Sih, Tiffany L. (2019) Diving into the deep-end: investigating tropical deep-reef fish assemblages. PhD thesis, James Cook University.

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Abstract

Increasing demand paired with declining catch rates from traditional fisheries has caused fishers from across the tropical Indian and Pacific Oceans to shift their focus towards deep-reef species. This trend is also seen in Australia; however, little is known about the local biology and ecology of these newly targeted species. Therefore, my objective was to combine multiple techniques, including underwater video, multibeam analysis of habitat, and otolith microchemistry, to examine the distribution, abundance, and species composition of a commercially important assemblage of deep-reef fishes. The information gathered from this project will assist in the resource management of these unique fish assemblages.

In this project I examined the biodiversity and ecology of deep-reef fishes at multiple spatial scales. I considered large depth gradients along the continental shelf-break to look at shifts in assemblage structure, but also broad geographic scales extending thousands of kilometres that had the potential to encapsulate multiple stocks. My specific aims were: (1) to describe deep-reef fish assemblages and examine fish-habitat associations for shelf-break environments in the Great Barrier Reef (GBR), Chapters 2 through 5; (2) to determine the utility of otolith microchemistry to identify regional stock structure, and then to apply the technique to fish populations across the Indian Ocean to the Central Pacific (Chapters 6 and 7).

In Chapter 2, I demonstrated that depth was a strong predictor of the distribution of fishes. Individual species had different depth distributions and few fish species overlapped between adjacent depth strata, indicating that these are unique assemblages that change with respect to depth. In general, species richness and abundance decreased with increasing depth. New species location records were found for Chromis circumaurea, Chromis okamurai, Chromis mirationis, Hoplolatilus marcosi and Bodianus bennetti in the GBR at lower mesophotic depths. After consulting various fish experts, three potentially new species from the genera Selenanthias, Chromis, and Bodianus species were detected. This was the first research project to use underwater video stations at multiple reefs down to 260 m depths in the GBR and in doing so this research has re-defined depth distributions of some fish assemblages and increased maximum depth records for a number of species.

Habitat was also important in predicting where deep-reef fish occur and there was high variation within depth strata (Chapter 3). Although species were often only found within a certain depth range, species' distribution and abundance was determined by localized habitat features. Furthermore, species distribution was dependent on the trophic group and degree of habitat specialization. Shelf-break slope environments had decreasing structural complexity with depth, such as greater proportion of plants and calcified reefs at shallower and middle depths and more mud, sand and rubble at the deepest depths. Depth, relative steepness, topographical relief and hardness of substrate differentiated where these species were distributed. Epibenthic cover and substrate were important factors in influencing fish distributions and the presence of encrusting organisms and calcified reef translated to higher abundance and diversity (Chapter 4). Deeper fishes had varying degrees of habitat specialization and these habitat preferences can have important management implications (Chapter 5). Closely related species (in the same genus) had varying levels of habitat association; these differences likely reflected their species-specific ecology and behaviour (i.e. what they eat, degree of movement). Species with stronger associations may be more easily targeted and directly or indirectly impacted by environmental changes.

I hypothesized that environmental variation among species would be reflected in the hard structures of the fish themselves and give some insight to population structure at multiple spatial scales. I investigated otolith elemental composition for commercially-valuable deep-reef fishes of the Pacific: Etelis coruscans (flame snapper) and Etelis sp. (ruby snapper, recently distinguished from the pygmy ruby snapper) to determine the most robust approach to elemental chemistry that would assist in revealing population structure (Chapter 6). Overlapping and non-overlapping elemental fingerprints clarified where deepwater fish resources should be considered a continuous stock or separate stocks between locations. I compared the two major methods of otolith chemistry; laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) had better discriminatory accuracy than solution-based inductively coupled plasma mass spectrometry. Using a smaller ablation spot size had greater temporal resolution when I used a transect of the cross-section of the otolith, from the core to the edge to represent the timeline, or life history, of the fish. Using specific locations of the otolith transect also increased the spatial discrimination of the elemental fingerprints. It was concluded that the spatial separation of the otolith edge was better for stock discrimination.

