xvEPA
United States
Environmental Protection
Agency
EPA/600/R-12/029 | April 2012 |www.epa.gov/ged
Field Manual for Coral Reef Assessments
Office of Research and Development
National Health and Environmental Effects Research Laboratory
Gulf Ecology Division
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Field Manual for
Coral Reef Assessments
Deborah L. Santavy
William S. Fisher
Jed G. Campbell
Robert L. Quarles
Gulf Ecology Division
National Health and Environmental Effects Research Laboratory
Office of Research and Development
U.S. Environmental Protection Agency
ISabine Island Dr.
Gulf Breeze, FL. 32561
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Notice and Disclaimer
The U.S. Environmental Protection Agency through its Office of Research and Development and
Office of Water funded and collaborated in the research and development of these field
protocols. It has been subjected to the Agency's peer and administrative review and has been
approved for publication as an EPA document. Mention of trade names or commercial products
does not constitute endorsement or recommendation for use.
This is a contribution to the EPA Office of Research and Development's Safe and Sustainable
Water Resources Program, Coral Reefs Project.
The appropriate citation for this report is:
Santavy DL, Fisher WS, Campbell JG and Quarles RL. 2012. Field Manual for Coral
Reef Assessments. U.S. Environmental Protection Agency, Office of Research and
Development, Gulf Ecology Division, Gulf Breeze, FL. EPA/600/R-12/029. April 2012.
This document can be downloaded from EPA's website at:
http://www.epa.gov/ged/publications.html
11
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Table of Contents
Notice and Disclaimer ii
List of Figures v
List of Tables vi
Acknowledgements vii
1.0 Introduction 1
1.1 Biological Water Quality Standards 2
1.2 Ecosystem Services 4
1.3 Measuring Coral Reef Condition 7
1.4 References 11
2.0 Visual Assessment of Reef Fish 14
2.1 What is measured? 14
2.2 Why is it measured? 14
2.3 What do we need? 15
2.4 How are data collected? 16
2.5 How are data managed? 18
2.6 How are indicators calculated? 18
2.7 References 19
3.0 Stony Coral Assessment 21
3.1 What is measured? 21
3.2 Why is it measured? 21
3.3 What is needed? 22
3.4 How are data collected? 24
3.5 How are data managed? 29
3.6 How are indicators calculated? 29
3.7 References 31
4.0 Marine Gorgonian Assessment 33
4.1 What is measured? 33
4.2 Why is it measured? 33
4.3 What do we need? 34
4.4 How are data collected? 37
in
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4.5 How are data managed? 38
4.6 How are indicators calculated? 38
4.7 References 39
5.0 Marine Sponge Assessment 40
5.1 What is measured? 40
5.2 Why is it measured? 40
5.3 What do we need? 41
5.4 How are data collected? 42
5.5 How are data managed? 45
5.6 How are indicators calculated? 45
5.7 References 46
6.0 Reef Rugosity, Live Coral Cover and Macroinvertebrate Assessments 47
6.1 What is measured? 47
6.2 Why is it measured? 47
6.3 What do we need? 48
6.4 How are data collected? 49
6.5 How are data managed? 50
6.6 How are indicators calculated? 51
6.7 References 51
Appendix A: Other Coral Reef Assessment Programs 53
Appendix B: Survey Data Sheets and Data Check List 55
Appendix C: Fish Species Codes, Biomass Coefficients and Trophic Guild Assignments 69
Appendix D: Estimating Surface Area of Gorgonians and Sponges 79
IV
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List of Figures
Figure 1-1: Coral reef communities provide benefits to humans 1
Figure 1-2: Coral reefs provide coastal protection 5
Figure 1-3: Benthic hard bottom maps 7
Figure 2-1: Fish contribute valuable ecological and economic services 14
Figure 2-2: Fish must be identified to species 15
Figure 2-3: Diagram offish survey transect using two divers 17
Figure 2-4: Fork length for different types offish 17
Figure 3-1: Stony corals assessments document the surface area 21
Figure 3-2: Examples of bleaching corals 23
Figure 3-3: Examples of coral disease 23
Figure 3-4: Boring clionid sponges on corals 23
Figure 3-5: Predation on coral tissue 24
Figure 3-6: Colony size and tissue estimates 25
Figure 3-7: Minimum size of coral colony 25
Figure 3-8: All coral colonies <1 m in diameter 26
Figure 3-9: All coral colonies > 1 m in diameter 27
Figure 3-10: Intact coral skeletons with no tissue 27
Figure 4-1: Marine gorgonian assessment for ecosystem services 33
Figure 5-1: Marine sponge assessment for ecosystem services 40
Figure 6-1: Rugosity is a measure of reef surface complexity 47
Figure 6-2: Examples low and high rugosity reefs 48
Figure 6-3: Macroinvertebrates included in the survey 49
Figure 6-4: Adult and juvenile forms of queen conch 50
Figure B-l: Fish Survey Data Sheet 56
Figure B-2: Stony Coral Survey Data Sheet 58
Figure B-3: Gorgonian Survey Data Sheet 60
Figure B-4: Gorgonian and Sponge Survey Data Sheet 62
Figure B-5: Sponge Survey Data Sheet 64
Figure B-6: Rugosity, Biosurvey and LPI Data Sheet 66
Figure B-7: Check List for Data Sheet Actions 67
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List of Tables
Table 1-1: Examples of biophysical measurements 6
Table 2-1: Potential fish indicators 19
Table 3-1: Examples of benefits derived from coral reef ecosystem services 22
Table 3-2: Stony Corals included in Western Atlantic and Caribbean assessments 28
Table 3-3: Regression equations for estimating 3D surface area of corals 31
Table 4-1: Gorgonian morphological shapes 36
Table 4-2: Regression equations to estimate surface area of gorgonians 38
Table 5-1: Sponge morphological shapes 44
Table 5-2: Regression equations to estimate surface area of sponges 45
Table A-1: Some current coral reef monitoring and assessment programs 54
Table C-l: Table offish species, a and P coefficients and trophic guilds 70
VI
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Acknowledgements
The production of this report would not have been possible without the participation of Charles
LoBue, Becky Hemmer, Peggy Harris, Sherry Vickery, Mel Parsons, Alan Humphrey, Scott
Grossman, Richard Henry, Danny Rodriguez, Dan Cooke, Patricia Bradley, and John McBurney.
Development of field protocols was made possible through collaboration with EPA Region 2,
Region 4, and Office of Water. Fish assessment protocols were introduced to us by Marc
Monaco, John Christenson, and Chris Jeffries (NOAA).
Photos are from: Alan Humphrey (EPA ERT), Charles LoBue (EPA Region 2), Peggy Harris
(EPA ORD/NHEERL/GED), and Mel Parsons (EPA Region 4).
The report was peer reviewed by Peggy Harris, Becky Hemmer, Sherry Vickery, Patricia
Bradley, Mel Parsons, Charles LoBue, Wendy Wiltse (U.S. EPA), and Janet Klemm, Florida
Department of Environmental Protection.
Key Words: coral reefs, coral reef assessment, fish, stony corals, octocorals, gorgonians,
sponges, rugosity, macroinvertebrates, assessment protocols, LPI, line point intercept
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1.0 Introduction
The U.S. Environmental Protection
Agency (EPA) is concerned over
the decline of coral reefs in U.S.
jurisdictions1 and around the
world. Coral reefs provide citizens
a variety of aesthetic and tangible
benefits. When human activity
impairs the physical, chemical or
biological integrity of a waterbody
containing a coral reef, it
contradicts the goals of the Clean
Water Act2 (Figure 1-1). Many
national, state and local policies
protect the quality of water and
habitat in U.S. watersheds and
coastal zones. Despite these
policies, reefs have declined
dramatically over the last forty
years, particularly in the Caribbean
Figure 1-1: Coral reef communities provide many important
benefits to humans but they are subject to impairment
through human activities.
and western Atlantic Ocean (Gardner et al. 2003). EPA has initiated two research programs with
potential to improve coral reef protection.
The Safe and Sustainable Water Resources Program (SSWR) supports development of coral reef
biological criteria. Research is focused on developing methods and tools to support implementation of
legally defensible biological standards for maintaining biological integrity, which is protected by the
Clean Water Act (CWA). Under CWA authority and following national guidelines established by EPA
(CWA §303), States and other jurisdictions3 promulgate water quality standards to protect the physical,
chemical and biological integrity of the nation's water bodies. States currently apply physical and
chemical standards at levels intended to be protective of aquatic biological inhabitants. More recently,
the importance of biological standards are gaining acceptance. Biological standards have the benefit of
directly measuring the cumulative effects of good and poor environmental conditions on the biological
community. Because the CWA is intended to protect aquatic resources from changes generated by
human activities (not from natural changes in the environment), the anticipated outcome is regulatory
protection that sustains reef condition equal or similar to a natural state.
The Sustainable and Healthy Communities Program (SHC) is founded on the recognition that natural
ecosystems, despite the many goods and services afforded, are undervalued by human society. The
services that ecosystems provide are too often considered free and limitless; consequently, their values
and benefits to humans are not routinely considered in policies and decisions (MEA 2005). Because we
U.S. jurisdictions with coral reefs include American Samoa, Commonwealth of Northern Mariana Islands, Florida, Guam,
Hawaii, Puerto Rico, Texas (Flower Garden Banks) and U.S. Virgin Islands.
2 Federal Water Pollution Control Act [As Amended ThroughP.L. 107-303, November 27, 2002] 33 U.S. Code 1251 et
seq.; also known as: The Clean Water Act Public Law 92-50033 U.S. Code 1251 et seq.
3 For the purpose of this document, when the term "State" is used it is intended to represent any U.S. jurisdiction, which
includes States, Territories, tribes and Commonwealths.
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generally protect only what we value, the goal of SHC is to quantify market and nonmarket values of
ecosystem services and incorporate them into decision-making processes at local, regional and national
levels. The anticipated outcome for coral reefs is a better understanding and recognition of reef value,
which should lead to decisions that are more protective of the coastal zone. In both EPA research
programs, development of appropriate reef assessment methods is critical.
1.1 Biological Water Quality Standards
EPA Assessment Needs. One of the most influential mechanisms available for aquatic resource
protection is the U.S. Clean Water Act. Unfortunately, the label "clean water" can mislead people to
think that only water quality is protected by the CWA. Protection of the nation's waters also includes
protection of biological systems such as coral reefs. States are responsible under the CWA to establish
water quality standards that define the goals and pollution limits for all waters within their jurisdictions,
including waters of the territorial seas4. In essence, water quality standards translate CWA goals into
measurable objectives, such as the protection and propagation offish, shellfish and wildlife, or
recreation in and on the water (EPA 1994). Water quality standards support the goal of the CWA to
maintain the physical, chemical and biological integrity of water bodies. States are responsible for water
quality criteria, but EPA provides national guidelines and oversight. There are three components of
water quality standards: designated uses, criteria, and antidegradation implementation plans. Most
important for this document is the development of criteria, although coral reef biocriteria cannot be
developed without formal recognition of coral reef protection as a designated use for the water body
(Bradley et al. 2010). Designated uses identify what you want to protect and criteria set the levels
(whether physical, chemical or biological) deemed necessary to achieve that protection.
Historically, jurisdictions have relied on enforcement of chemical and physical criteria to protect
biological integrity (Yoder and Rankin 1998). Yet, some chemical pollutants are hard to measure. In
addition, chemical and physical criteria do not reflect the cumulative impacts of multiple stressors on
biota. A better approach for measuring biological integrity is to assess biological changes. However,
states have been slow to adopt methods for evaluating biological integrity because the measurements are
generally more difficult, and variability is often greater than physical and chemical approaches. Many of
these challenges have now been overcome (EPA 2002) and biological criteria are used regularly in
freshwater and estuarine water bodies5 (EPA 1990, 2000). However, biological criteria are not currently
in place for marine resources, so the full potential of the CWA to protect coral reefs has not been
realized.
Biological criteria may refer to thresholds for expected or desired biological condition. Used in a
regulatory context, biocriteria are narrative or numeric
thresholds adopted by states as legally enforceable standards
of water quality. As such, biological criteria are no different
than chemical criteria for toxicants that establish concentration
limits—if the criteria are not met, the water body must be
reported as impaired (CWA §305b) and restorative actions
undertaken (CWA §303d). An important requirement for
measurements used in biological criteria is that they are able
to detect changes in condition caused by human action. The
Designated Uses:
What you want to protect
Criteria:
Levels or thresholds necessary
to achieve that protection
' The CWA identifies territorial seas as a belt of ocean waters extending three miles (or more in some states) from shore.
5 For examples, see EPA's biocriteria web site at .
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purpose of the CWA is to maintain water bodies in a natural condition free from impairment by
anthropogenic stresses. Serving this purpose, biological criteria are established to set a legal threshold
that distinguishes natural from impaired condition. The measurements used to identify impairment must,
therefore, be responsive (sensitive) to human disturbances. They must also be relevant to the designated
uses, which is why establishing designated uses for coral reef protection is so important. Designated
uses and biological criteria must be vetted through a public discussion, and methods and measurements
must be scientifically defensible and relevant. Anticipating that U.S. jurisdictions will eventually
incorporate coral reef protection as designated uses for marine waters, EPA has initiated studies to
identify reef measurements that reflect ecological integrity and are sensitive to human-generated
disturbances.
Water Quality Standard Measurement Needs. There are two critical requirements for measurements
used in biocriteria: 1) significance to biological integrity and 2) responsiveness to human disturbances.
Biological integrity was first defined as a balanced, integrated, adaptive community of organisms having
a species composition, diversity and functional organization comparable to that of the natural habitat of
a region (Karr and Dudley 1981). Many facets of an ecosystem are incorporated into the concept of
biological integrity. Not all of them can be measured, so measurements or sets of measurements are
selected to serve as indicators. The indicators are selected on the presumption that if these few indicator
measurements are equal or similar to the natural condition, then the water body as a whole supports
biological integrity and is attaining its designated uses. In freshwater biocriteria programs, there are
particular taxonomic groups (assemblages) recognized to have these characteristics (fish, phytoplankton
and insects). Selection of a variety of reef organisms would also reflect overall reef biological integrity,
and a few taxa are sure to be included. Stony corals, for example, provide much of the structural habitat
needed for a diverse reef community. Other key taxa, such as octocorals, sponges and fish may also
serve as indicators of reef biological integrity.
Water quality criteria, whether physical,
chemical or biological, must be measured with
indicators that distinguish anthropogenic effects
from natural changes in the environment. There
are two approaches for evaluating whether an
indicator will distinguish human disturbance—
controlled laboratory exposure-response studies
and empirical relationships drawn from field
studies. Exposure-response studies can be
especially useful for characterizing specific
effects of particular stressors on key organisms
such as stony corals. They are not, however,
effective for quantifying effects of multiple stressors and cumulative stresses over time. Moreover,
relationships established in laboratory settings must be validated in the field before they can be applied
in a regulatory process.
An acceptable field method for testing the sensitivity of indicators to human disturbance is to perform
the candidate measurement at various locations across (inside and outside) an area affected by known
(or measured) human activity. A consistent and logical response across the disturbance gradient implies
a sensitive indicator, at least for those particular disturbances at that particular location. Consistent
response means that the indicator values are in relative proportion to the distance from the center of the
disturbance, and logical response means that the direction of the response makes sense considering our
state of knowledge (e.g., taxa richness is expected to decrease, not increase, with greater human
Biological Integrity
A natural, fully functioning living system of
organisms and communities, plus the
processes that generate and maintain them.
The "living system" incorporates a variety of
scales—from individuals to landscapes—and is
embedded in a dynamic evolutionary and
biogeographic context (Karr 2006).
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Human Disturbance Gradients
An effective approach for identifying biological indicators that are responsive to human
disturbance is to apply candidate indicators across a zone of human disturbance. For
example, an industrial point source along the shore provides an opportunity to test and
evaluate candidate indicators. Those indicators that reflect a consistent and logical change
with distance from the center of disturbance can be considered responsive. The causative
agent of change does not need to be known to identify responsive indicators (metrics).
Industrial area
Land
Water
Stations
Replicates
Different habitat
Area of disturbance ~ 100 m •
disturbance). Ultimately, validation at other locations and for other stressor profiles is required for an
indicator to be considered a metric, acceptable for use in a state biocriteria monitoring program. It is also
important to examine co-varying factors, such as salinity and depth, which might influence biological
responses.
1.2 Ecosystem Services
EPA Assessment Needs. Although we have a great appreciation for coral reefs, society generally fails to
understand and appreciate the benefits they provide. Consequently, reefs and the services they provide
are not always considered in decisions that might affect them. Drawn by the diverse community of
unique and colorful marine organisms, coral reefs attract millions of tourists annually. Coral reefs also
provide very practical goods and services, including food products, aquarium fish, construction material,
beach nourishment, shoreline erosion control, flood protection and potential pharmaceutical products
which all support diverse economic opportunities. These services have led to numerous studies to
estimate the monetary worth of coral reefs6 (Spurgeon 1992; Costanza etal. 1997; Cesar etal. 2003;
Leeworthy et al 2004; Pendleton 2009; TEEB 2009).
6 Estimated global monetary value for coral reefs vary dependent on methods used; some examples are $377B y"1 (Costanza
et al. 1997), $30B y'1 (Cesar et al. 2003) and $172 B y'1 (TEEB 2009).
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Figure 1-2: Coral reefs provide coastal protection by
serving as a barrier to wave and tidal energy.
Several key reef attributes are
responsible for the delivery of these
ecosystem services (Principe et al.
2012). Stony corals form a strong
barrier to wave and tidal energy
that would otherwise erode
shorelines and damage valuable
coastal property (Figure 1-2). They
also provide a three-dimensional
(3D) structure that serves as habitat
for the diverse biological
community that has evolved with
them. Fish and shellfish harvested
for food depend on the stony coral
as habitat and nursery grounds.
Pharmaceuticals developed from
natural products are most often
discovered in reef areas with high
biological diversity (Fenical 1996).
Stony corals, and the reef
community that they harbor, can generate a strong tourism economy by attracting visitors, boaters,
recreational anglers and recreational divers.
Although stony corals are probably the greatest contributor, other reef organisms provide ecosystem
services. Fish and shellfish populations drive economies based on commercial, recreational and
subsistence fisheries. Octocorals and sponges, like stony corals, provide substantial habitat for rich reef
communities. In fact, some reef systems supporting recreational fisheries are composed primarily of
octocorals and sponges (e.g., southeast Florida). Sponges are commercially harvested, as are other
marine invertebrates such as lobsters, crabs and conchs.
Reef assessments to support quantification of ecosystem services must incorporate measurements of
those organisms that are relevant to the service endpoint. Reef protection of shorelines, for example,
depends on reef height, width, topography, depth and distance to shore among other variables (Lowe et
al. 2005). Provision of habitat, as another example, can be quantified as surface area and topography
(Dahl 1973; Alcala and Vogt 1997; Fisher 2007). Anticipating that highly valued ecosystem services
will influence decisions to protect coral reefs, EPA has initiated studies to identify and test potential
measures that can indicate or be transformed into indicators of ecosystem services.
Ecosystem Services Measurement Needs. Measurements to quantify ecosystem services need to focus on
key organisms or processes responsible for providing the service. Stony corals may well be the most
important reef inhabitant to benefit humans. To be useful in the context of ecosystem services,
measurement of stony corals should quantify those particular attributes that provide the services. For
example, measures of stony coral extent, distribution, colony size and topographic heterogeneity (reef
"roughness") are useful measurements for quantifying shoreline protection because they are all factors
in attenuating the shoreward energy of tides, waves and currents (Lowe et al. 2005; Monismith 2007).
Measures of stony coral surface area and topographic heterogeneity might be used to quantify the
amount of habitat and microhabitat provided by a coral reef to support an abundant and diverse
community of organisms (Dahl 1973; Alcala and Vogt 1997; Fisher et al. 2007; Monismith 2007).
