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RESEARCH ARTICLE
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Citation: Pomeroy AWM, Ghisalberti M, Peterson
M, Farooji VE (2023) A framework to quantify flow
through coral reefs of varying coral cover and
morphology. PLoS ONE 18(1): e0279623. https://
doi.org/10.1371/journal.pone.0279623
Editor: Atsushi Fujimura, University of Guam,
GUAM
Received: November 21, 2021
Accepted: December 12, 2022
Published: January 18, 2023
Copyright: © 2023 Pomeroy et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited.
Data Availability Statement: All data needed to
evaluate the conclusions in the paper are present in
the paper. The numerical model setup files, STL
files, underlying data for the figures, laboratory
experimental data and time average flow field data
used in this study are available from https://doi.org/
10.5281/zenodo.4281963. The STL files are also
available from The Hydrous (http://www.thehydro.
us).
Funding: AWP would like to acknowledge the
funding that was provided to this project in part by
an Australian American Fulbright Fellowship and
PLOS ONE | https://doi.org/10.1371/journal.pone.0279623 January 18, 2023
A framework to quantify flow through coral
reefs of varying coral cover and morphology
Andrew W. M. Pomeroy ID1,2¤*, Marco Ghisalberti1,2,3, Michael Peterson3, Vahid
Etminan Farooji1
1 Oceans Graduate School, The University of Western Australia, Crawley, Western Australia, Australia,
2 The UWA Oceans Institute, The University of Western Australia, Crawley, Western Australia, Australia,
3 School of Engineering, The University of Western Australia, Crawley, Western Australia, Australia
¤ Current address: School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
* a.pomeroy@unimelb.edu.au
Abstract
Flow velocities within coral reefs are greatly reduced relative to those at the water surface.
The in-reef flow controls key processes that flush heat, cycle nutrients and transport sedi-
ment from the reef to adjacent beaches, all key considerations in assessments of reef resil-
ience and restoration interventions. An analytical framework is proposed and tested with a
suite of high-resolution numerical experiments. We demonstrate a single parameter that
describes the total coral frontal area explains variation of horizontally averaged velocity
within a reef canopy across morphologies, densities, and flow depths. With the integration of
existing data of coral cover and geometry, this framework is a practical step towards the pre-
diction of near-bed flows in diverse reef environments.
Introduction
The hard coral colonies that form coral reef benthos are irregular in form and vary on spatial
scales that range from centimeters to kilometers. This irregular and complex form directly
modifies the in-reef flow that occurs between the seabed and the top of the coral colonies [1,
2]. While this in-reef flow is often well mixed, it can control biological processes such as the
capture of prey by corals [3], the rate of nutrient uptake [4] and coral respiration and calcifica-
tion [5]. It also governs a range of physical processes that are responsible for the attenuation of
waves [6–8] and currents [9] as well as the transport of reef-generated sediment [1, 10]. These
physical processes ultimately shape the adjacent shoreline and reduce the risk of coastal flood-
ing and erosion [11], which motivates many environmental restoration activities [12]. Given
the controlling influence of the flow within the reef benthos [13] as well as the role of benthos
on energy dissipation by drag in particular [9], there is a clear need for a practical framework
that allows the prediction of in-reef flow across a wide range of colony types, coral cover and
flow speeds.
Despite the wide range of coral species globally, coral colonies can be broadly classified
from a physical perspective based on their morphological form [14]. For example “plate” or
“table” morphologies such as Acropora hyacinthus [15] are characterized by large flat surfaces
1 / 15
PLOS ONE A framework to quantify flow through coral reefs