Fishery management decisions rely on accurate information of where natural boundaries in fish populations occur (i.e. stock structure), and it was predicted that the chemistry of otoliths could help in discriminating distinct groups or management units. Based on the outcomes of Chapter 6, I then extended LA-ICP-MS chemical analyses to assess fish populations from otolith samples collected by fisheries researchers from the Pacific Community (New Caledonia) and Fisheries Western Australia. Otoliths were from three broad regions (Indian Ocean, West Pacific and Central Pacific) and included multiple Pacific Island nations: New Caledonia, Tonga, Vanuatu, Samoa, Fiji, Papua New Guinea, Wallis and Futuna, and Monowai Seamount (international waters). Combined with samples I collected from the Indonesia, the GBR and Coral Sea (Australia), this sampling design included ten international Exclusive Economic Zones (EEZ), and three fishery management zones in Australia (Kimberley, Pilbara/Gascoyne and GBR/Coral Sea). This is the first project that applied otolith chemical analyses of multiple deep-reef species (E. coruscans, E. sp. and Etelis carbunculus, the pygmy ruby snapper) across a broad area (most of their distribution), for which identifying stock structure could assist management decisions and promote cooperation between adjoining nations. The potentially robust stocks identified were smaller than previously suggested, which is cause for concern. Smaller stocks may be more vulnerable to fishing pressure and local extirpation. For these locations precautionary management measures should be put in place that recognises these biological units until further evidence suggests otherwise.

My PhD research suggests that due to narrow depth distributions, deep-reef assemblages of fishes are vulnerable to overexploitation. Further, deep-reef fish depend on certain habitats and this can add an extra level of vulnerability if these depths and preferred habitat are isolated or uncommon. Deep reefs are critical ecological habitats and unique from shallower environments. Deep-reef ecosystems are still poorly understood, but they are an increasingly threatened component of the GBR and mesophotic reefs worldwide. Tropical deep-reef fish stocks are at risk of over-exploitation in the Indo-Pacific without sufficient information for fisheries management. Sensible protection of deeper areas will be critical if stocks are to be sustainably managed before they are lost. Deep-reef fisheries have been managed by EEZ rather than biological stocks. Here, I used elemental chemistry to identify biological units that could be useful for management strategies. Greater resolution of stock identity and pathways of connectivity in large biological stocks, is required to conserve the unique resources and unappreciated biodiversity of deep-reef fishes.

Item ID:	60377
Item Type:	Thesis (PhD)
Keywords:	deep reef, mesophotic, fish ecology, Great Barrier Reef, deepwater snapper, Baited Remote Underwater Video Stations (BRUVS), multi beam bathymetry, otolith chemistry, stock structure
Related URLs:	https://researchonline.jcu.edu.au/52877/ https://researchonline.jcu.edu.au/58334/
Copyright Information:	Copyright © 2019 Tiffany L. Sih.
Additional Information:	2 publications arising from this thesis are stored in ResearchOnline@JCU, at the time of processing. Please see the Related URLs field. The publications are: Chapter 2: Sih, Tiffany L., Cappo, Mike, and Kingsford, Michael J. (2017) Deep-reef fish assemblages of the Great Barrier Reef shelf-break (Australia). Scientific Reports, 7. 10886. Chapter 3: Sih, Tiffany L., Daniell, James J., Bridge, Thomas C. L., Beaman, Robin J., Cappo, Mike, and Kingsford, Michael J. (2019) Deep-reef fish communities of the Great Barrier Reef shelf-break: trophic structure and habitat associations. Diversity, 11. 26.
Funders:	Centre of Excellence for Coral Reef Studies, AIMS@JCU, Australian Institute of Marine Science, PADI Foundation, Holsworth Wildlife Research Endowment, Australian Coral Reef Society (ACRS), Australian Society for Fish Biology, GBRMPA Science for Management Awards
Projects and Grants:	GBRMPA Science for Management Awards, Australian Coral Reef Society Terry Walker Prize, Australian Society for Fish Biology Student International Travel Award, Great Barrier Reef Foundation Bommies Award, Holsworth Wildlife Research Fund, PADI Foundation grant
Date Deposited:	03 Feb 2020 02:42
FoR Codes:	06 BIOLOGICAL SCIENCES > 0602 Ecology > 060205 Marine and Estuarine Ecology (incl Marine Ichthyology) @ 50% 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070403 Fisheries Management @ 50%
SEO Codes:	96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 50% 96 ENVIRONMENT > 9605 Ecosystem Assessment and Management > 960507 Ecosystem Assessment and Management of Marine Environments @ 50%
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