MOLECULAR MARKERS,

NATURAL HISTORY

AND EVOLUTION

MOLECULAR MARKERS,

NATURAL BISTORY

AND EVOLUTION

JOHN C. AVISE

SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.

Copyright C> 1994 by Springer-Seienee+Business Media Dordreeht OriginaJly published by Chapman & Hali in 1994 Softcover reprint of the hardcover 1 st edition 1994

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Uhrary of Congress Cataloging-in-Publication Data

Avise. John C. Molecular markers, natural hislory & evolution/John C Avise.

P. Cm. Includes bibliographical referenees (p. ) and index. ISBN 978-0-412-03781-8 ISBN 978-1-4615-2381-9 (eBook) DOI 10.1007/978-1-4615-2381-9 J Biochemical markers. 2. Molecular evolutian. I. Title. QH438.4B55A95 1993 57487'328--dc20

93-20406 CIP

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Contents Preface

Part I. Background

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 3 WHY EMPLOY MOLECULAR GENETIC MARKERS? ......... 5

Molecular Data Are Genetic ........................... 5 Molecular Methods Open the Entire Biological World for Genetic

Scrutiny. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 6 Molecular Methods Access a Nearly Unlimited Pool of Genetic

Variability ...................................... 6 Molecular Data Can Distinguish Homology from Analogy ....... 8 Molecular Data Provide Common Yardsticks for Measuring

Divergence ..................................... 9 Molecular Approaches Facilitate Mechanistic Appraisals of

Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Molecular Approaches Are Challenging and Exciting .......... 12

WHY NOT EMPLOY MOLECULAR GENETIC MARKERS? ..... 15

2. History of Molecular Phylogenetics .................. 16 DEBATES AND DIVERSIONS FROM MOLECULAR

SYSTEMATICS ................................... 17 Empiricism and the Classical-Balance Debate ............... 17

Classical Versus Balance Views of Genome Structure ........ 17 Molecular Input to the Debate ......................... 20 Research Preoccupations of the Protein-Electrophoretic

Revolution .................................... 22 Empirical Approaches to the Variability/Fitness Conundrum .... 23

Genetic Theory and the Neutralist-Selectionist Debate .......... 26 Systematic Philosophy and the Phenetic-Cladistic Debate . ....... 34 Phylogenetic Data and the Molecule-Morphology Debate ........ 39

MOLECULAR PHYLOGENETICS ........................ 40 SUMMARY ........................................ 43

3. Molecular Tools .................................. 44 PROTEIN ASSAYS ................................... 44

Protein Immunology ................................. 44 Principles and Procedures ............................ 44 Data .......................................... 46

v

vi Contents

Protein Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 47 Principles and Procedures . . . . . . . . . . . . . . . . . . . . . . . . . .. 47 Data ......................................... 49

DNA ASSAYS ..................................... 53 DNA-DNA Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 53

Principles and Procedures . . . . . . . . . . . . . . . . . . . . . . . . . .. 53 Data ......................................... 55

Restriction Analyses ................................ 57 Animal Mitochondrial DNA ......................... 60 Plant Mitochondrial and Chloroplast DNA ............... 68 Single-copy Nuclear DNA .......................... 69 Ribosomal RNA Genes and other Middle-repetitive

Gene Families ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 75 Minisatellite Sequences and DNA Fingerprinting ........... 78

DNA Sequencing and the Polymerase Chain Reaction ......... 82 Principles and Procedures . . . . . . . . . . . . . . . . . . . . . . . . . .. 82 Data ......................................... 87

REFERENCES TO LABORATORY PROTOCOLS ............ 90 SUMMARy ....................................... 91

4. Interpretive Tools ................................ 92

CATEGORICAL SUBDIVISIONS OF MOLECULAR GENETIC

DATA ......................................... 92 Protein versus DNA Information . . . . . . . . . . . . . . . . . . . . . . .. 93 Qualitative versus Distance Data ....................... 93 Detached versus Connectible Information. . . . . . . . . . . . . . . . .. 97 Single-Locus versus Multilocus Data .. . . . . . . . . . . . . . . . . . .. 97 Utility of Data Along the Phylogenetic Hierarchy ............ 98