Additional examples for stony coral attributes are provided in Table 1-1.
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Table 1-1: Examples of biophysical measurements supporting quantitative estimates of
coral reef ecosystem services (human benefits) and the conceptual linkage between them.
Biophysical Measurement
Linkage
Ecosystem Service
Reef dimensions, topographic
complexity, roughness and
spatial arrangement; colony
size and height
Surface area and size;
heterogeneity of stony corals,
octocorals, and sponges; reef
topographic complexity
Taxa richness, unique taxa
Abundance and density of
organisms
Stony corals provide structures
that attenuate wave and
current energy, protecting
shorelines from erosion
Biogenic habitat provides
substrate for fish and
invertebrates harvested for
food; reef architecture traps
sediment (increased clarity for
photosynthesis and fish
predation) and aggregates
zooplankton for fish predation.
Increased reef rugosity
increases abundance of unique
fish and invertebrates
High density and biodiversity
adds to interspecies
competition and results in
unique chemical products
Increased diversity of flora and
fauna with more unique taxa
Unique flora and fauna
harvested for aquarium
industry
Biological abundance increases
predator-prey interactions
Shoreline protection: More coastal
land, higher land value, lower
insurance rates, security against
storms and flooding, protection
against human injury
Fisheries: More harvestable fish
and invertebrates, stronger
commercial and recreational
fisheries
Tourism/Recreation: Greater
attraction for tourists, increased
tourism industry
Natural products: Diverse biota
increases potential for medical or
pharmaceutical discoveries, leads
to reduction in human pain,
suffering and death
Tourism/Recreation: Diverse and
rare flora and fauna are
aesthetically pleasing
Fisheries: Unique flora and fauna
are available in the ornamental
fish/aquarium trade
Fisheries: Larger harvestable fish
and invertebrates, stronger more
sustainable fishing industry
Tourism/Recreation: greater
attraction for tourists, stronger
tourism industry
Natural products: Greater potential
for novel discoveries
Other reef species that are good assessment candidates include organisms that are harvested for food or
profit (food fish, ornamental fish, sponges, lobsters, crabs, conchs, urchins and algae) or that provide
biogenic habitat (sponges and octocorals). A species selected for estimating ecosystem services does not
have to represent a critical function of the ecosystem (a requirement for regulatory applications) but
does need to have a strong connection to benefits derived from the reef.
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Puerto Rico (SW)
Benthic Habilar Types
i lype
Figure 1-3: Benthic hard bottom maps for SW
Puerto Rico.
1.3 Measuring Coral Reef
Condition
Benthic Habitat Maps. To measure the
condition of coral reefs, we must first
know where they are located. Stony coral
and other reef-building organisms need
hard substrate ("hardbottom") to settle and
grow, and, therefore, are present in
patterns across the sea floor where
hardbottom substrate occurs. When
assessing coral condition, time spent
visiting locations without hardbottom
translates into wasted time and resources.
Until recently, little was known about the
exact locations of coral reefs. Sonar
mapping technology developed and in use
since 2000 has been used to create benthic
habitat maps that accurately depict hardbottom substrate (Rohmann etal. 2005; NOAA 2009). These
maps are useful because they delineate the extent of potential coral reef areas and provide an essential
tool to identify coral reef monitoring locations (Figure 1-3). The benthic maps of hardbottom substrate
can also be used for CWA reporting. EPA recommends that states report water body condition by
providing an estimate of the nearshore area that supports designated uses. For example, a state's report
of the biennial integrated water quality assessment might conclude, "70% of hardbottom areas support
the designated uses for coral reef habitat." To make this calculation, the area of hardbottom substrate
must be known. Hardbottom is specified because it is not particularly useful to report coral reef
condition for areas, such as soft sediment, that are incapable of supporting reefs.
Sampling Design. The most comprehensive assessment of any resource is a census, which counts every
member of the population. A census, however, is usually impractical because it is prohibitive in time
and expense, so different sampling designs are implemented to select a subset of the population (or
sample). How sampling
locations are selected depends
on the purpose of the survey. If
the results from the subset of
locations are intended to
represent all locations without
bias, then a random selection of
sampling locations is necessary.
A random design ensures that
every location has an equal and
known probability of being
included in the survey. If the
purpose of the study is to
address a specific question (not
represented by all locations),
then sampling random locations
Sampling Designs
Random sampling is the selection of representative stations such
that every location has an equal chance of being selected.
Each station is considered representative of the entire region
sampled.
Probabilistic sampling is a spatially balanced random design
employed to avoid station clumping that can sometimes
occur in randomization procedures.
Targeted sampling is the selection of stations at specific
locations to address particular questions. Information from
targeted sampling cannot be extended to represent other
locations or the region sampled.
is not appropriate. Instead,
locations should be "targeted" or selected based on a judgment of which locations will best address the
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question. For example, asking if greater numbers of herbivorous fish aggregate at reefs with high
rugosity can be answered by counting herbivorous fish at targeted locations with widely varying
rugosity.
Monitoring design. Monitoring programs are usually designed for status and trend reporting. Status
monitoring assesses the current condition of the resource and answers questions like "What is the size
distribution of stony corals in the region?" Trend monitoring detects change over time and will answer
questions like "Has taxa richness declined in the region during the last five years?" Surveys to address
status and trend questions must use randomly selected sampling locations to obtain a subset, which is
intended to represent all locations across the region. For trend sampling, the same stations are usually
revisited each year to reduce temporal variability, but sometimes new stations are selected for each
survey using a modified random sampling design. For regional reporting, EPA recommends
"probabilistic sampling", a specific type of random sampling which incorporates random locations
spatially balanced across the region (Peterson etal. 1999; Larsen etal. 2001; EPA 2008). This avoids
clumping of locations that can sometimes occur with simple random sampling. More details on
probabilistic sampling designs can be found in Bradley et al. 2010 and EPA's Aquatic Resource
Monitoring website (EPA 2008).
Monitoring Designs
Status monitoring assesses current condition and
answers questions such as "What is the percent
living coral?"
Trend monitoring assesses change in status over time
or space and can answer questions such as "Have
reef fish declined over the last ten years?"
Both random and targeted sampling
designs can be used in development of
coral reef biocriteria. For example, a
targeted site selection is used to
determine which indicators are
responsive to human disturbance.
Sampling stations are targeted inside,
across and outside an area of high human
activity (like a port, city or an industrial
area) to ensure responses will be
measured from both impacted and unimpacted locations (Fore et al. 2006; Fisher et al. 2008). Targeted
site selection can also be used during survey development to identify tradeoffs in data needs and
monitoring efficiency. Random site selection can be used to establish regional baselines for future
comparison in long-term monitoring programs and is recommended for regional reporting requirements
under the CWA (i.e., 305[b] reporting; see Brown etal. 2005). Examples of regional monitoring
programs for coral reef assessment include the Coral Reef Environmental Monitoring Program (CREMP
2010), Florida Keys coral disease surveys (Santavy et al. 2005), the Florida Reef Resilience Program
(FRRP 2010) and the EPA survey of Hawaiian bays and estuaries (Nelson etal. 2007). (See Appendix
A)
Survey Plan. Coral reef surveys, especially those to be used in a long-term monitoring program, are
expensive. Assessments usually require on-site, underwater
visits, which entail dive boats, scuba equipment, trained
divers and extensive survey time. An efficient survey plan
should be a high priority for any reef assessment program.
For long-term monitoring programs, inefficiencies are
replicated year after year, taking an unnecessary toll on
time and resources. A competent and efficient survey plan
may require many preliminary tests and analyses, but the
time is well spent.
Survey Plan
1. Define target population
2. Define sampling frame
3. Define sampling unit
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The first step in establishing a survey plan is to define the target population, the sampling frame and
sampling unit. To measure trends in a long-term monitoring program for coral reef condition, the target
population might include all stony corals in the region, but because a census is unobtainable for most
coral surveys, a subset of the population is sampled that is representative of the entire population. A
sampling frame characterizes which members of the target population will be used as a basis for
sampling. The sampling frame might identify different strata such as depth ranges, the distance from
shoreline or reef type classification (e.g., patch reef) to balance any bias in the target population. A
sampling unit is one of the elements into which the target population has been divided for purpose of
sampling. Each unit is considered individual and indivisible. If, for example, a station location is a
sampling unit, then the number of sites visited at that station must be aggregated for a station value. A
survey plan attempts to achieve an optimum balance between the objectives of the survey, the
responsiveness of the indicators (see below) and the available expertise and resources (monetary and
personnel needs).
Indicator Selection. Central to addressing a particular survey question are the measurements that are
made and the calculations (indicators) that stem from them. There are many potential indicators to
choose from (e.g., Jameson et al. 2001; Cooper et al. 2009), but not every indicator will be appropriate
for the intended purpose of the survey. For example, live coral cover may be suitable for assessing
trends in coral health but might not be suitable for estimating a reefs contribution to fish habitat or
shoreline protection. Each study might address a different set of questions, and each indicator
measurement will likely require different resources and expertise.
Selecting indicators should be a planned, iterative process of review, testing and analysis. Following
published guidelines for indicator development and evaluation can be very useful, and documenting how
each guideline is met will lend defensibility to later interpretation of results. Jackson et al. (2000)
present four phases of indicator evaluation—conceptual foundation, feasibility of implementation,
response variability and interpretation and utility. These phases describe an idealized progression for
indicator development that flows from fundamental concepts to methodology, to examination of data
from pilot or monitoring studies and lastly to how the indicator serves the program objectives.
Bradley et al. (2010) characterized a subset of guidelines that were important for coral reef biocriteria
development. Similarly, Hallock et al. (2003) used these
guidelines to evaluate the foraminiferan (FCrRAM) index
as an indicator of biological condition of coral reef
communities. A brief summary of how EPA stony coral
indicators described in Fisher (2007) are believed to meet
these guidelines is provided below:
Indicator Evaluation
1. Conceptual foundation
2. Feasibility of implementation
3. Response variability
4. Interpretation and utility
(Jackson et a/. 2000)
(1) Relevance to purpose: The condition of a reef
ecosystem can be characterized by the physical and
biological condition of stony corals. The pivotal role that stony corals play in reef ecology,
stemming from provision of habitat, is well known and amply addressed in the scientific literature7.
(2) Relevance to ecosystem structure and function: Stony corals provide the infrastructure of the reef
and create a physical and biological environment that attracts other species. Most reef organisms
o
depend on stony corals in some manner .
7 For example, Loya 1972; Birkeland 1987; Brown 1988; Jones and Kaly 1996; Done 1997; Kramer 2003.
8
Dahl 1973 states: "The production, occupation, and destruction of surface area are, therefore, basic reef processes, and the
balance between them is an essential aspect of the reef ecosystem. The efficient production of surface is a primary function of
-------
(3) Power to detect differences: Useful indicators have the statistical power to demonstrate change for
the number of stations surveyed. Measurement errors for stony coral calculations were found to be
smaller than natural variability across the stations (Fisher et al. 2007) and are expected to detect
differences among stations.
(4) Responsiveness to human influence: Stony coral indicators will respond in a consistent and logical
manner to a human disturbance gradient. Several indicators tested at St. Croix, USVI, were found
sensitive to a human disturbance gradient (Fisher et al. 2008).
(5) Feasibility of implementation: Stony coral indicator measurements can be easily obtained by divers
during a single dive. However, the number of stations that can be visited each year is dependent on
staff and resources. A rotating panel design for regional coverage can be used (Fore et al. 2006).
(6) Interpretation and utility for management: Management is supported when measurements reflect the
features that people value. Stony coral species richness, colony size and tissue condition are
defensible as surrogates for ecosystem integrity. Greater reef integrity supports fish nurseries,
shoreline protection and reef community habitat. Stony coral abundance and diversity provide a
significant attraction for snorkelers and divers (tourism)9.
Assessment Procedures. Clearly, there are two monitoring objectives for EPA—condition assessments
for setting useful thresholds as water quality standards and ecosystem services assessments to estimate
benefits provided from reef existence and function. There are numerous approaches available for
characterizing reef condition (see Appendix A) but not for ecosystem services. Both objectives can be
met with similar sampling designs and monitoring approaches, but the indicators and measurements
made to generate those indicators may differ (Principe et al. 2012). Recently, EPA has attempted to
develop a suite of indicators and measurements that could meet both objectives. The procedures are
outlined here with guidance on measurements and indicators for reef fish, stony corals, gorgonian
octocorals, sponges and macroinvertebrates, as well as reef rugosity and live coral cover. Although some
of the condition measurements (fish, stony corals, rugosity and live coral cover) are not new, they have
been adapted for an efficient survey plan that includes new services indicators (octocorals and sponges).
1. (25 x 4 m, 15
live
2. the
3. for of the the
the to the
4. If a can or the
The manual presents assessment methods as chapters in the order that the EPA Coral Assessment Team
conducts a survey. The fish assessment is completed first so the fish will not be disturbed prior to
counting. The fish surveyors lay the transect tape that is subsequently used for other surveys. During the
many reef organisms, and the control of surface by secondary occupants is a basic competitive force and a major determinant
of reef communities." (p. 240)
9 In a dive site preference study, divers were able to distinguish sites with greater fish species richness and abundance, stony
coral richness, abundance, tissue and structural complexity (Uyarra et al. 2009). In a choice-based valuation, degraded reef
attributes (including abundance and diversity offish and coral, and water clarity) at Eilat (Israeli Red Sea) represent a
$2.86M annual loss from recreational diving (Wielgus et al. 2003).
10
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fish count, the buddy diver can survey macroinvertebrates and estimate live coral cover using the linear
point intercept method. Once complete, the fish counter and buddy diver can conduct rugosity
measurements on their return to the marker buoy. Once the fish survey is complete, the stony coral
counter and octocoral/sponge counter can enter the water and complete their surveys. If available, it is
beneficial to have a fifth diver to take video or photographs, record transects and capture interesting and
unusual features at each study site.
1.4 References
Alcala MLR and Vogt H. 1997. Approximation of coral reef surfaces using standardized growth forms
and video counts. In: Proceedings of the 8th International Coral Reef Symposium 2:153-158.
Birkeland C. 1987. Comparison between Atlantic and Pacific tropical marine coastal ecosystems:
community structure, ecological processes and productivity. UNESCO Report in Marine Science
46, United Nations Educational, Scientific and Cultural Organization, Paris, France.
Bradley P, Fore L, Fisher W and Davis W. 2010. Coral Reef Biological Criteria: Using the Clean Water
Act to Protect a National Treasure. U.S. Environmental Protection Agency, Office of Research
and Development, Narragansett, RI. EPA/600/R-10/054 July 2010.
Brown BE. 1988. Assessing environmental impacts on coral reefs. In: Proceedings of the 6th
International Coral Reef Symposium 1:71-80.
Brown BS, Detenbeck NE and Eskin R. 2005. How probability survey data can help integrate 305(B)
and 303(D) monitoring and assessment of state waters. Environmental Monitoring and
Assessment 103: 41-57.
Cesar HJS, Burke L and Pet-Soede L. 2003. The Economics of Worldwide Coral Reef Degradation.
Cesar Environmental Economics Consulting, Arnhem, Netherlands.
Cooper TF, Gilmour JP and Fabricius KE. 2009. Bioindicators of changes in water quality on coral
reefs: review and recommendations for monitoring programs. Coral Reefs 28:589-606.
Coral Reef Evaluation and Monitoring Project (CREMP). 2010.
accessed June 2011.
Costanza R, D'Arge R, deGroot R, Farber S, Grasso M, Hannon B, Limburg K, Naeem S, O'Neill RV,
Paruelo J, Raskin RG, Sutton P and van den Belt M. 1997. The value of the world's ecosystem
services and natural capital. Nature 387:253-260.
Dahl AL. 1973. Surface area in ecological analysis: quantification of benthic coral-reef algae. Marine
Biology 23:239-249.
Done TJ. 1997. Decadal changes in reef-building communities: implications for reef growth and
monitoring programs. In: Proceedings of the 8* International Coral Reef Symposium 1:411-416.
Fenical W. 1996. Marine biodiversity and the medicine cabinet: the status of new drugs from marine
organisms. Oceanography 9:23-27.
Fisher WS. 2007. Stony Coral Rapid Bioassessment Protocol. EPA/600/R-06/167.
Fisher WS, Davis WP, Quarles RL, Patrick J, Campbell JG, Harris PS, Hemmer BL and Parsons M.
2007. Characterizing coral condition using estimates of three-dimensional colony surface area.
Environmental Monitoring Assessment 125:347-360.
Fisher WS, Fore LS, Hutchins A, Quarles RL, Campbell JG, LoBue C and Davis WP. 2008. Evaluation
of stony coral indicators for coral reef management. Marine Pollution Bulletin 56:1737-1745.
Florida Reef Resiliency Program (FRRP). 2010. accessed June 2011.
11
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Fore LS, Fisher WS and Davis WS. 2006. Bioassessment Tools for Stony Corals: Field Testing of
Monitoring Protocols in the US Virgin Islands (St. Croix). EPA-260-R-06-004. US EPA Office
of Environmental Information, Washington, DC. August 2006.
Gardner TA, Cote EVI, Gill JA, and Grant A. 2003. Long-term region-wide declines in Caribbean corals.
Science 301:958-960.
Hallock P, Lidz BH, Cockey-Burkhard EM and Donnelly KB. 2003. Foraminifera as bioindicators in
coral reef assessment and monitoring: The FORAM Index. Environmental Monitoring and
Assessment 81:221-238.
Jackson LE, Kurtz JC and Fisher WS. (Eds). 2000. Evaluation Guidelines for Ecological Indicators.
EPA/620/R-99/005. U.S. EPA, Office of Research and Development, Research Triangle Park,
NC. 107 Pp.
Jameson SC, Erdmann MV, Karr JR, Gibson GR and Potts KW. 2001. Charting a course toward
diagnostic monitoring: a continuing review of coral reef attributes and a research strategy for
creating coral reef indexes of biotic integrity. Bulletin of Marine Science 9:701-744.
Jones GP and Kaly VL. 1996. Criteria for selecting marine organisms in biomonitoring studies. In:
Detecting Ecological Impacts: Concepts and Applications in Coastal Habitats, pp. 29-48.
Academic Press, New York.
Karr JR. 2006. Seven Foundations of Biological Monitoring and Assessment. Biologia Ambientale 20:7-
18.
Karr JR and Dudley DN. 1981. Ecological perspective on water quality goals. Environmental
Management 5:55-68.
Kramer PA. 2003. Synthesis of coral reef health indicators for the Western Atlantic: results of the
AGRRA Program (1997-2000). Atoll Research Bulletin 496:1-58.
Larsen DP, Kincaid TM, Jacobs SE and Urquhart NS. 2001. Designs for evaluating local and regional
scale trends. BioScience 12:1069-1078.
Leeworthy VR, Wiley PC and Hospital JD. 2004. Importance-Satisfaction Ratings Five-year
Comparison, SPA and ER Use, and Socioeconomic and Ecological Monitoring Comparison of
Results 1995-96 to 2000-01. National Oceanic and Atmospheric Administration, Silver Spring,
MD. 67 pp.
Lowe RJJ, Falter L, Bandet MD, Pawlak G, Atkinson MJ, Monismith SG and Koseff JR. 2005. Spectral
wave dissipation over a barrier reef. Journal of Geophysical Research 110:4001-4016.
Loya Y. 1972. Community structure and species diversity of hermatypic corals at Eilat, Red Sea. Marine
Biology 13:100-123.
Millennium Ecosystem Assessment (MEA). 2005. Coastal Systems. Chapter 19. In: Hassan, RR
Scholes, and N Ash, (Eds.) Ecosystems and Human Well-being. Current State and Trends, 1:
513-549. Island Press, Washington, DC.