UWA-AIMS Postdoctoral Fellowship. This work
was supported by resources provided by the
Pawsey Supercomputing Centre with funding from
the Australian Government and the Government of
Western Australia. The funders had no role in study
design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing interests: The authors have declared
that no competing interests exist.
(Fig 1A), “massive” morphologies such as Porites lobata [15] form monolithic structures (Fig
1B), and “branching” morphologies such as Pocillopora edyouxi [16] create a complex porous
array (Fig 1C). A wide range of coral colonies globally are morphologically similar to these
three archetypes [17] and indeed these three species alone have been observed [18] throughout
many of the eco-regions where coral reefs are located (Fig 1D).
Many reef systems are current-dominated systems, such as those located in macro-tidal
regions [20] and reefs located in the relatively deep lagoons of barrier reefs [21] and atolls [22,
23]. For the more than two-thirds of reefs that experience wave-driven flows [24], there are
energetic wave-breaking zones on the forereef slope [2]. This can generate significant cross-
reef currents [25–27] and small depth-limited waves [8], such that the steady component of
the flow (and its attenuation by the reef) is still significant [28, 29]. In steady flows, the drag
exerted by the coral colonies creates a substantial reduction in the spatially-averaged in-reef
flow, relative to the near-surface flow [28, 30, 31]. In addition to this vertical variation, the gen-
eration of low-velocity wake regions behind coral colonies (and the individual ‘branches’ of
some species), means that in-reef flows exhibit significant horizontal variability [32]. Similar

Fig 1. The global distribution of the three archetypal benthos colony forms analyzed here (“table”, “massive” and “branching”). Recorded observations
[18] of the representative species (A) Acropora hyacinthus [15], (B) Porites lobata [15] and (C) Pocillopora edyouxi [16] are indicated by colored dots in (D)
with grey shading indicating ecoregions [19] where these broad morphology types are likely to be found [17]. Panels A-C compare example morphologies of
each representative species with the model forms embedded within numerical and experimental simulations (derived from reef colonies digitized in the field,
kindly provided by The Hydrous, http://www.thehydro.us). The three coral archetypes are broadly representative of a reef benthos observed globally.
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PLOS ONE A framework to quantify flow through coral reefs

processes of attenuation are also observed in oscillatory flows, except that this attenuation is
typically much less than that observed in steady flows [33]. Thus, quantification of steady flow
attenuation is of particular importance, has broad applicability and can serve as a foundation
to help explain the observed variation of in-reef flow with coral morphology and cover under
idealized conditions.
In this study, we present a practical framework for predicting the ratio of horizontally-aver-
aged in-reef and near-surface velocities for the three coral archetypes in Fig 1. Our numerical
approach considers steady currents over a single coral colony, with one of three morphologies
that broadly represent the global range, within a domain with cyclic boundaries (thus repre-
sentative of an infinite reef). We first present the theoretical basis for the framework. We then
explain how the framework was validated using high resolution Computational Fluid Dynam-
ics (CFD) numerical models. We also describe the parameter domain that we explore numeri-
cally to test the broad applicability of our framework as well as validate the numerical model in
the laboratory. Next we present the results from the validation and numerical simulations and
demonstrate the first-order accuracy of the predictive framework. Finally we discuss the per-
formance of the framework, how this framework can be extrapolated to mixed reef environ-
ments, as well as how the application of this framework may assist in understanding a wide
range of reef processes.

Methods
Analytical framework for in-reef velocity
The analytical framework presented here builds on previous work by others, such as that by
Lowe et al [33]. It predicts the ratio (β) of the horizontally- and depth-averaged in-reef velocity
(Uc, Fig 2) to the velocity well above the reef benthos (U1):
U1 DU
b¼ �1þ ; ð1Þ
Uc Uc

where ΔU is the difference between U1 and Uc.

