Tropical Forestry Tropical Forestry Volumes Already Published in this Series Tropical Forest Genetics by Finkeldey,R.,Hattemer,H.2007 ISBN:3-540-37396-9 Sampling Methods, Remote Sensing and GIS Multiresource Forest Inventory by Köhl,M.Magnussen,S.,Marchetti M.2006 ISBN:3-540-32571-9 Tropical Forest Ecology - The Basis for Conservation and Management by Montagnini,F.,Jordan C.2005 ISBN:3-540-23797-6 Reiner Finkeldey Hans H. Hattemer ● Tropical Forest Genetics With 44 Figures and 19 Tables Professor Dr.Reiner Finkeldey Professor Dr.Hans H.Hattemer Institute ofForest Genetics and Forest Tree Breeding Büsgenweg 2 D-37077 Göttingen Germany ISSN:1614-9785 ISBN-10 3-540-37396-9 Springer-Verlag Berlin Heidelberg New York ISBN-13 978-3-540-37396-4 Springer-Verlag Berlin Heidelberg New York Library ofCongress Control Number:2006931487 This work is subject to copyright.All rights are reserved,whether the whole or part ofthe material is con- cerned,specifically the rights oftranslation,reprinting,reuse ofillustrations,recitation,broadcasting,repro- duction on microfilm or in any other way,and storage in data banks.Duplication ofthis publication or parts thereofis permitted only under the provisions ofthe German Copyright Law ofSeptember 9,1965,in its current version,and permission for use must always be obtained from Springer.Violations are liable to pros- ecution under the German Copyright Law. Springer-Verlag is a part ofSpringer Science+Business Media springer.com © Springer-Verlag Berlin Heidelberg 2007 The use ofgeneral descriptive names,registered names,trademarks,etc.in this publication does not imply, even in the absence ofa specific statement,that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Editor:Dr.Dieter Czeschlik,Heidelberg Desk Editor:Anette Lindqvist,Heidelberg Production:SPi Typesetting:SPi Cover Design:Design & Production,Heidelberg Printed on acid-free paper 3/3152-HM 5 4 3 2 1 0 Preface This book is intended to provide information on fundamental genetic processes in tropical forests.It is based on lecture notes by the authors prepared for post- graduate students,mainly from tropical countries,ofthe M.Sc.course “Tropical and International Forestry”at the Faculty ofForest Sciences and Forest Ecology, Georg August University Göttingen,Germany.The intended readership is stu- dents,researchers and practitioners interested in the genetic variation ofspecies, in particular forest trees, living in complex forest ecosystems in the tropics. Particular emphasis is placed on the human impact on forest genetic resources in the tropics. Readers should be familiar with basics of classical and molecular genetics such as the structure and function of DNA (double-helix structure, replica- tion),polypeptide synthesis (transcription and translation),and the transmis- sion of genetic information during sexual reproduction (“Mendel’s rules”). This knowledge is easily available from recently published genetics textbooks; we recommend the book by Griffiths etal.(2000). The development of biochemical and molecular marker techniques and their application to species oftropical forests have greatly improved our knowl- edge ofgenetic variation patterns of“wild”plants in the tropics during the last two decades.Many examples in this book are based on gene marker techniques. We discuss the results of selected molecular studies and their implications for the development of sustainable management strategies for forest genetic resources.However,we refrain from providing details on laboratory techniques and statistical data analyses.Readers should consult the cited references or the book by Weising et