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Seascape ecology studies indicate that the spatial arrangement of habitat types and the topographic complexity of the seascape are major environmental drivers of fish distributions and diversity across coral reef ecosystems. Impairment of one component of an ecologically functional habitat mosaic and reduction in the architectural complexity of coral reefs is likely to lower the quality of habitat for many fish including important fished species. Documented declines in coral cover and topographic complexity are reported from a decade of long-term coral reef ecosystem monitoring in SW Puerto Rico. To examine broader scale impacts we use “reef flattening scenarios” and spatial predictive modeling to demonstrate how declining seascape complexity will lead to contractions and fragmentation in the local spatial distribution of fish. This change may result in impaired connectivity, cascading impacts to ecological functioning and reduced resilience to environmental stressors. We propose that a shift in perspective is needed towards a more holistic and spatially-explicit seascape approach to ecosystem-based management that can help monitor structural change, predict ecological consequences, guide targeted restoration efforts and inform spatial prioritization in marine spatial planning.
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Proceedings of the 63
Gulf and Caribbean Fisheries Institute November 1 - 5, 2010 San Juan, Puerto Rico
Importance of Seascape Complexity for Resilient Fish Habitat and Sustainable Fisheries
Biogeography Branch, Center for Coastal Monitoring and Assessment, National Oceanic and Atmospheric Administration,
Silver Spring, Maryland 20910 USA.
Marine Science Center, University of the Virgin Islands, 2 John Brewers Bay, St.
Thomas, VI00802, U.S. Virgin Islands. *
Seascape ecology studies indicate that the spatial arrangement of habitat types and the topographic complexity of the seascape
are major environmental drivers of fish distributions and diversity across coral reef ecosystems. Impairment of one component of an
ecologically functional habitat mosaic and reduction in the architectural complexity of coral reefs is likely to lower the quality of
habitat for many fish including important fished species. Documented declines in coral cover and topographic complexity are
reported from a decade of long-term coral reef ecosystem monitoring in SW Puerto Rico. To examine broader scale impacts we use
“reef flattening scenarios” and spatial predictive modeling to demonstrate how declining seascape complexity will lead to
contractions and fragmentation in the local spatial distribution of fish. This change may result in impaired connectivity, cascading
impacts to ecological functioning and reduced resilience to environmental stressors. We propose that a shift in perspective is needed
towards a more holistic and spatially-explicit seascape approach to ecosystem-based management that can help monitor structural
change, predict ecological consequences, guide targeted restoration efforts and inform spatial prioritization in marine spatial
KEY WORDS: Topographic complexity, seascape ecology, predictive modeling
Importancia de la Complejidad del Paisaje Marino para el Habitat Resistente
de Peces y las Pesquerías Sostenibles
PALABRAS CLAVE: Complejidad del paisaje marino, ecología marina, modelos de predicción
Importance de Complexité de Paysage Marin pour L'habitat Resilient
de Poissons et la Pêche Soutenable
MOTS CLÉS: Complexité de paysage marin, l’écologie marine, modélisation prédictive
Coral reef ecosystems exhibit complex spatial
heterogeneity in physical structure across a range of spatial
scales (Hatcher 1997). Studies that have applied a
multiscale landscape ecology approach have demonstrated
that the composition and spatial configuration of two-
dimensional seascape mosaics (Grober-Dunsmore et al.
2008, Huntington et al. 2010), as well as, the three-
dimensional terrain morphology are important drivers of
the distribution, abundance, and behavior of marine
organisms (Pittman and Brown 2011). Although more
studies are now incorporating two-dimensional models of
the seascape in marine ecology (such as thematic benthic
habitat maps), these are comprised of discrete patch types
and sharp discontinuities representing seascape heteroge-
neity only in the horizontal dimension, essentially, “a
flatscape”. Yet, the three-dimensional topographic
complexity of the seascape rarely is modeled at spatial
scales that are operationally meaningful for management
frameworks. In recent years, however, airborne remote
sensing techniques are providing highly accurate and
relatively fine resolution spatial representations of three-
dimensional seafloor structure (Brock et al. 2004).
Techniques such as bathymetric LiDAR (Light Detection
and Ranging) provide high resolution digital bathymetry
from which vertical seafloor complexity can be quantified
at multiple spatial scales. The seafloor heterogeneity can
then be analysed as a terrain using tools more typically
applied in terrestrial geomorphology and industrial
meterology, where measures of troughs and peaks and
anomalies in surface roughness are important. Using a
wide range of surface metrics, Pittman et al. (2009) and
Pittman and Brown (2011) demonstrated the utility of
LiDAR bathymetry (and lidar derived vertical seafloor
complexity) for predicting the distribution and abundance
of fish and corals in southwest Puerto Rico.
However, structurally complex coral reefs are proving
vulnerable in the face of rapid environmental change.
Human activity in the coastal zone - combined with
hurricanes, bio-erosion, disease and thermal stress - have
resulted in region-wide loss and degradation of biogenic
structure created by reef forming scleractinian corals
(Hughes et al. 2003, Gardner et al. 2003). Furthermore, the
loss of structure and any recovery from loss may be
compounded by ocean acidification, with as yet unknown
impacts for Caribbean coral reefs. A pan-Caribbean meta-
analysis using data on coral reef rugosity estimated that
coral reef complexity had declined by more than 50% since
its 1960’s levels (Alvarez-Filip et al. 2009) (Figure 1). A
concurrent decline in the abundance of a wide range of fish
species across the region has also occurred that is thought
to be partly a result of habitat degradation (Paddack et al.
Pittman, S.J. et al. GCFI:63 (2011) Page 421
2009). These declines are likely to have triggered cascad-
ing impacts throughout the ecosystem (Cheal et al. 2008),
adding fresh impetus to the urgent need to understand
broad-scale environmental correlates, such as topographic
complexity that influence species distributions across
tropical seascapes (Pittman and Brown 2011).
