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Population Genetic Structure of Freshwater Catfish

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Population Genetic Structure of Freshwater Catfish 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. Except as permitted under the Copyright Act, no part of this reproduction may be reproduced by any process, electronic or otherwise, without the specific written permission of the copyright owners. Neither may information be stored electronically in any form whatsoever without such permission. DISCLAIMER The publishers do not warrant that the information in this report is free from errors or omissions. The publishers do not accept any form of liability, be it contractual, tortuous or otherwise, for the contents of this report for any consequences arising from its use or any reliance placed on it. The information, opinions and advice contained in this report may not relate to, or be relevant to, a reader’s particular circumstance. ISSN 1837-2112 Note: Prior to July 2004, this report series was published by NSW Fisheries as the ‘NSW Fisheries Final Report Series’ with ISSN number 1440-3544. 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
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