Monismith SG. 2007. Hydrodynamics of coral reefs. Annual Review Fluid Mechanics 39:37-55.
National Oceanic and Atmospheric Administration (NOAA). 2009. Center for Coastal Monitoring and
Assessment: Biogeography Branch.
Nelson WG, Brock R, Lee H, Lamberson JO and Cole FA. 2007. Condition of Estuaries and Bays of
Hawaii for 2002: A Statistical Summary. U.S. EPA, Washington, DC, EPA/620/R-07/001.
Pendleton L. 2009. The Economic and Market Value of America's Coasts and Estuaries: What's at
Stake? Coastal Ocean Values Press, Washington, DC.
Peterson SA, Urquhart NS and Welch EB. 1999. Sample representativeness: a must for reliable regional
lake condition estimates. Environmental Science Technology 33:1559-1565.
12
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Principe PP, Bradley P, Yee SH, Fisher WS, Johnson ED, Allen P and Campbell D. 2012. State of the
Science on Linkages among Coral Reef Conditions, Functions, and Ecosystem Services. EPA
Report: EPA/600/R-11/206.
Rohmann SO, Hayes JJ, Newhall RC, Monaco ME and Grigg RW. 2005. The area of potential shallow-
water tropical and subtropical coral ecosystems in the United States. Coral Reefs 24:370-383.
Santavy DL, Summers JK, Engle VD and Harwell LM. 2005. The condition of coral reefs in South
Florida using coral disease as an indicator. Environmental Monitoring and Assessment 100:129-
152.
Spurgeon JPG. 1992. The economic valuation of coral reefs. Marine Pollution Bulletin 24:529-536.
The Economics of Ecosystems and Biodiversity (TEEB). 2009. The Economics of Ecosystems and
Biodiversity for National and International Policymakers, accessed
June 2011.
U.S. Environmental Protection Agency (EPA). 1990. Biological Criteria: National Program Guidance
for Surface Waters. EPA-440/5-90-004.
U.S. Environmental Protection Agency (EPA). 1994. Water Quality Standards Handbook: Second
Edition. EPA-823-B-94-005. .
U.S. Environmental Protection Agency (EPA). 2000. Estuarine and Coastal Marine Waters:
Bioassessment and Biocriteria Technical Guidance. EPA-822-B-00024.
U.S. Environmental Protection Agency (EPA). 2002. Biological Assessments and Criteria: Critical
Components of Water Quality Programs. EPA 822-F-02-006.
U.S. Environmental Protection Agency (EPA). 2008. Handbook for Developing Watershed Plans to
Restore and Protect Our Waters. EPA 841-B-08-002.
accessed June 2011.
Uyarra MC, Watkinson AR and Cote JM. 2009. Managing diver tourism for the sustainable use of coral
reefs: validation diver perceptions of attractive site features. Environmental Management 443:1-
16.
Wielgus J, Chadwick-Furman NE, Zeitouni N and Shechter M. 2003. Effects of coral reef attribute
damage on recreational welfare. Marine Resources Economics 18:225-237.
Yoder CO and Rankin ET. 1998. The role of biological indicators in a state water quality management
process. Environmental Monitoring and Assessment 51:61-88.
13
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2.0 Visual Assessment of Reef Fish
2.1 What is measured?
Reef fish are surveyed visually to
document the species, numbers and
sizes of all reef fishes within a 25 m
r\
x 4 m underwater transect (100 m ).
Data are used to estimate
abundance, species richness and
biomass for the fish populations,
which can be subsequently classified
by taxonomy and trophic guilds
(Randall 1967). This protocol is a
noninvasive, rapid underwater
assessment and is similar to that
performed by the National Oceanic
and Atmospheric Administration
(Menza et al. 2006; Caldow et al.
2009).
Figure 2-1: Fish on reefs contribute valuable ecological
and economic services.
2.2 Why is it measured?
Reef fish are major components of coral reef ecosystems and provide valuable economic and ecological
services, particularly food provisioning via subsistence and commercial fishing (Figure 2-1). The World
Health Organization (WHO 2010) reports that the protein derived from seafood (fish, crustaceans and
mollusks) accounts for 13-16% of the animal protein consumed by people globally. Reef fish are also a
major attraction for recreational anglers, snorkelers and divers, supporting lucrative tourism and
recreational industries (Hall 2001; Brander et al. 2007). Additionally, reef fish are harvested for the
aquarium trade (Chan and Sadovy 2000).
Fish play an important ecological role in maintaining the stability and sustainability of coral reefs. They
have a primary role in the trophodynamics of the reef system: fish consumption of algae and predation
on other fish is critical to maintaining a trophic balance across the reef ecosystem. For example,
herbivores (e.g., parrotfishes, damselfishes, and surgeonfishes) crop algae that might otherwise
overgrow corals and sustain the infrastructure of reefs (Burkepile and Hay 2008). Invertivores (e.g.,
grunts, angelfish) aid in balancing the proliferation of corallivores (e.g., butterflyfishes, snails), which
consume coral tissue. Overfishing of all these trophic groups can be attributed as major threats to the
persistence of coral reefs and could provide mechanisms for ecological phase shifts, for example, from
coral to algal-dominated communities (Sale 1977; Jackson et al. 2001). While various programs have
been established to generate policies for sustainable reef fisheries (e.g., Ault etal. 2005, 2006), an
increased understanding offish on reefs as indicators of coral reef ecosystem condition will provide
greater protection for coral reef ecosystems.
14
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Figure 2-2: Fish must be identified to species, and
abundance and size class estimations made while
swimming 25 m in 15 minutes.
2.3 What do we need?
2.3.1 Surveyor skills
Surveyors must be able to count and
identify reef fishes to the genus and
preferably species level. They also have
to be able to make size estimates
quickly while swimming along a 25 m
transect (Figure 2-2). Expertise is
acquired through reference materials
and field training (e.g., Humann and
DeLoach 2006). Familiarity with local
species can be obtained from region-
specific literature. Resources for fish
identification provide comprehensive
descriptions, diagrams, behavioral
characteristics and photographic
records of the targeted species
(Humann and DeLoach 2002).
Additional training to refine
identification skills is acquired by underwater training with an experienced surveyor who highlights
target species, prominent physical characteristics, habitat preferences and behavioral patterns for
accurate identification.
Surveyors are trained to estimate fish size under water, using premeasured objects as calibration tools.
Training should include pacing the 25 m swim for a duration of 15 minutes. Measurement bias will
occur if the survey time is substantially over or under the required 15 minutes. If there is more than one
fish surveyor, then variability among surveyors (measurement error) must be determined. Each surveyor
collects data independently, while they simultaneously swim side-by-side in the same transect.
Differences in surveyor experience and training are common causes of measurement bias. Increased
training should minimize this error (Menza et al. 2006).
2.3.2 Equipment
- Fish Survey Data Sheets printed on underwater paper (Figure B-l)
- Fish species codes (Appendix C for Caribbean species)
- Underwater slate or clipboard
- Underwater pencils10 or pens with surgical tubing or rubber bands to attach to slate
- Flexible fiberglass metric measuring tape at least 30 m in length on reel
- Optional: underwater digital camera
The metric measuring tape is on a reel to allow deployment during the fish survey and is clearly marked
at 1 m increments. A convenient way to attach the tape to the substrate is to modify the end of the tape
with a small diameter bungee cord and snap clip. The bungee cord is wrapped around an object on the
substrate and clipped back on itself to secure the tape in place. If there are substantial currents and the
transect will be used for other types of surveys (e.g., stony coral assessment), it is recommended that the
tape be weighted with a thin lead line to reduce movement. An underwater camera is useful for
recording fish with questionable identities for later verification with existing literature.
Recycled wood pencils will disintegrate. Always bring multiple pencils or pens.
15
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2.4 How are data collected?
1) Preparation: Record survey information on the Fish Survey Data Sheet (Figure B-l), ensuring
each page is numbered consecutively and taking care to transcribe the date, location, and
surveyor name prior to entering water. Set a weighted marker buoy from the surface at the
desired sampling location using GPS coordinates. If multiple assessments for other organisms
and measurements will be made, the fish survey should always be completed first. The fish
surveyor and buddy diver enter the water with slate, pencils, data sheets, transect line (30 m
tape), and fish species codes (optional: lead line and camera). Divers descend slowly and avoid
movements that would disturb fish and take care to adjust buoyancy. No other divers should be
present during the fish survey to reduce fish disturbance, herding or congregating. The transect
location and direction is selected as the best available reef habitat (usually based on stony coral
coverage) within 20 m of the marker buoy weight. The transect tape is attached securely to the
sea floor, and a visual reference point 25 m at the other side of the selected habitat should be
estimated as a target to swim towards. The depths at the 0 m and 25 m marks of the transect tape
are recorded.
2) Transect: The fish surveyor begins swimming, documenting fish abundance, species and size
classes while reeling out the 25 m tape along a single direction across the best available habitat.
Depending on current, swimming is at a medium pace so that the measuring tape is deployed at a
relatively constant rate and reaches 25 m in about 15 minutes. Longer or shorter swimming
periods could affect comparison of results across stations. The buddy diver remains behind the
fish surveyor and can perform other tasks such as coral cover (LPI) or macroinvertebrate counts
(See Chapter 6).
3) Procedure: Completion of the survey should take 15 minutes regardless of habitat type or number
offish present to standardize data collection among sites. The fish surveyor looks forward at all
times and documents only those fish that occur within 2 m to each side (delineating the 4 m
width of the transect perimeter) in the entire water column. Fish above or below the surveyor's
line of sight should be documented as far as visibility allows, but not past the 25 m length or the
4 m width of the transect (Figure 2-3). The surveyor may move off the centerline to check for
fish under ledges or in holes, but should never look back to the transect area already surveyed.
4) Measurements:
a) Species abundance: Fish within the 100 m transect area are recorded to the lowest
taxonomic level possible. All fish greater than 1 cm in size are included in the assessment.
Four letter codes, consisting of the first two letters of the genus and the first two letters of the
species, are used for reporting (Caribbean species in Appendix C). If common names are
recorded on the data sheet under water, then corresponding scientific codes need to be
transcribed on data sheet and used for data entry purposes. In the case that two species have
the same four-letter code, letters are added to the species name until a unique code occurs. If
the fish cannot be classified to at least family level, then a brief description is taken and the
fish is photographed for later identification. All procedures must be standardized prior to the
survey.
16
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-3u*-
_! 1C m
£tJ 111
Diver s Direction
;
E
.
Figure 2-3: Diagram offish transect using two divers in a 4 m x 25 m belt transect (100 m2).
All fish encountered in the water column or on the reef are included in the visual
assessment.
b) Fish size: Each fish is scored in 5 cm size class increments up to 35 cm using visual
estimation of fork length. If an individual is greater than 35 cm, an estimate of the actual fork
length is made. The fork length is measured from the snout (with closed mouth) to the fork at
the base of the tail or caudal fin (Figure 2-4).
Figure 2-4: Fork length for
different types offish. The fork
length is meaured from the tip
of the snout (with closed
mouth) to the base of the
caudal fin.
5) Post-Survey: The survey is complete at the 25 m mark and the depth is recorded again. If
additional surveys will follow (e.g., stony corals) the transect tape is secured beyond the 25 m
mark and, if needed, a lead line is installed to anchor it down. Otherwise, the tape is reeled back
to the starting point and all equipment retrieved. After the dive all data sheets are verified for
completeness and any questionable records reconciled by the surveyor. Data sheets are rinsed
with freshwater and dried.
17
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2.5 How are data managed?
Surveyors must review data sheets for legibility, completeness, and correct use of standardized
fish codes. Changes are made to the data sheet and should be initialed. A checklist for data sheet
review is provided in Figure B-7. Any photographs taken to verify taxonomic description are
examined and archived with an appropriate file name. Data are delivered to the data recorder
who transcribes it from the underwater data sheets into electronic spreadsheets for archiving and
data analysis. After data have been electronically entered, they are reviewed for accuracy and
verified simultaneously by the surveyor and recorder. When complete, both the recorder and the
surveyor sign and date the data sheets, which are scanned and archived.
2.6 How are indicators calculated?
All data are summarized and procedures are applied to identify outliers, errors, and
inconsistencies to be considered prior to data analyses. These procedures can include summary
statistics, box plots and stem and leaf plots. Fish community ecological attributes such as species
richness, abundance, density, length distributions, biomass and diversity indices can be
calculated at different taxonomic levels and by trophic guilds (Table 2-1).
Biomass (W) for each fish (equation 2-1) is calculated using the measured length (L) in cm and
published length-weight relationships specific for species, represented as values for a and P
coefficients that were obtained from FishBase (Froese and Pauly 2007; Table C-l).
p
W = aL (equation 2-1)
Population biomass is estimated by pooling all individuals of one species by either abundance or
density. Biomass estimations for species with no published length-weight relationships are
calculated using terms for the closest congener based on morphology. Additionally, fish
classified by trophic guild are compared by abundance and biomass. These trophic guilds
include: herbivores, piscivores, invertivores, detritivores and zooplanktivores (Randall 1967)11.
11 Herbivores: fish that eat algae and vegetation. Piscivores: carnivorous fish that eat other fish. Invertivores: fish
that eat invertebrates usually separated by sessile [corals (corallivores), sponges, etc.)] and mobile forms
(crustaceans, polycheates, mollusks, etc.). Detritivores: fish that eat bottom materials and detritus. Zooplanktivores:
fish that eat zooplankton.
18
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Table 2-1: Potential fish indicators used to describe characteristics of reef fish. Most
indicators can be expressed as total or mean values classified by species or other taxonomic
level and trophic guilds. (Equations detailed in Caldow et al. 2009 and Mensa et al. 2006).
Indicator
Description
Units
Formula
Species richness (total or mean)
Density (total or mean)
Length size (mean or frequency)
Biomass (total or mean)
Shannon diversity index (H)
Pielou evenness index (J)
Abundance (total or mean)
Frequency of occurrence
# offish species at site
# fish /area=relative
abundance
Fork length, total length,
body length
Total weight of all
individuals, estimated
wet weight
Index of richness &
abundance
Index of biodiversity
Total # individuals
Proportion of sampled
sites that a given
species is present
#/100 m2
S=Z species
No. fish/100m2
cm
g/100m2
Unitless
Unitless
# individuals
Unitless
W =
H' =
J' = H'/lnS
a and (3 are coefficients obtained from FishBase (Froese and Pauly 2007) for calculating biomass (see Appendix
C). Biomass for species with no published length-weight relationships can be calculated using terms for the closest
congener based on morphology.
2.7 References
Ault JS, Bohnsack JA, Smith SG and Luo J. 2005. Towards sustainable multispecies fisheries in
the Florida USA coral reef ecosystem. Bulletin of Marine Science 76:595-622.
Ault JS, Smith SG, Bohnsack JA, Luo J, Harper DE and McClellan DB. 2006. Building
sustainable fisheries in Florida's coral reef ecosystem: positive signs in the Dry Tortugas.
Bulletin of Marine Science 78:633-654.
Brander LM, Beukering PV and Cesar HJ. 2007. The recreational value of coral reefs: A meta-
analysis. Ecological Economics 63:209-218.
Burkepile DE and Hay ME. 2008. Herbivore species richness and feeding complimentarity affect
community structure and function: the case for Caribbean reefs. Proceedings of the
National Academy of Sciences USA 105:16201-16206.
Caldow CR, Edwards CK, Hile SD, Menza C, Hickerson E and Schmahl GP. 2009.
Biogeographic Characterization of Fish Communities and Associated Benthic Habitats
within the Flower Garden Banks National Marine Sanctuary: Sampling Design and
Implementation of SCUBA Surveys on the Coral Caps. NOAA Technical Memorandum
NOS NCCOS 81. Silver Spring, MD. 134 pp.
19
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Chan TTC and Sadovy Y. 2000. Profile of the marine aquarium fish trade in Hong Kong.
Aquarium Sciences and Conservation 2:197-213.
Froese R and Pauly D. 2007. FishBase. World Wide Web electronic publication.
Version (09/2007).
Hall CM. 2001. Trends in ocean and coastal tourism: the end of the last frontier? Ocean and
Coastal Management 44:601-618.
Humann P and DeLoach N. 2002. 3r Edition, Reef fish identification: Florida, Caribbean,
Bahamas. New World Publications, Jacksonville, FL. 426 pp.
Humann P and DeLoach N. 2006. 4rd Edition, Reef fish identification: Florida, Caribbean,
Bahamas. DVD, ReefNet Inc.
Jackson JBC, Kirby MX, Berger WH, Bjorndal KA, Botsford LW, Bourque BJ, Bradbury RH,
Cooke R, Erlandson J, Estes JA, Hughes TP, Kidwell S, Lange CB, Lenihan HS, Pandolfi
JM, Peterson CH, Steneck RS, Tegner MJ and Warner RR. 2001. Historical overfishing
and the recent collapse of coastal ecosystems. Science 293:629-637.
Menza C, Ault J, Beets J, Bonsack J, Caldow C, Christensen J, Friedlander A, Jeffrey C, Kendall
M, Luo J, Monaco M, Smith S and Woody K. 2006. A Guide to Monitoring Reef Fish in
the National Park Service's South Florida/Caribbean Network. NOAA Technical
Memorandum NOS NCCOS 39. 169pp.
Randall JE. 1967. Food habits of the reef fishes of the West Indies. Studies in Tropical
Oceanography 5:665-847.
Sale PF. 1977. Maintenance of high diversity in coral reef fish communities. American Naturalist
111:337-359.
World Health Organization (WHO). 2010. World Health Organization: Global and regional food
consumption patterns and trends
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3.0 Stony Coral Assessment
3.1 What is measured?
Stony coral surveys document the
taxa, 3D size, amount of tissue on
coral colonies and the occurrence of
adverse health conditions such as
bleaching, disease or overgrowth by
boring sponges. These characteristics
can provide estimates of stony coral
abundance, density, species
diversity, richness, reef surface area
and complexity, and relative health
of coral colonies. This method is an
update of EPA's Stony Coral Rapid
Bioassessment Protocol (Fisher
2007).
3.2 Why is it measured?
Figure 3-1: Stony coral assessments document the surface
area of corals and provide important information about
ecosystem and ecological services.
Stony corals form the permanent architecture of coral reefs. Because stony corals provide habitat
for many other types of organisms, humans benefit from the opportunity for tourism, recreation,
and fishing (Figure 3-1). Stony corals also provide shoreline protection from erosion and
inundation during storms or even normal high wind and wave conditions. They also support high
abundances of extremely diverse organisms that produce secondary metabolites potentially
useful for pharmaceutical s and other biochemical needs. Stony corals are a main attraction for
divers and snorkelers, who enjoy the beautiful colors and interesting shapes. Protection of stony
corals and the services they provide, are critical for future provision of coral reef ecosystem
services (Table 3-1).
The coral reef infrastructure supports many of the ecological interactions and functions
characteristic of a dynamic reef ecosystem. It also contributes to biodiversity by providing
essential habitat for sponges, octocorals, fish and a myriad of invertebrate and plant species. The
stony coral assessment procedure characterizes the biophysical condition of stony corals by
comparing species and populations across reef types, study areas and geographic regions (Fisher
2007). The condition of stony corals and the reef is related to water quality and human
disturbances in watersheds and coastal zones (Fisher etal. 2006, 2008). Moreover, data from
these measurements can be used to determine whether stony corals attain established thresholds
(biocriteria) or to estimate the type and quantity of ecosystem services they provide.
21
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Fable 3-1: Examples of benefits derived from coral reef ecosystem services that
rely on a stony coral infrastructure (in economic categories, Principe et al. 2012].