The ecological significance of LiDAR derived
seafloor complexity to marine fish provides the key to a
new cost-effective tool for forecasting and hindcasting
some impacts to fish from changes to the surface complexi-
ty of coral reef ecosystems. The ability to predict impacts
will support the development of realistic expectations for
recovery and restoration for coral reef areas that are either
accreting or eroding and will help anticipate the effects of
reductions in habitat suitability for commercially important
food fish. Here we highlight the importance of topographic
complexity in maintaining intact coral reef ecosystems in
SW Puerto Rico using data collected by the National
Oceanic and Atmospheric Administration’s Biogeography
Branch. Using in-situ monitoring data we show a decline in
both live coral cover and the structural complexity of coral
reefs in SW Puerto Rico during the past decade. Then
using simulated flattening of surface complexity for the
entire study area, we predict and map the impact that
declining complexity will have on habitat suitability for
positive influence of structural complexity on marine
faunal distributions and ecological processes, but the
majority of evidence comes from relatively fine-scale
studies conducted across meter and sub-meter spatial
scales. Recent evidence demonstrates that high resolution
(1 - 4 m) measures of topographically complexity collected
across tropical seascapes (100s - 1000s meters), also
provides powerful predictive capability for modeling
broader scale spatial patterns of biodiversity and species
distribution. In SW Puerto Rico, Pittman et al. (2009)
compared a wide range of measures of topographic
complexity derived from LiDAR bathymetry and found
that the “slope of the slope” (a first derivative of slope)
contributed most to models of fish species richness and
distributions of individual species. Models and mapped
predictions for individual species were subsequently
refined by inclusion of the statistical interactions between
slope of the slope and the geographical location across the
insular shelf (distance to shore & shelf) in SW Puerto Rico
(Pittman & Brown 2011). For example, in SW Puerto
Rico, high habitat suitability for Stegastes planifrons
(threespot damselfish) increased almost linearly with
increasing complexity, although spatially the species was
restricted by the interaction with depth and by cross-shelf
location. Similarly, studies from Jamaica, Belize, Cayman
Islands, Florida and Bahamas demonstrated that the
availability of shallow water topographically complex
microhabitats were the most important proximal controls
on S. planifrons distribution and abundance (Precht et al.
2010). Threshold effects are also evident where, below a
certain level of complexity, the habitat becomes sub-
optimal for a species and can no longer support its
occurrence at that location. Identifying these critical
threshold values and describing the associated precursor
conditions that lead to tipping points will be crucial for
anticipating the ecological consequences of eroding and
collapsing coral reefs.
Study area
The coral reef ecosystems of the insular shelf of
southwestern Puerto Rico (Figure 2) exist as a spatial
mosaic of habitat types dominated by coral reefs, seagrass-
es, mangroves and patches of sand. The seafloor is highly
heterogeneous in assemblage composition and topographic
structure resulting in a diverse and productive fish
community, with important ecological, economic and
cultural value. Like many Caribbean coral reef ecosystems
the study area has experienced environmental changes on
land and sea that have resulted in loss of structural and
functional integrity. The environmental history and
ecology of the region was documented in Pittman et al.
Figure 1. Changes in reef rugosity across the Caribbean
between 1969 and 2008. Steepest decline occurred be-
tween 1969-1985 and rugosity after the mid-2000s was at
the lowest levels recorded in the time series (Adapted from
Alvarez-Filip et al. 2009).
two species of fish associated with Caribbean coral reefs.
Seafloor Terrain Complexity as an Important Spatial
Predictor for Coral Reef Ecosystems
It is generally accepted as axiomatic in ecology that
within a region, environments with greater architectural
complexity support higher species richness and higher
abundance for certain species than nearby environments
with low complexity (MacArthur and MacArthur 1961).
Coral reef ecosystems have been shown to exemplify the
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Gulf and Caribbean Fisheries Institute
Underwater Survey Methods for Fish and Benthic
Underwater visual surveys of fish and benthic habitat
were conducted semi-annually (Jan/Feb and Sept/Oct)
across the insular shelf at La Parguera (322 km
) between
2001 and 2008 as part of a broader long-term monitoring
program. Survey sites (n = 1,018) were selected using a
stratified-random sampling design whereby sites were
randomly located within two mapped strata (i.e., hardbot-
tom and softbottom) derived from National Oceanic and
Atmospheric Administration's nearshore benthic habitat
Fish surveys were conducted within a 25 m long and 4
m wide (100 m
) belt transect deployed along a randomly
selected bearing (0 - 360°). Constant swimming speed was
maintained for a fixed duration of fifteen minutes to
standardize the search time. Abundance data for five
common species were converted to presence-only data.
Fish data are available online at
To conduct benthic habitat surveys and collect
percentage cover data on scleractinian corals, an observer
placed a 1 m
quadrat at five random locations along the
fish transect. The quadrat was divided into 100 smaller
squares (10 x 10 cm). Corals were identified to genus (and
species where possible) and percent cover was estimated to
the nearest 0.1 %. Rugosity was measured with a six meter
chain (1.3 cm chain link) draped over the contoured surface
at two positions along the fish transect. The straightline
horizontal distance was measured with a tape. An index of
rugosity was calculated as the ratio of contoured surface
distance to linear distance, using R = 1-d/l, where d is the
contoured distance and l is the horizontal distance (6 m).
Chain-and-tape rugosity was only measured over hardbot-
tom sites in the study area.
Spatial Predictive Modeling
Fish species occurrence (or species presence) data
from underwater visual surveys was linked statistically to a
suite of spatial predictors derived from LiDAR bathymetry
following the multiscale analytical approach of Pittman
and Brown (2011). Topographic complexity was modeled
as the slope of the slope averaged in a 25 m radius moving
window across the entire study area from the landward
fringe to the shelfedge. MaxEnt (Maximum Entropy
Distribution Modeling) software (Phillips et al 2006;
Phillips and Dudik 2008) was used to model and map
spatial predictions as probabilities of species presence.
Using MaxEnt we exploit the strength of the fish-terrain
relationship to develop preliminary and exploratory models
of species distributions under varying scenarios of reef
flattening. Using GIS tools, our slope of the slope layer
was uniformly reduced across the entire terrain by 25 % to
represent the estimated decadal decline for SW Puerto
Rican coral reefs, and 50 % approximating Caribbean-wide
declines since the 1960s. This was used as a proof-of-
concept for our initial forecasting experiments. Predictions
of high habitat suitability (using consistent probability
threshold for each scenario) were then re-mapped for two
common fish species: i) a herbivorous scraper, Scarus
taeniopterus (Princess parrotfish); and ii) an indicator of
live coral cover, Stegastes planifrons (threespot damsel-
fish). Mapped predictions were overlain and examined for
differences in spatial patterning and area of suitability
habitat under different reef flattening scenarios was
quantified and compared to measure the change.