Fig 2. Conceptual model of the flow above and within benthos on a coral reef. For a given water depth (H), the near-surface flow velocity (U1) is greater
than that within the reef region (Uc), which is defined by the height of the benthos (h) above the seabed. The plan area (Ap) and frontal area (Af) are shown for
the three archetypal coral forms in Fig 1 (“Table”, “Massive” and “Branching”). Note that Af is not simply the total coral area projected into the flow; rather, it is
the sum of the projected areas of all coral surfaces.
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PLOS ONE A framework to quantify flow through coral reefs

The attenuation of the in-reef flow occurs due to the substantial drag forces imposed by
coral reef colonies. For a given coral colony, this drag is typically described through a quadratic
law relating the drag force (FD) to the depth-averaged in-reef flow velocity (Uc) and the area of
the coral colony projected into the flow (the “frontal area” in Fig 2, Af):

1
FD ¼ rC A U 2 ; ð2Þ
2� D f c

where ρ is the density of water, CD is a drag coefficient and ϕ is the porosity of the reef colony,
which was calculated by treating the canopy as a box with the upper limit defined at the top of
the coral morphology (z = h); the porosity is then equal to one minus the ratio of coral solid
volume to box volume. We discuss the limitations of this approach to some morphologies such
as plate corals later in the discussion. While complex forms such as branched corals (e.g., Pocil-
lopora edyouxi) have been suggested to act as bluff bodies [34], Af is not simply the total coral
area projected into the flow; rather, it is the sum of the projected areas of all coral surfaces (as
all coral surfaces will exert drag and create flow attenuation). What this means is that, for
example, for a branching coral each branch along the flow direction axis contributes to
increase Af. We note this is not trivial for practical applications and we propose an approach to
address this later. In this study, we evaluate the area projected into the incoming flow of each
individual element (e.g., each individual branch) of each morphology and define Af as the sum
of these projected areas.
When this is extrapolated to the reef scale, the drag force exerted per unit reef area and unit
fluid density is:

1
fD ¼ C l U2; ð3Þ
2� D f c

where λf (which is non-dimensional) is the total benthos frontal area per unit reef surface area.
Below we show that λf is a critically-important determinant of the in-reef flow. While evalua-
tion of CD for a complex coral reef colony is not straightforward, measured values tend to lie
in the range 0.5–2 [35–39]. Rather than try to quantify small changes in drag coefficient with
coral and flow characteristics, we instead assume a constant value of CD = 1 for all coral mor-
phologies. This assumption is borne out of practical necessity, as utilization of the framework
presented here requires assumption of a coral drag coefficient value (which is otherwise not
easily predicted). Later we discuss the implications of our choice and the need for a practical
strategy to define CD, particularly for ‘non-front-facing’ morphologies.
For the case where the current is driven by a surface slope (e.g., tidal currents, wave break-
ing induced currents, etc.), conservation of momentum over the entire depth (H) and for a
given water surface slope (S) requires a balance of the driving hydraulic gradient (left hand
side of Eq 4) and the reef benthos drag (Eq 3, right hand side of Eq 4):

1
gHS ¼ C l U2; ð4Þ
2� D f c

which can then be rearranged as:

!12
2�gHS
Uc ¼ : ð5Þ
CD lf

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PLOS ONE A framework to quantify flow through coral reefs

The shear stress at the top of the reef benthos (τc) can also be deduced from a momentum
balance, such that the shear velocity at the top of the benthos (u� ) is given by:
rffiffiffi
tc 1=2
u� � ¼ ðgðH hÞSÞ ; ð6Þ
r

where g is the gravitational acceleration constant and h is the average height of the reef ben-
thos. In flows over rough colonies, the shear velocity increases linearly with the velocity differ-
ence across the benthos (ΔU):
u� � kDU; ð7Þ

where k is a coefficient of proportionality [40]. Substitution of (5), (6) and (7) into (1) yields:
1=2 � � ��1=2
u ðgðH hÞSÞ CD lf h
b¼1þ � ¼1þ � �1=2 ¼ 1 þ k
�
1 ð8Þ
kUc � H
k 2�gHS
CD lf

pffiffi
with k� ð¼ 1= 2kÞ a modified coefficient. Eq 8 implies that flow attenuation within a reef ben-
thos tends to zero (i.e. β ! 1) in the limits of both vanishing benthos frontal area (λf!0) and
emergence of the benthos from the water (h/H ! 1). Later in the discussion we propose how
this framework can be applied in practice.