MOLECULAR CLOCKS .............................. 100 General Concepts . ................................. 100 Clock Calibrations and Controversies .................... 103 Absolute and Relative Rate Comparisons .................. 106 Closing Thoughts About Molecular Clocks ................. 108

PROCEDURES FOR PHYLOGENY RECONSTRUCTION ....... 109 Distance Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

UPGMA Cluster Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 Fitch-Margoliash Method . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 Neighbor-Joining Method ........................... 114 Distance Wagner Method ........................... 115 Comparison of Distance Matrix Methods ................ 119

Contents vii

Character-State Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 Hennigian Cladistics .............................. 121 Maximum Parsimony . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Conclusions About Phylogenetic Procedures . ............... 124 GENE TREES VERSUS SPECIES TREES .................. 126 SUMMARY ....................................... 138

Part II. Applications 5. Individuality and Parentage ....................... 141

GENETIC IDENTITY VERSUS NON-IDENTITY ............. 141 Human Forensics .................................. 141 Ramets and Genets ................................. 147

Background and Concepts .......................... 147 Spatial Distributions of Clones ....................... 150 Ages of Clones .................................. 155

Genetic Mosaics ................................... 159 Clonal Reproduction in Microorganisms .................. 160 Gender Determination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

PARENTAGE ...................................... 168 Paternity Analysis .................................. 172

Multiple Paternity in Animals .. . . . . . . . . . . . . . . . . . . . . . . 172 Paternity in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 Sperm and Pollen Competition, Precedence ............... 182

Maternity Analysis ................................. 185 SUMMARY ....................................... 188

6. Kinship and Intraspecific Phylogeny ................ 190

CLOSE KINSHIP AND FAMILY STRUCTURE .............. 190 Eusocial Colonies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 Noneusocial Colonies and Groups . ...................... 199 Kin Recognition ................................... 203

GEOGRAPHIC POPULATION STRUCTURE AND GENE FLOW .................................... 204 Autogamous Mating Systems .......................... 210 Gametic and Zygotic Dispersal . ........................ 213

Pollen and Seeds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Marine Gametes and Larvae ......................... 215 Direct Estimates of Dispersal Distances ................. 221

Vagility, Philopatry, and Dispersal Scale . ................. 222 Physical Dispersal Barriers . . . . . . . . . . . . . . . . . . . . . ..... 223 Philopatry to Natal Site ............................ 224

Vlll Contents

Gender-biased Dispersal and Gene Flow ................. 227 Non-neutrality of Some Molecular Markers ............... 230 Historical Demographic Events ....................... 232

PHYLOGEOGRAPHY ................................ 233 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233 Case Histories .................................... 236

The Origin of Green Turtles on Ascension Island . . . . . . . . . . . 236 Migratory Histories of Monarch Butterflies ............... 236 Interbrood Switching in Periodical Cicadas ............... 237 Natural Selection and Biogeographic History in the Killifish ... 238 Human Populations-Out of Africa? ................... 238 Genealogical Concordance and the Sharp-tailed Sparrow . . . . . . 241 Phylogeography of a Regional Fauna .. . . . . . . . . . . . . . . . . . 242

General Conclusions About Intraspecific Phylogeography ....... 246 MICROTEMPORAL PHYLOGENY ...................... 248 SUMMARY ....................................... 250

7. Speciation and Hybridization ...................... 252

THE SPECIATION PROCESS .......................... 257 How Much Genetic Change Accompanies Speciation? ......... 257

Traditional Perspectives ............................ 257 Molecular Evidence ............................... 261

Do Speciations Entail Severe Population Bottlenecks? ......... 264 Are Speciation Rates and Divergence Rates Correlated? ....... 267 Can Speciation Occur Sympatrically? .................... 269

Flocks of Fishes ................................. 269 Host- or Habitat-Switching in Insects ................... 272

Can Related Species be Diagnosed Reliably? ............... 274 Should a Phylogenetic-Species Concept Replace the BSC? ...... 278

HYBRIDIZATION AND INTROGRESSION ................. 280 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280