Changes to Coral Reef Structure in SW Puerto Rico
and the Wider-Caribbean
Underwater visual census from 572 sites where
benthic cover had been estimated semi-annually over a
seven year period (2001 - 2007) revealed significant
declines in live coral cover (Figure 3). Monitoring beyond
2007 showed continued decline to < 4% mean live coral
cover across the region by 2010. At these same sites,
measures of surface complexity using the chain-tape
method indicated that coral reefs had “flattened” signifi-
cantly in the past 10 years by an estimated 25 % (Figure 4).
Simulated Flattening of Coral Reef Complexity to
Model and Map Impacts to Fish
When the predictions from models using variable
levels of flattening were overlain in a GIS, visual examina-
tion of differences in the spatial patterning of high
suitability habitats for both species indicated a clear
contraction in range as terrain complexity declined. In
addition, the suitable habitat became more fragmented
Figure 2. Study area of SW Puerto Rico showing LiDAR
derived bathymetry across the insular shelf and the
locations of stratified-random biological survey sites
conducted between 2001 and 2008 by NOAA’s Biogeogra-
phy Branch.
Pittman, S.J. et al. GCFI:63 (2011) Page 423
leaving patches that were small islands of suitable habitat
surrounded by large expanses of sub-optimal areas (Figure
5). Suitable habitat for Princess parrotfish (Scarus
taeniopterus) contracted by 30 % with a 25 % flattening of
terrain complexity, and as much as 66 % was lost when
terrain was flattened by 50 %. With 25 % flattening,
habitat was lost from the edges of large contiguous patches
of suitable coral reef, probably where structure had already
existed near the lower thresholds of suitability. With a 50
% flattening patches of suitable habitat fragment even
more and few large contiguous patches remain, whereas
the number of small patches with relatively small interiors
of habitat increased across the seascape.
When impacts to threespot damselfish (Stegastes
planifrons) habitat suitability were assessed with a 25 %
flattening of terrain complexity, model comparison
revealed a 56 % loss of suitable habitat. Considerable
heterogeneity was observed in the patterns of loss, with
some clustering of high loss areas along many of the
shallow fringing reef slopes around mid-shelf islands and
the coral reefs between the Laurel, San Cristobal, and El
Palo reefs. Species-specific differences in the magnitude of
lost habitat (i.e. higher for threespot damselfish under a 25
% flattening scenario) are likely to relate to the specificity
for habitat requirements determined by a species’, relative
position along the specialist-generalist gradient of habitat
use, and how close the existing structural complexity is to
the threshold of a particular species. A small decline in
complexity would be expected to have a greater impact on
habitat suitability for areas with complexity already near
the tipping point for unsuitable habitat for a particular
species. See also color figures of predictions for entire
study area in non-print electronic version of the manuscript
(Figures 1 & 2 Appendix 1).
Understanding the ecological consequences of losing
structural complexity of coral reefs is a crucial knowledge
gap in our understanding of impacts to coral reef ecosys-
tems (Wilson et al. 2010). Long-term monitoring data
collected over multiple years across a wide range of coral
reef habitat types has provided an early warning of broad
scale declines in the structural complexity of coral reefs in
SW Puerto Rico. This structural decline was likely
exacerbated by the longer-term trends of declining
Figure 3. Trend in mean live coral cover (%) for the SW
Puerto Rico study area estimated from semi-annual
surveys conducted between 2001 and 2008 by NOAA’s
Biogeography Branch (source: Pittman et al. 2010).
Figure 4. Decline in rugosity of coral reefs in
the SW Puerto Rico study area over a ten year
period (2001 and 2010) based on chain-tape
measurements conducted by NOAA’s Biogeog-
raphy Branch.
Figure 5. Predicted habitat suitability for threespot
damselfish (Stegastes planifrons) across a subset of the
SW Puerto Rico study area using i.) Unaltered LiDAR-
derived topographic complexity; and ii) Numerically
flattened topographic complexity to simulate 10 year
declines for coral reefs in SW Puerto Rico. MaxEnt was
used for modeling predictions.
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Gulf and Caribbean Fisheries Institute
impacts to topographic complexity will vary by depth,
distance to shore, type and intensity of human activities,
coral community composition and possibly even patch
characteristics. Studies by Alvarez-Filip et al. (2011b)
showed that annual rates of change in reef complexity
varied significantly between coral reefs across the
Caribbean. Yet patterns of change can also be counterintu-
itive. For example, Alvarez-Filip et al. (2011a) found that
coral reef topographic complexity (measured as rugosity)
had declined more in marine protected areas than in
comparable unprotected areas in the Caribbean. The
authors speculate that bioerosion from increasing herbivo-
rous fish populations may have been the cause.
Simulating the spatial impact of these stressors even
across the local seascape is a complicated challenge with
insufficient information currently available to inform such
as model. Development of proxies, however, would allow
us to compare a range of scenarios to examine resultant
impacts. Integration of data available from detailed
ecological studies and long-term monitoring programs
should enable us to begin to piece together sufficient
information to develop reliable scenarios of structural
change which can then be utilized to predict impacts on a
wide range of marine biota. Such spatial predictions can
then be analyzed using spatial pattern metrics from
landscape ecology to quantify and investigate the losses
and gains and the magnitude of fragmentation in local
patterns of species distributions and biodiversity. Frag-
mentation of suitable habitat may disrupt movement
patterns of individuals, impair metapopulation connectivity
leading to isolated dysfunction patches with reduced
population viability, shifts in community composition and
cascading effects through foodwebs and resiliency of
ecosystems. However, existing exploratory studies
indicate that species with different habitat requirements
and preferences will respond differently to changes in
structural complexity; it will be important to identify any
species-specific sensitivities and critical threshold beyond
which an area no longer provides suitable habitat.
High resolution LiDAR data show strong potential as
a data type that, when combined with comprehensive
underwater visual survey data and analyzed with sophisti-
cated spatial predictive modeling algorithms, can help
determine thresholds in topographic complexity below
which habitat no longer supports viable populations of
specific fish species.
