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Type: Theses
Title: Diet of the Australian sea lion (Neophoca cinerea): an assessment of novel DNA-based and contemporary methods to determine prey consumption
Author: Peters, Kristian John
Issue Date: 2017
School/Discipline: School of Biological Sciences
Abstract: A fundamental prerequisite in the conservation and management of endangered species is knowledge of diet, because diet provides information on habitat use and resource requirements. However, understanding diet in marine mammals is difficult because direct feeding events are rarely observed. To overcome these limitations, many studies use the identification of skeletal remains (hard parts) recovered from faeces, or regurgitates. Yet, for the endangered Australian sea lion (Neophoca cinerea) (ASL), one of the rarest pinniped species in the world, diet remains a key knowledge gap that impedes our understanding of the species ecology and connectedness to other taxa in the marine ecosystem. When this thesis commenced, knowledge of ASL diet was based on few hard part studies comprising small sample sizes, which were limited in temporal and spatial extent. Knowledge of prey utilised by ASL was poor because prey hard parts are completely digested, or, if recovered in faeces, heavily eroded. Therefore, traditional methods of dietary analysis are ‘unreliable’ and biased toward robust prey. However, limitations notwithstanding, the analysis of Australian sea lion diet via traditional methods still provides useful information on prey species consumed that cannot be readily obtained using other methods. For example, alternative biochemical methods, such as fatty acid and stable isotope analyses, have provided important insights into habitat use the broader trophic levels of prey consumed by ASL; however, they are yet to provide reliable taxonomic information on the diversity of prey species consumed, at least not without first having a thorough understanding of Australian sea lion prey. Given the paucity of information on ASL diet, I initially aimed, as presented in Chapter 2, to investigate the diet of the ASL at different breeding colonies in South Australia. This initial study provided insights into some of the prey taxa consumed by ASL, which were subsequently used to develop a range of DNA-based dietary analyses to determine consumption of different prey. In order to apply DNA-based dietary analysis methods to wild populations, it was important to assess the application of different methods in a controlled environment to understand methodological constraints and refine the methods. In Chapter 3, I present feeding trials on captive ASL, with the aim to: i) assess end-point PCR and quantitative real-time PCR (qPCR) DNA-based techniques to determine their suitability to amplify and detect prey in ASL faeces and, ii) compare the DNA diet results with prey detected and identified using traditional hard-part methodology. Having successfully applied faecal DNA-based methods in a controlled feeding experiment to identify different prey, I applied DNA-based methods to faecal samples collected from two ASL breeding colonies in South Australia and identified a range of prey. The aims of Chapter 4 were to: (i) determine the diversity of prey taxa by sequencing a large number of clones from a few individuals, (ii) compare the prey taxa recovered at two study sites, and (iii) determine whether pooling faecal DNA from multiple individuals provides a useful means to characterise diet at the colony/population level. Finally, Chapter 5 utilised and extended the information gained from using the DNA-based faecal analyses presented in previous chapters, by integrating next-generation sequencing (NGS). Next-generation sequencing has the capacity to provide a greater depth of DNA sequencing than the cloning-sequencing approach, with the method potentially improving prey diversity information for the ASL. The aim of this study was to use DNA-based faecal analysis and NGS technology at one breeding colony to investigate seasonal and annual variation in prey consumed by ASL.
Advisor: Goldsworthy, Simon D.
Ophel-Keller, Kathy
Dissertation Note: Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Biological Sciences, 2017.
Keywords: Australian sea lion
diet
DNA
PCR
predator-prey
otariid
clone
next generation pyrosequencing
Research by Publication
Provenance: This electronic version is made publicly available by the University of Adelaide in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. This thesis may incorporate third party material which has been used by the author pursuant to Fair Dealing exceptions. If you are the owner of any included third party copyright material you wish to be removed from this electronic version, please complete the take down form located at: http://www.adelaide.edu.au/legals
DOI: 10.4225/55/5b10900bb84be
Appears in Collections:Research Theses

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