Numerical model
To demonstrate that the framework in Eq 8 is applicable across a range of coral morphologies,
we conducted numerical simulations of flow through colonies of the three coral archetypes
(Fig 2). Values of β were estimated across a wide range of coral cover (the ratio of the total
coral colony planar area to the total reef surface area, Fig 2), flow depth and speed, and colony
orientations relative to the flow (Table 1).
High-resolution computational fluid dynamics (CFD) simulations were conducted to
obtain detailed information about the vertical and horizontal structure of the 3D in-reef flow
across a wide range of system variables (Table 1) and coral morphologies (Table 2). We main-
tained the same coral morphology dimensions in the numerical model that were used in the
laboratory validation. Large Eddy Simulations (LES) were run in the CFD solver OpenFOAM
[41], which has proven a reliable tool for modelling complex flow around bluff bodies [42] and
through aquatic canopies [43], including coral reef benthos [44]. A dynamic kinetic energy
subgrid-scale model was employed [as in 45].
One coral colony was placed in the horizontal center of the computational domain (as
shown in Fig 4B). Cyclic boundary conditions were implemented on all four vertical domain
walls, such that the model represents an infinite, uniformly-arranged array of each

Table 1. The range of parameter values considered in the numerical simulations for each archetype coral colony morphology.
Morphology Form Table Massive Branching
Example Species Acropora hyacinthus Porites lobata Pocillopora edyouxi
Coral cover (%) 0.10, 0.15, 0.20, 0.25, 0.30, 0.40 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.40, 0.50 0.10, 0.15, 0.20, 0.25, 0.30, 0.40
Depth H (m) 0.16 0.06, 0.10, 0.16, 0.20, 0.30, 0.40, 0.50 0.16†
Flow direction (˚) 0 0†, 45, 90, 180 0
-1 †
Depth-averaged velocity [m s ] 0.16 0.16 0.05, 0.16, 0.50
†
Default values for simulations

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PLOS ONE A framework to quantify flow through coral reefs

Table 2. Geometry of each archetypal coral colony morphology used in the numerical models and experimental validation.
Morphology Form Table Massive Branching
Example Species Acropora hyacinthus Porites lobata Pocillopora edyouxi
Height, h (cm) 3.4 5.1 5.6
Plan area, Ap (cm2) 76.7 50.7 63.6
Frontal area, Af (cm2) 17.1 θ = 0˚ 29.9 95.1
θ = 45˚ 33.6
θ = 90˚ 38.1
θ = 180˚ 29.6

Af is not simply the total coral area projected into the flow; rather, it is the sum of the projected areas of all coral surfaces (as all coral surfaces will exert drag and create
flow attenuation).
Ap was calculated as the coral area projected onto a horizontal plane (i.e. as seen from above).

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morphology [46–48]. Coral cover was adjusted by varying the horizontal domain size. While
this approach to modelling an irregular natural reef system may appear simplified, we note
that, at reef-scale, the drag imposed by regular and random arrays with the same cover is, to
first order, equivalent. This has been demonstrated for cylinder arrays, for which the average
drag is approximately the same for regular and random arrays (noting that at the individual
element level, the drag can indeed vary) [43]. Thus, given that our aim is to computationally
resolve the horizontally-averaged in-reef velocity, we believe that this simplification is both
practically necessary and appropriate.
The numerical domain was generated using utilities in the OpenFOAM package. The
blockMesh utility was used to generate the grid, which was then adjusted via the snappyHex-
Mesh tool to fit the mesh to the surface of the coral morphology. Coral surfaces and the under-
lying bed were specified as no-slip boundaries, with the upper surface of the domain (i.e. the
water surface) treated as a non-zero-velocity, zero-flux slip boundary. Four mesh sizes were
tested to determine the point of mesh insensitivity (defined as the mesh size where velocity val-
ues changed by less than 3%).
All simulations were initially run for 60 s to ensure the flow reached quasi-steady state,
determined from time series of the horizontally averaged velocity at z = h/2. After the initial
spin up, each simulation was continued for a minimum of 10 flow-through periods, during
which the velocity data were obtained. While LES provides time-dependent flow output, only
the steady-state velocities are presented here. Critically, model results were validated against
data from laboratory flume experiments.

