Taxonomy, Biogeography and Population Genetic Structure of the Southern Australian Intertidal Barnacle Fauna
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Taxonomy, biogeography and population genetic structure of the southern Australian intertidal barnacle fauna Katherine L York Subtnittcd in total fulfihncnt of the requirements of the degree of Doctor of Philosophy Decetnber, 2008 Departrnent of Genetics 'T'hc University of Melbourne Produced on archival quality paper Declaration This is to certify that: (i) this thesis comprises only my original work towards the PhD except where indicated in the Preface; (ii) due acknowledgement has been made in the text to all other material used; (iii) this thesis is less than I 00,000 words in Ient::,rth, exclusive of table, figures, bibliographies and appendices Parts of the work have been published in the following paper: York, K.L., l3lacket, M.J., and Appleton, B.R. (2008) The Bassian Isthmus and the major ocean currents of southeast Australia influence the phytogeography and population structure of a southern Australian intertidal barnacle Calomerus polymerus (Darwin). Molecular Ecology 17: 1948-1961 Katherine York Abstract Barnacles are a unique organism in that they have both a planktonic larval stage followed by an irreversibly sessile adult stage. Widely distributed throughout the world, they have been studied by tnany prominent scientists, with much of the work undertaken focusing on ecology and taxonomy. However, most of the taxonomic work had been undertaken based on morphological characteristics, with phylogenetic studies only undertaken more recently. Many of these studies have failed to include Australian species, most of which are endemic to the continent. Newly produced and Genbank records of mitochondrial DNA sequence were used to confirm the taxonomic status of Australian species. The status of most species was confirmed, with a few notable exceptions. In particular, data analysis suggested the existence of cryptic species within Elminius modestus. In addition, the divergence between these three species and Elminius kingii was great enough to warrant the introduction of a new genus, Austrominius. This genus now contains three species, A. modestus, A. adelaidae and A. covertus. The two-phase life history of barnacles also made them the ideal organism for the study of the dynamics of the southern Australian marine environment. Three marine biogeographic provinces are recognised in the region, with both historical and contemporary ecological factors predicted to be responsible. In order to investigate the biogeography and hydrography of the region, both tnitochondrial sequence data and n1icrosatellite data were used to investigate the phylogeography and population genetic ii structure of Catomerus polymerus. The mitochondrial data showed a deep phylogeographical split, dividing the species into eastern and western lineages. Dating this split using a molecular clock indicated that the repeated emergence of the Bassian Isthmus during glacial periods was most likely responsible, having provided a barrier to gene flow between the two lineages. However, subsequent geneflow during interglacial periods prevented the lineages from diverging into two separate species. Analysis of the microsatellite data indicated that the species comprised four groups or subregions; one in South Australia, one in New South Wales and eastern Victoria, one in central Victoria, and one in western Victoria and Tasmania. Further analysis of the data indicated that these subregions could be due to the influence of the major ocean currents (Leeuwin, East Australian and Zeehan currents), and the reduction in gene 'flow across two biogeographic breaks (Ninety Mile Beach, The Coorong). This correlates reasonably well with the previously recognised biogeographic provinces. Finally, mitochondrial data were used to examine the phytogeography of two species of barnacle, Chthamalus antennatus and Chamaesipho tasmanica. In contrast with the study of C.polymerus, these species did not show any significant structure across their entire distribution. There are a number of possible explanations for this, with most relating to the longevity and durability of the larvae. However, it is also possible that these species could colonise southern Tasmania during the glacial periods, thereby being unaffected by the present of the Bassian Isthmus, and maintaining a single pamnictic population. iii Preface The following work was carried out by, or in conjunction with others Chapter 4: Microsatellite isolation in Catomerus polymerus was carried out with the supervision of M. Blacket iv Acknowledgments There are many people without whom my PhD would not have been possible. Firstly, my supervisor Belinda Appleton, who provided the perfect balance of supervision and friendship. Without Belinda, this project would not have existed, but I am grateful also for being able to take the project in my own direction. Thank you for all the advice and guidance, all the chats and the fun times too! I have enjoyed and appreciated having a supervisor that I can really talk to, about both work and anything else. Thank you also to Joanne Srnissen, who provided the original idea which started the project. Without you I would never have even thought about working on barnacles, let alone had any idea about all the different species. Thank you also for providing all the vital literature and background information that got this project up and running. I am also grateful to Mark Blacket, who guided me through the process of creating a microsatellite library from start to finish. Without you I would have been lost. Thank you also for spending ti1ne showing me the many different ways to analyse mitochondrial data. Many thanks also to the Genetics Department, and the Appleton Lab in particular. There are many people who have been there, day-to-day, throughout my PhD who have been 1nore help than they realise. Not just for help in the lab with different techniques, but also for the distraction when I've needed a break. v There are also many people and organisations which I must thank for their help with field work. Permits were provided by New South Wales Fisheries, Victorian Department of Sustainability and Environment, South Australia Primary Industries and Resources SA, and Tasmania Department of Primary Industries and Water. There have been numerous people who have come along on field trips, including Melanie Norgate, Fallon Mody, Kate Ryan, Dale Appleton, Cadel Appleton, Elissa York, Melissa Stahle and Suzanne York. Thank you also to Parks Victoria, who provided funding for much of this research. Last, but most importantly, are the family and friends who have supported me over the last 3 ~ years. Without you, I would not have been able to be this dedicated. My friends have been there to cheer me up and distract me when I needed a break. My family have also provided countless support and encouragement. However, my acknowledgements would not be complete without specifically thanking my mum, Suzanne. For the encouragement and support throughout my entire education, and for believing that I can achieve whatever I want. For continuing to support me through another 3 ~ years of study. For cooking me dinner when I get home late. For travelling around half of Australia with me collecting barnacles. For being interested i.n what I do, and trying to understand when I'm talking science. And most of all, for loving Ine. Without you, I would not be where I am today. vi Table of Contents Declaration .............................................................................................. i Abstract ................................................................................................ ii Preface ................................................................................................ iv Ack.nowledgements ................................................................................... v Contents ............................................................................................... vii Figures ............................................................................................... xiii '"fables .................... ; ............................................................................ xiv Chapter 1 Introduction ..•...•.....................................................................1 1.1 General Description .............................................................................. 2 1.2 Reproduction ...................................................................................... 3 1.3 Taxonomy and Phylogenetics of the Cirripedia .............................................. 5 I .4 Biogeography .....................................................................................7 1.5 Markers for Use in Phytogeographic and Biogeographic Studies ........................ 13 1.5.1 Mitochondrial DNA (mtDNA) Structure ....................................... 14 1.5.2 Use ofmtDNA in Phylogenetics ................................................ 15 1.5.3 Microsatellite Evolution ........................................................... 17 1.5.4 Use of Microsatellites in Studies of Population Genetic Structure .......... 19 1.6 Overall Aims .................................................................................... 20 Chapter 2 General Materials and Methods ...................................................22 2.1 Sample Collection ...............................................................................23 vii 2.1.1 Whole Individuals ...................................................................23 2.1.2 Partial Samples of Catomerus Polymerus