Direct Extractive Uses
Commercial fishing
Subsistence fishing
Aquarium fish
Sport fishing
Coral jewelry
Pharmaceutical harvesting
Non-pharmaceutical harvesting
Indirect Uses
Fish habitat
Nutrients
Reduced flooding
Less storm damage
Fewer deaths from storms and flooding
Reduced erosion from storms and flooding
Mangrove and seagrass protection
Sealife nursery protection
Global life support
Direct Non-extractive Uses
Scuba diving
Snorkeling
Boating
Pharmaceutical chemicals
Non-pharmaceutical natural products
Non-uses
Existence value
Cultural value
Option value
Quasi-option value
Bequest value
Instrumental value
Intrinsic value
Scientific value
Scarcity value
3.3 What is needed?
3.3.1 Surveyor skills
Surveyors must be able to identify corals to genus and species, measure coral colony dimensions
and estimate the proportion of tissue in relation to the overall size of the colony. Surveyors can
note any bleaching (Figure 3-2), disease (Figure 3-3), and invasive growth of clionid sponges
(Figure 3-4), taking care to distinguish from predation damage (Figure 3-5). (For detailed
disease, predation, bleaching and overgrowth descriptions see regional specific websites: GCDD
2012; NOAA CDHC 2012; NOAA CORIS 2012). If more than one surveyor is required, then
variability among surveyors (measurement error) must be determined.
3.3.2 Equipment
- Stony Coral Survey Data Sheets printed on underwater paper (Figure B-2)
- Species (Table 3-2) and disease code sheets
- Underwater slate or clipboard
- Underwater pencils or pens12 with surgical tubing or rubber bands to attach to slate
- Flexible fiberglass metric measuring tape on reel at least 30 m in length
-1m length rod or PVC pipe to delineate transect width
- 0.5 m or 1 m measuring tool marked in 5 cm increments (e.g., PVC tube)
- Optional: underwater digital camera
Recycled wood pencils will disintegrate. Always bring multiple pencils or pens.
22
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Bleached Corals
Figure 3-2: Examples of bleaching corals, including paling (left), partially (center) and severely
bleached (right) colonies.
Diseased Corals
Figure 3-3: Examples of coral disease, black band disease (left), white plague (center), and white
pox (right).
Boring Sponges on Corals
Figure 3-4: Boring clionid sponges on corals. Dark brown sponge (left) and orange boring
sponges (center and right) dissolve coral skeletons.
23
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Predation on Corals
Figure 3-5: Predation on coral tissue by snails (left), damselfish (center) and parrotfish (right).
The metric measuring tape should be on a reel to allow easy deployment and should be clearly
marked at 1 m increments. If the fish survey was conducted, the tape will have been previously
deployed. The tape can be attached to the substrate with a small diameter bungee cord and snap
clip on the end of the tape. The bungee cord is wrapped around an object on the substrate and
clipped back on itself. An underwater camera is beneficial to record corals of uncertain identity
for later verification with existing literature.
3.4 How are data collected?
1. Preparation: Record survey information on the Stony Coral Survey Data Sheet (Figure B-
2), ensuring that each page is numbered consecutively and taking care to enter the date,
location, and surveyor name prior to entering water. Set a weighted marker buoy from the
surface at the desired sampling location using GPS coordinates. If multiple assessments for
other organisms and measurements are made, the fish survey should always be conducted
first and then the transect tape will be in place. If only a coral survey is performed, the
coral surveyor and dive buddy enter the water with transect line (30m tape on reel), slate,
pencils, 1 m rod, measuring tool, data sheets, and stony coral species codes, (optional lead
line and camera). The transect location and direction is selected as the best available reef
habitat, (usually based on stony coral coverage) within 20 m of the marker buoy weight.
The transect tape is securely fastened to the seafloor and deployed 25 m in a straight line.
Depth is recorded and colony measurements begin at the 0 m mark of the transect tape. If
strong currents exist, the transect line can be secured by tie wrapping the lead line to it. If
there is very high coral coverage, the transect length can be reduced, but changes must be
clearly noted on each data sheet.
2. Transect: Position the 1 m rod on the right side (looking forward) and orthogonal to the
transect tape, parallel to the seafloor. As the survey progresses, the 1 m rod is moved along
the transect tape to delineate the 1 m transect width. If the rod can be laid directly on the
seafloor, it can be used to mark the surveyors progress along the transect line.
3. Procedure: The surveyor records all stony coral data from the transect on the data sheet by
identifying each colony to genus and species (Table 3-2), measuring the maximum height
and diameter of the colony, and estimating the percent of coral tissue (as opposed to bare
skeleton) on the colony. HydrocoralsM/7//pora complanata andMillipora alcicornis can be
included in the assessment of Caribbean corals. Colony height is the greatest distance of the
colony from the substrate and maximum diameter is the greatest distance parallel to the
substrate. All measurements are recorded to the nearest 5 cm with appropriate rounding.
24
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4. Percent tissue (living coral) is estimated for the whole colony in 3D, not simply from the
aerial planar view and is recorded in 10% increments (Figure 3-6). If condition indicators
are included, the surveyor can note any disease, bleaching, or clionid boring sponges on the
colony.
Figure 3-6: Colony size and tissue estimates are made from the entire colony surface, not merely
from an overhead planar view.
5. Rules for inclusion: Certain conventions have been adopted to determine which colonies
are included within the survey transect.
a. The entire coral colony skeleton, including live and dead areas, must have one
dimension greater than 10 cm (any dimension—height, diameter, or length) to be
included in survey (Figure 3-7). Smaller coral colonies can be assessed if
recruitment data are desired.
Figure 3-7: Minimum size of coral
colony is 10 cm in any dimension,
including length, diameter, or
height. Yellow color denotes coral
skeleton, which may or may not be
covered by tissue.
Transect
line
25
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If greater than fifty percent of the colony falls within the transect perimeter, the
entire colony is included in the survey transect, even in cases where the tissue
falls outside the transect perimeter (Figure 3-8).
Figure 3-8: All coral
colonies 21 m in diameter
are included in transect if
£50% of colony is con-
tained within 1 m transect
(yellow). If <50% of colony
is in transect, the colony is
excluded (green). Check-
ered portions denote coral
tissue, clear colored por-
tion denotes dead coral
and exposed skeleton.
Data for colony size and tissue estimates are collected from the entire colony, not
merely from the portion that is contained within the transect perimeter or only
from the top (aerial view) of the colony.
Large colonies (> 1 m in diameter) that span the transect perimeter are counted
and measured even if the majority of the colony lies outside the transect perimeter
(Figure 3-9). If they do not span the transect perimeter, they are not counted.
Colonies within the transect perimeter with no tissue, but with visible calices to
indicate recent mortality are counted and measured. If identification to genus is
not possible from the calices, the taxon is reported as "unknown" (Figure 3-10).
26
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6. Post Survey: The survey is completed at the 25-meter mark of the tape and the depth is
recorded again. If stony corals are the last to be assessed, the surveyor detaches the transect
tape from the seafloor, rolls up the transect line, retrieves all equipment and returns to the
surface. After the dive, all data sheets are verified for accuracy, completeness and legibility
and any questionable records reconciled by the surveyor. Data sheets are rinsed with
freshwater and dried.
Figure 3-9: All coral colonies > 1
m in diameter are included in
transect if the colony spans the
entire 1 m width of the transect
(yellow), otherwise it is excluded
(green). Checkered portions
denote coral tissue, clear colored
portion denotes dead coral and
exposed skeleton.
Figure 3-10: Intact coral skeletons with no tissue are included in the assessment if the colony
can be identified to species or genus by calices or skeletal morphology.
27
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Table 3-2: Stony corals included in Western Atlantic and Caribbean assess-
ments (Humann and DeLoach 2002) with the three letter identification code
and the morphological conversion factor for calculating 3-D surface area.
Genus and Species
Acropora cervicornis
Acropora palmata
Acropora prolifera
Agaricia agaricites
Agariciafragilis
Agaricia humilis
Agaricia lamarcki
Agaricia tenuifolia
Cladocora arbuscula
Col pophy Ilia natans
Dendrogyra cylindrus
Dichocoenia stokesii
Diploria clivosa
Diploria labyrinthiformis
Diploria strigosa
Eusmilia fastigiata
Faviafragum
Leptoseris cucullata
Isophyllastrea rigida
Isophyllia sinuosa
Madracis decactis
Mad rods formosa
Madracis mirabilis
Madracis pharensis
Manicina areolata
Meandrina meandrites
Millepora complanata
Montastraea annularis
Montastraea cavernosa
Montastraea faveolata
Man tastraea franksi
Mussa angulosa
Mycetophyllia aliciae
Mycetophyllia danaana
Mycetophyllia ferox
Mycetophyllia lamarckiana
Oculina varicosa
Porites astreoides
Porites colonensis
Porites divaricata
Porites furcata
Porites porites
Siderastrea siderea
Solenastrea bournoni
Solenastrea hyades
Stephanocoenia intersepta
ID Code
Acer
Apal
Apro
Aaga
Afra
Ahum
Alam
Aten
Carb
Cnat
Dcyl
Dsto
Deli
Dlab
Dstr
Efas
Ffra
Lcuc
Irig
Isin
Mdec
Mfor
Mmir
Mpha
Mare
Mmea
Mcom
Mann
Mcav
Mfav
Mfra
Mang
Mali
Mdan
Mfer
Mlam
Ovar
Past
Pcol
Pdiv
Pfur
Ppor
Ssid
Sbou
Shya
Sint
Conversion Factor
4
4
4
1
1
1
1
3
2
2
3
2
2
2
2
3
2
1
2
2
3
3
3
1
2
2
3
3
2
2
2
2
1
1
1
1
3
2
1
3
3
3
2
2
3
2
28
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3.5 How are data managed?
Surveyors must review data sheets for legibility, completeness and correct use of standardized
codes for species and disease. A checklist for data sheet actions is provided in Figure B-7. Any
photographs taken to verify taxonomic description should be examined and appropriate changes
made and initialed on the original data sheet. Data are delivered to the data recorder who
transcribes from the underwater data sheets into an electronic spreadsheet for archiving and data
analysis. After the data have been electronically entered, they are verified for accuracy and
validated simultaneously by the surveyor and recorder. When complete, both the recorder and
surveyor sign and date the data sheets, which are scanned and archived.
3.6 How are indicators calculated?
All data are summarized, and procedures are applied to identify outliers, errors, and
inconsistencies to be considered prior to data analyses. These procedures can include summary
statistics, box plots, and stem and leaf plots. The three core measurements taken in the survey
(species, size, and percent tissue area) allow calculation of several indicators reflecting aspects of
community composition as well as physical status and biological condition of the colonies. They
were first proposed in Fisher (2007) and have been used in subsequent studies.
Community Composition
Abundance: number of colonies
r\
Density: number of colonies per m sea floor
Relative species abundance: abundance of a selected species per total abundance
Species (taxa) richness: number of species occurring in a reef or region
Species frequency of occurrence: proportion of sites where a species is present
Species diversity: index of taxa richness and relative abundance
Community composition: relative abundance of species with discretionary biological,
physical or regulatory attributes (e.g., tolerance, branching, protected status)
Physical Status
Total surface area (TSA): total 3D colony surface area (m2) including both living and
dead portions
9 99
3D total coral cover (3DTC): TSA per m sea floor (m /m )
Average colony surface area (CSA): TSA per total abundance (m )
Population structure: size distribution of colony abundance or other attribute for single
species
Community structure: size distribution of colony abundance or other attribute for all coral
species
Biological Condition
Percent live tissue (%LT): proportion of live coral tissue on each colony
Live surface area (LSA): live 3D surface area (m2) = TSA*(% LT)
3D live coral cover (3DLC): LSA per m2 sea floor (m2/m2)
%LSA: comparative index of live and total surface area [(LSA/TSA) *100]
The concept of measuring an organism's surface area is not new (Dahl 1973; Szmant-Froelich
1985; Roberts and Ormond 1987; Babcock 1991; Alcala and Vogt 1997; Bak and Meesters
29
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1998), but it has not been widely applied in coral reef studies because of the relative convenience
of measuring 2D projected colony surface area (live coral cover). Yet there are several possible
approaches to estimate the true surface area of coral colonies. Some studies have used the surface
area of geometric surrogates to estimate colony surface area from size classes or measurements
of field colony dimensions (Alcala and Vogt 1997; Bak and Meesters 1998; Fisher et al. 2007,
2008). Others have used photographic approaches, using computer software to convert multiple
2D photographic images into 3D colony surface area estimates (Bythell et al. 2001; Cocito et al.
2003; Courtney et al. 2007).
The simplest method is to assign a surface index value (Dahl 1973) to a circular footprint based
on colony morphology. A circular colony footprint is assumed because colony growth is usually
radial. The surface area of a circular footprint is Tir2 (r = radius) and the surface area of a
hemispherical colony is 27ir2 so the surface index for a hemispherical colony is 2. As colony
morphology becomes increasingly complex the surface index increases. To accommodate some
of the irregularities in colony formation, "r" is measured as the average of colony height and half
the maximum colony diameter. In general, surface indices were rated 1 for flattened species
morphology, 2 for hemispherical, 3 for lobed and domed morphologies and 4 for branched
colonies (Table 3-2 for Caribbean species). Currently, this coarse but simple method is
recommended for estimating 3D surface area of stony corals.
More accurate regression equations have been developed to estimate 3D surface area for nine
species of Caribbean stony corals (Table 3-3). The equations are derived from log-linear
regression models from colony measurements and photographic reconstructions of coral colonies
(Courtney et al. 2007). Several of the estimations require three colony measurements instead of
the two routinely taken. The percent difference of the regression estimates from the photographic
reconstruction (actual) are relatively small, less than 10%, for the hemispherical, spherical, and
low mounding colony morphologies (unpublished data, Fisher). More complex morphologies,
such as branching or other irregular shapes, do not have accurate regression equations for
estimating surface area; therefore none is recommended. EPA currently uses the morphological
surrogate approach (Table 3-2) to estimate 3D colony surface area.
30
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Table 3-3: Regression equations for estimating 3D surface area for nine coral species. Percent
difference is calculated from the actual measured surface area using a photographic reconstruc-
tion method. h=maximum colony height, d=maximum colony diameter (Courtney etal. 2007)
Species
Colpophyllia natans
Dichocoenia stokesii
Diploria labyrinthiformis
Siderastrea siderea
Stephanocoenia intersepta
Porites astreoides
Meandrina meandrites
Porites porites
Acropora palmata
Equation
2n(h+ d/2)
0.904 log(h)+1.165 log(d/2)+0.610
0.904 log(h)+1.165 log(d/2)+0.610
0.904 log(h)+1.165 log(d/2)+0.610
0.904 log(h)+1.165 log(d/2)+0.610
0.846 log(h)+0.723 log(d/2)+0.510
log(h+[d/2])+0.656
0.904 log(h)+1.165 log(d/2)+0.610
0.846 log(h)+0.723 log(d/2)+0.510
log(h+[d/2])+0.656
0.846 log(h)+0.723 log(d/2)+0.510
log(h+[d/2])+0.656
% Difference
from Actual
5%
10%
5%
5%
5%
5%
6%
12%
21%
Shape
hemisphere
sphere
sphere
flattened dome
sphere
low mound
low mound
branching
branching
3.7 References
Alcala MLR and Vogt H. 1997. Approximation of coral reef surfaces using standardized growth
forms and video counts. In: Proceedings of 8th International Coral Reef Symposium
2:1453-1458.
BabcockRC. 1991. Comparative demography of three species of scleractinian corals using age-
and size-dependent classifications. Ecological Monographs 61:225-244.
Bak RPM and Meesters EH. 1998. Coral population structure: the hidden information of colony
size-frequency distributions. Marine Ecology Progress Series 162:301-306.
Bythell JC, Pan P and Lee J. 2001. Three-dimensional morphometric measurements of reef
corals using underwater photogrammetry techniques. Coral Reefs 20:193-199.
Cocito S, Sgorbini S, Peirano A and Malle M. 2003. 3-D reconstruction of biological objects
using underwater video technique and image processing. Journal of Experimental Marine
Biology and Ecology 297:57-70.
Courtney LA, Fisher WS, Raimondo S, Oliver LM, and Davis WP. 2007. Estimating 3-
dimensional colony surface area of field corals. Journal of Experimental Marine Biology
and Ecology 351:234-242.
Dahl AL. 1973. Surface area in ecological analysis: quantification of benthic coral-reef algae.
Marine Biology 23:239-249.
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Fisher WS. 2007. Stony Coral Rapid Bioassessment Protocol. U. S. Environmental Protection
Agency, Office of Research and Development. EPA/600/R-06/167, Washington, DC. 60
pp.
Fisher WS, Davis WP, Quarles RL, Patrick J, Campbell JG, Harris PS, Hemmer B and Parsons
M. 2007. Characterizing coral condition using estimates of three-dimensional colony
surface area. Environmental Monitoring and Assessment 125:347-360.
Fisher WS, Fore LS, Hutchins A, Quarles RL, Campbell JG and Davis WS. 2008. Evaluation of
stony coral indicators for coral reef management. Marine Pollution Bulletin 56:1737-
1745.
Fisher WS, Santavy DL, Davis WP and Courtney LA. 2006. Regional Monitoring of Coral
Condition in the Florida Keys. In: Monitoring Science and Technology Symposium:
Unifying Knowledge for Sustainability in the Western Hemisphere. (Eds) Aguirre-Bravo
C, Pellicane PJ, Burns DP and Draggan S. Proceedings RMRS-P-42CD. Fort Collins,
CO: US Dept Agriculture, Forest Service, Rocky Mountain Research Station, pp. 304-
311.
Global Coral Disease Database (GCDD). 2012. Western Atlantic Diseases.
Humann P and DeLoach N. 2002. Reef Coral Identification. New World Publications, Inc.,
Jacksonville, FL. 287 pp.
National Oceanographic and Atmospheric Administration Coral Disease and Health Consortium
(NOAA CDHC). 2012. Coral Disease Identification Key.
National Oceanographic and Atmospheric Administration Coral Reef Information System
(NOAA CORIS). 2012. Major Reef-building Coral Diseases.
Principe P, Bradley P, Yee S, Fisher W, Johnson E, Allen P and Campbell D. 2012. Quantifying
Coral Reef Ecosystem Services. U.S. Environmental Protection Agency, Office of
Research and Development, Research Triangle Park, NC.EPA/600/R-11/206.
Roberts CM and Ormond RFG. 1987. Habitat complexity and coral reef fish diversity and
abundance on Red Sea fringing reefs. Marine Ecology Progress Series 41:1-8.
Szmant-Froelich A. 1985. The effect of colony size on the reproductive ability of the Caribbean
coral Montastraea annularis (Ellis and Solander). In: Proceedings of 5th International
Coral Reef Congress 4:295-300.
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4.0 Marine Gorgonian Assessment
4.1 What is measured?
Marine gorgonian (Octocorallia)
surveys document the size and
morphology of each colony to
estimate the surface area
contribution to reef habitat.
Height and maximum diameter
are measured for each gorgonian
classified by colony morphology
(not taxonomy). The dimensions
are converted to 3D colony
surface area using a formula
derived for each morphological
type. Additional data collection
can include taxonomic
identification and reporting of
adverse health conditions (e.g.,
bleaching, disease, predation). Data provide estimates of gorgonian abundance, density, surface
area and, if included in the protocol, physical condition and taxa richness.
Figure 4-1: Marine gorgonian assessments allow evalua-
tion of ecosystem services such as habitat for fish, ma-
rine Pharmaceuticals and aesthetic qualities.
4.2 Why is it measured?
Marine gorgonians provide many important ecosystem services (Figure 4-1). The rich
biochemical diversity of gorgonians provides bioprospecting opportunities for new marine
chemicals and pharmaceuticals (Fenical 1996). Cnidaria have contributed over 10% of the
marine biochemicals isolated with pharmaceutical potential (Hunt and Vincent 2006). Marine
gorgonians are also partially responsible for tourism and recreational opportunities; in particular,
large colorful colonies attract snorkelers and divers, while the fish that use them as habitat attract
recreational fishers.