The SW Puerto Rico study area has experienced
marked deterioration in coral reef health concurrent with
an increase in stressors and a significant decline of
commercially targeted fish, with some local extirpations of
several large-bodied and late maturing species (Jeffrey et
al. 2010, Pittman et al. 2010). It is conceivable, however,
that even if fishing were restricted or excluded in the study
branching acroporid species and a shift to a macroalgal
dominated benthic community (Pittman et al. 2010, Jeffrey
et al. 2010). Together these changes are analogous to
changes detected in a Caribbean-wide analyses of rugosity,
whereby reductions in coral cover were followed by loss of
architectural complexity with little evidence of a time-lag
(Alvarez-Filip et al. 2009 and 2011b). Elsewhere in the
region, shifts in coral dominance from Acropora and
Montastraea spp. to more stress-resistant and lower
complexity species such as Agaricia and Porites spp. has
been documented (Alvarez-Filip et al. 2011b). Where
Montastraea annularis is still an important reef-building
species, growth rates have declined over the past 15 years
(Edmunds and Elahi 2007) and Porites astreoides has
increased (Green et al. 2008). This trend is expected to
have major consequences for fish communities, but the
spatially explicit implications of reducing terrain surface
complexity has not before been examined for Caribbean
Although, the ecological ramifications through the
ecosystem are still largely unknown, we now know that
many fish species and assemblage variables correlate with
LiDAR derived measures of terrain surface complexity,
which provides opportunities to manipulate the three-
dimensional surface structure and investigate correspond-
ing impacts to habitat suitability for fishes. This modeled
relationship provides a cost-effective technique to forecast
(and hindcast) effects of varying surface complexity. Our
proof-of-concept modeling here was a first step in this new
direction, yet developing realistic spatial simulations of
flattening at relevant spatial scales is challenging. The
information required to map the spatial patterns and
processes that influence bioerosion, bleaching and physical
collapse across highly heterogeneous and connected land-
sea ecosystems is still lacking. Neither is information
readily available on the likely rates of change at operation-
ally relevant scales. Nevertheless, evidence that structural
complexity is declining in many regions is mounting.
Ecological impacts will need to be anticipated to ensure
that management actions are well targeted and that
expectations for recovery after protection are ecologically
We recognize that more spatially complex scenarios
are required to refine our predictions since a uniform
flattening is likely to be over-simplistic. Depth will likely
be an important consideration, since impacts to deeper
coral reefs may be very different to shallow reefs and
shallow sheltered reefs may be very different than shallow
exposed reefs. Clearly, stressors operate across a hierarchy
of scales. Impacts to coral reef structure from hurricanes,
bioeroders and direct human activities are spatially
heterogeneous processes operating at relatively local
scales, whereas thermal stress and ocean acidification
operate at considerable broader spatio-temporal scales.
Regardless of the type of stressors involved, differential
Pittman, S.J. et al. GCFI:63 (2011) Page 425
region at some point in the future, the role of degraded
benthic habitat must be considered when setting and
communicating expectations for rates of recovery and in
assessing the suitability of habitat for the most vulnerable
and large-bodied fish species. Based on the present
trajectory in ecosystem health and stressors, future habitat
structure in this region may no longer be capable of
offering the necessary ecological functions of food and
refuge that it once did; instead it may be impaired to a
point where only sub-optimal habitat remains. Therefore,
such coral reefs are likely to recover more slowly com-
pared with coral reefs with greater structural integrity.
Changes in topographic complexity should not be consid-
ered the only seascape measures of habitat suitability for
fish associated with coral reefs, since fish are highly
mobile and many key species require mosaics of connected
habitat to maintain viable populations. Therefore, resource
management agencies and associated monitoring programs
interested in maintaining or restoring sustainable fisheries
must also consider other components of seascape change,
such as loss of seagrasses and mangroves, which may
reduce the availability of critical resources for fish species
or reduce connectivity across ontogenetic life stages
(Pittman et al 2007, Grober-Dunsmore et al. 2009).
Through interconnectedness, loss and degradation of these
surrounding habitat mosaics can also influence the
suitability of coral reefs as fish habitat independent of
declining coral reef complexity.
Managing Habitat Mosaics and Terrains for Resilient
Ecosystems and Sustainable Fisheries
We propose that a shift towards a more holistic and
spatially-explicit approach to ecosystem-based manage-
ment is needed and that a seascape approach can help
guide targeted restoration efforts and ecologically relevant
spatial prioritization in marine spatial planning. Specifical-
ly, we recommend:
i) A shift in emphasis from monitoring, managing
and restoring individual habitat types to a focus
on protecting and restoring optimal seascape
types based on ecological requirements of species
and communities,
ii) Identifying and prioritizing seascape types that
support high biodiversity, productivity and key
species of concern,
iii) Understanding vulnerability of mosaic integrity to
environmental stressors in order to predict the
consequences of impaired structure for mosaic
function including connectivity,
iv) Utilizing terrain morphology and benthic habitat
maps to predict diversity patterns, map essential
fish habitat including critical life history spaces
such as nursery areas and spawning areas,
v) Identifying tipping points in habitat structure
beyond which abrupt change is expected to help
anticipate impacts and set targets for restoration,
vi) Developing management strategies and actions
that reduce threats to structural integrity and
actively help to re-build lost structure.
We thank Richard Appeldoorn of the University of Puerto Rico for
inviting us to participate in the theme session on Management of Coral
Reef Ecosystems at the 63
GCFI meeting in San Juan, Puerto Rico. We
are grateful to all of our scientific divers for many years of data
collection. Funding for research and conference attendance was provided
by NOAA’s Coral Reef Conservation Program and NOAA’s Biogeogra-
phy Branch.
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... This was further demonstrated by significant relationships between fish abundances and soft coral cover. The complex spatial heterogeneity of coral reefs is a major driver of the distribution, diversity and behaviour of reef-associated fishes (Pittman et al. 2010) and as such, it is important to explore relationships with all habitat-forming organisms. ...
The composition of coral reef habitats strongly influences associated fish assemblages. As habitat formers, soft corals constitute a morphologically diverse component of coral reefs, although their importance as fish habitat is largely unquantified. Our study assessed relationships between soft and hard coral habitats and assemblages of reef-associated fishes on inshore reefs of the Whitsunday Islands, focussing on pomacentrids, chaetodontids and pomacanthids. Study sites varied in hard and soft coral cover and were assessed by the level of exposure to previous cyclone damage. The soft coral community was dominated by Sinularia spp. and constituted an average of 11.4% of benthic cover compared to 16% hard coral cover. At fine spatial scales (250 m ² ), significant positive relationships between soft coral cover and abundance occurred for 2 species of pomacentrids (Amblyglyphidodon curacao and A. leucogaster) as well as total Chaetodontidae and Pomacanthidae. Further, it was clear that some taxa were associated with specific soft corals. For example, A. curacao , Pomacentrus lepidogenys and Chelmon rostratus were observed associating with branching digitate Sinularia , with a more structurally complex soft coral morphology. The combination of high and medium cover of hard and soft corals supported distinct assemblages of fishes and the highest abundances of many species at the scale of sites (1000 m ² ). Our results indicate that soft corals provide valuable habitat, supporting diverse fish assemblages by contributing to habitat mosaics on coral reefs. These findings suggest that the ecological role of soft corals has been underestimated and therefore holds direct implications for the management of coral reefs.