al. (2005) if they require additional information in this regard. No advanced knowledge concerning modern molecular or statistical methods for the analysis ofgenetic variation patterns is necessary to follow the argumentation of this book. Comprehensive data on DNA sequences are becoming available for more and more plants,including forest trees.The first project aimed at sequencing the full genome of a forest tree (Populus trichocarpa) has recently been com- pleted (Brunner etal.2004).However,only very few genomic data are currently VI Preface available for tropical forest trees; tropical forest genetics is still in a “prege- nomic era.”Thus,the focus ofthis book in on population genetics processes in natural and managed tropical forests rather than on genomics and related, newly emerging fields of research in forest genetics. Acknowledgements The authors are grateful to Oliver Gailing for critically reading Sect.12.5.4 to Barbara Vornam and Martin Ziehe for assistance in literature search and in word processing,and to Wolfgang Tambour for preparing Figures 7.1,7.2,7.5, and 12.4. July 2006 Reiner Finkeldey Hans H.Hattemer Contents 1 Introduction – Genetics of Tropical Forests 1 Part A Genetic Processes in Tropical Forests 3 2 Population Genetics – an Overview 5 2.1 Introduction 5 2.2 The Population 5 2.3 Variation at Gene Loci 6 2.3.1 The Molecular Basis ofGenetic Variation 6 2.3.1.1 Molecular Markers 7 2.3.1.2 Biochemical Markers – Isozymes 12 2.3.2 The Gene As a Unit ofHeredity 13 2.3.3 The Mode ofInheritance 14 2.3.4 Definition and Classification ofGene Markers 15 2.4 Genetic Structures Within Populations 16 2.4.1 Allelic and Genotypic Structures 16 Example 2.1:Genetic Structures at an Isozyme Gene Locus in Dalbergia sissoo 17 2.4.2 Variation at Uniparentally Inherited Markers 18 Example 2.2:Diversity ofcpDNA Haplotypes in D.sissoo 18 2.5 Evolution and Evolutionary Factors 19 2.6 Phenotypic Variation 21 2.7 Recommended Literature 22 3 Genetic Variation of Tropical Forest Plants 23 3.1 Introduction 23 3.2 Genetic Inventories 23 3.3 Measurement ofGenetic Variation 24 3.3.1 Genetic Variation Within Populations 24 3.3.1.1 Genetic Multiplicity 25 3.3.1.2 Genetic Diversity 25 3.3.2 Genetic Differentiation Among Populations 27 3.3.2.1 Genetic Distances 27 3.3.2.2 Genetic Differentiation 27 VIII Contents 3.4 Genetic Variation in Tropical Forest Species – General Trends 28 3.5 Case Studies on Genetic Variation Patterns 31 Example 3.1:Genetic Variation at Isozyme Gene Loci in Natural Populations ofAcacia auriculiformis 31 Example 3.2:Genetic Differentiation Among Populations ofEugenia dysentericafrom the Brazilian Cerrado 33 Example 3.3:Genetic Variation ofSwietenia macrophylla Across the Brazilian Amazon 33 Example 3.4:Genetic Variation ofEndangered Australian Species ofthe Genus FontaineaAssessed with RAPD Markers and by DNA Sequences 34 Example 3.5:Genetic Variation ofShorea leprosulaand Shorea parvifoliain Indonesia Assessed at AFLP Loci 35 Example 3.6:Genetic Variation ofCedrela odorataat cpDNA 37 3.6 Recommended Literature 39 4 Sexual and Asexual Reproduction in Tropical Forests 41 4.1 Introduction 41 4.2 Sexual Reproduction 41 4.2.1 Sexual Types and Sexual Systems 42 4.2.2 Sexual Systems 44 4.2.3 Sexual Structures and Sexual Function 47 4.3 Asexual Reproduction 49 4.3.1 Vegetative Reproduction 50 4.3.2 Apomixis 51 4.4 Recommended Literature 52 5 Gene Flow and Migration 53 5.1 Introduction 53 5.2 Gene Flow Through Pollen 54 5.2.1 Pollination and Fertilization 54 5.2.2 Pollen Vectors in Tropical Forests 54 5.2.2.1 Pollination by Wind (Anemogamy) 54 5.2.2.2 Pollination by Animals (Zoogamy) 55 5.2.3 