Population genetic structure of freshwater catfish (Tandanus tandanus) in the Murray-Darling Basin and coastal catchments of New South Wales: Implications for future re-stocking programs Meaghan Rourke and Dean Gilligan Industry & Investment NSW Narrandera Fisheries Centre Buckingbong Road Narrandera, NSW 2700 Australia Recreational Freshwater Fishing Trust Project No. DPI FT48 June 2010 Industry & Investment NSW - Fisheries Final Report Series No. 123 ISSN 1837-2112 Population genetic structure of freshwater catfish (Tandanus tandanus) in the Murray-Darling Basin and coastal catchments of New South Wales: Implications for future re-stocking programs. June 2010 Authors: Meaghan Rourke and Dean Gilligan Published By: Industry & Investment NSW (now incorporating NSW Fisheries) Postal Address: Narrandera Fisheries Centre, PO Box 182, Narrandera, NSW, 2700 Internet: www.industry.nsw.gov.au © Industry & Investment NSW and the NSW Recreational Fishing Trust This work is copyright. 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Then, following the formation of the NSW Department of Primary Industries the report series was published as the ‘NSW Department of Primary Industries – Fisheries Final Report Series’ with ISSN number 1449-9967. The report series is now published by Industry & Investment NSW as the ‘Industry & Investment NSW – Fisheries Final Report Series’ with ISSN number 1837-2112. Contents i TABLE OF CONTENTS TABLE OF CONTENTS.................................................................................................................................I LIST OF TABLES.........................................................................................................................................III LIST OF FIGURES ......................................................................................................................................III ACKNOWLEDGEMENTS..........................................................................................................................IV NON-TECHNICAL SUMMARY ................................................................................................................. V 1. GENERAL INTRODUCTION.............................................................................................................. 7 1.1. Current status of Tandanus tandanus ........................................................................................... 7 1.2. Potential actions to promote population recovery ........................................................................ 9 1.3. Potential genetic impacts of stocking.......................................................................................... 10 1.4. Tandanus tandanus genetic structure ......................................................................................... 11 1.5. Project aims................................................................................................................................. 11 2. ISOLATION AND CHARACTERISATION OF FRESHWATER CATFISH MICROSATELLITE LOCI ................................................................................................................ 12 2.1. Introduction................................................................................................................................. 12 2.2. Methods, results and discussion.................................................................................................. 12 3. PHYLOGEOGRAPHIC STRUCTURE OF FRESHWATER CATFISH IN THE MURRAY- DARLING BASIN AND COASTAL CATCHMENTS OF NEW SOUTH WALES...................... 16 3.1. Introduction................................................................................................................................. 16 3.2. Methods....................................................................................................................................... 19 3.2.1. Sampling and DNA extraction...................................................................................................... 19 3.2.2. Laboratory procedures.................................................................................................................. 19 3.2.3. Data analysis................................................................................................................................. 19 3.3. Results ....................................................................................................................................... 21 3.3.1. Genetic variation .......................................................................................................................... 21 3.3.2. Phylogenetic structure .................................................................................................................. 21 3.4. Discussion ................................................................................................................................... 27 3.4.1. Biogeography ............................................................................................................................... 28 3.4.2. Management implications............................................................................................................. 30 4. MICROSATELLITE POPULATION GENETIC STRUCTURE OF FRESHWATER CATFISH WITHIN THE MURRAY-DARLING BASIN AND COASTAL CATCHMENTS OF NSW....... 31 4.1. Introduction................................................................................................................................. 31 4.2. Methods....................................................................................................................................... 32 4.2.1. Sample collection ......................................................................................................................... 32 4.2.2. DNA extraction and microsatellite genotyping ............................................................................ 33 4.2.3. Genetic diversity and differentiation ............................................................................................ 34 4.2.4. Population structure...................................................................................................................... 34 4.2.5. Assignment tests........................................................................................................................... 34 4.2.6. Population bottleneck ................................................................................................................... 35 4.2.7. Effective population size .............................................................................................................. 35 4.3. Results ....................................................................................................................................... 36 4.3.1. Hardy-Weinberg and genotypic disequilibrium............................................................................ 36 4.3.2. Genetic diversity........................................................................................................................... 36 4.3.3. Genetic structure........................................................................................................................... 38 4.3.4. Population structure...................................................................................................................... 42 4.3.5. Assignment tests........................................................................................................................... 48 4.3.6. Population bottleneck ................................................................................................................... 49 4.3.7. Effective population size .............................................................................................................. 49 4.4. Discussion ................................................................................................................................... 50 4.4.1. Population structure and genetic diversity.................................................................................... 50 4.4.2. MDB group................................................................................................................................... 50 4.4.3. NSW north coast........................................................................................................................... 50 Catfish genetic structure Rourke and Gilligan ii Contents 4.4.4. Tandanus sp. 1 ..............................................................................................................................51 4.4.5. Translocation history in the NSW central and south