... The restricted depths could be explained by a greater light availability and increased primary productivity at the shallowest areas (Sigman and Hain, 2012), thus providing more suitable habitats for the species. Moreover, rocky habitats with high complexity have been identified to be more profitable for many fish species (García-Charton and Pérez-Ruzafa, 2001;García-Charton et al., 2004;Pittman et al., 2011;Abecasis et al., 2014), as they provide refuge and shelter against predators and increase accessibility to food (Gratwicke and Speight, 2005;Claudet et al., 2011). Additionally, eastness contributed to marginality only in area with low density of fish (Table 2). ...
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Marine Protected Areas (MPAs) are useful tools for the conservation of fishes, providing that they include the essential habitats for the focal species. Habitat selection may depend on external (i.e., environmental conditions, food availability, and shelter) and internal (i.e., density-dependent processes) factors. Additionally, most fishes undergo ontogenetic shifts along their life cycles, thus, understanding the habitat requirements at each stage is of great interest for the correct design and functioning of MPAs. Here, we evaluated habitat preferences of high-level predatory fishes, namely Epinephelus marginatus, Epinephelus costae, Mycteroperca rubra, Dentex dentex, Sciaena umbra and Sphyraena viridensis to assess differences between species, maturity stages and density of fish. To do so, we applied Species Distribution Models (SDMs) in protected and unprotected areas along the coast of Murcia (SE Spain) to determine if those areas are properly located for the conservation of the focal species. We included three areas with different density of fishes. One area with high density in the long-term protected Cabo de Palos-Islas Hormigas MPA, and two with low density in the newly established Cabo Tiñoso MPA and the unprotected area of Cabo Cope. We evaluated the environmental variables that affect the occurrence of the species at two life stages, before and after achieving size at maturity. SDMs showed that bathymetry, habitat complexity and rocky bottoms were the most important drivers determining species distribution in both areas with high and low density of fish, although there were differences in the contribution of the variables at each location. Additionally, we found that habitat requirements were different for the immature and mature individuals, generally being the immatures the most sensitive to changes in habitats. Both MPAs and the unprotected area largely included areas of high suitability for the studied species, indicating that the MPAs are established in proper areas, and suggesting another area for the establishment of a new MPA to enhance a MPA network in the region.
... Although there are challenges to effectively use citizen-generated data to monitor invasive species on a global scale (Earp and Liconti, 2020;Johnson et al., 2020), it can be a useful tool to detect and monitoring the bioinvasion processes (present study). In this sense, special emphasis has been placed on the underwater seascape, as highlighted in previous works performed in other research fields (Pittman et al., 2011;Gobert et al., 2014;Cheminée et al., 2016;Schejter et al., 2017;Ceraulo et al., 2018). The monitoring of an area by comparative images reflecting "before" and "after" scenarios due to bioinvasion processes as a proxy of BACI analyses (Before After Control Impact) (Underwood, 1994;Montefalcone et al., 2008;Conner et al., 2015;Donázar-Aramendía et al., 2018, may offer key information on the degree of affection that the local ecosystem has suffered and the risk of its prevalence in the area. ...
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The invasive macroalga Rugulopteryx okamurae represents an unprecedented case of bioinvasion by marine macroalgae facing the European coasts. Since the first apparition of the species in the Strait of Gibraltar in 2015, its fast dispersion along the introduced habitats constitutes a real challenge to develop monitoring strategies that ahead of its impacts. The present study uses three different approaches to address impacts on the benthic ecosystems, at the same time offers relevant data for future management actions in El Estrecho Natural Park (PNE). Information obtained by monitoring permanent sentinel stations revealed a significant loss in resident species coverage after the moment of maximum growth in 2017. Thus, despite coverage of R. okamurae did not strongly varied in the latter years, impacts generated remain high in the habitats studied. Estimations of the invasive species coverage by combining cartographic image analysis and in situ data predicted a major occupation (over 85% coverage) between 10 and 30 m, coinciding with the maximum rocky surface areas (m 2) mapped on the PNE. Furthermore, a Citizen Science research collaboration evidenced impacts on the benthic seascape through an ad hoc exploration of images that allowed a "before" and "after" comparison of the invasion process in the same geographic locations. This has made it possible to graphically demonstrate severe changes in the underwater seascape and, therefore, the general impact of this new biological invasion. The spatial colonization estimations combined with the impacts reported by both scientific [Sessile Bioindicators in Permanent Quadrats (SBPQ) sentinel stations] and civilian (Citizen Science) monitoring methodologies claim the urgent development of further studies that allow the design of monitoring strategies against R. okamurae expansion across the Mediterranean and Atlantic waters.
... For example, Debrot et al. [62] documented significant habitat deterioration of seagrasses and mangroves in one of the largest inland bays on Curaçao (Spanish Water), which is the most important nursery habitat for many fishes on the island [63]. Confirming earlier studies relating reef complexity and the abundance of reef-associated fishes [21,64,65] and species other than fish [66], this example is only serves to illustrate that in addition to fishing, several forms of habitat degradation also contribute to the observed declines of at least certain fish species. ...
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Effective assessments of the status of Caribbean fish communities require historical baselines to adequately understand how much fish communities have changed through time. To identify such changes and their causes, we compiled a historical overview using data collected at the beginning (1905–1908), middle (1958–1965) and end (1984–2016) of the 20th century, of the artisanal fishing practices and their effects on fish populations around Curaçao, a small island in the southern Caribbean. We documented historical trends in total catch, species composition, and catch sizes per fisher per month for different types of fisheries and related these to technological and environmental changes affecting the island’s fisheries and fish communities. We found that since 1905, fishers targeted species increasingly farther from shore after species occurring closer to shore had become rare. This resulted in surprisingly similar catches in terms of weight, but not composition. Large predatory reef fishes living close to shore (e.g., large Epinephelid species) had virtually disappeared from catches around the mid-20th century, questioning the use of data from this period as baseline data for modern day fish assessments. Secondly, we compared fish landings to in-situ counts from 1969 to estimate the relative contributions of habitat destruction and overfishing to the changes in fish abundance around Curaçao. The decline in coral dominated reef communities corresponded to a concurrent decrease in the abundance and diversity of smaller reef fish species not targeted by fishers, suggesting habitat loss, in addition to fishing, caused the observed declines in reef fish abundance around Curaçao.