Simulation cases and data analysis

We conducted 21 simulations across the three archetype coral colony morphologies with vari-
able coral cover (5–50%, Table 1). For these simulations, default values of the depth-averaged
velocity (0.16 m s-1) and water depth (0.16 m) were maintained. To determine the impact of
additional system variables on flow attenuation, we maintained a coral cover of 20% and varied
(i) the water depth (0.06–0.50 m) for a massive morphology, (ii) the angle of the flow (0-180˚)
relative to the orientation for a massive morphology, and (iii) the depth-averaged inflow veloc-
ity (0.05–0.50 m s-1) for the branched morphology. Given that our framework is physically-
based, a computationally expensive factorial study was not required here. Rather, it was more
important that the key variables controlling the in-reef flow were firstly identified, and then
varied over realistic field ranges.
To validate the numerical model, laboratory experiments were conducted in a small (30 cm
x 30 cm) open-channel flow flume (Fig 3A). Experiments employed the massive and branched

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Fig 3. (A) Example of an experimental setup of the branching morphology used for directly measuring velocities in reefs comprised of
3-D printed coral specimens. (B) Comparison of within- and above-reef velocities predicted by the model with those observed in the
laboratory. There is excellent agreement between model and experimental velocity values (RMSE = 0.008).
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morphologies 3D printed at the same scale as in the numerical model (Table 2). The morphol-
ogies were arranged in the flume to form a 2.0-m-long reef flat of specific coral cover (10%,
20% and 30%). Flow velocities above and within the artificial reef benthos were measured at 25
Hz using an Acoustic Doppler Velocimeter located 1.6–2.0 m downstream of the front of the
reef. To obtain accurate spatially-averaged in-reef and near-surface velocities, the mean veloc-
ity was measured at 6–10 points in horizontal planes both within and above each reef. Repre-
sentative velocities (Uc and U1) were taken as depth-averaged values of horizontally-averaged
velocities in a 3-cm-tall profile: from z = 0.5–3.5 cm (spanning 0.1 ≲ z/h ≲ 1) for the in-reef
velocity and from z = 7.0–10.0 cm (spanning 1.3 ≲ z/h ≲ 3) for the near-surface velocity. This
provided mean in-reef and above reef velocities with standard errors that were, on average,
10% and 1% respectively. The measured spatially-averaged flow velocities above and within
the coral benthos agreed with model results to within an average of 4% (Fig 3B). This demon-
strates that the use of a single coral in numerical simulations (with cyclic boundary conditions)
generates high-fidelity estimates of the in-reef velocity, and of the velocity ratio β.

Results
Spatial variation of velocity in reef flows
Vertical profiles of the temporally- and horizontally-averaged velocity (<u>(z)) are shown in
Fig 4A for all three colony types with a coral cover of 20%. In all cases, there is a region of
roughly uniform, attenuated flow that extends from the seabed to the top of the coral colonies
(i.e. 0 < z/h < 1), and a uniform high-velocity region well above the colonies. These regions
are separated by a strong shear layer [24] where the flow velocity changes rapidly. In the
numerical model, we evaluated the near-surface velocity (U1) as that 0.01 m below the water
surface, and Uc as the mean velocity in the region 0 < z < h across the entire horizontal extent
of the domain (i.e. a horizontally- and vertically-averaged velocity, Fig 4A). While the choice