Frequencies and Geographic Settings of Hybridization ....... 280 Case History Involving Treefrogs . . . . . . . . . . . . . . . . . . . . . . 284

Hybrid Zone Asymmetries ............................ 287 Differential Introgression Across a Hybrid Zone ........... 287 Haldane's Rule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289 Differential Mating Behaviors ........................ 291 Differential Gametic Exchange ....................... 293 Reticulate Evolution Evidenced by cpDNA Phylogenies ...... 295

Speciation by Hybridization ........................... 297

Contents ix

Diploid or Homoploid Speciation ...................... 297 Origins of Unisexual Biotypes ........................ 299

SUMMARY ....................................... 305

8. Species Phylogenies and Macroevolution ............. 306

RATIONALES FOR PHYLOGENY ESTIMATION ............ 307 Phylogenetic Mapping of Organismal Traits . . . . . . . . . . . . . . . . 307

Anatomical Features .............................. 308 Behavioral, Physiological, and Life History Features ........ 315

Biogeographic Assessment . ........................... 321 Vicariance Versus Dispersal ......................... 321 Common Ancestry Versus Convergence ................. 326 Recent Islands, Ancient Inhabitants .................... 328

Academic Pursuit of Genealogical Roots .................. 329 SPECIAL APPROACHES TO PHYLOGENY ESTIMATION ..... 331

DNA-DNA Hybridization and Avian Systematics . ............ 331 Mitochondrial DNA and the Higher Systematics of Animals ..... 334

Eccentric mtDNA Markers .......................... 334 mtDNA Sequences ............................... 336

Chloroplast DNA and the Higher Systematics of Plants ........ 337 Eccentric cpDNA Markers .......................... 337 cpDNA Restriction Sites and Sequences ................. 339

Slowly Evolving Gene Sequences and Deep Phylogenetic Branches ................... . . . . . . . . . . . . . . . . . . . 341

PROSPECTUS FOR A GLOBAL PHYLOGENY .............. 350 SPECIAL TOPICS IN MOLECULAR PHYLOGENETICS ....... 352

Horizontal Gene Transfer ............................ 352 Phylogeny of Retroviruses and Transposable Elements ......... 354 Molecular Paleontology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356

SUMMARY ....................................... 359

9. Conservation Genetics ............................ 361

ISSUES OF HETEROZYGOSITY ........................ 362 Molecular Heterozygosity in Rare and Threatened Species ...... 362 Does Reduced Molecular Heterozygosity Matter? ............ 366

ISSUES OF PHYLOGENY ............................. 370 Parentage and Kinship .............................. 371 Population Structure and Intraspecific Phylogeny ............ 372

Genetic Partitions Within Rare and Threatened Species ....... 373 Stock Identification ............................... 375 Conclusions About Intraspecific Phylogeography ........... 380

x Contents

Speciation and Conservation Biology . .................... 382 Recognition of Endangered Species .................... 382 Molecular Forensics and Law Enforcement ............... 386

Hybridization and Introgression ........................ 388 Biological Issues ................................. 388 Legal Issues .................................... 391

Species Phylogenies and Macroevolution .................. 393 SUMMARY ....................................... 396 CONCLUSION ..................................... 397

Literature Cited .................................... 399

Index to Taxonomic Genera .......................... 501

General Index ...................................... 507

Preface

I never cease to marvel that the DNA and protein markers magically appearing on laboratory gels and autoradiographs 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 reproduction in unicellular eukaryotes predominantly sexual or clonal? In the absence of recombinationally derived genetic variability, how long do evolutionary lineages persist in parthenogenetic all-female "species"? Do social groups within various species of insects, fishes, and other organisms consist of close relatives whose behavior might have evolved under the influence of kin selection? How often does intraspecific brood parasitism occur in birds, whereby females "dump" eggs in the nests offoster parents? When distinctive morphotypes exist among related fishes within a lake, do these reflect species' differences (as opposed to developmental switches within a species), and, if so, did the species flock arise in situ? Do migratory marine turtles return to natal sites for nesting? How often has carnivory evolved among plants? What are the evolutionary origins of mitochondrial DNA and chloroplast DNA within eukary­otic cells? Are transposable elements the phylogenetic precursors of retroviruses, or vice versa? Can plate tectonics and continental drift account for the presence of large flightless birds in Australia, South America, and Africa? Have demo­graphic bottlenecks diminished genetic variability in some populations to the extent that they can no longer adapt to environmental challenges? How distinct genetically are the taxa currently afforded protection under the Endangered Spe­cies Act? These are but a small sample of the diverse problems addressed and answered (at least provisionally) through use of molecular genetic markers.