... Future tropical and temperate reef fish predictive modeling studies could benefit from including a combination of both 2D and 3D covariables. LiDAR-derived habitat complexity can also provide a cost-effective spatial approach for forecasting the potential impacts to fish communities through changes in reef complexity at local (e.g., hurricanes, direct anthropogenic stressors) and regional spatial-temporal scales (e.g., climate-induced thermal stress and ocean acidification) ( Pittman et al. 2011). Major findings could relate directly to the spatial scale of the analysis ( Estes et al. 2018) and LiDAR provides the flexibility to explore relationships between the seascape and fish assemblage structure at multiple scales. ...
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LiDAR (light detection and ranging) allows for the quantification of three‐dimensional seascape structure, which is an important driver of coral reef communities. We hypothesized that three‐dimensional LiDAR‐derived covariables support more robust models of coral reef fish assemblages, compared to models using 2D environmental co variables. Predictive models of coral reef fish density, diversity, and biomass were developed using linear mixed effect models. We found that models containing combined 2D and 3D covariables outperformed models with only 3D covariables, followed by models containing only 2D covariables. Areas with greater three‐dimensional structure provide fish more refuge from predation and are crucial to identifying priority management locations that can potentially enhance reef resilience and recovery. Two‐dimensional seascape metrics alone do not adequately capture the elements of the seascape that drive reef fish assemblage characteristics, and the application of LiDAR data in this work serves to advance seascape ecology theory and practice in the third dimension. LiDAR (light detection and ranging) allows for the quantification of three‐dimensional seascape structure, which is an important driver of coral reef communities. We found that three‐dimensional LiDAR‐derived covariables support more robust models of coral reef fish assemblages, compared to simpler models (e.g., models using 2D environmental variables). Furthermore, areas with greater three‐dimensional structure provide fish more refuge from predation and are crucial to identify biodiversity hotspots, areas of greater potential fish biomass and locations to prioritize for spatial management.
... Around the island of St John, USVI, reef edges are associated with high topographical complexity (Figure 14), a biogeomorphological pattern that is also associated with high coral cover and fish species richness. The ecological significance of topographical complexity as a key contributor to the geographical distribution of fish richness highlights serious ecological consequences for the long-term capacity of reefs to support high diversity given the recent widespread declines in the topographical complexity of Caribbean reefs (Alvarez-Filip, Dulvy, Gill, Côté, & Watkinson, 2009;Pittman, Costa, Jeffrey, & Caldow, 2010;Rogers, Blanchard, & Mumby, 2014). In general, seascape predictors played an important contribution only at relatively fine spatial scales across the scale range. ...
Geographical patterning of fish diversity across coral reef seascapes is driven by many interacting environmental variables operating at multiple spatial scales. Identifying suites of variables that explain spatial patterns of fish diversity is central to ecology and informs prioritization in marine conservation, particularly where protection of the highest biodiversity coral reefs is a primary goal. However, the relative importance of conventional within-patch variables versus the spatial patterning of the surrounding seascape is still unclear in the ecology of fishes on coral reefs. A multi-scale seascape approach derived from landscape ecology was applied to quantify and examine the explanatory roles of a wide range of variables at different spatial scales including: (i) within-patch structural attributes from field data (5 × 1 m2 sample unit area); (ii) geometry of the seascape from sea-floor maps (10–50 m radius seascape units); and wave exposure from a hydrodynamic model (240 m resolution) for 251 coral reef survey sites in the US Virgin Islands. Non-parametric statistical learning techniques using single classification and regression trees (CART) and ensembles of boosted regression trees (TreeNet) were used to: (i) model interactions; and (ii) identify the most influential environmental predictors from multiple data types (diver surveys, terrain models, habitat maps) across multiple spatial scales (1–196,350 m2). Classifying the continuous response variables into a binary category and instead predicting the presence and absence of fish species richness hotspots (top 10% richness) increased the predictive performance of the models. The best CART model predicted fish richness hotspots with 80% accuracy. The statistical interaction between abundance of living scleractinian corals measured by SCUBA divers within 1 m2 quadrats and the topographical complexity of the surrounding sea-floor terrain (150 m radius seascape unit) measured from a high-resolution terrain model best explained geographical patterns in fish richness hotspots. The comparatively poor performance of models predicting continuous variability in fish diversity across the seascape could be a result of a decoupling of the diversity-environment relationship owing to structural degradation leading to a widespread homogenization of coral reef structure.
... The scale and extent of these datasets however, are often small and patchy (Hughes et al., 2005;Knudby et al., 2013), making them unsuitable for large scale MSP endeavors (Collie et al., 2013). Seascape properties, such as benthic cover and structural complexity can be used as proxies or surrogates of important ecosystem properties, including biodiversity, species distributions, ecological processes, and ecosystem goods and services (Mellin et al., 2011;Mumby et al., 2008;Pittman et al., 2010). This information is increasingly obtained through remote sensing methods, allowing data collection on large scales (see Diaz et al. (2004) for a review of methods). ...
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The cartography of ecological units at a detailed level requires differentiating them by the associations of coral species, but also by the use of physical and biotic attributes. Remote sensors have limitations to perform this type of discrimination; this is not only due to the spectral response of the coral species, which is very similar, but also to their variation in abundance, which can be considerable within the same ecological unit; the abundance can be so low, that their identification can go unnoticed when interpreting satellite images. In order to provide clues to propose criteria for the delimitation of ecological units, in the present study, and through the use of Bray-Curtis similarity index and multivariate analyzes, spatial distribution patterns of biotic assemblages and their relationship with the geomorphology in the Seaflower Biosphere Reserve were identified and analyzed, both, at the level of reef complexes [Serrana, Roncador, Quitasueño and Providence Island (SRQP)], and in the particular case of San Andrés Island (SAI) coral reefs. In general, spatial distribution trends among the identified biotic assemblages were recognised with respect to geomorphology, when they nested to one or two specific geomorphological units. This shows that the geomorphological units, rather than indicate the presence of a particular ecological unit, provide indications of a series of possibilities. In some cases, the patterns were expressed within the geomorphological units, which suggest the need to carry out analyses at a more detailed geomorphological scale. On the other hand, the increase in the abundance of macroalgae seems to create noise in the identification of ecological units, and that these present a high abundance does not necessarily indicate that the richness or the coral abundance should be low, which implies the need to establish delimitation thresholds. It is concluded that in order to establish criteria for the delimitation of ecological units at higher detail, the spatial distribution patterns of biotic assemblages are indispensable. Consequently, four criteria are proposed for the delimitation of ecological units (1. Biotic, 2. Biotic-Geomorphology-Zoning, 3. Biotic-Cover (Remote sensing), 4. Biotic-Macroalgae), which in addition to including biotic assemblages and geomorphological aspects, they must be complemented with various physical attributes that make up the landscape of these coral areas.
