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FRDC Final Report Design Standard Research to underpin better understanding and management of western Gemfish stocks in the Great Australian Bight Andy Moore1&2, Jenny Ovenden2, Carlos Bustamante2 1 Australian Bureau of Agricultural and Resources Economics and Sciences 2 Molecular Fisheries Laboratory, University of Queensland September 2017 FRDC Project No 2013/014 © 2017 Fisheries Research and Development Corporation. All rights reserved. ISBN: 978-1-74323-347-4 ISSN – 189-3128 Technical report no: 17.1 Research to underpin better understanding and management of western Gemfish stocks in the Great Australian Bight FRDC 2014/014 2016 Ownership of Intellectual property rights Unless otherwise noted, copyright (and any other intellectual property rights, if any) in this publication is owned by the Fisheries Research and Development Corporation; the Australian Bureau of Agricultural and Resource Economics and Sciences; and the University of Queensland. This publication (and any information sourced from it) should be attributed to Moore, A., Ovenden, J., & Bustamante, C., 2017, Research to underpin better understanding and management of western Gemfish stocks in the Great Australian Bight, Australian Bureau of Agricultural and resource Economics and Sciences, Canberra, September 2017. Creative Commons licence All material in this publication is licensed under a Creative Commons Attribution 3.0 Australia Licence, save for content supplied by third parties, logos and the Commonwealth Coat of Arms. Creative Commons Attribution 3.0 Australia Licence is a standard form licence agreement that allows you to copy, distribute, transmit and adapt this publication provided you attribute the work. A summary of the licence terms is available from creativecommons.org/licenses/by/3.0/au/deed.en. The full licence terms are available from creativecommons.org/licenses/by/3.0/au/legalcode. Inquiries regarding the licence and any use of this document should be sent to: [email protected] Disclaimer The authors do not warrant that the information in this document is free from errors or omissions. The authors do not accept any form of liability, be it contractual, tortious, or otherwise, for the contents of this document or for any consequences arising from its use or any reliance placed upon it. The information, opinions and advice contained in this document may not relate, or be relevant, to a readers particular circumstances. Opinions expressed by the authors are the individual opinions expressed by those persons and are not necessarily those of the publisher, research provider or the FRDC. The Fisheries Research and Development Corporation plans, invests in and manages fisheries research and development throughout Australia. It is a statutory authority within the portfolio of the federal Minister for Agriculture, Fisheries and Forestry, jointly funded by the Australian Government and the fishing industry. Researcher Contact Details FRDC Contact Details Name: Andy Moore Address: 25 Geils Court Address: 18 Marcus Clarke St Deakin ACT 2600 Canberra ACT 2601 Phone: 02 6285 0400 Phone: 02 6272 3090 Fax: 02 6285 0499 Email: [email protected] Email: [email protected] Web: www.frdc.com.au In submitting this report, the researcher has agreed to FRDC publishing this material in its edited form. Contents Contents ................................................................................................................................................. iii Acknowledgments ................................................................................................................................ vi Executive Summary ............................................................................................................................ vii Introduction ......................................................................................................................................... 10 Objectives ............................................................................................................................................. 13 Method .................................................................................................................................................. 14 Population Sampling ........................................................................................................................14 Genomic DNA extraction ................................................................................................................16 Next generation sequencing and assembly of the mitochondrial genome of the Gemfish ..............17 De novo development of microsatellite markers using next generation sequencing .......................17 Sanger sequencing of regions of the mitochondrial genome ...........................................................18 Laboratory .................................................................................................................................18 Computer analysis .....................................................................................................................18 Microsatellite genotyping ................................................................................................................19 Laboratory .................................................................................................................................19 Computer analysis .....................................................................................................................20 Genotyping single nucleotide polymorphisms (SNP)......................................................................22 Laboratory .................................................................................................................................22 Computer analysis .....................................................................................................................24 Results .................................................................................................................................................. 25 Sampling summary, including biological characteristics ................................................................25 Sampling achieved ....................................................................................................................25 Reproductive status and timing of spawning ............................................................................25 Length frequency .......................................................................................................................27 Sequence variation in mitochondrial DNA ......................................................................................28 Summary statistics .....................................................................................................................28 Network of mtDNA control region haplotypes .........................................................................29 MtDNA haplotype variation among population samples ..........................................................29 Microsatellite genotyping ................................................................................................................32 Summary statistics .....................................................................................................................32 Tests for conformance to Hardy-Weinberg genotypic proportions and linkage disequilibrium ...........................................................................................................................34 Genetic diversity of populations from microsatellite genotypes...............................................38 Population genetic structure from microsatellite genotypes .....................................................39 Immigrant and admixture analysis ............................................................................................41 SNP genotyping ...............................................................................................................................42 Summary statistics .....................................................................................................................43 Fst and DAPC analyses of SNP data .........................................................................................45 Discussion ............................................................................................................................................. 48 Conclusion ............................................................................................................................................ 53 Implications ........................................................................................................................................ 54 Recommendations ............................................................................................................................... 55 Further development .......................................................................................................................55 Extension and Adoption ...................................................................................................................... 56 Project coverage ...............................................................................................................................56 Project materials developed ............................................................................................................... 57 Appendices ..........................................................................................................................................
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