Depth as refuge: depth gradients in ecological pattern, process, and risk mitigation among coral reef fishes

MacDonald, Chancey (2018) Depth as refuge: depth gradients in ecological pattern, process, and risk mitigation among coral reef fishes. PhD thesis, James Cook University.

PDF (Thesis)
Download (3MB) | Preview
View at Publisher Website:


The impacts of anthropogenic habitat disturbance are often asymmetric along environmental gradients and among taxa. For species that cannot successfully utilize post disturbance habitats, the ability to occupy positions on spatial gradients that fall outside of disturbance regimes may offer a key refuge. However, decreasing resource availability or quality, and changing ecological and behavioural dynamics along gradients may result in substantial physiological costs for fringe-dwelling organisms. Assessments of potential refuges therefore require nuanced spatially gradated ecological assessments that are often absent and difficult to attain.

Coral reefs are now heavily impacted by climate related disturbance, and the greatest rates of biotic attrition among reef fishes generally occur within species obligated to associate with live corals. Because key drivers of future coral loss (i.e. warm water bleaching and storm events) may attenuate with depth, deep reefs hypothetically offer a refuge to vulnerable fishes. However, because of access difficulties, most ecological studies on coral reef organisms occur in shallow waters of <15 m.

In Chapter 2, I investigated the natural depth distributions, depth-related variation in community structure and coral habitat associations for 123 reef fish species at 6 depths between 0m and 40m, and from inner-bay to offshore reefs. The results indicated that depth is a stronger driver of reef fish assemblages than cross shelf gradients, though complex coral habitats and some associated fish species more frequently occupy deeper depths further from shore. Total live hard coral cover did not decline with depth in Kimbe Bay, though the cover of habitat-providing complex corals declined with depth. The major break in the community assemblage of reef fishes occurred between 5 m and 10 m, and 25% of species were limited to the shallowest 5m. However, 25% of species occurred at all depths between 0m and 30m, and 12% between 0m and 40m. In addition, I show that 85% of species with strong associations with live complex coral habitats occurred at depths of 20m or below. I therefore conclude that deep reef habitats in Kimbe Bay can provide a substantial refuge potential if reef degradation does attenuate with depth and the ecological costs of occupying deep periphery habitats are not prohibitive to long-term population maintenance.

In Chapters 3 to 6, I utilized the Chaetodontidae family (Butterflyfishes) to further investigate how a broad suit of behaviours and ecological dynamics that influence the distribution, vulnerability and success of a wide range of taxa in multiple biomes interrelate and vary among reef fishes along a broad coral reef depth gradient, from 0 – 40 m.

Interrelationships among distribution breadth, abundance, and degree of resource specialization form the basis of many general models in ecology, as well as extinction-risk assessments in conservation biology. Species with narrow distributions, low abundance and high resource specialisation are more vulnerable to environmental change and risk increases when vulnerability traits are combined. In Chapter 3, I evaluate whether depth may mediate these risks in coral-specialist fishes. Contrary to expectation, the most coral-specialized species were also the most abundant and the most broadly distributed. Further, no specialist-species had combined vulnerability traits, and no specialists were wholly restricted to shallow-water. Chapter 3 demonstrates that interrelationships among vulnerability traits and occupancy depths do not necessarily follow traditional ecological expectations on coral reefs, but they do work to mediate substantial risks for species vulnerable to shallow-reef habitat declines.

Chapters 2 and 3 demonstrate that many ecologically vulnerable reef fish species may offset the risks associated with shallow-water habitat losses by utilising deep habitats. However, the refuge potential of deep peripheral habitats may be mediated by the potentially substantial costs of securing sparsely distributed resources, which can limit survival and reproductive output. Further, depth-related resource shifts are likely to be more detrimental to dietary specialists than to generalists. In Chapter 4, I use extensive and intensive in-situ behavioural observations in combination with physiological condition measurements to examine the costs and benefits of resource-acquisition along the depth-gradient in two obligate corallivore reef fishes with contrasting levels of dietary specialisiation. I demonstrate that the space utilised to secure coral-resources increases towards deeper depths, as expected. However, increased territory sizes result in equal or greater total resources secured within deep territories. Foraging-distance, pairing-behaviour, body condition and fecundity did not decline with depth, but competitive interactions did. Unexpectedly, therefore, coral-specialist fishes selecting high-quality coral patches in deep water access equal or greater resources than their shallow-reef counterparts, with no extra costs.