The structure of seafloor terrain affects the distribution and diversity of animals in all seascapes. Effects of terrain on fish assemblages have been reported from most ecosystems, but it is unclear whether bathymetric effects vary among seascapes or change in response to seafloor modification by humans. We reviewed the global literature linking seafloor terrain to fish species and assemblages (96 studies) and determined that relief (e.g. depth), complexity (e.g. roughness), feature classes (e.g. substrate types) and morphology (e.g. curvature), have widespread effects on fish assemblages. Research on the ecological consequences of terrain have focused on coral reefs, rocky reefs, continental shelves and the deep sea (n ≥ 20 studies), but are rarely tested in estuaries (n = 7). Fish associate with a variety of terrain attributes, and assemblages change with variation in the depth and aspect of bathymetric features in reef and shelf seascapes, and in the deep sea. Fish from different seascapes also respond to distinct metrics, with fluctuations in slope of slope (coral reefs), rugosity (rocky reefs) and slope (continental shelves, deep sea) each linked to changes in assemblage composition. Terrain simplification from coastal urbanization (e.g. dredging) and resource extraction (e.g. trawling) can reduce fish diversity and abundance, but assemblages can also recover inside effective marine reserves. The consequences of these terrain changes for fish and fisheries are, however, rarely measured in most seascapes. The key challenge now is to examine how terrain modification and conservation combine to alter fish distributions and fisheries productivity across diverse coastal seascapes.
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It could be argued that in recent decades conservation biology has been a field centred on damage limitation – controlling biodiversity loss, human-wildlife conflict, park boundaries, etc. However, 20 years from now, it could well have transformed into a ‘crisis’ science, characterized by last ditch efforts to prevent species extinctions, attempts to resurrect ‘phoenix’ species extirpated in previous decades, translocations of species to new or restored habitats in response to territory lost to climate change or other perturbations and increasingly invasive mediation in biological processes to prop up failing ecosystems and crumbling food webs. In concert with growing concerns for species declines and environmental degradation in past decades, our tools for protecting and conserving our environmental heritage have become more sophisticated and refined. Twenty years from now, we will still be fighting some of the same conservation battles, together with some new ones, but our conservation tools will have evolved.
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The functional roles of certain reef fishes are considered to facilitate recovery of reef ecosystems following coral mortality. Maintenance of high fish species diversity and associated functional diversity are thought to represent an ‘ecological insurance’ against ecosystem degradation. We examined responses of reef fish communities to varied levels of coral decline on 22 individual reefs of the Great Barrier Reef over an 11 yr period. Using 7 measures of species diversity, we found that fish diversity rarely decreased due to coral declines, even on 7 reefs that suffered massive coral losses (cover decreased by >75%). However, maintenance of fish diversity on those 7 reefs belied major changes in fish communities that involved increases in abundance of large herbivores and decreases in abundance of both coral-dependent fishes and species with no obvious dependence on coral. The magnitude of change in species abundances increased linearly with the magnitude of coral decline. While the proportion of species that increased or decreased in abundance varied considerably among reefs, 45 to 71% of fish species decreased in abundance on some reefs. Ecological function is related to abundance, so such decreases are likely to indicate reduced ecosystem function. Our results suggest that: (1) reef fish diversity may not be a reliable indicator of reef resilience and (2) predicted declines in coral cover due to global warming are likely to cause changes in the structure of reef fish communities, but the nature of these changes and associated capacity of reef fishes to assist ecosystem recovery will vary among reefs.
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The architectural complexity of coral reefs is largely generated by reef-building corals, yet the effects of current regional-scale declines in coral cover on reef complexity are poorly understood. In particular, both the extent to which declines in coral cover lead to declines in complexity and the length of time it takes for reefs to collapse following coral mortality are unknown. Here we assess the extent of temporal and spatial covariation between coral cover and reef architectural complexity using a Caribbean-wide dataset of temporally replicated estimates spanning four decades. Both coral cover and architectural complexity have declined rapidly over time, with little evidence of a time-lag. However, annual rates of change in coral cover and complexity do not covary, and levels of complexity vary greatly among reefs with similar coral cover. These findings suggest that the stressors influencing Caribbean reefs are sufficiently severe and widespread to produce similar regional-scale declines in coral cover and reef complexity, even though reef architectural complexity is not a direct function of coral cover at local scales. Given that architectural complexity is not a simple function of coral cover, it is important that conservation monitoring and restoration give due consideration to both architecture and coral cover. This will help ensure that the ecosystem services supported by architectural complexity, such as nutrient recycling, dissipation of wave energy, fish production and diversity, are maintained and enhanced.
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The ecosystem concept has been applied to coral reefs since the time of Charles Darwin, perhaps because of the apparent integrity of the biotic-abiotic nexus. The modern model of the ecosystem as a hierarchy with emergent properties is exemplified in reefs as massive structures formed by small colonial organisms, the self-similarity of these structures across large spatial scales, and the uniformity of function by diverse biological communities. Emergent properties arise through the integration of processes up the levels of organization and larger spatial and temporal scales encompassed by a whole reef. The organic response of reef morphology to hydrodynamic forcing, the constancy and conservatism of organic production across a broad range of environments, and the global persistence of reefs in the face of massive evolutionary change in species diversity are interpreted as emergent properties. Coral reefs, of course, function by the same basic laws as other ecosystems, but there is cause to view them as an end member of a continuum because of their structural complexity and high internal cycling. Well-defined boundary conditions mean that highly integrative measures of ecosystem process based on physical and biogeochemical models (e.g. community metabolism) have provided the main applications of systems ecology to questions of coral reef function. Organism-population approaches are being reconciled with form-functional models to yield new insights to ecosystem processes and interactions among reefs and adjacent systems. The form and metabolism of reef production are strongly affected by phase shifts in benthic community structure, and most reef systems are more open to trans-boundary fluxes and external forcing than the early models suggest. The attractive paradigm of the reef as a self-sufficient ecosystem is dying slowly as research focus shifts from atolls to more open fringing and bank barrier reefs, and organic inputs to system production are measured. Coral reefs contribute little in a net sense to global ecosystem processes, but on an areal basis their exports of organic products are significant. Holistic models and measures of ecosystem processes incorporate the unusual whole-part relationship of reefs and are practically essential to answering the key questions facing coral reef science in the next millennium.