Marine gorgonians supply biogenic habitat for reef fish and other invertebrates (Gratwicke and
Speight 2005). Gorgonians can serve as a nursery for fish and invertebrates, which may be
especially important when stony coral habitat is in decline (Wolff et al. 1999; Kuffner et al.
2007). Although gorgonians are prominent reef inhabitants, they are often excluded from
monitoring programs. This is partially because they are not widely recognized for their important
functional contributions to reef environments, and partially because taxonomic distinctions can
be difficult. In this approach, classification is based on morphology, categorized by
predetermined shapes, which can be easier to apply than taxonomy. Size of the colony, combined
with its morphological shape can be used to estimate the contribution to 3D reef habitat (Santavy
et al. in review). If taxonomic expertise is available, both taxonomic and morphological
classification schemes can be used to provide additional information.
33
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4.3 What do we need?
4.3.1 Surveyor skills
The surveyor must be able to discern gorgonians from stony corals, sponges, tunicates,
hydrozoans, zooanthids, bryozoans and other marine organisms and classify gorgonians into
morphological groups as described below. If taxonomic classification and adverse biological
conditions are included, the surveyor must be able to distinguish species (or at least genera) and
signs of adverse conditions. Condition information can be acquired with little additional training,
whereas taxonomic training requires a greater time investment. Reporting of taxonomic and
adverse colony health is facilitated with an underwater camera to record questionable taxa or
conditions for comparison with existing literature.
4.3.2 Equipment
- Gorgonian Survey Data Sheet (Figure B-3) or combined Gorgonian and Sponge Survey Data
Sheet (Figure B-4) printed on underwater paper
- Gorgonian morphological codes (Table 4-1)
- Underwater slate with clipboard
- Underwater pencils or pens13 with surgical tubing or rubber bands to attach to slate
- Flexible fiberglass metric measuring tape on reel at least 30 m in length
- 0.5 m or 1 m linear measuring instrument marked in 5 cm increments (e.g., PVC tube)
- 1 m2 (1m x 1m) or 0.5 m2 (70.7cm x 70.7cm) quadrat (PVC tubing)
- Optional: automatic underwater digital camera
- Optional: 30m lead line with 30 tie wraps
Routinely, a single diver surveys both gorgonians and sponges and uses a single data sheet that
accommodates data for both groups (Figure B-4). Depending on the goals of the study, it is
possible to survey only gorgonians, in which case the surveyor would use the Gorgonian Survey
Data Sheet (Figure B-3). If any other survey is conducted, the tape will already be in place. If
not, the measuring tape is deployed from the reel and can be attached to the substrate with a
small diameter bungee cord and snap clip on the end of the tape. The bungee cord is wrapped
around an object on the substrate and clipped back on itself to secure the tape in place. If the
transect will be used for other types of surveys (e.g., stony coral, sponge) and there is a
significant current, it is recommended that the tape be weighted with a thin lead line to reduce
movement. An underwater camera is beneficial to record uncertain gorgonians that can be used
later to clarify unknown or questionable identifications with existing literature.
13
Recycled wood pencils will disintegrate. Always bring multiple pencils or pens.
34
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4.3.3 Morphological classification scheme
Gorgonian colonies (subclass Octocorallia, Order Gorgonacea) are classified into general
morphologies using descriptive terms that denote the shape and proportions of a colony without
regard for taxonomic affiliation (Santavy etal. in review). Basic categories include: sea fans, sea
rods, sea whips, sea plumes and encrusting forms (see Table 4-1). In general, sea rods, sea whips
and sea plumes are distinguished by the differences in branch and branchlet diameters, which
affect the surface area of the colony.
Sea fans
Planar sea fans consist of a reticulate structural array occurring on a single plane
resembling a flat fan.
Three-dimensional sea fans have multiple fan structures with varied planar
arrangements arising from a central stalk thus significantly increasing the
structure's surface area.
Sea rods single or branched, rods are usually 15-30 mm in diameter.
Unbranched sea rods are simple, single or multiple upright rod structures arising from a
single basal expansion.
Planar sea rods resemble a candelabra (or menorah) with multiple rods occurring in a
single plane.
Branched and bushy sea rods are characterized by arborescent (tree-like) forms and
bifurcation. Branched colonies are distinguished from bushy colonies by the former
having abundant branching arising above the holdfast, usually not forming an
obvious main stem.
Sea whips branches are usually 5-15 mm in diameter.
Branched and bushy sea whips are characterized by arborescent forms varying in
complexity in number of branches, types of branching and degree of bifurcation.
Branched colonies are distinguished from bushy colonies by the former having
abundant branching arising above the holdfast, usually not forming an obvious
main stem. They can be with or without angular branches in cross section as
found in Pterogorgia.
Sea plumes branches are usually less than 5 mm in diameter.
Sea plumes have branched morphology that resemble ostrich feathers. They have the
smallest diameter of branches and branchlets, the most consistent branch axial
diameter and the longest branchlets of all gorgonians.
Encrustinggorgonians have a characteristic crust that spreads over the substrate, with little
height. These provide little vertical substrate for habitat.
35
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Table 4-1: Gorgonian morphological shapes with simulated models
and in situ examples.
Gorgonian Morphology
Simulated
Model
Sea Fans
(Gorgonia
ventalina,
Leptogorgia)
(Gorgonia
flabellum)
Sea Rods
branch and
branchlet
diameter >
15 - <30mm
Planar
Three-
dimensional
Unbranched
(digitate form,
Briareum)
Branched
(Plexaura)
Bushy
(Eunicea
fusca)
Planar
(Eunicea
tourneforti)
Sea Whips
branch &
branchlet
diameter >5 -
<15mm
Branched
(Pterogorgia)
Bushy
(Pterogorgia
guadalupensi)
Sea Plumes
smallest branch &
branchlet diameter
usually <5mm
(Muriceopsis fI avid a,
Pseudopterogorgia)
Encrusting Gorgonians
(Briareum, Erythopodium)
36
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4.4 How are data collected?
1. Preparation: Survey information is recorded on the survey data sheet (Figure B-3 or B-
4), ensuring each page is numbered consecutively and taking care to enter the date,
location and surveyor name prior to entering the water. A weighted marker buoy is set
from the surface at the desired sampling location using GPS coordinates. If multiple
assessments for other organisms and measurements are to be made, the fish survey
should always be done first. If only the gorgonian survey is done, the gorgonian
surveyor and buddy enter the water at the site with transect line (30m tape on reel),
quadrat, measuring tool, data sheets, gorgonian morphology codes, slate and pencils
(optional camera). The transect location and direction are selected as the best available
reef habitat (usually based on stony coral coverage) within 20 m of the buoy weight. The
transect tape is securely fastened to the seafloor and extended 25 m in a straight line. (If
the gorgonian assessment is preceded by a fish assessment, the transect tape is already
set by the fish surveyors). Depths are recorded at the 0 m and 20 m marks.
2. Transect: The quadrat is placed at 0 m, 5 m, 10m, 15m and 20 m marks along the 25 m
transect tape. If there is insufficient time because there are too many organisms to count
in one dive, the quadrat can be placed at only three locations. Alternatively, five smaller
quadrats (0.5 m2) could be used along same five marks. The quadrat is positioned and
secured against current and wave action. The quadrat or grid number indicating its
position along the transect line is recorded on the data sheet.
3. Procedure: Every gorgonian > 10 cm (in any dimension) that falls within the quadrat is
classified as one often gorgonian morphologies (Table 4-1). Colony height (greatest
distance from substrate) and maximum diameter (parallel to the substrate) are measured
to the nearest 5 cm.
4. Optional measurements:
a. If condition is assessed, notations of bleaching, disease or other abnormality can
be noted in the remarks column.
b. If taxonomy (genus, species) is reported, this can be noted in the remarks column.
c. If many individuals with the same morphology and approximately the same size
occur within the same grid, they can be grouped for recording purposes. The total
number of similar gorgonians can be noted as ticks in the remarks column.
d. If encrusting gorgonians are documented, then maximum diameter and width
(dimension orthogonal to the maximum diameter at its midpoint) are measured to
the nearest 5 cm increment.
5. Post Survey: The survey is completed at 21 m mark and the depth is again recorded. If
gorgonians are the last assemblage to be assessed, the surveyor detaches the transect
tape from the seafloor, rolls up the transect line, retrieves all equipment and returns to
the surface. After the dive, all data sheets are verified for accuracy, completeness and
legibility, and any questionable records reconciled by the surveyor. Data sheets are
rinsed with freshwater and dried.
37
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4.5 How are data managed?
Surveyors must review data sheets for legibility, completeness and correct use of standardized
codes. Changes are made to the data sheet and should be initialed. A checklist for data sheet
actions is in Figure B-7. Any photographs taken to verify taxonomic or morphological
description are examined and archived with appropriate file name. Data are delivered to the data
recorder who transcribes from the underwater data sheets into electronic format for archiving and
data analysis. After the data have been electronically entered, they are verified for accuracy and
validated simultaneously by the surveyor and recorder. When complete, both the recorder and
the surveyor sign and date the data sheets, which are scanned and archived.
4.6 How are indicators calculated?
All data are summarized and procedures are applied to visualize outliers, errors, and other
inconsistencies to be considered prior to data analyses. These procedures can include summary
statistics, box plots, and stem and leaf plots. Morphological measurements (height and diameter)
are entered into the appropriate regression equation (Table 4-2) to estimate surface area of
individual specimens. The regressions were developed from simulated models with measurement
errors (Santavy et al. in review) (Appendix D). Community ecological attributes such as
richness, abundance, density, diversity and cover can be calculated using morphological instead
of taxonomic classifications.
Table 4-2: Regression equations to estimate surface area of
gorgonians with different morphology. d=maximum
diameter, h= height, w=maximum planar width
Gorgonian
Morphology
Surface Area
Estimations
Sea Fans planar
Sea Fans 3D
Sea Rods planar
Sea Rods unbranched
Sea Rods branched
Sea Rods bushy
Sea Whips branched
Sea Whips bushy
Sea Plumes
Encrusting
SA=0.68h2+0.66d2-3.61
SA=0.0113h3+106d-1190
SA=76.4 d-806
SA=0.341d3+11.2h-127
SA=1.46d2+399
SA=0.0288h3+ 939
SA=31.2h-0.0069h3-248
SA=0.0672d3+1610
SA=4.77h2-2990
SA=dw
38
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4.7 References
Fenical W. 1996. Marine biodiversity and the medicine cabinet: the status of new drugs from
marine organisms. Oceanography 9:23-27.
Gratwicke B and Speight MR. 2005. Effects of habitat complexity on Caribbean marine fish
assemblages. Marine Ecology Progress Series 292:301-310.
Hunt B and Vincent ACJ. 2006. Scale and sustainability of marine bioprospecting for
Pharmaceuticals. Ambios 35:57-64.
Kuffner IB, Brock JC, Grober-Dunsmore R, Bonito VE, Hickey TD and Wright CW. 2007.
Relationships between reef fish communities and remotely sensed rugosity measurements
in Biscayne National Park, Florida, USA. Environmental Biology of Fish 78:71-82.
Santavy DL, Courtney LA, Fisher WS, Quarles RL and Jordan SJ. (in review, 2012) Estimating
the surface area of marine gorgonians and sponges in the field. Hydrobiologia.
Wolff N, Grober-Dunsmore R, Rogers CS and Beets J. 1999. Management implications offish
trap effectiveness in adjacent coral reef and gorgonian habitats. Environmental Biology
of Fish 55:81-90.
39
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5.0 Marine Sponge Assessment
Figure 5-1: Marine sponge assessments allow important
ecological and economic services to be evaluated by
measuring surface area.
5.1 What is measured?
Marine sponge (Porifera)
surveys document the size and
morphology of each organism to
estimate the surface area
contribution of sponges to reef
habitat. Height and maximum
diameter are measured for each
sponge classified by colony
morphology instead of
taxonomy. The dimensions are
converted to 3D colony surface
area using a formula derived for
each morphological type.
Additional data collection can
include taxonomic identification
and reporting of adverse health
conditions (e.g., bleaching,
disease, predation). Data will provide estimates of sponge abundance, density, surface area and,
if included in the protocol, physical condition and taxa richness.
5.2 Why is it measured?
Marine sponges provide many important ecosystem services (Figure 5-1). The diversity of
sponges in reef habitats provides bioprospecting opportunities for new marine biochemicals and
Pharmaceuticals (Fenical 1996). Porifera possess unique biological compounds that have
contributed nearly 65% of the marine biochemicals isolated with pharmaceutical potential (Hunt
and Vincent 2006). Large and colorful marine sponges attract snorkelers and divers making them
partially responsible for tourism and recreational opportunities. The fish that use them as habitat
attract recreational fishers. Finally, a small commercial fishery for marine sponges still exists
today.
Marine sponges have diverse functional roles that directly influence coral reefs and the survival
of many associated organisms. Sponges provide habitat for fish and other invertebrates
(Gratwicke and Speight 2005), reinforce reef structure by cementation, contribute to nitrogen and
carbon cycling through the metabolic activity of their microbial symbionts, and efficiently filter
sediment, algae and small organisms from the water column (Wulff 2006). Although-sponges are
one of the most prominent sessile invertebrates on coral reefs, they are often overlooked in
monitoring programs. This may be in part because sponge taxonomic classification is
confounded by high diversity and morphological plasticity. In this approach, classification is
based on morphology rather than taxonomy (Santavy et al. in review); however, if taxonomic
40
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expertise is available both classification schemes can be used to provide additional information
for assessing biological condition.
5.3 What do we need?
5.3.1 Surveyor skills
The surveyor must be able to discern sponges from stony corals, octocorals, tunicates,
hydrozoans, zooanthids, bryozoans and other marine organisms and must be able to classify
sponges into morphological groups as described below. Signs of adverse biological conditions
can be accomplished with little additional training, whereas taxonomic classification to
distinguish species (or at least genera) requires a significant time investment. Taxonomic and
adverse health reporting can be facilitated with an underwater camera to record questionable taxa
or conditions for comparison with existing literature.
5.3.2 Equipment
- Sponge Survey Data Sheet (Figure B-5) or combined Gorgonian and Sponge Survey Data Sheet
(Figure B-4) printed on underwater paper
- Sponge morphological codes
- Underwater slate with clipboard
- Underwater pencils or pens14 with surgical tubing or rubber bands to attach to slate
- Flexible fiberglass metric measuring tape on reel at least 30 m in length
- 0.5 m measuring tool marked in 5 cm increments (e.g., PVC tube)
- 1 m2 (1m x 1m) or 0.5 m2 (70.7 cm x 70.7 cm) quadrat (PVC tubing)
- Optional: automatic underwater camera
- Optional: 30m lead line with 30 tie wraps
Usually a single diver surveys both gorgonians and sponges, and uses a single data sheet that
accommodates data for both groups (Figure B-4). Depending on the goals of the study, it is
possible to survey only sponges, in which case the surveyor would use the Sponge Survey Data
Sheet (Figure B-5). The metric measuring tape should be on a reel to allow easy deployment and
should be clearly marked at 1 m increments. If any other survey is conducted, the tape will
already be in place. The tape can be attached to the substrate with a small diameter bungee cord
and snap clip on the end of the tape. The bungee cord is wrapped around an object on the
substrate and clipped back on itself to secure in place. If the transect will be used for other types
of surveys (e.g., coral, sponge), and there is a significant current, it is recommended that the tape
be weighted with a thin lead line to reduce movement. The lead line can be attached to the
transect line with tie wraps every meter. An underwater camera is beneficial to record uncertain
sponges that can be used later to clarify unknown or questionable identifications with existing
literature.
5.3.3 Morphological classifications
Marine sponges (class Demospongiae) are classified into ten morphological forms, including
barrel, vase, globe, mound, tube, rod, ropey branching, bushy, encrusting, and boring types
(Table 5-1). Each group is defined by shape and relative proportions without regard to taxonomic
affiliation or surface texture (Santavy et al. in review). Although species generally exhibit a
particular shape, two individuals of the same species could be classified into two different
14
Recycled wood pencils will disintegrate. Always bring multiple pencils or pens.
41
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morphological groups. For example, Cribrochalina vasculum could be classified as either a
barrel or a vase sponge.
Barrel sponges resemble a cylinder with a flat bottom, and can exhibit varying degrees of
surface relief and side slope.
Vase sponges are tapered at the base and wider at the top. An individual sponge can have
one or multiple vases.
Globe sponges include spherical, hemispherical or elliptical shapes that can vary in
height and diameter. The surfaces are mostly convex and have minor irregularities.
Mound sponges are amorphous with an irregular shape, devoid of symmetry or
resemblance to a simple geometric figure. They often are described as lobate or having a
lumpy surface.
Tube sponges have large hollow cylinders resembling tubes or pipes that can be either
singular or multiple; individuals sometimes have 12 or more tubes.
Rod sponges have solid cylinders without large openings. Rods lack branching and are
usually single, digitate (finger-like), upright cylinders. Multiple rods can originate from a
common base with no branching (stoloniferous).
Bushy sponges resemble large arborescent upright shapes with branching in multiple
planes originating from a common stalk or base. They appear similar to bushes or
branched forms.
Branching ropey sponges are similar to small rod sponges but appear tangled and
intertwined as a rope. This sponge has digitate branching in one or more planes and can
have irregular or regular branching, appearing as arborescent (tree-like) or tangled rods in
any or multiple planes. The branching forms can be either simple or complex.
Encrusting sponges resemble veneer-like overgrowth with very little colony height.
Dimensions of an encrusting sponge are recorded as maximum diameter and width of the
colony orthogonal to and at the midpoint of the maximum diameter.
Boring sponges also resemble veneer-like overgrowth and are distinguished from
encrusting sponges by penetration of the coral's surface and skeleton. Dimensions of a
boring sponge are recorded as maximum diameter and width of the colony orthogonal to
and at the midpoint of the maximum diameter.
5.4 How are data collected?
1) Preparation: Survey information is recorded on the survey data sheet (Figure B-5 or B-4),
ensuring each page is numbered consecutively and taking care to include date, location,
and surveyor name prior to entering the water. A weighted marker buoy is set from the
surface at the desired sampling location using GPS coordinates. If multiple assessments
for other organisms are to be made, the fish survey should always be done first. If only a
42
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sponge survey is done, the sponge surveyor and buddy enter the water at the site with
measuring tape on reel, quadrat, measuring tool, data sheets, sponge morphology codes,
pencils and slate (optional: camera). The transect location and direction are selected as
the best available reef habitat (usually based on stony coral coverage) within 20 m of the
buoy weight. The transect tape is securely fastened to the seafloor and extended 25 m in a
straight line. (If the sponge assessment is preceded by a fish assessment, the transect tape
is already set by the fish surveyors). Depths are recorded at the 0 m and 20 m marks.
2) Transect: The quadrat is placed at 0 m, 5 m, 10m, 15m and 20 m along the 25 m transect
tape. If there is insufficient time to complete the quadrats because there are too many
organisms to count in one dive, the quadrat can be placed at only three locations.
Alternatively, five smaller quadrats (0.5 m2) could be used along same five marks. The
quadrat is positioned against current and wave action. The quadrat or grid number
indicating its position along the transect line is recorded on the data sheet.
3) Procedure: Every sponge > 10 cm (in any dimension) falling within the quadrat is
classified as one often sponge morphologies (Table 5-1). If the base of sponge is in the
quadrat, it is considered in the transect. Colony height (greatest distance from substrate)
and maximum diameter (parallel to the substrate) are recorded to the nearest 5 cm.
