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Population Genetics of Hakea Carinata F. Muell. Ex Meissner (Proteaceae)

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Population Genetics of Hakea Carinata F. Muell. Ex Meissner (Proteaceae) :ríl 1l îy 2" . ¿..r3 Population Genetics of Høkea carinata F. Muell. ex Meissner (Proteaceae) A thesis submitted in fulhlment of the requirements for the award of the degree of Doctor of Philosophy from The University of Adelaide by Gary Starr B.A.(Hons) Department of Applied and Molecular Ecology October 200L THE UNTVERSITY OF ADELAIDE AUSTRALIA I)eclaration This work contains no material which has been accepted for the award of any other degree or diploma in any university or other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis, when deposited in the University Library, being available for loan and photocopying. .'Gary Starr Date: 2 If.ol ll Abstract This study is an examination of the population genetic structure and gene flow in a sclerophyllous plant species, Hakea carinata,that is endemic to South Australia. The species has a naturally fragmented geographic distribution. It survives in very small populations by using a predominantly selfing mating system, however this is combined with very low levels of gene flow and substantial differentiation between populations. The distribution of genetic diversity in H. carinata was represented by a sample of 30 populations covering the range of the species. The level of genetic diversity in the species is concomitant with expectations for similar woody perennial shrubs, but populations contain little variation and most is represented as between population differences. Overall gene flow between populations is insufficient to prevent further population differentiation. Outcrossing is very low and unexpected for widely distributed species in the Proteaceae. Geographical clustering of populations coincides with genetic similarity. Isolation by distance can be used to explain the greater differentiation between furthest populations. Populations that are relatively close still appear to be exchanging too few genes to prevent differentiation. Clustering of related individuals occurs within populations, with neighbourhoods comprising approximately five individuals. Little if any gene flow occurs between individuals more than 100 m apart in continuous stands. Isolation by distance is detectable within populations down to l0 m between plants. Ecological observations show that autogamy may be the main source of seed set, as insect visitors to flowers appear not to effect significant levels of fertilisation. The behaviour of insect visitors equates with the low rate of outcrossing. Hakea carinata demonstrates a high degree of isolation by distance. The investigations in this study provide important information on an evolutionary process that rnay becone more prevalent as the effects of habitat fragmentation increase worldwide. lll Acknowledgments I extend my appreciation to the many people who assisted me to undertake this work. I thank Dr. Susan Carthew, my supervisor, for the way in which she shared her experience with me and enabled me to see and correct the flaws in my work. Valuable assistance was received from Drew Tyre, Ben Sparrow, Ian Overton,Frazet McGregor, Jo Chivell, and Michelle Lorimer, most of whom were fellow students having similar experiences. Mark Adams of the Evolutionary Biology Unit, SA Museum taught me how to operate a genetics lab and offered advice on the analysis of genetic data. His book was my bible. Paul O. Lewis of the University of New Mexico provided advice in using the power of his computer program GDA (Genetic Data Analysis), after we had worked out the bugs. Bryan K. Epperson of the Department of Forestry, Michigan State University advised on adjusting predicted values from his papers on spatial autocorrelation so that they reflected my sampling scheme. Bill Barker of the SA Herbarium assisted with the selection of subject species and encouraged and complimented my work whenever we met. David Ayre of the University of V/ollongong provided valuable comments on a draft of Chapter 3. Seed was collected under permits from SA Department of Environment and Natural resources No. Q23476 and SA Department of Primary Industry: Forestry Nos. 06920 and 10988. lv TABLE OF CONTENTS CHAPTER 1. INTRODUCTION........ I CHAPTER 2. A SURVEY OF GENETIC VARIATION AT THE LEVEL OF THE SPECIES . 12 2.1 INrRoDUcrroN ................l2 2,2 METHoDS l3 2.2.2 Electrophoresis. 14 2.2.3 Statistical Analysis I8 2,4 DISCUSSION 25 CHAPTER 3. GENE FLOW BETWEEN POPULATIONS........... 28 3.I INTRODUCTION 28 3.2 MATERIALS AND METHoDS 29 3.2.1 Sampled Populqtions 29 3.4 DISCUSSIoN 39 CHAPTER 4. SPATIAL STRUCTURE WITHIN POPULATION.............. .............. 