As demonstrated in Chapter 4, the capacity for species to successfully occupy range peripheries is enhanced by their ability to mediate costs related to decreases in quantities and quality of key resources. In Chapter 5, I investigate the capacity to of species to employ variation in dietary strategies and energy acquisition along depth gradients. I focus on two obligate corallivores with differing levels of dietary specialization, as well as their mixotrophic coral prey. Total resource availability and total feeding effort did not decline toward deep-range peripheries in either fish species, but availability of preferred Acropora resources did decline. The more specialized species exhibited limited feeding plasticity along the depth gradient, and selective feeding effort on the preferred coral genus Acropora increased rather than decreased with depth. In contrast, the generalist's diet varied greatly with depth, reflecting changes in prey composition. Unexpectedly, the nutritional content of Acropora did not decline with depth, with shifts in δ¹³C and δ¹⁵N indicating increased coral heterotrophy in deeper water may offset declines in light energy. Mixed modelling of stable isotopes in amino acids of fish muscle tissue revealed a parallel increase in plankton-sourced carbon among deep-resident fish. Therefore, deep ranges appear to be supported by multiple mechanisms of dietary versatility, but for specialist species this versatility occurred at the resource level (corals), rather than among the consumers (fish). This dietary variability and trophic plasticity may act to buffer costs and bolster refuge potentials associated with dwelling at deep range peripheries, even among taxa with differential functional strategies.

In Chapter 6, I utilize two natural experiments to 1) demonstrate that a natural habitat disturbance event (a crown of thorns sea-star outbreak) can result in differential impacts and outcomes on shallow and deep populations of the coral obligate reef fish Chaetodon baronessa that favour the persistence of deep population; and 2) individual fishes are able to migrate downward, away from territories in degrading shallow-water habitats to inhabit healthy deep-reef habitats when made available via experimental competitor removal.

Overall, my thesis highlights how interrelationships among vulnerability traits, occupancy depths, and deep coral habitats, offer some risk mitigation among taxa currently thought to express high vulnerability to global-scale coral declines in shallow-water. The thesis further demonstrates how various combinations of stability and plasticity in resource specialization, space use, effort, food availability and quality, diet, feeding behaviour, and body condition, may aid the successful exploitation of deep refuges by species with contrasting functional traits. Finally, severe habitat disturbance can differentially impact fish and habitat survival between shallow and deep reefs, and individual fish are demonstrably able to utilize downward vertical migration away from declining shallow-water habitat to access higher-quality deep-water habitats where prior residence is not established.

Item ID: 64468
Item Type: Thesis (PhD)
Keywords: body condition, carbon pathways, coral habitat availability, coral reef fish, depth distributions, depth gradient, depth refuge, ecological costs, energy acquisition, environmental gradients, fish-habitat relationships, functional strategies, marginal habitats, range margin, reef fishes, refuge
Related URLs:
Copyright Information: Copyright © 2018 Chancey MacDonald.
Additional Information:

Three publications arising from this thesis are stored in ResearchOnline@JCU, at the time of processing. Please see the Related URLs. The publications are:

Chapter 2: MacDonald, Chancey, Bridge, Tom C.L., and Jones, Geoffrey P. (2016) Depth, bay position and habitat structure as determinants of coral reef fish distributions: are deep reefs a potential refuge? Marine Ecology - Progress Series, 561. pp. 217-231.

Chapter 4: MacDonald, Chancey, Jones, Geoffrey P., and Bridge, Tom (2018) Marginal sinks or potential refuges? Costs and benefits for coral-obligate reef fishes at deep range margins. Proceedings of the Royal Society of London Series B, Biological Sciences, 285 (1890). 20181545.

Chapter 5: MacDonald, Chancey, Bridge, Tom C.L., McMahon, Kelton W., and Jones, Geoffrey P. (2019) Alternative functional strategies and altered carbon pathways facilitate broad depth ranges in coral-obligate reef fishes. Functional Ecology, 33 (10). pp. 1962-1972.

Date Deposited: 23 Sep 2020 04:45
FoR Codes: 06 BIOLOGICAL SCIENCES > 0602 Ecology > 060205 Marine and Estuarine Ecology (incl Marine Ichthyology) @ 100%
SEO Codes: 96 ENVIRONMENT > 9603 Climate and Climate Change > 960305 Ecosystem Adaptation to Climate Change @ 50%
96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 50%
Downloads: Total: 72
Last 12 Months: 6
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page