Modelling physical and biological drivers of larval retention in reef systems

Cetina Heredia, Paulina (2012) Modelling physical and biological drivers of larval retention in reef systems. PhD thesis, James Cook University.

PDF (Thesis)
Download (11MB) | Preview
View at Publisher Website:


Larval dispersal has major effects on ecological and evolutionary processes. Thus, a thorough understanding of mechanisms driving larval transport, and estimates of larval retention, are necessary to inform the conservation and management of marine biodiversity. The overall aim of this thesis was to investigate physical and biological factors driving larval transport in coral reef systems, with particular emphasis on the effect of lee‐reef eddies, swimming behaviour, and their interaction.

In the second chapter, I quantified the extent to which lee‐reef eddies with different dynamics influence retention of passive larvae close to reefs. Simulations of particle transport at individual reefs with idealized shapes, under the influence of unidirectional and tidal flows, were conducted with the Sparse Hydrodynamic Ocean Code (SHOC), a three dimensional hydrodynamic model, using a reef‐scale spatial resolution. I then tested how accurately the Island Wake Parameter (I), a dimensionless number that indicates the degree of turbulence of flow past obstacles under stationary flows in shallow waters, characterized the qualitative nature of the simulated flow past reefs. Theoretical considerations suggest that I~1 implies the formation of stable eddies that remain attached downstream of the reef, and I>10 implies the formation of unstable eddies that detach and dissipate or are advected downstream. I found that the Island Wake Parameter captured adequately the qualitative nature of the flow past idealized reefs. Unidirectional flows induced the formation of stable eddies and were associated with I~1, while tidal flows induced the detachment and downstream advection of eddies and were associated with I>10. These eddies provoked the recirculation of particles, prolonging retention times. Thus, stable eddies (small I values) induced long retention times, and unstable eddies (large I values) induced short retention times. Indeed, a nonlinear regression indicated that the Island Wake Parameter explained 81‐92% of the variability in retention time among idealized reefs across the range of flow regimes considered. This suggests that the Island Wake Parameter is a useful predictor of the formation and duration of eddies past reefs with idealized shapes under unidirectional and tidal flows, and that eddies and their life‐spans are key determinants of the retention of passive particles close to reefs.

The findings above suggest that the Island Wake Parameter may be useful for approximating retention of particles close to reefs, when well‐calibrated, reef‐scale circulation models are not unavailable. To investigate this possibility further, I aimed, first, to examine how well the Island Wake Parameter characterizes the flow past real reefs under nonstationary flows, and second, under these more realistic circulation regimes, to determine effect of eddies on retention of passive larvae, and test the robustness of the relationship between the Island Wake Parameter and mean retention times. To achieve these objectives, in Chapter 3, I implemented SHOC with a reef‐scale spatial resolution (~300 m) within the central Great Barrier Reef (GBR), encompassing 14 middle and 6 outer shelf reefs with various shapes (crescentic, lagoonal, planar and patchy), ranging from 1.9 to 27.5 km2 in size. Comparison of the model outcomes against observed time series of temperature, sea level and currents through correlation, principal components, and spectral analyses, showed that the model reproduces the dynamics in the region adequately. In particular, it characterizes well the formation of eddies downstream of reefs, and the upwelling events associated with these eddies.

Having validated the central GBR model, I turned in Chapter 4 to simulating passive larval transport over two spawning events, and to quantifying retention time at individual reefs. The Island Wake Parameter proved successful at discerning between the presence and absence of eddies. In turn, the presence of eddies, and their duration, strongly influenced larval retention: the longest retention times occurred at reefs where eddies were long‐lived, and the shortest retention times when eddies did not form at all. Finally, a common functional relationship characterized how mean retention time depends on the Island Wake Parameter, both for idealized reefs under simplified flows (from Chapter 2), and for reefs along the central GBR under realistic circulation. These results indicate, first, that lee‐reef eddies and their dynamics are accurately depicted by the Island Wake Parameter, and second, that lee‐reef eddies are key drivers of passive larval transport close to reefs. Because the Island Wake Parameter is a simple function of upstream flow velocity, reef geometry, and vertical diffusion, these findings suggest that first‐order estimates of larval retention may be obtained from relatively coarse‐scale characteristics of the flow, and basic features of reef geomorphology. Such approximations may be a valuable tool for modelling meta‐population dynamics over large spatial scales, where explicitly characterizing fine‐scale flows around reefs would require extensive computational resources and model calibration.

The results of Chapters 2 and 4 indicate that the potential of lee‐reef eddies to retain particles is limited by eddy life‐span. Stable eddies can facilitate self‐recruitment of species whose larvae are passive, or weak swimmers, for a few days after release. However, mean currents along the central GBR are intense and provoke unstable eddies that only retain larvae for periods of less than a day. This suggests that other mechanisms, such as swimming behaviour, might play an important role in larval retention and dispersal patterns of species whose larvae take weeks or months to develop, such as reef fishes.

Consequently, the objective of the fifth chapter was to quantify the extent to which horizontal swimming behaviour of larvae that exploit lee reef eddies can influence retention close to reefs. I incorporated larval behaviour within SHOC's Lagrangian algorithm to simulate the transport of larvae that swim towards regions where lee reef eddies form. The implemented swimming speed of larvae increased with age according to an empirical relationship for Lutjanids. Simulations were conducted at idealized reefs under alternative circulation regimes that produced stable eddies, unstable eddies, and no eddies. Larvae were assumed to be advected into the reef's vicinity at different stages of their development, and the proportion of retained larvae at the end of the pelagic larval duration was quantified for each larval stage and circulation regime. Depletion of energy reserves by swimming was also considered, based on published data. Results indicate that the potential for swimming behaviour to increase retention close to reefs is highly sensitive to the extent to which larval feeding is sufficient to replenish energy reserves, and on the presence and duration of eddies. If food sources are sufficiently available throughout the planktonic stage to replenish energy expended during swimming, then larval swimming behavior suffices to enhance retention close to reefs and facilitate self‐recruitment. However, if food is scarce, the presence of favourable circulation structures, such as eddies with long life‐spans, or vertical migration combined with currents flowing in varying directions with depth, are necessary for self-recruitment, and crucial to enhance the retention of late‐stage pelagic larvae that arrives close to reefs.

Item ID: 36289
Item Type: Thesis (PhD)
Keywords: coral reefs; eddies; GBR; Great Barrier Reef; island wake parameter; island wakes; larvae; larval behavior; larval behaviour; larval dispersal; larval transport; lee-reef; retention time
Related URLs:
Additional Information:

Publications arising from this thesis are available from the Related URLs field. The publications are:

Cetina-Heredia, Paulina, and Connolly, Sean R. (2011) A simple approximation for larval retention around reefs. Coral Reefs, 30 (3). pp. 593-605.

Date Deposited: 05 Aug 2015 05:38
FoR Codes: 04 EARTH SCIENCES > 0405 Oceanography > 040503 Physical Oceanography @ 50%
06 BIOLOGICAL SCIENCES > 0602 Ecology > 060205 Marine and Estuarine Ecology (incl Marine Ichthyology) @ 50%
SEO Codes: 96 ENVIRONMENT > 9699 Other Environment > 969902 Marine Oceanic Processes (excl. Climate Related) @ 34%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 33%
97 EXPANDING KNOWLEDGE > 970104 Expanding Knowledge in the Earth Sciences @ 33%
Downloads: Total: 115
Last 12 Months: 3
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page