issues regarding patterns, processes, or mechanisms of molecular evolu­
tion (Ayala 1976a; Nei and Koehn 1983; Selander et al. 1991b; Takahata and
Clark 1993); statistical or mathematical aspects of population-genetic or
phylogenetic theory (Nei and Kumar 2000; Page and Holmes 1998); or
detailed methodological procedures of data acquisition and analysis (Baker
2000; Ferraris and Palumbi 1996; Hillis et al. 1996; Karp et al. 1998). Some
textbooks and edited volumes have approached more closely what is
attempted here (Baker 2000; Caetano-Anolles and Gresshoff 1997; Carvalho
1998; Hoelzel 1992; Hoelzel and Dover 1991a), but most of them are either
popularized accounts (Avise 2001a, 2002) or else are restricted to research
topic, laboratory method, or taxonomic group (Avise 2000a; Hollingsworth
et al. 1999; Kocher and Stepien 1997; Mindell 1997; Phillips and Vasil 2001;
Sibley and Ahlquist 1990; Soltis et al. 1992). No other classroom textbook or
reference work quite fills the niche toward which this book is aimed: the
wide world of biological applications for molecular genetic markers in the
contexts of ecology, behavior, natural history, evolution, and organismal
phylogeny.
The first edition of Molecular Markers included references to about 2,200
studies from the then-neophyte fields of molecular ecology and evolution,
and this second edition approximately doubles that total count of citations
from the primary literature. Thus, this compendium is again intended to
provide a thorough introduction to relevant research that can serve both as
an educational tool and stimulus for students, and ah extensive reference
guide for practicing researchers. Despite this coverage, an encyclopedic
treatment of all relevant studies is no longer feasible because of the explo­
sive growth of molecular ecology and evolution since the early 1990s. Thus,
by necessity I have been selective in the choice of additional examples to
illustrate various topics. I also retained many of the citations and examples
(albeit updated) from the first edition, in part to provide historical perspec­
tive (research approaches in molecular ecology and evolution have them­
selves evolved), and in part to give due credit to pioneering works that
should not be forgotten. Indee;d, an important goal of this book is to describe
not only the current state of biological knowledge derived from molecular
markers, but also to trace how that current state of affairs has come to be.
Like its predecessor, this second edition is not intended to be a detailed
"how to" book on laboratory details and analytical methods of molecular
ecology and evolution (although sufficient background is provided for
beginners). Rather, this book is more of a "what-has-been-and-can-be-done"
treatment intended to stimulate ideas and pique the research curiosity of
young biology students and seasoned professionals alike. I hope this reno­
vated edition will be read and enjoyed in this imaginative spirit of scientif­
ic adventure.
Dedication
This book is dedicated in part to my current and former graduate students,
postdocs, and research technicians: Charles Aquadro, Marty Ball, Eldredge
Bermingham, Brian Bowen, Robert Chapman, Beth Dakin, Andrew
DeWoody, Michael Douglas, Anthony Fiumera, Matt Hare, Glenn Johns,
Adam Jones, Steve Karl, Lou Kessler, Trip Lamb, Mark Mackiewicz, Judith
Mank, Joe Neigel, Bill Nelson, Guillermo Orti, John Patton, Devon Pearse,
Brady Porter, Paulo Prodohl, Joe Quattro, Carol Reeb, Nancy Saunders, Kim
Scribner, DeEtte Walker, and Kurt Wollenberg. Without them, my own
involvement in molecular ecology and evolution would hardly have been
possible, and not nearly so much fun. DeEtte Walker in particular has been
of invaluable assistance in all phases of this book's preparation. I also want
to thank Drs. Jeff Mitton and Loren Rieseberg for helpful suggestions on this
second edition. Over the years, my laboratory has been supported by grants
primarily from the National Science Foundation, the University of Georgia,
the Sloan Foundation, and most recently the Pew Foundation.
I want to dedicate this book also to my family—Joan, Jennifer, Edith,
and Dean—all of whom have given unwavering support.
Preface to the
FirstEdition"
I never cease to marvel that the DNA and protein markers magically emerg­
ing from molecular-genetic analyses in the laboratory can reveal so many
otherwise hidden facets about the world of nature. Can individual plants
sometimes exist as genetic mosaics derived from multiple zygotes? Is repro­
duction by unicellular organisms predominantly sexual or clonal? What is
the typical evolutionary lifespan of parthenogenetic all-female lineages,
given that they lack recombinational genetic variation that otherwise might
enable them to respond to changing environments? What is the genetic
makeup of social groups within various species of insects, fishes, mammals,
and other organisms whose behaviors might have evolved under the influ­
ence of kin selection? In birds and other taxa, how often does intraspecific
brood parasitism occur, wherein females surreptitiously "dump" eggs into
the nests of soon-to-be foster parents? Do migratory marine turtles return to
their natal sites for nesting? How often has camivory evolved among plants?
What are the evolutionary origins of cytoplasmic genomes within eukaryot­
ic cells? How old are the fossils from which DNA can be extracted? How and
how often have horizontal gene transfers taken place between distant forms
of life? Have demographic bottlenecks diminished genetic variability to the
extent that some populations can no longer adapt to environmental chal­
lenges? How useful is the criterion of phylogenetic distinctiveness as a guide
to prioritizing taxa and regional biotas for conservation efforts? These are but
a small sample of the diverse problems addressed and answered (at least
provisionally) through the use of molecular genetic markers.
This treatment of molecular natural history and evolution is written at
a level appropriate for advanced undergraduates and graduate students, or
^Reprinted with slight modifications from the First Edition (1994).