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Fig 4. (A) Vertical profiles of the temporally- and horizontally-averaged velocity (<u>) for the archetypal coral
forms. The shading represents the vertical region used to calculate the depth-averaged in-reef velocity (Uc). (B) The
significant horizontal variability (at z/h = 0.5) of the instantaneous flow field within a reef consisting of the branched
morphology.
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of how U1 and Uc are evaluated non-trivially impacts the value of β, it does not alter the vali-
dation of the framework and the predictive capacity developed in this paper.
There is also substantial horizontal variability of the in-reef flow velocity (Fig 4B). For the
branched colony case in Fig 4, there are distinct regions of low flow within its branches, as well
as within its wake, with faster channelized flow in the gaps between adjacent colonies. Far
above the branching colony the flow velocity is 0.20 m/s, while at mid-height (z/h = 0.5) the
velocity is 0.048 ± 0.055 m/s (horizontal mean ± spatial standard deviation, Fig 4B).

Impact of key system parameters on flow attenuation

A wide range of β was observed in this study (1.4–5.3, Fig 5) across a relevant range of key sys-
tem variables (coral cover, coral morphology, water depth, coral orientation relative to the
flow and flow velocity). Here, we demonstrate the extent of flow attenuation, and its sensitivity
to coral morphology and other system parameters.
Coral cover. For all morphologies, there is a linear increase of β (from 1) with increasing
coral cover (Fig 5A). For a given water depth, coral cover is the parameter with the greatest
influence on β, with the greatest values for cover exceeding 30%.
Morphology. For given coral cover, the branching form consistently generates the great-
est flow attenuation (Fig 5A). This is due to all the individual branches contributing to a signif-
icantly enhanced total frontal area per unit reef surface area (Table 2). That is, for a fixed

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Fig 5. The extent of flow attenuation β for the three archetypal coral forms is impacted by: (A) the colony coral cover,
(B) the water depth H, (C) the angle of the approaching flow to the morphology θ, and (D) the near-surface velocity
U1. Where particular parameters were not varied, they took the default values in Table 1: coral cover of 20%, a depth
of 0.16 m, a depth-averaged velocity of 0.16 m s-1 and θ = 0˚. The coral cover and water depth have the greatest
influence on β. The grey lines demonstrate general trends, but do not represent a particular functional form.
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amount of biomass, corals that have thin, branching entities (that maximizes the organismal
frontal area) will impact flow velocity much more so than a near-spherical shaped form (a
shape which may minimize organismal frontal area).
Water depth. Consistent with Eq 8, β increases with the water depth in shallow flow
before becoming independent of water depth in deeper flow (here when H � 0.3 m, or H/h >
6, Fig 5B).
Orientation. β is moderately sensitive to the orientation of the coral morphology relative
to the flow for the massive morphology (Fig 5C), as the frontal area projected into the flow
changes (and thus λf in Eq 8). Here, an orientation of 0˚ indicates that the narrow end of the
massive morphology is oriented into the flow (see Fig 1). For a 90˚ change in the flow direc-
tion, there is a 27% increase in the frontal area projected by the morphology, and a corre-
sponding 30% increase in β (Fig 5C).
Flow velocity. There is negligible variation of β with the depth-averaged velocity (Fig 5D).
This implies that the model Reynolds numbers (Re = Ud/ν, where ν is fluid kinematic viscosity
and d is a characteristic width), which are indicative of field values, are sufficiently high that β
is independent of Reynolds number (and thus velocity itself).