4) Optional measurements:
a. If condition is assessed, notations of bleaching, disease or other abnormality can
be noted in the remarks column.
b. If taxonomy (genus, species) is reported, this can be noted in the remarks column.
c. If many individuals with the same morphology and approximately the same size
class (height x diameter within 5 cm increments) occur within the same grid, they
can be grouped for recording purposes. The total number of similar sponges can
be noted as ticks in the remarks column.
d. If encrusting and boring sponges are documented, then maximum diameter and
width (dimension orthogonal to the maximum diameter at its midpoint) are
measured to the nearest 5 cm increment.
5) Post-Survey: The survey is completed at the 21 m mark and the depth is recorded again.
If sponges are the last assemblage to be assessed, the surveyor detaches the transect tape
from the seafloor, rolls up the transect line, retrieves all equipment and returns to the
surface. After the dive, all data sheets are verified for accuracy, completeness and
legibility and any questionable records reconciled by the surveyor. Data sheets are rinsed
with freshwater and dried.
43
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Table 5-1: Sponge morphological shapes with simulated
models and in situ examples.
Sponge Morphology
(spp. example)
Simulated
Model
in situ
Example
Barrel
(Xestospongia muta,
Verongula reiswigi)
Vase
(Callyspongia plicifera,
Callyspongia vaginalis)
Globe
(tricinia strabilina,
Spheciospongia vesparium)
Tube
(Aplysina archeri, Aplysina
fistularis)
Mound
(Oligoceras hemorrhages,
Iriciniafelix)
Rod
(Aplysina cauliformis,
Niphates erecta)
Bushy
(Aplysina fulva)
Branched Ropey
(lotrochota birotulata)
Encrusting
(Amphimedon compressa,
Chrondrilla caribensis)
Boring
(all Clionids)
'
fc " 3
SK; ..^
44
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5.5 How are data managed?
Surveyors must review data sheets for legibility, completeness and correct use of standardized
codes. Changes are made to the data sheet and should be initialed. A checklist for data sheet
actions is in Figure B-7. Any photographs taken to verify morphological or taxonomic
description should be examined and archived with appropriate file name. Data are delivered to
the data recorder who transcribes from the underwater data sheets into electronic format for
archiving and data analysis. After the data have been electronically entered, they are verified for
accuracy and validated simultaneously by the surveyor and recorder. When complete, both the
recorder and the surveyor sign and date the data sheets, which are scanned and archived.
5.6 How are indicators calculated?
All data are summarized, and procedures are applied to visualize outliers, errors, and other
inconsistencies to be considered prior to data analyses. These procedures can include summary
statistics, box plots, and stem and leaf plots. Morphological measurements (height and diameter
dimensions) are entered into the appropriate regression equation (Table 5-2) to estimate surface
area of individual specimens. The regressions were developed from simulated models and
measurement errors provided in Santavy et al. (in review) (Appendix D). For barrel, vase and
tube sponge morphologies, surface areas are calculated using both outside and inside surfaces.
Community ecological attributes such as richness, density, diversity indices and abundance can
be calculated using morphological as well as taxonomic classifications if taxa are recorded.
Table 5-2: Equations to estimate surface area of
sponges with different morphology. d=maximum
diameter, h=height, w=maximum planar width
Sponge
Morphology
Barrel
Vase
Globe
Mound
Tubes
Rods
Bushy
Ropey Branched
Encrusting & Boring
Regression
Equations
SA=4.31d"+0.827hr+108
SA=3.71h-161
SA=1.88h2 +0.0573d3+83.3
SA=30.0h+18.7d-193
SA=0.493d3+109
SA=7.69h+1.83d3-33.5
SA=0.462h2+0.834d2+19.3
SA=18.8d+7.97h-132
SA=dw
45
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5.7 References
Fenical W. 1996. Marine biodiversity and the medicine cabinet: the status of new drugs from
marine organisms. Oceanography 9:23-27.
Gratwicke B and Speight MR. 2005. Effects of habitat complexity on Caribbean marine fish
assemblages. Marine Ecology Progress Series 292:301-310.
Hunt B and Vincent ACJ. 2006. Scale and sustainability of marine bioprospecting for
Pharmaceuticals. Ambios 35:57-64.
Santavy DL, Courtney LA, Fisher WS, Quarles RL and Jordan SJ. (in review 2012). Estimating
the surface area of marine gorgonians and sponges in the field. Hydrobiologia.
Wulff JL. 2006. Rapid diversity and abundance decline in a Caribbean coral reef sponge
community. Biological Conservation 127:167-176.
46
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6.0 Reef Rugosity, Live Coral Cover and
Macroinvertebrate Assessments
6.1 What is measured?
Reef rugosity is surveyed to
infer topographical
complexity of the coral reef
surface. A rugosity index is
applied as a reef-scale
indicator of reef contour or
roughness (Figure 6-1). It is
determined using a chain-
transect method that compares
the length of a chain draped
along the coral and bottom of
a reef to the length of a taut
line across the same linear
distance.
Figure 6-1: Rugosity is a measure of reef surface
complexity.
Linear point intercept (LPI) method is used to estimate the percent planar live coral coverage on
the reef This method uses points along a transect to quantify no coral, live coral, or dead coral
coverage lying underneath each point.
Selected macroinvertebrates that contribute to ecological and ecosystem services are enumerated
by visual count census. Invertebrates targeted for Caribbean surveys are queen conch (Strombus
gigas) recorded as adult or juvenile, spiny lobster (Panilaurus argus), reef crabs larger than 20
cm, sea urchins and long-spined sea urchins (Diadema antillarum).
The three assessments are presented together because they are easily completed simultaneously.
6.2 Why is it measured?
Vertical relief and topographical complexity of coral reefs are assessed by measuring rugosity,
which is a coarse estimate of reef contour (McCormick 1994; Alvarez-Filip et al. 2009) (Figure
6-2). Several studies have applied a rugosity index to estimate physical habitat provided by a reef
(McCormick 1994; Rogers et al. 1994; Lang 2003). The rugosity index estimates complexity by
sampling the two-dimensional (2D) vertical contour of stony corals and non-coral substrate along
the draped line. This generates a unitless value that can be used for relative comparisons across
stations and reefs. The chain-transect method estimates topography by extrapolation. While
rugosity accounts for important vertical dimensions, it is only captured in one horizontal
dimension and might not be as useful as 3D estimates of colony size and complexity.
47
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Many past reef assessments have used 2D coral coverage as an indicator of reef condition. In
order to compare results from 3D coral cover assessments with other studies, it is recommended
that LPI also be assessed (Loya 1978).
Selected commercially and ecologically important macroinvertebrates are documented to
indicate their population status on reefs. Queen conch, spiny lobsters and some crabs are
harvested for food and consequently have been declining throughout the Caribbean for decades.
Queen conch is a threatened and endangered species, protected in Florida, with catch limits
enforced in Puerto Rico and United States Virgin Islands. Sea urchins (especially Diadema
antillarum ) have an important herbivory role on reefs and are considered a keystone species. An
epizootic in the 1980s decimated Diadema antillarum populations throughout the Western
Atlantic (Lessios 2005).
Figure 6-2: Examples of low rugosity (left) and high rugosity (right) reefs.
6.3 What do we need?
6.3.1 Surveyor skills
Only basic skills for underwater work are required for these assessments. For rugosity, a chain is
draped over stony corals at several locations and its length measured. For LPI, one characterizes
whether coral is present and whether it is alive or dead underneath each meter mark along a 25 m
transect. For macroinvertebrates, one must be able to recognize the queen conch (Strombus
gigas\ the spiny lobster (Panilaurus argus), crabs larger than 20 cm, sea urchins and distinguish
the long-spined sea urchin (Diadema antillarum) (Figure 6-3). The queen conch is recorded by
maturity level. An adult conch has a flared lip on the edge of its shell and a juvenile does not
(Fig. 6-4).
6.3.2 Equipment
- Rugosity, Biosurvey and LPI Data Sheet on underwater paper (Figure B-6)
- Underwater slate with clipboard
- Several underwater pencils or pens15 with surgical tubing or rubber bands to attach to slate
- Flexible fiberglass metric measuring tape on reel at least 30 m in length marked 1 m increments
' Recycled wood pencils will disintegrate. Always bring multiple pencils or pens.
48
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- Second flexible fiberglass metric measuring tape on reel at least 10 m in length
-6m length linked chain or line with pencil weights inserted (to minimize reef damage)
Figure 6-3: Macroinvertebrates
included in the survey are large
crabs (top left), spiny lobster
(Panilaurus argus), and the black
sea urchin (Diadema antillaruni).
6.4 How are data collected?
1) Preparation: Survey information is recorded on the Rugosity, Biosurvey and LPI Data
Sheet (Figure B-6), ensuring each page is numbered consecutively and taking care to
include date, location, and surveyor name prior to entering the water. A weighted marker
buoy is set from the surface at the desired sampling location using GPS coordinates. If
multiple assessments for other organisms and measurements are to be made, the fish
survey should always be done first. Often the fish surveyors can do these surveys after
they finish while the other surveyors are assessing corals, gorgonians and sponges. If
only this survey is done, the surveyor and buddy diver enter the water at the site with two
measuring tape, 6 m linked chain, slate, pencils and data sheets. The best available habitat
within 20 m of the buoy weight is selected for the survey. The transect tape is securely
fastened to the seafloor and extended 25 m in a straight line. (If the rugosity, LPI and
macroinvertebrate surveys are preceded by a fish assessment or other group, the transect
tape is already set up.) Depths at the 0 and 20 m mark are recorded.
2. Rugosity: Divers perform five rugosity measurements at the 0, 5, 10, 15 and 20 m
marks along the 25 m transect using a separate tape measure, laid parallel but not on top
49
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of the transect tape. The linked chain is placed such that it follows the relief of
hardbottom substrate. The chain is placed on top of any hard substrate encountered, but
not on top of gorgonians or sponges since only hardbottom rugosity is being measured.
To avoid these organisms, place the chain around or along the bottom to avoid placing
on branches, but it can drape over the base. An effort should be made to ensure the chain
is touching the substrate at all points along transect without doubling back on itself. The
second diver can adjust the chain as the surveyor lays it over the substrate to ensure it
has the best contact. A surveyor records the linear distance above the 6 m chain draped
across the coral colonies in the transect, using another measuring tape. The tape must be
pulled taut to determine the linear distance (NOAA CCMA 2008).
LPI Survey: Divers evaluate the presence or absence of coral under the 25 m transect
tape at every meter mark between 0 m and 25 m, including each end. If coral is present
then it is recorded as either live or dead coral.
Macroinvertebrate Abundance: Divers
count the designated macroinvertebrates
within 2 m on either side of the 25 m tape
measure (survey area 4 m x 25 m =100
m ). The survey can be done while
deploying the 25 m tape or by the
rugosity surveyors on their way back
from the end of the 25 m tape. Large
crabs, lobsters, sea urchins and conch are
visually noted. The surveyors should
search the reef surface for relief such as
holes, overhangs, or crevices deep within
the reef framework for these often
contain hidden invertebrates. Record
whether the conch is an adult or juvenile
based on the shell's lip structure (Figure
6-4).
Figure 6-4: Adult and juvenile forms of queen
conch (Strombusgigas). The adult has a flared
lip that the juvenile form lacks. (Photo credit:
)
5. Post-Survey: When the survey is completed, the depth is recorded at the 25 m end. If
this is the last survey to be completed, all survey gear is retrieved and returned to the
surface. The surveyor detaches the transect tape from the seafloor, rolls up the transect
line and returns to the surface. After the dive, all data sheets are verified for accuracy,
completeness and legibility and any questionable records reconciled by the surveyor.
Data sheets are rinsed with freshwater and dried.
6.5 How are data managed?
Surveyors must review data sheets for legibility, completeness and correct use of standardized
codes. A checklist for data sheet actions is in Figure B-7. Data are transcribed from the
underwater data sheets into electronic format for archiving, data management and data analysis.
After the data have been electronically entered, they are verified for accuracy and validated
simultaneously by the surveyor and recorder. When complete, both the recorder and the surveyor
sign and date the data sheets, which are scanned and archived.
50
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6.6 How are indicators calculated?
Rugosity is the ratio of the overall length of chain draped over the reef contour divided by the
straight horizontal distance between the beginning and the end of the chain. Therefore, if 6 m of
chain is laid out over a 4 m horizontal distance, the rugosity is 6/4 = 1.5 for that segment.
Rugosity will always be > 1. Higher values relate to increased rugosity or reef relief.
LPI is recorded as the number of points of each coral class divided by the total number of points
evaluated. This results in estimates for planar coverage of coral vs. no coral, and live coral vs.
dead coral (exposed skeleton).
Key macroinvertebrates are reported as density to compare their presence across stations.
Strombus gigas are reported as either adults or juveniles based on the presence of a flared lip.
6.7 References
Alvarez-Filip L, Dulvy NK, Gill JA, Cote EVI and Watkinson AR. 2009. Flattening of Caribbean
coral reefs: region-wide declines in architectural complexity. Proceedings of the Royal
Society of Britain B 276:3019-3025.
Lang JC. 2003. Status of coral reefs in the western Atlantic: results of initial surveys, Atlantic
and Gulf Rapid Reef Assessment (AGRRA) program. Atoll Research Bulletin 496:1-630.
Lessios HA. 2005. Diadema antillarum populations in Panama twenty years following mass
mortality. Coral Reefs 24:125-127.
Loya Y. 1978. Plotless and transect methods. Ed: DR Stoddart and RE Johannes. In: Coral reefs:
research methods. UNESCO Paris, pp. 197-217.
McCormick M. 1994. Comparison of field methods for measuring surface topography and their
associations with a tropical reef fish assemblage. Marine Ecology Progress Series 112:87-
96.
National Oceanographic and Atmospheric Administration, Center for Coastal Monitoring and
Assessment (NOAA CCMA). 2008. Detailed Methods for Characterization and
Monitoring of Coral Reef Ecosystems and Associated Biological Communities.
.
Rogers C, Garrison G, Grober R, Hillis Z-M and Franke MA. 1994. Coral Reef Monitoring
Manual for the Caribbean and Western Atlantic. US Virgin Islands National Park
Service.
51
-------
52
-------
Appendix A: Other Coral Reef Assessment
Programs
53
-------
Table A-l: Some current coral reef monitoring and assessment programs, including websites.
Program
Atlantic and Gulf Rapid Reef Assessment
Australian Institute of Marine Science
British Virgin Islands Dept. Environ. &
Fisheries
Caribbean Coral Reef Ecosystem
Assessment Monitoring Project
Coral Reef Assessment and Monitoring
Program
Coral Reef Evaluation and Monitoring
Project
US Environmental Protection Agency
International Union for the Conservation
of Nature
Reef Check
Regional Organization for Conservation of
Environment of Red Sea & Gulf of Aden
Acrony
AGRRA
AIMS
BVIDEF
CCMA
CRAMP
CREMP
EPA
IUCN
RC
PERSGA
Website
www.agrra.org
www.aims.gov.au/docs/research/monitor
ing/reef/latest-surveys. html
www.bvidef.org/main/
ccma.nos.noaa.gov/ecosystems/coralreef/
reef fish/
cramp.wcc.hawaii.edu
ocean.floridamarine.org/iknms wqpp/pa
ges/cremp.html
www.epa.gov/bioiwebl/pdf/EPA-260-R-
06-004StonyCoralsUSVIField
Testing .pdf
cmsdata.iucn.org/downloads/resilience
assessment fmal.pdf
www.reefcheck.org
www.persga.org/
Year
G
OJD
QQ
1998
1985
2005
2000
1998
1996
2006
2005
2007
2008
•a
C
U
Present
Present
Present
Present
1999
2007
2006
Present
Present
2009
Ocean
NW Atlantic
Pacific/Coral Sea
Caribbean Sea
Caribbean Sea
N Pacific Ocean
NW Atlantic
Caribbean Sea
Worldwide
Worldwide
Red Sea &
Gulf Aden
Country
Caribbean nations & US
Australia
British Virgin Islands
US Virgin Islands &
Puerto Rico, Florida Keys
Hawaii
Florida Keys
US Virgin Islands
Tropical nations
Tropical nations
Middle East Asia
Taxa Assessed
VI
"re
s_
O
U
X
X
X
X
X
X
X
X
X
X
-E
C/5
b
X
X
X
X
X
X
X
X
0)
m
01
"^
X
X
X
X
X
X
X
(/)
0)
OX
E
O
a
in
X
X
X
(/)
"re
o
U
o
ts
O
X
X
X
O 0)
!_ *-»
u re
re £
5 -0
a, aj
4-1
s_
0)
>
C
X
X
X
X
X
X
-------
Appendix B: Survey Data Sheets and Data Check
List
55
-------
Figure B-l: Fish Survey Data Sheet
FISH SURVEY DATA SHEET
Surveyor
Tender
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
FISH ID
Station
Date
Page
Depth ft
of
start
end
Size (cm)
<5
5-10
10-15
15-20
20-25
25-30
30-35
>35
Entered by:
QAby:
Date:
Date:
56
-------
FISH SURVEY DATA SHEET
Surveyor
Tender
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
FISH ID
Station
DATE
Page
Depth ft
of
start
end
Size (cm)
<5
5-10
10-15
15-20
20-25
25-30
30-35
>35
Entered by:
QA by:
Date:
Date:
57
-------
Figure B-2: Stony Coral Survey Data Sheet
STONY CORAL SURVEY DATA SHEET
Date
Station
Surveyor
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Taxon
% Live
Tissue
Height
max (cm)
Entere
QAby
Diameter
max (cm)
Disease
Page of
Depth ft
Bleach
Clionid
dby: Date:
: Date:
58
-------
STONY CORAL SURVEY DATA SHEET
Date
Station
Surveyor
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Taxon
% Live
Tissue
Height
max (cm)
Entere
QAby
Diameter
max (cm)
Disease
Page of
Depth ft
Bleach
Clionid
dby: Date:
: Date:
59
-------
Figure B-3: Gorgonian Survey Data Sheet
GORGONIAN SURVEY DATA SHEET
Date
Station Page of
Surveyor Depth ft
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Grid#
Gorgonian
Shape
Height
(cm)
Diameter
(cm)
Remarks
Entered by:
QAby:
Date:
Date:
60
-------
GORGONIAN SURVEY DATA SHEET
Date
Station Page of
Surveyor Depth ft
31
32
33
34
35
36
37
38
39
40
44
42
43
44
45
46
47
48
49
50
51
55
53
54
55
56
57
58
59
60
Grid#
Gorgonian
Shape
Height
(cm)
Ent
QA
Diameter
(cm)
Remarks
e red by: Date:
by: Date:
61
-------
Figure B-4: Gorgonian and Sponge Survey Data Sheet
Date
Surveyor
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Grid#
GORGONIAN & SPONGE SURVEY DATA SHEET
Station
Gor/Spo
Height
Dia max
Page of
Depth ft
Morphological Description
Entered by:
QA by:
Date:
Date:
62
-------
Date
Surveyor
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Grid#
GORGONIAN & SPONGE SURVEY DATA SHEET
Station
Gor/Spo
Height
Ent
QA
Dia max
Page of
Depth ft
Morphological Description
e red by: Date:
by: Date:
63
-------
Figure B-5: Sponge Survey Data Sheet
SPONGE SURVEY DATA SHEET
Date (Station Page of
Surveyor Depth ft
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Grid#
Sponge
Shape
Height
(cm)
Ent
QA
Diameter
(cm)
Remarks
eredby: Date:
by: Date:
64
-------
SPONGE SURVEY DATA SHEET
Date
Station Page of
Surveyor Depth ft
31
32
33
34
35
36
37
38
39
40
44
42
43
44
45
46
47
48
49
50
51
55
53
54
55
56
57
58
59
60
Grid#
Sponge
Shape
Height
(cm)
Diameter
(cm)
Remarks
Entered by:
QAby:
Date:
Date:
65
-------
Figure B-6: Rugosity, BioSurvey and LPI Data Sheet
Rugosity, BioSurvey and LPI Data Sheet
Date:
Station:
Surveyor:
Depth:
Oi
Oi
Draped Chain = 6 m
Rep # Linear Distance (tape)
Notes
0 m
5 m
10m
15m
20 m
Entered by:
Mark(m) OBS Mark(m) OBS Mark(m) OBS
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
Observations (OBS):
Live Coral - LC
Dead Coral - DC
No Coral - NC
#Biota within 2m on both sides of line
Queen Conch (flared)
Queen Conch (juv)
Spiny Lobster
Slipper Lobster
Large Crabs
Sea Urchin Diadema
Sea Urchin
Other
Notes:
Date:
QAby:
Date:
-------
Figure B-7: Check List for Data Sheet Actions
Prior dive:
Complete date, location, and surveyor specific
information at top of data sheet.