This treatment of molecular natural history and evolution is written at a level appropriate for the advanced undergraduate or graduate student, or for scientists in fields such as ecology, genetics, ethology, molecular biology, population biology, and conservation biology who may wish a readable introduction or refresher to the burgeoning application of molecular markers to problems in their disciplines. I hope to have captured and conveyed the genuine excitement that can be brought to such fields when genetic attributes with known patterns of inheritance are applied to organismal-Ievel issues. I also hope to have provided a wellspring of research ideas for those entering the field. My goal has been to present material in a manner that is technically straightforward, without sacri-

xi

xii Preface

ficing the richness of underlying concepts and biological applications. For the reader, the only necessary prerequisites are an introductory knowledge of genet­ics and an acute interest in the natural biological world.

Why is a treatment of this topic necessary when numerous excellent texts in molecular evolution already are available? Recent publications in the field have focused on (a) proteins and DNA as primary objects of interest from a molecular perspective; (b) broad conceptual issues regarding patterns and processes of molecular evolution; (c) statistical or mathematical aspects of population genet­ics theory; (d) procedures of molecular data analysis; or (e) descriptions of laboratory methods. Some books have approached more closely what is at­tempted here, but are restricted either to topic, laboratory method, or taxonomic group. Hoelzel and Dover (1991a) and Hoelzel (1992) have produced fine in­troductions to molecular ecology, but to my knowledge, no extended available treatment explicitly addresses the multifaceted biological applications for mo­lecular genetic markers from the perspectives of population biology, natural history, and organismal phylogeny.

The field of molecular evolution is at a stage where reflection on the past 30 years may provide useful historical perspective, as well as a springboard to the future. The mid-1960s witnessed an explosion of interest in molecular techniques with the seminal introduction of protein electrophoretic approaches to popUlation genetics and evolutionary biology. In the late 1970s, attention shifted to methods of DNA analysis, primarily through restriction enzymes, and in the 1980s, mitochondrial DNA analyses and DNA fingerprinting approaches gained im­mense popUlarity. Recently, the introduction ofPCR-mediated DNA sequencing has brought the field close to a final technical fruition by providing the first ready access to the "ultimate" genetic data, nucleotide sequences themselves. None­theless, it would be a mistake to conclude that direct sequence information invariably provides the preferred or most accessible pool of genetic markers for all biological applications. Several alternative assays retain tremendous power and utility and, because of ease, cost, amount of genetic information accessed, or simplicity of data interpretation, continue to be the techniques of choice for many evolutionary problems. Ecologists, as well as molecular geneticists, some­times are unaware of the arguments for and against various molecular genetic approaches, and one major goal of this book is to clarify these positions.

In scientific advance, timing and context are all-important. Imagine for sake of argument that DNA sequencing methods had been widely employed for the past 30 years and that only recently had protein-electrophoretic approaches been introduced. No doubt a headlong rush into allozyme techniques would ensue, on justifiable rationales that (a) the methods are cost-effective and technically sim­ple, (b) the variants revealed reflect independent Mendelian polymorphisms at several loci scattered around the genome (rather than as linked polymorphisms in a single stretch of DNA), and (c) the amino acid replacement substitutions

Preface Xlll

uncovered by protein electrophoresis (as opposed to the silent base changes often revealed in DNA assays) might bring molecular evolutionists closer to the real "stuff" of adaptive evolution. To carry the argument farther, suppose that mo­lecular genetic methods had been employed throughout the last century but that an entrepreneurial scientist finally ventured into the world of nature and discov­ered organismal phenotypes and behaviors. Finally, the interface of gene prod­ucts with the environment would have been revealed! Imagine the sense of excitement and the research prospects!