Predictive capacity of analytical framework

Assuming an invariant drag coefficient, the analytical framework presented in Eq 8 predicts
that (β─1) will increase with α1/2, where
� �
lf h
a¼ 1 : ð9Þ
� H

Indeed, across all the numerical simulations conducted here and across all the dimensions
of variation considered in Fig 5 (coral morphology, coral cover, water depth, orientation angle

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PLOS ONE A framework to quantify flow through coral reefs

Fig 6. The performance of the predictive model (Eq 8) in collapsing the effects of reef colony morphology, coral
cover, water depth, orientation and flow velocity into a single predictor variable for in-reef flow attenuation. The
solid markers indicate the coral cover cases for the three archetypal coral forms. The open markers indicate cases
where depth, orientation or velocity (as indicated in brackets in the legend) were varied systematically for one coral
morphology. The equation for the line of best fit is indicated on the plot, with the shading representing the 95%
prediction interval.
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and flow velocity), there is an excellent agreement between the data and the prediction curved
for β and α (R2 = 0.70, Fig 6). The measure of this agreement increases to R2 = 0.86 when the
three noticeably different table cases are excluded (we discuss the reason for this in the next
section). The line of best fit in this figure represents the relationship β─1 � α1/2. The agree-
ment of the data across morphologies as well as the agreement of the functional forms of the
line of best fit and Eq 8 validate the analytical framework presented here (which has a single
predictor variable, α).

Discussion
Predictability of flow on coral reefs
The agreement of the data with the curve of β on α (Fig 6) is a fundamentally-important result,
as it implies that the canopy-averaged in-reef flow attenuation within the benthos of a coral
reef can be predicted through knowledge of three core parameters regardless of coral species:
the benthos frontal area per unit reef area, the height of the benthos and the water depth. Devi-
ations from the predicted curve (Eq 8) are likely to be associated with changes in the true val-
ues of coral drag coefficient CD, which can be reasonably expected to vary according to
morphology but were assumed constant in our estimation of α. For example, the numerical
experiments show slightly greater flow attenuation for the table colony with high coral cover
(Fig 6). This deviation can be explained by a unique feature of this morphology: namely, the
large plan area (rather than frontal area) of these colonies. This geometry has the effect of pro-
viding flow resistance in the form of skin friction that is not embedded within the analytical
framework (and ultimately serves to increase the effective value of the drag coefficient in Eq 3).
Consistent with this unaccounted-for flow resistance, the flow attenuation of the table colony
is higher than would otherwise be expected. A better understanding of the variation of CD with
coral morphology would assist to constrain these deviations and we suggest that initial efforts
could focus on accounting for non-front-facing morphologies (e.g., table corals). While CD is
expected to vary based on the flow and morphology, this variation is somewhat small relative
to the natural variation of other components that make up the predictor variable (α). Further-
more, the scale at which inhomogeneity of coral morphologies affects drag warrants further
investigation. While studies of cylinder arrays suggest that the average drag is similar for both
homogeneous and inhomogeneous arrays, at an individual colony scale the drag can be

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expected to be different [43]. Notwithstanding these areas that required further investigation,
to first-order we suggest that the general model (Fig 6) is appropriate for estimating in-reef
velocities across the full range of morphologies.