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Connectivity across the seascape is expected to have profound consequences for the behavior, growth, survival, and spatial distribution of marine species. A landscape ecology approach offers great utility for studying ecological connectivity in tropical marine seascapes. Landscape ecology provides a well developed conceptual and operational framework for addressing complex multi-scale questions regarding the influence of spatial patterning on ecological processes. Landscape ecology can provide quantitative and spatially explicit information at scales relevant to resource management decision making. It will allow us to begin asking key questions such as ‘how much habitat to protect?’, ‘What type of habitat to protect?’, and ‘Which seascape patterns provide optimal, suboptimal, or dysfunctional connectivity for mobile marine organisms?’. While landscape ecology is increasingly being applied to tropical marine seascapes, few studies have dealt explicitly with the issue of connectivity. Herein, we examine the application of landscape ecology to better understand ecological connectivity in tropical marine ecosystems by: (1) reviewing landscape ecology concepts, (2) discussing the landscape ecology methods and tools available for evaluating connectivity, (3) examining data needs and obstacles, (4) reviewing lessons learned from terrestrial landscape ecology and from coral reef ecology studies, and (5) discussing the implications of ecological connectivity for resource management. Several recent studies conducted in coral reef ecosystems demonstrate the powerful utility of landscape ecology approaches for improving our understanding of ecological connectivity and applying results to make more informed decisions for conservation planning. KeywordsSeascape ecology–Landscape ecology–Connectivity–Spatial scale–Pattern metrics–Fish
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The NASA Experimental Advanced Airborne Research Lidar (EAARL), a temporal waveform-resolving, airborne, green wavelength LIDAR (light detection and ranging), is designed to measure the submeter-scale topography of shallow reef substrates. Topographic variability is a prime component of habitat complexity, an ecological factor that both expresses and controls the abundance and distribution of many reef organisms. Following the acquisition of EAARL coverage over both mid-platform patch reefs and shelf-margin bank reefs within Biscayne National Park in August 2002, EAARL-based optical indices of topographic variability were evaluated at 15 patch reef and bank reef sites. Several sites were selected to match reefs previously evaluated in situ along underwater video and belt transects. The analysis used large populations of submarine topographic transects derived from the examination of closely spaced laser spot reflections along LIDAR raster scans. At all 15 sites, each LIDAR transect was evaluated separately to determine optical rugosity (Ro tran ), and the average elevation difference between adjacent points (Av(δE ap )). Further, the whole-site mean and maximum values of Ro tran and Av(δE ap ) for the entire population of transects at each analysis site, along with their standard deviations, were calculated. This study revealed that the greater habitat complexity of inshore patch reefs versus outer bank reefs results in relative differences in topographic complexity that can be discerned in the laser returns. Accordingly, LIDAR sensing of optical rugosity is proposed as a complementary new technique for the rapid assessment of shallow coral reefs.
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Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape.
Conference Paper
Coral reef ecosystems comprise of interconnected habitats including mangrove forests, seagrass beds, unconsolidated sediments, and coral reef and hardbottom substrates, all of which provide shelter and sustenance for fishes that form the basis of important fisheries in the Caribbean. Monitoring of such habitats in Southwestern Puerto Rico from 2001 to 2007 revealed complex spatial patterns in benthic composition that often correlated with the distribution and abundance of fishes. Depth and rugosity of substrates correlated positively with coral cover and taxa richness and influenced the abundance and size-class structure of parrotfishes. Measures of benthic composition were also useful in Maxent predictions of potential occurrence and size-class distribution of scarid assemblages. Benthic characterizations provide the basis for identifying species-habitat relationships, increase our understanding of spatial patterns in the distributions of habitats, and illustrate important and crucial linkages for the successful management of coral reef fisheries and other important marine resources.
On Caribbean reefs, a striking trend of the last 25 years has been the decline in cover of the framework-building coral Montastraea annularis, a species that has dominated reefs throughout the region for millennia. Clearly, such losses are important ecologically, but to evaluate their significance fully, they need to be placed in the context of the proximal causes and balanced against the potential for gains in cover through growth and recruitment. In this study, a population of M. annularis in St. John, U. S. Virgin Islands, was censused annually from 1988 to 2003 to quantify coral cover and construct a size-based demographic model. The model was developed to explore the mechanisms of change in coral cover and to ascertain likely trajectories for future population growth. Over the study period, the cover of M. annularis declined from 41% in 1988, to; 12% by 1999 (a 72% decline) but remained unchanged statistically for the last five years of the study. Between 1988 and 2003, colony abundances declined by 57% (from 47 colonies/m(2) to 20 colonies/m(2)), and the losses were driven mostly by the death and fission of medium to large colonies (i.e., >= 151 cm(2)). By 2003, the population had proportionally more small colonies (70% were <= 50 cm(2)) and fewer large colonies (3% were > 250 cm(2)) than in 1988 (60% and 6%, respectively), and the changes in population structure had accelerated >= 14% in terms of the rate of change in population size and the time necessary to attain equilibrium of colony size structure. Importantly, this analysis revealed an ongoing and imminent population decline coincident with the recent period of apparently stable coral cover. Fifty-year projections indicate the strong likelihood of extirpation of M. annularis at this particular site in St. John (in contrast to a continuation of constant low cover) and suggest that the 1988 population structure cannot be restored by recruitment. It is unlikely that the population decline will reverse until there is an amelioration of the conditions that kill individual colonies.
On most coral reefs, the percentage cover of scleractinian corals has declined greatly over the last 30 yr; some species that are more resistant to mortality have been less affected than others. Porites astreoides is one species that has become a more prominent com- ponent of coral reef communities throughout the Caribbean. Analyses of coral reefs in shallow water (5 to 6 m depth) at 6 locations spanning a 4100 km arc of the Caribbean were used to evaluate the contri- bution of P. astreoides to contemporary reefs. Photo- quadrats recorded in 2003/2004 were used to esti- mate the percentage cover and colony density of P. astreoides, and colony size-frequency structure was analyzed to gain insight into demographic processes. At all locations, reefs were characterized by
Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time-consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use ‘‘default settings’’, tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence-only data. We evaluate our method on independently collected high-quality presenceabsence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce ‘‘hinge features’ ’ that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore ‘‘background sampling’’ strategies that cope with sample selection bias and decrease model-building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence-only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model