These fanciful scenarios are raised to emphasize a point-molecular ap­proaches carry immense popularity at the present time, but they nonetheless provide but one of many avenues toward the goal of understanding the natural histories and evolutionary biologies of organisms. Studies of morphology, ecol­ogy, and behavior undeniably have shaped the great majority of our perceptions about the natural world. Molecular approaches are especially exciting at this point in time because they open new empirical windows and novel insights on these traditional subjects.

In this book, I have attempted to identify and highlight select case histories where molecular methods have made significant contributions to natural history and evolutionary biology. The treatment is not intended to be exhaustive, be­cause literally thousands of studies have utilized genetic markers. Rather, I have tried to choose classic, innovative, or otherwise interesting examples illustrative of the best that molecular methods have to offer. The literature is represented through 1992. Overall, I have attempted to retain a balanced taxonomic perspec­tive that includes examples from plants, animals, and microbes, and indeed I hope that common threads will be evident that tie together the similar classes of biological questions that frequently apply to such disparate organisms.

This book is organized into two parts. Part I provides introductory material and background: the rationale for molecular approaches in natural history and evolution (Chapter 1); the history of molecular phylogenetics (Chapter 2); out­lines of various laboratory methods and the nature of the genetic data each

. molecular method provides (Chapter 3); and descriptions of some of the inter­pretive tools of the trade, including molecular clock concepts and phylogenetic methods as applied to molecular data (Chapter 4).

Part n departs significantly from previous books in molecular evolution by emphasizing empirical examples of significant biological applications for mo­lecular genetic markers. Topics are arranged along a phylogenetic hierarchy ranging from micro- to macro-evolutionary: the assessment of genetic identity! nonidentity and parentage (Chapter 5); kinship and intraspecific phylogeny (Chapter 6); speciation, hybridization, and introgression (Chapter 7); and assess­ment of the deeper phylogenetic structures in the evolutionary tree of life (Chap­ter 8). A concluding chapter deals with the relevance of molecular studies to conservation biology and to the preservation of genetic diversity (Chapter 9).

xiv Preface

I would like to dedicate this book to my current and fonner graduate students and research technicians, without whom most of our work would not have been possible, nor nearly as much fun: Charles Aquadro, Marty Ball, Eldredge Ber­mingham, Brian Bowen, Robert Chapman, Michael Douglas, Matt Hare, Steve Karl, Lou Kessler, Trip Lamb, Joe Neigel, Bill Nelson, Jay Parker, John Patton, Joe Quattro, Carol Reeb, Nancy Saunders, Kim Scribner, DeEtte Walker, and Kurt Wollenberg. Recent graduate students were forced to read early drafts of several chapters, and they responded by providing numerous helpful criticisms. Drs. Fred Allendorf, Jim Hamrick and Linda Maxson read drafts of the entire book and suggested numerous improvements. Excellent criticisms of individual sections or chapters were kindly provided by Drs. Jeff Palmer, David Stock, Gary Olsen, and Carl Woese. Of course, I remain responsible for any errors or omissions. I am also indebted to my own advisors in graduate school-Robert K. Selander, Michael H. Smith, and Francisco J. Ayala-for getting me started; and to my wonderful colleagues at the University of Georgia-Wyatt Anderson, Jim Hamrick, Jonathan Arnold, Marjorie Asmussen, John McDonald, Mike Arnold, and others-for keeping me going. Much of this book was written during a sabbatical supported by the Sloan Foundation, and I am indebted to my host Denny Powers for providing a wonderful working environment at the Hopkins Marine Station of Stanford University. Over the years, my laboratory has been supported by grants primarily from the National Science Foundation and the National Geographic Society.

I especially want to dedicate this book to my wife Joan, with whom I have collaborated to put into practice the fitness concepts that we evolutionary biol­ogists so often discuss. The result was the light of my life, Jennifer. Finally, I want to thank my parents, Dean and Edith, for unwavering support.