Implementation of framework in practice

To apply this framework, four key data are required: (1) a spatial map of reef benthos species
(to ultimately determine reef frontal area and porosity), (2) the height (h) of the reef benthos,
(3) the total water depth (H) and (4) the surface velocity (U1). We recognize that not all of this
data will always be available, however we believe that it can be practically obtained. Spatial
maps of reef benthos are routinely assembled by diver [49, 50], drone [51], aerial [52] or satel-
lite [53, 54] methods. These maps of coral cover and occasionally species composition, which
are more important than the orientation of the reef benthos to the flow, can be used to inform
the choice of λf/ϕ (the component of α that is determined by coral cover and morphology).
This requires quantitative allometric relationships between λf/ϕ and the more easily-obtained
measure of coral cover. For the three archetypes employed here, indicative forms of such rela-
tionships are presented in Fig 7. We believe that these curves represent the typical range of
forms of the λf/ϕ-coral cover relationship, a table coral minimizes frontal area per unit biomass
while branches serve to maximize it. Such curves can be developed for other morphological
forms with relative ease using techniques such as CT scanning [55] of colony fossils.
The three remaining pieces of data are less difficult to determine. The geometric height of
the benthos can be obtained in a number of different ways including from representative spot
measurements or vessel mounted echo-sounders [56], as well as from aerial LIDAR [31],
Structure from Motion imagery [51, 57, 58] or even from satellite imagery [59]. The water
depth can be determined from surface elevation data or in situ hydrodynamic measurements
with wave or tide gauges [60]. Finally, the near-surface velocity can be obtained by surface
tracking of objects such as drifters [61] or by tilt meters and acoustic instruments [1, 51, 62]
that can measure velocity well above, but not within, the reef. All methods are commonly used
in hydrodynamic and monitoring studies.
An obvious consideration is how this framework can be applied to a reef composed of a
range of coral species. The nature of this framework is such that mixed benthos can be charac-
terized as the sum of the frontal areas of its constituent parts, contributing to a ‘total’ value of
λf/ϕ in Fig 6. Importantly, the canopy frontal area per unit reef surface area controls the resis-
tance exerted on the flow through form drag. Practically, this area can be estimated spatial
maps of reef benthos and allometric relationships of the form shown in Fig 7.

Implications for coral reef process understanding, resilience and

restoration
Traditional approaches used to describe the hydrodynamic impact of coral reef benthos is
through a friction coefficient that describes the impact of reef on the overlying flow [35]. This
approach, however, does not allow prediction of the flow within the benthos, which is relevant
to the wide range of reef processes that govern coral reef health and function. The framework
proposed in this study enables this flow to be estimated through the inclusion of Eq 8 within
established numerical models (for example as a wall-type function) and, importantly, without
the need to explicitly resolve the physical structure of the benthos in these models at regional
scales. This is a major step forward in understanding the range of environmental transport
processes on reef systems (of, for example, heat, nutrients and in some cases biota), the future
of reef-adjacent coasts (i.e., the supply and loss of sediment) and quantitative design of reef res-
toration activities.

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PLOS ONE A framework to quantify flow through coral reefs

Fig 7. The allometric relationship between coral cover and the resultant value of λf/ϕ for three archetypal benthos
colony forms (“table”, “massive” and “branching”) which are based on observations of the representative species
Acropora hyacinthus [15], Porites lobata [15] and Pocillopora edyouxi [16], respectively. The markers indicate
data from the numerical simulations. The shaded area roughly represents the range of typical values based on the
results of this study.
https://doi.org/10.1371/journal.pone.0279623.g007

Acknowledgments
The authors would like to thank Erika Woolsey at The Hydrous who provided the digital coral
models used in this study. We would also like to thank Sai Htin Aung, Campbell Kirk, Phui
Joan Lai and Cody Narlock who undertook the laboratory validation experiments at the Uni-
versity of Melbourne as well as Taylor Simpkins at the University of Western Australia, Curt
Storlazzi and Benjamin Norris at the US Geological Survey for their feedback on the study and
manuscript.

Author Contributions
Conceptualization: Andrew W. M. Pomeroy, Marco Ghisalberti.
Formal analysis: Andrew W. M. Pomeroy, Marco Ghisalberti, Michael Peterson, Vahid Etmi-
nan Farooji.
Methodology: Andrew W. M. Pomeroy, Marco Ghisalberti, Michael Peterson, Vahid Etminan
Farooji.

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PLOS ONE A framework to quantify flow through coral reefs

Project administration: Andrew W. M. Pomeroy.

Supervision: Andrew W. M. Pomeroy, Marco Ghisalberti.
Validation: Andrew W. M. Pomeroy, Michael Peterson.
Visualization: Andrew W. M. Pomeroy, Michael Peterson.
Writing – original draft: Andrew W. M. Pomeroy, Marco Ghisalberti.
Writing – review & editing: Andrew W. M. Pomeroy, Marco Ghisalberti, Michael Peterson,
Vahid Etminan Farooji.

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