During dive:
Accurately report data, using established codes and
formating for assessment.
Post dive:
Check for completion of date, location, and surveyor
specific information.
_Check for completion and adherence of recorded data to
standards in protocols.
_Research any uncertain taxa information especially those
photographed.
_Wash data sheet in freshwater, hang and allow to dry.
_Verify data sheet for completeness and accuracy.
Deliver data sheet to data recorder.
67
-------
68
-------
Appendix C: Fish Species Codes, Biomass
Coefficients and Trophic Guild Assignments
69
-------
Table C-l: Table offish species found in the tropical Western Atlantic and Caribbean Sea. Both common names and taxonomic classification at the family, genus and species level are presented,
which include the four letter species code used to record data. Estimates for biomass are made by employing values for the a and P coef-ficients derived from FishBase (Froese and Pauley 2007).
Five trophic guilds for fish were derived from Randall 1967 (as used in Mensa et al. 2006 and Caldrow et al. 2009). Abbreviations for the trophic guilds are: H= herbivore, Ml = mobile invertivore,
P = piscavors, SI = sessile invertivore, Z = zooplanktonivore, and D = detritavor.
Species Code
ABHI
ABSA
ABTA
Acanthemblemaria UNK
Acanthurus UNK
ACAS
ACBA
ACCH
ACCO
ACDE
ACMA
ACPO
ACQU
ACSP
AENA
ALAF
ALCI
ALSC
ALVU
AMPI
ANSU
ANVI
APAU
APBI
APIA
APMA
Apogon UNK
APPS
APQU
APTO
ARRH
ASPU
ASST
Atherinomorus UNK
AUMA
BASO
Family
Belonidae
Pomacentridae
Pomacentridae
Chaenopsidae
Acanthuridae
Chaenopsidae
Acanthuridae
Acanthuridae
Acanthuridae
Syngnathidae
Chaenopsidae
Ostraciidae
Ostraciidae
Chaenopsidae
Myliobatidae
Serranidae
Carangidae
Monacanthidae
Albulidae
Cirrhitidae
Haemulidae
Haemulidae
Apogonidae
Apogonidae
Apogonidae
Apogonidae
Apogonidae
Apogonidae
Apogonidae
Apogonidae
Sparidae
Apogonidae
Apogonidae
Atherinidae
Aulostomidae
Gobiidae
Genus
Ablennes
Abudefduf
Abudefduf
Acanthemblemaria
Acanthurus
Acanthemblemaria
Acanthurus
Acanthurus
Acanthurus
Acentronura
Acanthemblemaria
Acanthostracion
Acanthostracion
Acanthemblemaria
Aetobatus
Alphestes
Alectis
Aluterus
Albula
Amblycirrhitus
Anisotremus
Anisotremus
Apogon
Apogon
Apogon
Apogon
Apogon
Apogon
Apogon
Apogon
Archosargus
Astrapogon
Astrapogon
Atherinomorus
Aulostomus
Bathygobius
Species
Ablennes hians
Abudefduf saxatilis
Abudefduf taurus
Acanthemblemaria sp.
Acanthurus sp.
Acanthemblemaria aspera
Acanthurus bahianus
Acanthurus chirurgus
Acanthurus coeruleus
Acentronura dendritica
Acanthemblemaria maria
Acanthostracion polygonia
Acanthostracion quadricomis
Acanthemblemaria spinosa
Aetobatus narinari
Alphestes afer
Alectis ciliaris
Aluterus scriptus
Albula vulpes
Amblycirrhitus pinos
Anisotremus surinamensis
Anisotremus virginicus
Apogon aurolineatus
Apogon binotatus
Apogon lachneri
Apogon maculatus
Apogon sp.
Apogon pseudomaculatus
Apogon quadrisquamatus
Apogon townsendi
Archosargus rhomboidalis
Astrapogon puncticulatus
Astrapogon stellatus
Atherinomorus sp.
Aulostomus maculatus
Bathygobious soporator
Common Name
Flat needlefish
Sergeant major
Night sergeant
Tube Blenny
Surgeonfish
Roughhead blenny
Ocean surgeonfish
Doctorfish
Blue tang
Pipehorse
Secretary blenny
Honeycomb cowfish
Scrawled cowfish
Spinyhead blenny
Spotted eagle ray
Mutton hamlet
African pompano
Scrawled filefish
Bonefish
Redspotted hawkfish
Black margate
Porkfish
Bridle cardinalfish
Barred cardinalfish
Whitestar cardinalfish
Flamefish
Cardinalfish
Twospot cardinalfish
Sawcheek cardinalfish
Belted cardinalfish
Sea bream
Blackfin cardinalfish
Conchfish
Silverside
Trumpetfish
Frillfin goby
Trophic
Guild
P
SI
H
Ml
H
Ml
H
H
H
MI/SI
Ml
MI/SI
SI
Ml
Ml
Ml
MI/P
SI/Z
Ml
Z
Ml
Ml
Z
Z
Z
Z
Z
Z
Z
Z
H
Ml
Ml
Z
P
Ml
a Coef.
0.0007
0.017
0.017
0.0077
0.0286
0.0077
0.0191
0.0225
0.0305
0.0004
0.0077
0.0179
0.0014
0.0077
0.0059
0.0174
0.0412
0.0022
0.0279
0.0026
0.0233
0.0148
0.0157
0.0157
0.0157
0.0157
0.0157
0.02
0.0157
0.0157
0.018
0.017
0.017
0.0079
0.004
0.0144
Length:Weight
B Coef. Conversion
3.13
3.12
3.12
2.962
3
2.962
3.08
3
3
3.0768
2.962
3
3.418
2.962
3.13
3
2.85
3
2.89
3.427
3.01
3.167
3.073
3.073
3.073
3.073
3.073
2.943
3.073
3.073
3.102
3.077
3.077
3.1938
2.866
3
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.885
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
-------
Species Code
BAVE
BelonidaeUNK
BOBO
BOLU
BOOC
BOPU
BORU
BothusUNK
CABAJ
CABAR
CACA
CACR
CAHI
CAJA
CALA
Calamus UNK
CALI
CALU
CAMA
CANO
CanthigasterUNK
CAPENNA
CAPENNAT
CAPU
CaranxUNK
CARD
CARU
CASU
GEAR
CEAU
CECR
CEFU
ChaenopsisUNK
CHAN
CHCA
CHCY
CHFA
CHIN
CHLI
CHMU
Family
Balistidae
Belonidae
Gobiidae
Bothidae
Bothidae
Labridae
Labridae
Bothidae
Sparidae
Carangidae
Sparidae
Carangidae
Carangidae
Tetraodontidae
Carangidae
Sparidae
Carcharhinidae
Carangidae
Monacanthidae
Sparidae
Tetraodontidae
Sparidae
Sparidae
Monacanthidae
Carangidae
Tetraodontidae
Carangidae
Balistidae
Pomacanthidae
Pomacanthidae
Serranidae
Serranidae
Chaenopsidae
Diodontidae
Chaetodontidae
Pomacentridae
Ephippidae
Pomacentridae
Chaenopsidae
Pomacentridae
Genus
Balistes
UNK
Bollmannia
Bothus
Bothus
Bodianus
Bodianus
Bothus
Calamus
Caranx
Calamus
Caranx
Caranx
Canthigaster
Caranx
Calamus
Carcharhinus
Caranx
Cantherhines
Calamus
Canthigaster
Calamus
Calamus
Cantherhines
Caranx
Canthigaster
Caranx
Canthidermis
Centropyge
Centropyge
Cephalopholis
Cephalopholis
Chaenopsis
Chilomycterus
Chaetodon
Chromis
Chaetodipterus
Chromis
Chaenopsis
Chromis
Species
Balistes vetula
UNK
Bollmannia boqueronensis
Bothus lunatus
Bothus ocellatus
Bodianus pulchellus
Bodianus rufus
Bothus sp.
Calamus bajonado
Caranx bartholomaei
Calamus calamus
Caranx crysos
Caranx hippos
Canthigaster jamestyleri
Caranx latus
Calamus sp.
Carcharhinus limb at us
Caranx lugubris
Cantherhines macrocerus
Calamus nodosus
Canthigaster sp.
Calamus penna
Calamus pennatula
Cantherhines pullus
Caranx sp.
Canthigaster rostrata
Caranx ruber
Canthidermis sufflamen
Centropyge argi
Centropyge aurantonotus
Cephalopholis cruentata
Ceph alopholis fulva
Chaenopsis sp.
Chilomycterus antennatus
Chaetodon cop/stratus
Chromis cyanea
Chaeto dip terus faber
Chromis insolata
Chaenopsis limbaughi
Chromis multilineata
Common Name
Queen triggerfish
Needlefish
White-eye goby
Peacock flounder
Eyed flounder
Spotfin hogfish
Spanish hogfish
Lefteye Flounder
Jolthead porgy
Yellow jack
Saucereye porgy
Blue runner
Crevalle jack
Goldface toby
Horse-Eye jack
Porgy
Blacktip shark
Blackjack
America whitespotted filefish
Knobbed porgy
Puffer
Sheepshead porgy
Pluma
Orangespotted filefish
Jack
Sharpnose puffer
Bar jack
Ocean triggerfish
Cherubfish
Flameback angelfish
Graysby
Coney
Pike blenny
Bridled burrfish
Foureye butterflyfish
Blue chromis
Atlantic spadefish
Sunshinefish
Yellowface pikeblenny
Brown chromis
Trophic
Guild
Ml
P
MI/SI
P
MI/P
Ml
Ml
P
Ml
P
MI/SI
P
MI/P
MI/SI
P
Ml
P
P
SI
Ml
MI/SI
Ml
Ml
H
P
MI/SI
P
MI/Z
H
H/SI
P
MI/P
Ml
Ml
SI
Z
SI
Z
Ml
Z
a Coef.
0.0864
0.0013
0.0035
0.0098
0.0098
0.0145
0.0145
0.0098
0.0672
0.034
0.0429
0.0524
0.0518
0.0197
0.021
0.0447
0.0061
0.0251
0.0561
0.0077
0.0197
0.0196
0.0178
0.0683
0.0224
0.0197
0.0065
0.0217
0.0314
0.0314
0.0121
0.0174
0.0077
0.0236
0.047
0.0202
0.0407
0.0202
0.0077
0.0202
Length:Weight
P Coef. Conversion
2.784
3.08
3.766
3.189
3.189
3.053
3.053
3.189
2.822
2.84
2.801
2.69
2.734
2.9174
2.97
2.8662
3.01
2.84
2.653
3.13
2.9174
3
3.11
2.563
2.9457
2.9174
2.748
3
2.7995
2.7995
3.082
3
2.962
3.124
2.86
2.9595
2.25
2.9595
2.962
2.9595
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.828
1
1
0.926
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
-------
Species Code
CHOCELLATA
CHOCELLATU
CHSC
CHSE
CHST
CLPA
ClupeidaeUNK
CODI
COEI
COEL
COGL
COLI
COPE
Coryphopterus UNK
COTR
CRRO
CTSA
CTST
DAAM
DAVO
Decapterus UNK
DEIN
DEMA
DIAR
DIBI
DIFO
DIHOLB
DIHOLO
DIHY
DOME
ECCA
ECNA
ECNE
Elacatinus UNK
ELCH
ELDI
ELEV
Family
Chaenopsidae
Chaetodontidae
Pomacentridae
Chaetodontidae
Chaetodontidae
Labridae
Clupeidae
Gobiidae
Gobiidae
Syngnathidae
Gobiidae
Gobiidae
Gobiidae
Gobiidae
Congridae
Scaridae
Gobiidae
Gobiidae
Dasyatidae
Dactylopteridae
Carangidae
Serranidae
Carangidae
Sparidae
Serranidae
Serranidae
Sparidae
Diodontidae
Diodontidae
Labridae
Muraenidae
Echeneidae
Echeneidae
Gobiidae
Gobiidae
Gobiidae
Gobiidae
Genus
Chaenopsis
Chaetodon
Chromis
Chaetodon
Chaetodon
Clepticus
UNK
Coryphopterus
Coryphopterus
Cosmocampus
Coryphopterus
Coryphopterus
Coryphopterus
Coryphopterus
Conger
Cryptotomus
Ctenogobius
Ctenogobius
Dasyatis
Dactylopterus
Decapterus
Dermatolepis
Decapterus
Diplodus
Diplectrum
Diplectrum
Diplodus
Diodon
Diodon
Doratonotus
Echidna
Echeneis
Echeneis
Elacatinus
Elacatinus
Elacatinus
Elacatinus
Species
Chaenopsis ocellata
Chaetodon ocellatus
Chromis scotti
Chaetodon sedentarius
Chaetodon striatus
Clepticus parrae
UNK
Coryphopterus dicrus
Coryphopterus eidolon
Cosmocampus elucens
Coryphopterus
glaucofraenum
Coryphopterus lipernes
Coryphopterus
personatus/hyalinus
Coryphopterus sp.
Conger triporiceps
Cryptotomus roseus
Ctenogobius saepepallens
Ctenogobius stigmaticus
Dasyatis americana
Dactylopterus volitans
Decapterus sp.
Dermatolepis inermis
Decapterus macarellus
Diplodus argenteus
caudimacula
Diplectrum bivittatum
Diplectrum formosum
Diplodus holbrooki
Diodon holocanthus
Diodon hystrix
Doratonotus megalepis
Echidna catenata
Echeneis naucrates
Echeneis neucratoides
Elacatinus sp.
Elacatinus chancei
Elacatinus dilepis
Elacatinus evelynae
Common Name
Bluethroat pikeblenny
Spotfin butterflyfish
Purple reeffish
Reef butterflyfish
Banded butterflyfish
Creole wrasse
Herring
Colon goby
Pallid goby
Shortfin pipefish
Bridled goby
Peppermint goby
Masked/Glass goby
Goby
Manytooth conger
Bluelip parrotfish
Dash goby
Marked goby
Southern stingray
Flying gurnard
Scad
Marbeled grouper
Mackerel scad
Silver porgy
Dwarf sand perch
Sand perch
Spottail pinfish
Balloonfish
Porcupinefish
Dwarf wrasse
Chain moray
Sharksucker
Whitefin sharksucker
Goby
Shortstripe goby
Orangesided goby
Sharknose goby
Trophic
Guild
Ml
SI
Z
MI/SI/D
SI
Z
Z
MI/H
MI/H
MI/Z
MI/H
MI/H
MI/H
MI/H
MI/P
H
MI/H
MI/H
SI
Ml
Z
P
Z
H/MI
MI/SI
P
H
Ml
Ml
MI/SI
Ml
Z/D
Z/D
SI
SI
SI
SI
a Coef.
0.0077
0.0318
0.0202
0.0251
0.0222
0.0135
0.0009
0.0345
0.0345
0.0006
0.0345
0.0345
0.0345
0.0345
0.0002
0.0505
0.0345
0.0345
0.0014
0.0217
0.0078
0.0017
0.0078
0.0205
0.0094
0.0114
0.0205
0.0219
0.533
0.0049
0.0012
0.127
0.127
0.008
0.008
0.008
0.008
P Coef.
2.962
2.984
2.9595
3.076
3.14
3.043
3.62
2.68
2.68
3
2.68
2.68
2.68
2.68
3.41
3.182
2.68
2.68
2.672
2.8
3.14
3
3.14
2.9902
3.1121
3.078
2.9902
3
2.276
3.51
3
2.113
2.113
3.137
3.137
3.137
3.137
Length:Weight
Conversion
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.936
0.905
1
0.905
1
1
1
1
1
1
1
1
1
1
1
1
1
1
-------
U)
Species Code
ELLO
ELMU
ELOC
ELPR
ELS A
EMAT
Emblemariopsis UNK
EMPA
EngraulidaeUNK
Enneanectes UNK
ENNI
EPAD
EPGU
EPMO
EPST
EQLA
EQPU
Eucinostomus UNK
EUGU
EUJO
EUME
FITA
GACU
GECI
GICI
GNTH
Gobiidae UNK
GOGR
GRLO
GYFU
GYMI
Gymnothorax UNK
GYMO
GYVI
HAAL
HAAU
HABI
HACAR
HACAU
HACH
Family
Gobiidae
Gobiidae
Gobiidae
Gobiidae
Gobiidae
Inermiidae
Chaenopsidae
Chaenopsidae
Engraulidae
Tripterygiidae
Muraenidae
Serranidae
Serranidae
Serranidae
Serranidae
Sciaenidae
Sciaenidae
Gerreidae
Gerreidae
Gerreidae
Gerreidae
Fistulariidae
Carcharhinidae
Gerreidae
Ginglymostomatidae
Gobiidae
Gobiidae
Gobiidae
Grammatidae
Muraenidae
Muraenidae
Muraenidae
Muraenidae
Muraenidae
Haemulidae
Haemulidae
Labridae
Haemulidae
Labridae
Haemulidae
Genus
Elacatinus
Elacatinus
Elacatinus
Elacatinus
Elacatinus
Emmelichthyops
Emblemariopsis
Emblemaria
UNK
Enneanectes
Enchelycore
Epinephelus
Epinephelus
Epinephelus
Epinephelus
Equetus
Equetus
Eucinostomus
Eucinostomus
Eucinostomus
Eucinostomus
Fistularia
Galeocerdo
Gerres
Ginglymostoma
Gnatholepis
UNK
Gobiosoma
Gramma
Gymnothorax
Gymnothorax
Gymnothorax
Gymnothorax
Gymnothorax
Haemulon
Haemulon
Halichoeres
Haemulon
Halichoeres
Haemulon
Species
Elacatinus louisae
Elacatinus multifasciatus
Elacatinus oceanops
Elacatinus prochilos
Elacatinus saucrum
Emmelichthyops atlanticus
Emblemariopsis sp.
Emblemaria pandionis
UNK
Enneanectes sp.
Enchelycore nigricans
Epinephelus adscensionis
Epinephelus guttatus
Epinephelus morio
Epinephelus striatus
Equetus lanceolatus
Equetus punctatus
Eucinostomus sp.
Eucinostomus gula
Eucinostomus jonesii
Eucinostomus melanopterus
Fistularia tabacaria
Galeocerdo cuvier
Gerres cinereus
Ginglymostoma cirratum
Gnatholepis thompsoni
UNK
Gobiosoma grosvenori
Gramma loreto
Gymnothorax funebris
Gymnothorax miliaris
Gymnothorax sp.
