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Genetic Implications of Culturing Australasian Snapper (Chrysophrys Auratus) from Wild-Caught Eggs for Stock Enhancement

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Genetic Implications of Culturing Australasian Snapper (Chrysophrys Auratus) from Wild-Caught Eggs for Stock Enhancement Genetic implications of culturing Australasian snapper (Chrysophrys auratus) from wild-caught eggs for stock enhancement Natasha Danielle Prokop BSc (Marine Science); BComm (Journalism) 2015 Murdoch University, Western Australia School of Veterinary and Life Sciences With support from i Declaration I declare that this thesis is my account of my research and contains, as its main content, work that has not previously been submitted for a degree at any tertiary education institution. ____________________________________ _____________________ Natasha Prokop Date ii Abstract This thesis represents the first study into the genetic implications of culturing a marine finfish from wild-caught eggs (the ACAAR technique), for use in stock enhancement. This technique should facilitate the capture of genetic diversity in the cultured fish, while also dispensing with the need to maintain a large broodstock in the hatchery. This study was conducted with Chrysophrys auratus from Cockburn Sound in Western Australia. Nine, polymorphic microsatellite loci were used to compare the genetic composition between a sample of wild adults of C. auratus from spawning aggregations in Cockburn Sound and a sample of juveniles cultured using the ACAAR technique. The levels of genetic diversity present in the wild sample, in terms of allelic richness and heterozygosity, were maintained in the juveniles cultured using this technique and their release would likely pose little risk to genetic diversity in the wild. Overall, the allelic compositions were similar between the wild adult and cultured juveniles samples, although some rare alleles were absent in each population due to sampling bias, and bottleneck effects in the cultured juveniles. The levels of inbreeding and relatedness detected in the cultured juveniles were low, and similar to that of the wild adult sample, suggesting that juvenile releases would be unlikely to increase levels of inbreeding in the wild. It is also likely that a large number of effective breeders ( > 133) contributed to the cultured juveniles, thereby lowering the risk of inbreeding, or reductions to the wild effective population size, upon release. These findings together suggest that the ACAAR technique poses a limited risk to the genetic integrity of the wild population, should these fish be released for stock enhancement. It may also serve as a suitable alternative to traditional culturing for other aggregate spawning marine finfish. Further, suggestions are made for the improvement of the ACAAR culturing technique and for improvements to the genetic analyses. iii Table of contents Declaration .................................................................................................................................... ii Abstract ........................................................................................................................................ iii Table of contents .......................................................................................................................... v List of Figures ............................................................................................................................ viii List of Tables ................................................................................................................................ x Acknowledgements .................................................................................................................... xii Chapter One – Introduction ...................................................................................................... 1 1.1 Context of introduction ........................................................................................................... 1 1.2 Active fisheries management .................................................................................................. 1 1.2.1 Stock enhancement for the management of fisheries.................................................................... 2 1.3 Genetic effects of stock enhancement .................................................................................... 4 1.3.1 Tools for assessing the genetic effects of enhancements ............................................................. 5 1.3.1.1 Microsatellites ............................................................................................... 5 1.3.2 Potential genetic effects of traditional stock enhancement .......................................................... 7 1.3.2.1 Effects during culturing ................................................................................ 9 1.3.2.2 Effects in the wild ....................................................................................... 12 1.3.3 The salmonid bias and marine enhancements .............................................................................. 14 1.3.4 Managing genetic effects .................................................................................................................. 18 1.3.5 Novel techniques ................................................................................................................................ 20 1.4 This study ............................................................................................................................. 21 1.4.1 Project overview ................................................................................................................................. 21 1.4.2 Study species general biology .......................................................................................................... 23 1.4.2.1 Taxonomy ................................................................................................... 23 1.4.2.2 Distribution ................................................................................................. 24 1.4.2.3 Reproduction and recruitment ..................................................................... 24 1.4.3 Study species threats and management .......................................................................................... 27 1.4.4 Motivation for enhancement ............................................................................................................ 29 1.4.4.1 Practicality .................................................................................................. 29 1.4.4.1.1 Egg collection ................................................................................ 29 1.4.4.1.2 Culture technologies....................................................................... 30 1.4.4.1.3 Funding .......................................................................................... 30 1.4.4.2 Responsible enhancement ........................................................................... 31 1.4.4.2.1 Recruitment limitation ................................................................... 31 1.4.4.2.2 Genetic implications....................................................................... 31 1.4.5 Significance and need for this study ............................................................................................... 32 v 1.4.5 Study objectives .................................................................................................................................. 33 Chapter Two – Methods ........................................................................................................... 34 2.1 Sampling design and collection ............................................................................................ 34 2.1.1 Sample site ........................................................................................................................................... 34 2.1.2 Sampling design .................................................................................................................................. 35 2.1.2.1 Wild adults (2014) ...................................................................................... 36 2.1.2.2 Cultured juveniles ....................................................................................... 36 2.1.2.3 Wild adults (2013) ...................................................................................... 39 2.2 DNA extraction ..................................................................................................................... 40 2.2.1 Screening of nuclear DNA ............................................................................................................... 41 2.3 Polymerase chain reaction (PCR) ......................................................................................... 42 2.3.1 Microsatellite loci ............................................................................................................................... 42 2.3.2 PCR amplification .............................................................................................................................. 43 2.3.3 Screening of PCR product ................................................................................................................ 44 2.3.4 Fragment length analysis .................................................................................................................. 44 2.4 Data analyses ........................................................................................................................ 46 2.4.1 Locus selection ...................................................................................................................................
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