Conservation and the Genetics of Populations

Fred W. Allendorf is a Regents Professor at the University of Montana and a Professorial Research Fellow at Victoria University of Wellington in New Zealand. He has published over 200 articles on the population genetics and conservation of fish, amphibians, mammals, invertebrates, and plants. He is a past President of the American Genetic Association, and has served as Director of the Population Biology Program of the National Science Foundation. He has taught conservation genetics at the University of Montana, University of Oregon, University of Minnesota, University of Western Australia, Victoria University of Wellington, and the US National Conservation Training Center.

Gordon Luikart is an Associate Professor at the Flathead Lake Biological Station of the University of Montana and a Visiting Scientist in the Center for Investigation of Biodiversity and Genetic Resources at the University of Porto, Portugal. He is also an award winning (Bronze Medal) Research Scientist with the Centre National de la Recherche Scientifique at the University Joseph Fourier in Grenoble, France. His research focuses on the conservation and genetics of wild and domestic animals, and includes over 100 publications. He was a Fulbright Scholar at La Trobe University, Melbourne, and he is a member of the IUCN Specialist Group for Caprinae (mountain ungulates) conservation.

Sally N. Aitken is a Professor in the Department of Forest Sciences and Director of the Centre for Forest Conservation Genetics at the University of British Columbia. She studies the population, conservation, ecological genetics, and genomics of forest trees. S he received her PhD from the University of California, Berkeley, and she was a faculty member at Oregon State University. She has received the Canadian Forestry Scientific Achievement Award, a Killam Faculty Research Fellowship, and a Killam Teaching Prize. She teaches forest biology, alpine ecology, and conservation genetics, and she is involved in forest genetic conservation initiatives in North America and Europe.

Guest Box authors, ix

Preface to the second edition, xi

Preface to the first edition, xiii

List of symbols, xv

PART I: INTRODUCTION, 1

1 Introduction, 3

Guest Box 1: L. Scott Mills and Michael E. Soulé, The role of genetics in conservation, 13

2 Phenotypic variation in natural populations, 14

Guest Box 2: Chris J. Foote, Looks can be deceiving: countergradient variation in secondary sexual color in sympatric morphs of sockeye salmon, 32

3 Genetic variation in natural populations: chromosomes and proteins, 34

Guest Box 3: E. M. Tuttle, Chromosomal polymorphism in the white-throated sparrow, 52

4 Genetic variation in natural populations: DNA, 54

Guest Box 4: Louis Bernatchez, Rapid evolutionary changes of gene expression in domesticated Atlantic salmon and its consequences for the conservation of wild populations, 74

PART II: MECHANISMS OF EVOLUTIONARY CHANGE, 77

5 Random mating populations: Hardy- Weinberg principle, 79

Guest Box 5: Paul Sunnucks and Birgita D. Hansen, Null alleles and Bonferroni 'abuse': treasure your exceptions (and so get it right for Leadbeater's possum), 93

6 Small populations and genetic drift, 96

Guest Box 6: Menna E. Jones, Reduced genetic variation and the emergence of an extinction-threatening disease in the Tasmanian devil, 115

7 Effective population size, 117

Guest Box 7: Craig R. Miller and Lisette P. Waits, Estimation of effective population size in Yellowstone grizzly bears, 134

8 Natural selection, 136

Guest Box 8: Paul A. Hohenlohe and William A. Cresko, Natural selection across the genome of the threespine stickleback fish, 154

9 Population subdivision, 156

Guest Box 9: M.K. Schwartz and J.M. Tucker, Genetic population structure and conservation of fisher in western North America, 185

10 Multiple loci, 187

Guest Box 10: Robin S. Waples, Estimation of effective population size using gametic disequilibrium, 203

11 Quantitative genetics, 205

Guest Box 11: David W. Coltman, Response to trophy hunting in bighorn sheep, 229

12 Mutation, 230

Guest Box 12: Michael W. Nachman, Color evolution via different mutations in pocket mice, 242

PART III: GENETICS AND CONSERVATION, 245

13 Inbreeding depression, 247

Guest Box 13: Lukas F. Keller, Inbreeding depression in song sparrows, 268

14 Demography and extinction, 270

Guest Box 14: A. G. Young, M. Pickup, and B. G. Murray, Management implications of loss of genetic diversity at the selfincompatibility locus for the button wrinklewort, 293

15 Metapopulations and fragmentation, 296

Guest Box 15: Robert C. Vrijenhoek, Fitness loss and genetic rescue in stream-dwelling topminnows, 313

16 Units of conservation, 316

Guest Box 16: David J. Coates, Identifying units of conservation in a rich and fragmented flora, 350

17 Hybridization, 352

Guest Box 17: Loren H. Rieseberg, Hybridization and the conservation of plants, 375

18 Exploited populations, 377

Guest Box 18: Gu?rún Marteinsdóttir, Long-term genetic changes in the Icelandic stock of Atlantic cod in response to harvesting, 393

19 Conservation breeding and restoration, 395

Guest Box 19: Robert C. Lacy, Understanding inbreeding depression: 25 years of experiments with Peromyscus mice, 419

20 Invasive species, 421

Guest Box 20: Richard Shine, Rapid evolution of introduced cane toads and native snakes, 438

21 Climate change, 440

Guest Box 21: S. J. Franks, Rapid evolution of flowering time by an annual plant in response to climate fluctuation, 453

22 Genetic identification and monitoring, 455

Guest Box 22: C. Scott Baker, Genetic detection of illegal trade of whale meat results in closure of restaurants, 481

Appendix: Probability and statistics, 484

A1 Paradigms, 485

A2 Probability, 487

A3 Statistical measures and distributions, 489

A4 Frequentist hypothesis testing, statistical errors, and power, 496

A5 Maximum likelihood, 499

A6 Bayesian approaches and MCMC (Markov Chain Monte Carlo), 500

A7 Approximate Bayesian Computation (ABC), 504

A8 Parameter estimation, accuracy, and precision, 504

A9 Performance testing, 506

A10 The coalescent and genealogical Information, 506

Guest Box A: James F. Crow, Is mathematics necessary?, 511

Glossary, 513

References, 531

Index, 587

Color plates section between page 302 and page 303