Juanita Renwick Thesis
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POPULATION STRUCTURE AND GENETIC DIVERSITY OF SOUTHEAST QUEENSLAND POPULATIONS OF THE WALLUM FROGLET, CRINIA TINNULA (TSCHUDI). Juanita Renwick B. App. Sci. (Hons) School of Natural Resource Sciences Queensland University of Technology Brisbane, Australia This dissertation is submitted as a requirement of the Doctor of Philosophy Degree 2006 KEYWORDS Crinia tinnula; population genetic structure; phylogeography; Pliocene; mitochondrial DNA; 12S; COI; wallum; southeast Queensland. ii ABSTRACT Genetic diversity is a fundamental attribute that contributes to a species evolutionary survival. In recent times, conservation managers have recognized the need to preserve genetic diversity of declining species, and have also acknowledged the utility of genetic markers for describing genetic and ecological relationships within and among populations. Information obtained from genetic studies can be used in conjunction with information on population demography, land use patterns and habitat distribution to develop effective management strategies for the conservation of species in decline. The wallum froglet, Crinia tinnula, is one of Australia’s smallest habitat specialist anurans. In recent years there has been a dramatic decrease in population numbers of this species. The habitat to which C.tinnula is endemic (‘wallum’ habitat) is restricted to low coastal plains along the southeast Queensland and northern New South Wales coastline. As human populations in this region expanded, the coastal areas have undergone significant development and large areas of wallum habitat have been cleared. The effect has been to convert once largely continuous patches of coastal heathland in to a matrix of small habitat patches within an area undergoing rapid urban expansion. This study aimed to document levels and patterns of genetic diversity and to define the population structure of C.tinnula populations within southeast Queensland, with the objective of defining possible conservation management units for this species. Results from 12S and COI mitochondrial markers clearly showed that two distinct evolutionary lineages of C.tinnula are present within southeast Queensland. The high level of divergence between lineages and strict geographic partitioning suggests long term isolation of C.tinnula populations. It is hypothesized that ancestral C.tinnula populations were once confined to wallum habitat refugia during the Pliocene resulting in phylogeographic delineation of ‘northern’ and ‘southern’ C.tinnula clades. Populations within each geographic region show evidence of range contraction and expansion, with subsequent restricted gene flow. Levels of genetic diversity appear, largely, to be the product of historical associations rather than contemporary gene flow. A revision of the current systematics of C.tinnula is required to ensure that discrete population groups are recognized as distinct evolutionary lineages and will therefore be protected accordingly. iii TABLE OF CONTENTS KEYWORDS...................................................................................................................................ii ABSTRACT....................................................................................................................................iii TABLE OF CONTENTS................................................................................................................iv LIST OF FIGURES ......................................................................................................................viii LIST OF TABLES..........................................................................................................................ix LIST OF APPENDICES.................................................................................................................xi STATEMENT OF ORIGINAL AUTHORSHIP ...........................................................................xii Chapter One: General Introduction .................................................................................................1 1.1 Relevance of genetics to conservation biology .......................................................... 1 1.2 Population genetic structure ....................................................................................... 2 1.2.1 Earth history events that shape population structure ........................................... 6 1.3 The use of molecular markers to describe genetic variation and population structure.................................................................................................................................. 7 1.4 Declining frog populations......................................................................................... 9 1.5 Case Study: The Wallum Froglet (Crinia tinnula).................................................. 11 1.6 Thesis structure and Aims ........................................................................................ 13 Chapter Two: General Methods.....................................................................................................15 2.1 The study area .......................................................................................................... 15 2.1.1 Biogeography of the wallum.............................................................................. 15 2.1.2 Biogeography of the coastal sand islands of southeast Queensland .................. 19 2.2 The study species; Crinia tinnula............................................................................. 21 2.2.1 Systematics ........................................................................................................ 21 2.2.2 Morphology ....................................................................................................... 22 iv 2.3 Sampling design and sample collection ................................................................... 24 2.4 Laboratory methods: Mitochondrial DNA techniques ............................................ 28 2.4.1 Outgroup species................................................................................................ 29 2.4.2 DNA extraction.................................................................................................. 29 2.4.3 Polymerase chain reaction (PCR) ...................................................................... 29 2.4.4 Temperature gradient gel electrophoresis (TGGE)............................................ 30 2.4.5 Sequencing......................................................................................................... 34 2.5 Laboratory methods: Nuclear DNA techniques ...................................................... 35 2.5.1 Development of microsatellite genomic library................................................. 35 2.5.2 Primer design and optimisation of PCR............................................................. 36 2.5.3 Amplification of F2.5 ........................................................................................ 37 2.5.4 Amplified fragment length polymorphism (AFLP)........................................... 38 2.5.5 Data analyses ..................................................................................................... 40 Chapter Three: Historical Population Structure Inferred from Mitochondrial 12S rRNA.............44 3.1 Introduction .............................................................................................................. 44 3.2 Materials and methods.............................................................................................. 47 3.2.1 Sampling localities and sample numbers........................................................... 47 3.2.2 DNA extraction and amplification of 12S rRNA mitochondrial DNA fragment.......................................................................................................................... 48 3.2.3 Temperature gradient gel electrophoresis (TGGE), Heteroduplex analysis (HA) and Sequencing..................................................................................................... 49 3.2.4 Data analysis...................................................................................................... 50 3.3 Results ...................................................................................................................... 52 3.3.1 Mitochondrial DNA sequences.......................................................................... 52 3.3.2 Sequence variation............................................................................................. 53 3.3.3 Neutrality tests ................................................................................................... 54 v 3.3.4 Test for clock-like evolution.............................................................................. 54 3.3.5 Population genetic diversity and structure......................................................... 56 3.3.6 Population structure across the natural distribution of C.tinnula....................... 61 3.3.7 Genetic comparisons within Crinia genus......................................................... 64 3.3.8 Phylogenetic analyses........................................................................................ 65 3.3.9 Genetic structure within regions ........................................................................ 67 3.4 Discussion ................................................................................................................ 73 3.4.1 Broad scale population structure.......................................................................