Gymnothorax moringa
Gymnothorax vicinus
Haemulon album
Haemulon aurolineatum
Halichoeres bivittatus
Haemulon carbonarium
Halichoeres caudalis
Haemulon chrysargyreum
Common Name
Spotlight goby
Greenbanded goby
Neon goby
Broadstripe goby
Leopard goby
Bonnetmouth
Blenny
Sailfin blenny
Anchovies
Triplefin
Viper moray
Rock hind
Red hind
Red grouper
Nassau grouper
Jackknife fish
Spotted drum
Mojarra
Silver jenny
Slender mojarra
Flagfin mojarra
Bluespotted cornetfish
Tiger shark
Yellowfin mojarra
Nurse shark
Goldspot goby
Goby
Rockcut goby
Fairy basslet
Green moray
Goldentail moray
Moray eel
Spotted moray
Purplemouth moray
Margate (White)
Tomtate
Slippery dick
Caesar grunt
Painted wrasse
Smallmouth grunt
Trophic
Guild
SI
SI
SI
SI
SI
P/Z
z
z
H/SI/MI
MI/P
Ml
MI/P
Ml
P
Ml
Ml
Ml
Ml
Ml
MI/Z
P
P
MI/SI
MI/P
H
MI/H
MI/H
MI/Z
MI/P
MI/P
P
P
P
MI/SI
SI/Z
Ml
Ml
Ml
SI/Z
a Coef.
0.008
0.008
0.008
0.008
0.008
0.0148
0.0077
0.005
0.0141
0.0017
0.0153
0.036
0.0122
0.0157
0.0011
0.0011
0.014
0.014
0.0923
0.0128
0.0053
0.0025
0.013
0.0105
0.0035
0.0345
0.0345
0.0128
0.0041
0.0011
0.001
0.001
0.0043
0.014
0.011
0.0094
0.0404
0.0052
0.0141
P Coef.
3.137
3.137
3.137
3.137
3.137
3.105
2.962
3.1355
3.05
3
3
2.839
3.035
3
3.844
3.844
3.25
3.25
2.65
2.91
2.59
3.26
2.69
2.892
3.766
2.68
2.68
3.036
2.856
2.574
3.158
3.158
2.876
3.09
3.2
3.15
2.74
3.375
3.08
Length:Weight
Conversion
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.903
0.672
1
1
0.705
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
-------
Species Code
HACY
Haemulon UNK
HAFL
HAGA
Halichoeres UNK
HAMACR
HAMACU
HAME
HAPA
HAPI
HAPL
HAPO
HARA
HASC
HASP
HAST
HECR
HELD
Hippocampus UNK
HIRE
HO AD
HOBE
HOCI
Holacanthus UNK
HORU
HOTR
HYAB
HYCH
HYGU
HYIN
HYNI
Hypoplectrus UNK
HYPU
HYUN
IN VI
Jenkinsia UNK
KYSE
LABI
Lactophrys UNK
LAFI
Family
Labridae
Haemulidae
Haemulidae
Labridae
Labridae
Haemulidae
Labridae
Haemulidae
Haemulidae
Labridae
Haemulidae
Labridae
Labridae
Haemulidae
Labridae
Haemulidae
Priacanthidae
Congridae
Syngnathidae
Syngnathidae
Holocentridae
Pomacanthidae
Pomacanthidae
Pomacanthidae
Holocentridae
Pomacanthidae
Serranidae
Serranidae
Serranidae
Serranidae
Serranidae
Serranidae
Serranidae
Serranidae
Inermiidae
Clupeidae
Kyphosidae
Ostraciidae
Ostraciidae
Labrisomidae
Genus
Halichoeres
Haemulon
Haemulon
Halichoeres
Halichoeres
Haemulon
Halichoeres
Haemulon
Haemulon
Halichoeres
Haemulon
Halichoeres
Halichoeres
Haemulon
Halichoeres
Haemulon
Heteropriacanthus
Heteroconger
Hippocampus
Hippocampus
Holocentrus
Holacanthus
Holacanthus
Holacanthus
Holocentrus
Holacanthus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Hypoplectrus
Inermia
Jenkinsia
Kyphosus
Lactophrys
Lactophrys
Labrisomus
Species
Halichoeres cyanocephalus
Haemulon sp.
Haemulon flavolineatum
Halichoeres garnoti
Halichoeres sp.
Haemulon macrostomum
Halichoeres maculipinna
Haemulon melanurum
Haemulon parra
Halichoeres pictus
Haemulon plumierii
Halichoeres poeyi
Halichoeres radiatus
Haemulon sciurus
Halichoeres sp.
Haemulon striatum
Heteropriacanthus cruentatus
Heteroconger halis
Hippocampus sp.
Hippocampus reidi
Holocentrus adscensionis
Holacanthus bermudensis
Holacanthus ciliaris
Holacanthus sp.
Holocentrus rufus
Holacanthus tricolor
Hypoplectrus aberrans
Hypoplectrus chlorurus
Hypoplectrus guttavarius
Hypoplectrus indigo
Hypoplectrus nigricans
Hypoplectrus sp.
Hypoplectrus puella
Hypoplectrus unicolor
Inermia vittata
Jenkinsia sp.
Kyphosus sectatrix
Lactophrys bicaudalis
Lactophrys sp.
Labrisomus filamen tosus
Common Name
Yellowcheek wrasse
Grunt
French grunt
Yellowhead wrasse
Wrasse
Spanish grunt
Clown wrasse
Cottonwick
Sailors choice
Rainbow wrasse
White grunt
Blackear wrasse
Puddingwife
Bluestriped grunt
Mardi gras wrasse
Striped grunt
Glasseye snapper
Brown garden eel
Pipefish
Longsnout seahorse
Squirrelfish
Blue angelfish
Queen angelfish
Angelfish
Longspine squirrelfish
Rock beauty
Yellowbelly hamlet
Yellowtail hamlet
Shy hamlet
Indigo hamlet
Black hamlet
HAMLET
Barred hamlet
Butter hamlet
Boga
Herring
Chub (Bermuda/Yellow)
Spotted trunkfish
Trunkfish
Quillfin blenny
Trophic
Guild
Ml
SI/Z
MI/SI
Ml
Ml
Ml
SI
Ml
Ml
Ml
Ml
Ml
Ml
Ml
Ml
Z
Z
Z
MI/SI
MI/SI
Ml
SI
SI
SI
Ml
SI
Ml
Ml
Ml
Ml
MI/P
Ml
Ml
MI/P
Z
Z
H
MI/SI
MI/SI
Ml
a Coef.
0.0094
0.011
0.0207
0.0052
0.0126
0.0176
0.0028
0.0557
0.028
0.0052
0.0259
0.0052
0.0131
0.0218
0.0126
0.0175
0.0188
0.0006
0.0015
0.0015
0.0208
0.0319
0.0337
0.0337
0.015
0.0428
0.009
0.009
0.009
0.009
0.009
0.009
0.009
0.011
0.0078
0.0009
0.0174
0.0294
0.0309
0.0341
Length:Weight
P Coef. Conversion
3.15
3.2
3
3.375
3.0673
3.06
3.693
2.63
2.89
3.375
3
3.375
3.038
3
3.0673
3.099
3
3.2486
3
3
3
2.899
2.9
2.9
3.059
2.858
3.04
3.04
3.04
3.04
3.04
3.04
3.04
3.182
3.14
3.62
3.08
3
3
2.72
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.905
1
1
1
1
1
-------
Species Code
LAMA
LANU
LATRIG
LATRIQ
LIRU
LOCY
LOMI
LUAN
LUAP
LUBU
LUCY
LUGR
LUJO
LUMA
LUSY
Lutjanus UNK
MAAU
MABI
MABO
MAGI
Malacoctenus UNK
MAMA
MAPL
MATR
MAVE
MEAT
MENI
MICA
MICH
Microgobius UNK
MISI
MOCI
Monacanthus UNK
MOTU
MUCE
MUMA
Muraenidae UNK
MYBO
MYBR
Mycteroperca UNK
Family
Labridae
Labrisomidae
Ostraciidae
Ostraciidae
Serranidae
Gobiidae
Opistognathidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Lutjanidae
Labrisomidae
Myliobatidae
Labrisomidae
Labrisomidae
Labrisomidae
Labrisomidae
Malacanthidae
Labrisomidae
Labrisomidae
Megalopidae
Balistidae
Gobiidae
Pomacentridae
Gobiidae
Gobiidae
Monacanthidae
Monacanthidae
Monacanthidae
Mugilidae
Mullidae
Muraenidae
Serranidae
Ophichthidae
Serranidae
Genus
Lachnolaimus
Labrisomus
Lactophrys
Lactophrys
Liopropoma
Lophogobius
Lonchopisthus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Lutjanus
Malacoctenus
Manta
Malacoctenus
Malacoctenus
Malacoctenus
Malacoctenus
Malacanthus
Malacoctenus
Malacoctenus
Megalops
Melichthys
Microgobius
Microspathodon
Microgobius
Microgobius
Monacanthus
Monacanthus
Monacanthus
Mugil
Mulloidichthys
UNK
Mycteroperca
Myrichthys
Mycteroperca
Species
Lachnolaimus maximus
Labrisomus nuchipinnis
Lactophrys trigonus
Lactophrys triqueter
Liopropoma rubre
Lophogobius cyprinoides
Lonchopisthus micrognathus
Lutjanus analis
Lutjanus apodus
Lutjanus buccanella
Lutjanus cyanopterus
Lutjanus griseus
Lutjanusjocu
Lutjanus mahogoni
Lutjanus synagris
Lutjanus sp.
Malacoctenus aurolineatus
Manta birostris
Malacoctenus boehlkei
Malacoctenus gilli
Malacoctenus sp.
Malacoctenus macropus
Malacanthus plumieri
Malacoctenus triangulatus
Malacoctenus versicolor
Megalops atlanticus
Melichthys niger
Microgobius carri
Microspathodon chrysurus
Microgobius sp.
Microgobius signatus
Monacanthus ciliatus
Monacanthus sp.
Monacanthus tuckeri
Mugil cephalus
Mulloidichthys martinicus
UNK
Mycteroperca bonaci
Myrichthys breviceps
Mycteroperca sp.
Common Name
Hogfish
Hairy blenny
Trunkfish
Smooth trunkfish
Peppermint basslet
Crested goby
Swordtail jawfish
Mutton snapper
Schoolmaster
Blackfin snapper
Cubera snapper
Gray snapper
Dog snapper
Mahogany snapper
Lane snapper
Snapper
Goldline blenny
Giant manta
Diamond blenny
Dusky blenny
Scaly blenny
Rosy blenny
Sand tilefish
Saddled blenny
Barfin blenny
Tarpon
Black durgon
Seminole goby
Yellowtail damselfish
Goby
Microgobius signatus
Fringed filefish
Filefish
Slender filefish
Striped mullet
Yellow goatfish
Moray Eel
Black grouper
Sharptail eel
Grouper
Trophic
Guild
Ml
Ml
Ml
SI
Ml
H/SI/MI
Z
Ml
MI/P
MI/P
MI/P
MI/P
MI/P
MI/P
MI/P
MI/P
MI/Z
P/Z
MI/Z
MI/Z
MI/Z
MI/Z
Ml
Ml
MI/Z
P
H/Z
Z
H
H
Z
H/Z
H/Z
Z/D
Z/D
MI/Z
MI/P
P
Ml
P
a Coef.
0.0104
0.0341
0.375
0.0309
0.0128
0.0035
0.0119
0.0221
0.0189
0.0747
0.0093
0.0182
0.0085
0.0428
0.0387
0.0167
0.0341
0.0164
0.0089
0.0089
0.0195
0.0341
0.027
0.0089
0.0089
0.012
0.0058
0.0079
0.0239
0.0079
0.0079
0.0256
0.0256
0.0256
0.0148
0.0207
0.001
0.0069
0.001
0.0135
Length:Weight
P Coef. Conversion
2.706
2.72
2.1
3
3.036
3.766
2.995
2.95
3
2.735
2.88
2.94
3.2
2.719
2.844
2.9773
2.72
3
3
3
2.6477
2.72
2.696
3
3
2.984
3.554
3
3.082
3
3
2.7
2.7
2.7
2.903
3
3.158
3.205
3
3.0418
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.895
1
1
1
1
1
-------
Species Code
MYIN
MYJA
MYOC
MYPH
Myrichthys UNK
MYTI
MYVE
NELO
NEMA
OCCH
ODDE
OGNA
OPAU
Opistognathus UNK
OPMACC
OPMACR
OPOP
OPWH
OXST
PAAC
PABA
PAFU
PAMA
PESC
POAR
Pomacanthus UNK
POPA
PRAC
PRAR
PRHI
PSMA
PTHE
RERE
RYBI
RYSA
SABU
SACO
SAVE
Scarus UNK
SCCO
Family
Serranidae
Holocentridae
Ophichthidae
Serranidae
Ophichthidae
Serranidae
Serranidae
Gobiidae
Holocentridae
Lutjanidae
Sciaenidae
Ogcocephalidae
Opistognathidae
Opistognathidae
Blenniidae
Opistognathidae
Ophichthidae
Opistognathidae
Gobiidae
Sciaenidae
Callionymidae
Serranidae
Blenniidae
Pempheridae
Pomacanthidae
Pomacanthidae
Pomacanthidae
Chaetodontidae
Priacanthidae
Gobiidae
Mullidae
Microdesmidae
Echeneidae
Serranidae
Serranidae
Holocentridae
Holocentridae
Holocentridae
Scaridae
Scaridae
Genus
Mycteroperca
Myripristis
Myrichthys
Mycteroperca
Myrichthys
Mycteroperca
Mycteroperca
Nes
Neonifon
Ocyurus
Odontoscion
Ogcocephalus
Opistognathus
Opistognathus
Ophioblennius
Opistognathus
Ophichthus
Opistognathus
Oxyurichthys
Pareques
Paradiplo grammus
Paranthias
Parablennius
Pempheris
Pomacanthus
Pomacanthus
Pomacanthus
Prognathodes
Priacanthus
Priolepis
Pseudupeneus
Ptereleotris
Remora
Rypticus
Rypticus
Sargocentron
Sargocentron
Sargocentron
Scarus
Scarus
Species
Mycteroperca interstitialis
Myripristis jacobus
Myrichthys ocellatus
Mycteroperca phenax
Myrichthys sp.
Mycteroperca tigris
Mycteroperca venenosa
Nes longus
Neonifon marianus
Ocyurus chrysurus
Odontoscion dentex
Ogcocephalus nasutus
Opistognathus aurifrons
Opistognathus sp.
Ophioblennius macclurei
Opistognathus macrognathus
Ophichthus ophis
Opistognathus whitehursti
Oxyurichthys stigmalophius
Pareques acuminatus
Paradiplogrammus bairdi
Par an th ias furcifer
Parablennius marmoreus
Pempheris schomburgkii
Pomacanthus arcuatus
Pomacanthus sp.
Pomacanthus paru
Prognathodes aculeatus
Priacanthus arenatus
Priolepis hipoliti
Pseudupeneus maculatus
Ptereleotris helenae
Remora remora
Rypticus bistrispinus
Rypticus saponaceus
Sargocentron bullisi
Sargocentron coruscus
Sargocentron vexillarium
Scarus sp.
Scarus coeruleus
Common Name
Yellowmouth grouper
Blackbar soldierfish
Goldspotted eel
Scamp
Snake eel
Tiger grouper
Yellowfin grouper
Orangespotted goby
Longjaw squirrelfish
Yellowtail snapper
Reef croaker
Shortnose batfish
Yellowhead jawfish
Jawfish
Redlip blenny
Banded jawfish
Spotted snake eel
Dusky jawfish
Spotfin goby
Highhat
Lancer dragonet
Atlantic creolefish
Seaweed blenny
Glassy sweeper
Gray angelfish
Angelfish
French angelfish
Longsnout butterflyfish
Bigeye
Rusty goby
Spotted goatfish
Hovering goby
Common remora
Freckled soapfish
Greater soapfish
Deepwater squirrelfish
Reef squirrelfish
Dusky squirrelfish
Parrotfish
Blue parrotfish
Trophic
Guild
P
Ml
Ml
P
Ml
P
P
MI/SI
Ml
MI/Z
Z
Ml
Z
MI/Z
H
Ml
MI/P
Ml
MI/SI
Ml
MI/SI
Z
Z
SI/Z
SI
SI
SI
MI/SI
MI/Z
Ml
Ml
Z
Z
MI/P
MI/P
Ml
Ml
Ml
H
H
a Coef.
0.0188
0.111
0.001
0.0144
0.001
0.0094
0.0069
0.0035
0.0185
0.0155
0.0105
0.0154
0.0093
0.0093
0.0324
0.0093
0.002
0.0093
0.012
0.0087
0.023
0.0135
0.0109
0.0439
0.0345
0.0345
0.0203
0.0318
0.013
0.0133
0.0229
0.0091
0.0042
0.0128
0.0121
0.0162
0.0162
0.0162
0.0177
0.0124
Length:Weight
P Coef. Conversion
2.94
2.72
3
3
3
3.12
3.14
3.766
2.9705
3
3.007
3.063
2.99
2.99
2.379
2.99
3
2.99
2.9554
3.202
3.121
3.043
3.0249
2.62
2.968
2.968
3.126
2.984
3.039
3.041
2.958
3
3
3.036
3.082
3.07
3.07
3.07
3
3.111
0.987
0.926
1
0.978
1
0.974
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0.946
1
1
1
1
1
1
0.952
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Species Code
TRFA
TRGO
Triglidae UNK
TYCR
XYMA
XYNO
Xyrichtys UNK
XYSP
Family
Carangidae
Carangidae
Triglidae
Belonidae
Labridae
Labridae
Labridae
Labridae
Genus
Trachinotus
Trachinotus
UNK
Tylosurus
Xyrichtys
Xyrichtys
Xyrichtys
Xyrichtys
Species
Trachinotus falcatus
Trachinotus goodei
UNK
Tylosurus crocodilus
Xyrichtys martinicensis
Xyrichtys novacula
Xyrichtys sp.
Xyrichtys splendens
Common Name
Permit
Palometa
Searobin Family
Houndfish
Rosy razorfish
Pearly razorfish
Razorfish
Green razorfish
Trophic
Guild
MI/P
P
MI/P
P
Ml
Ml
MI/Z
Z
a Coef.
0.531
0.204
0.0096
0.0013
0.01
0.048
0.01
0.01
Length:Weight
P Coef. Conversion
2.803
3
3.0538
3.08
3
2.234
3
3
1
0.776
1
1
1
1
1
1
00
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Appendix D: Estimating Surface Area of
Gorgonians and Sponges
79
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Estimating the Surface Area of Marine Gorgonians and Sponges in the Field
Deborah L. Santavy, Lee A. Courtney, William S. Fisher,
Robert L. Quarles and Stephen J. Jordan
US EPA, NHEERL, Gulf Ecology Division
Gulf Breeze, FL. USA 32561
Abstract
An approach to estimate the three dimensional surface area (SA) of gorgonians and
sponges was developed to assess in situ habitat provision. The empirical method for
estimating habitat SA contributed by sponges and gorgonians used colony height,
diameter and morphology which can be easily obtained during underwater surveys. While
developed for shallow-water (<25 m) organisms that occur in the Western Atlantic
Ocean, a similar approach might be applicable to other regions and deep-water reefs.
Computer-simulated images were developed to represent natural populations of each
morphological type. Population characteristics were compiled from field measurements
and taxonomic literature. Modeling software was used to determine the SA of each
simulated image. Stepwise regression analysis was used to generate models for
estimating SA for different morphological types using height and diameter as variables
that included linear, quadratic and cubic terms. Regression models and geometric
surrogates were compared to known SA for each morphology using covariate analysis.
Regression models were more robust than geometric surrogates, exhibiting greater
accuracy at range extremes and, explaining over 90% of the variation. Results indicated
that regression models fit better than geometric surrogates, particularly for estimates of
small and large individuals. The regression models for all morphologies exhibited
forecast errors of less than 20%. Application of these methods in combination with
estimates for stony corals can be used to estimate biogenic habitat, which is an important
ecosystem service of coral reef ecosystems. The approach using regression models to
estimate surface area easily documented in field surveys, is relatively rapid, low tech and
non-invasive.
80
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SCIENCE
&EPA
United States
Environmental Protection
Agency
Office of Research and Development
Washington, DC 20460
Official Business
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$300
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