Pollen Dispersal Assessed by Marker-Based Studies 60 5.2.3.1 Dispersal ofRare Alleles 60 Example 5.1:Gene Dispersal in a Clonal Seed Orchard ofTeak (Tectona grandis) 60 5.2.3.2 Paternity Analyses 61 Example 5.2:Gene Flow Through Pollen in Neobalanocarpus heimiiand Dipterocarpus tempehes(Dipterocarpaceae) 62 Example 5.3:Pollen Dispersal in Three Neotropical Tree Species with Different Spatial Distribution Patterns on Barro Colorado Island 63 Contents IX 5.2.3.3 Model-Based Estimates ofPollen Dispersal 64 Example 5.4:Pollen Dispersal in Dinizia excelsa(Fabaceae) 64 5.2.4 Efficiency ofPollen Vectors for Gene Flow 65 5.3 Migration ofSeeds 65 5.3.1 Seed Vectors 65 5.3.1.1 Abiotic Seed Dispersal 65 5.3.1.2 Biotic Seed Dispersal 66 5.3.2 Efficiency ofSeed Dispersal 66 5.4 Long-Distance Gene Flow and Migration in Tropical Forest Species 67 5.5 Recommended Literature 68 6 Mating Systems 69 6.1 Introduction 69 6.2 Random Mating and Panmixis 70 6.2.1 Heterogeneity ofPollen Allele Frequencies 70 6.2.2 Panmixis and Hardy–Weinberg Structures 72 6.3 Selfing and Outcrossing Rates 73 6.3.1 Estimates ofSelfing Rates Based on Rare Alleles 74 Example 6.1:Estimates ofSelfing Rates in Teak (Tectona grandis) Populations 74 6.3.2 Estimates ofSelfing Rates Based on a Mixed Mating Model 76 6.3.3 Estimates ofSelfing Rates Based on Nonmaternal Alleles 76 6.4 Inbreeding and Inbreeding Depression 78 6.4.1 Genetic Consequences ofInbreeding 78 6.4.2 Inbreeding Depression 80 Example 6.2:Inbreeding Depression in Eucalypts 80 6.5 Incompatibility and Self-Sterility 82 6.5.1 Incompatibility 82 6.5.2 Self-Sterility 84 6.6 Environmental Effects on Mating 84 6.7 Recommended Literature 85 7 Adaptation and Coevolution 87 7.1 Introduction 87 7.2 Physiological and Evolutionary Adaptation 87 Example 7.1:Viability Selection During Early Life Stages ofPlatypodium elegans 89 7.3 Species Interactions and Coevolution 90 Example 7.2:Figs and Their Pollinators 91 7.4 Recommended Literature 97 8 Phylogenies and Evolution Above the Species Level 99 8.1 Introduction 99 8.2 The Evolution ofSpecies Diversity in the Tropics 99 X Contents 8.2.1 Species Diversity in Tropical Forests 99 8.2.2 Evolution Above the Species Level 101 8.3 Molecular Phylogenies 102 Example 8.1:A Molecular Phylogeny ofIndonesian Dipterocarpoideae 103 Example 8.2:Evolution ofthe Genus Inga 104 8.4 Recommended Literature 106 Part B Applications of Genetics to Tropical Forestry 109 9 Fragmentation of Forests 111 9.1 Introduction 111 9.2 The Genetic Status ofFragmented Tree Populations 113 Example 9.1:Genetic Impact ofFragmentation on a Rain Forest Canopy Tree 116 Example 9.2:Connectivity ofPopulation Fragments ofa Medium-Sized Dry-Forest Tree 119 9.3 Genetic Preconditions for Restoration and Persistence 123 9.4 Recommended Literature 127 10 Genetic Aspects of the Management of Natural Tropical Forests 129 10.1 Introduction 129 10.2 Selective Logging 130 10.2.1 Effective Population Density After Logging 131 10.2.2 The Question ofDysgenic Selection 135 10.3 Natural Regeneration 136 10.4 Genetic Aspects ofthe Manipulation ofDynamic Processes in Natural Forests 137 10.5 Genetic Aspects ofSustainability in Natural Tropical Forests 140 10.6 Recommended Literature 146 11 Provenance Research 147 11.1 Introduction 147 11.2 Definitions 148 11.3 Historical Development 150 11.4 Provenance Tests 151 11.4.1 Types ofField Experiments in Provenance Research 153 11.4.2 Traits Studied in Field Trials 155 11.4.3 Design,Conduct,and Analysis ofProvenance Trials 156 11.4.3.1 Collection ofMaterial for Provenance Trials 156 11.4.3.2 Production ofPlanting Stock 159 11.4.3.3 Experimental Design 159