43 4,1 INTRODUCTION 43 4.2.1 Study Organism and Site. 45 4.2.2 Data Analysis 47 4.4 DISCUSSIoN 59 CHAPTER 5. FLOWERING OF HAKEA CARINATA 65 5.I INTRODUCTION 65 5.2 MATERIALS AND METHODS 67 5.2.1 Study Species 67 5.2.2 Flowering Phenologt...... 68 5.2.3 Pollinqtor Visitation and Fruit Set 70 72 5.3 RESULTS IJ 5.3.1 Flowering Phenologt 73 5.3.2 Pollinator Visitation qnd Fruit Set 74 5.3.3 Autogamy Test 84 v REFERENCES 92 APPENDIX 1. ALLELE FREQUENCIES.............. 100 APPENDIX 2. HERBARIUM VOUCHER SPECIMENS......... ............103 vi CHAPTER I.. INTRODUCTION Evolution is the change in genetic composition of a population over successive generations. Individuals are descended from the previous generation but are not identical to them, and these changes accumulate over time as generations succeed each other. Individuals do not change over their lifetime, apart from the slow accumulation of mutations. Populations, however, do change over time. The genetic composition of a population is the sum of the genetic composition of all the individuals in the population. Differential survival and reproductive success of individuals result in changes to the population genetic composition. Population genetics and the evolutionary forces that result in changes to population genetic structure have been the subject of enthusiastic study since the 1920's and 1930's, including work by Wright (1931) and Dobzhansky (1937). The study of population genetics seeks to understand how evolutionary processes change the genetic composition of populations over time. Foremost of the evolutionary processes studied are selection and migration, otherwise known as gene flow. Selection is the differential survival and reproductive success of some genotypes over others, resulting in a greater representation of these genes in the next generation. Gene flow is the movement of genes within and between populations, resulting in changed population genetic composition between generations. These forces, together with other random processes such as the sampling of genes from the parent population that is the consequence of sexual reproduction, combine to cause populations to evolve over time. These evolutionary forces are mostly invisible and as such cannot be viewed directly. To enable them to be studied it is necessary for a whole repertoire of scientific and statistical tools to be used to detect and differentiate between them. Primary among these is to observe present day population genetic composition. Study of the amount and distribution of genetic variation results in a picture at a point in time of the genetic structure of populations. These observed pattems of genetic variation in populations can be used to elucidate past and present evolutionary processes. Furthermore, an I Chapter 1. lntroduction understanding ofpast and present evolutionary processes can suggest the evolutionary future of populations and entire species. These speculations on the evolutionary future of species are a central component of conservation biology, as we seek to understand the process of extinction and how to conserve what remains. Conservation biology seeks to maintain, as much as possible, the evolutionary processes within species in the face of increasing environmental changes brought about by human activity. Species extinction rates have dramatically increased in the last four hundred years (Holsinger 1996). Solutions are needed if we are to minimise extinction rates as much as possible. Much has been made of the importance of maintaining levels of genetic variation in species as a major goal of conservation biology (Ellstrand 1992, Lande 1988, Levin and Kerster 1974, Ouborg et al. 1999). The loss of genetic variation in species as a result of human activity, usually caused by reduction in population sizes or a change in mating systems, makes species more vulnerable to extinction (Ellstrand and Elam 1993, Holsinger 1993). The connections between levels of genetic variation, population genetic structure, and the probability of extinction still require study if we are to properly understand them. The term "Genetic variation" refers to the range of genetic material of which species are composed. The variation is differences between individuals in DNA sequence at gene loci. A specific gene locus will perform the same function in every individual, but minor differences in DNA sequence between them may lead to slightly different properties of the protein produced by the gene. These genetic variants may have future selective advantages or disadvantages as a result of their properties, but in most cases genetic variants appear functionally equivalent and co-exist within populations. The advantage for a species in having a high level of genetic variation is that in the event of changed environmental circumstances,
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