Random Vs Repetitive Photo Quadrat Comparison at a Long-Term Coral Reef Monitoring Site, Sian Ka’An Biosphere Reserve, Quintana Roo, Mexico

RANDOM VS REPETITIVE PHOTO QUADRAT COMPARISON AT A LONG-TERM CORAL REEF MONITORING SITE, SIAN KA’AN BIOSPHERE RESERVE, QUINTANA ROO, MEXICO

Gary Haralson

November, 2006

A Thesis Submitted In Partial Fulfillment of the Requirements for the Degree of

MASTER OF SCIENCE

Texas A&M University-Corpus Christi Environmental Science Program Corpus Christi, Texas

Approved: ______Date:______Dr. John W. Tunnell, Jr., Chair

______Dr. Quenton Dokken, Member

______Dr. Roy L. Lehman, Member

______Dr. Frank Pezold, Dean College of Science and Technology

ABSTRACT

Stewardship of the environment is the goal of any ecosystem management program. Marine Protected Areas (MPA’s) have the added burden that much of their charge is largely inaccessible to humans. Areas such as coral reefs at present time are studied mainly through the use of

SCUBA (Self Contained Underwater Breathing Apparatus). SCUBA allows us access to coral reefs, but at the same time limits our ability to make lengthy observations. Monitoring methods need to be developed to obtain as much information in the least amount of time and at the same time take all safety precautions possible for the researchers.

Methodologies used to monitor coral reefs can be problematic, and they are often dependent upon trained personnel conducting extensive field studies in remote locations. Development of a monitoring method for benthic coral communities requiring minimally skilled personnel and field time would be beneficial. This study examines two photographic methods (random and repetitive) of collecting field data conducted on coral reefs at Rancho Pedro Paila, located approximately 20 km south of

Tulum, Mexico, in the Sian Ka’an Biosphere Reserve. Photographic images were analyzed using Coral Point Count with Excel extensions

(CPCe). Field work was conducted annually (May 2001-2005) as part of a long term monitoring program conducted by university students as part of a coral reef ecology class at Texas A & M-Corpus Christi.

Percent coverage for hard corals, octocorals, sponges, macroalgae, and jig where analyzed for both random and repetitive photographic methods to compare if either method was better for monitoring coral reefs and if one denoted change easier. Levene, Kruskal-Wallis, ANOVA, and

Tukey tests were used to analysis each respective method.

The random photographic method proved to be the better method for analyzing the character of the coral reef by being the more efficient and effective method. Less field time is needed to gather more data by the random photographic method, resulting in larger data sets at a lower cost.

Which method was more effective at depicting change was inconclusive.

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TABLE OF CONTENTS

Page

ABSTRACT……………………………………………………………………...ii

LIST OF FIGURES ………………………………………………………….....v

LIST OF TABLES ……………………………………………………………..vii

LIST OF APPENDICES ………………………………………………………..x

ACKNOWLEDGMENTS ………………………………………………………xi

INTRODUCTION …………………………………………………………….…1

STUDY SITE ……………………………………………………………….….11

MATERIALS AND METHODS ……………………………………………...12

RESULTS …………………………………………………………………….…16

DISCUSSION ……………………………………………………………….….44

CONCLUSIONS AND RECOMMENDATIONS …………………...…….…53

LITERATURE CITED ………………………………………………………...57

APPENDIX ………………………………………………………………….….62

LIST OF FIGURES

Page

Figure 1. Location map of Rancho Pedro Paila, Sian Ka’an Biosphere Reserve, Quintana Roo, Mexico…………………..11

Figure 2. Comparison of mean hard coral percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila……………………………………………...23

Figure 3. Comparison of mean octocoral percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila……………………………………………...23

Figure 4. Comparison of mean sponge percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila……………………………………………...24

Figure 5. Comparison of mean macroalgae percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila……………………………………………...24

Figure 6. Comparison of mean jig percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila………………………………………………………….…...25

Figure 7. Comparison of mean hard coral percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila……………………………………………………………….32

Figure 8. Comparison of mean octocoral percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila……………………………………………...33

Figure 9. Comparison of mean sponge percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila……………………………………………...33

Figure 10. Comparison of mean macroalgae percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila……………………………………………...34

Figure 11. Comparison of mean jig percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila……………………………………………...34

Page Figure 12. Mean hard coral percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method………………………………………………..36

Figure 13. Mean octocoral percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method………………………………………………..37

Figure 14. Mean sponge percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method………………………………………………..37

Figure 15. Mean macroalgae percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method………………………………………………..38

Figure 16. Mean jig percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method………………………………………………..38

Figure 17. Percent coverage by category for random photographic method on shallow reef zone at Rancho Pedro Paila in 2001 and 2005………………………………………………...40

Figure 18. Percent coverage by category for repetitive photographic method on shallow reef zone at Rancho Pedro Paila from 2003 to 2005……………………………………………….40

Figure 19. Percent coverage by category for random photographic method on mid reef zone at Rancho Pedro Paila in 2001 and 2005………………………………………………...41

Figure 20. Percent coverage by category for repetitive photographic method on mid reef zone at Rancho Pedro Paila from 2002 to 2005……………………………………………….42

Figure 21. Percent coverage by category for random photographic method on deep reef zone at Rancho Pedro Paila in 2001 and 2005………………………………………………...43

Figure 22. Percent coverage by category for repetitive photographic method on deep reef zone at Rancho Pedro Paila from 2002 to 2005……………………………………………….44

LIST OF TABLES

Page Table 1. Levene test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001…….…………………………………………………...17

Table 2. Kruskal-Wallis test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001……………………………………………….18

Table 3. ANOVA test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001…………………………………………………………18

Table 4. Tukey test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001……………………………………………………...….19

Table 5. Levene test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005…….…………………………………………………...19

Table 6. Kruskal-Wallis test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001……………………………………………….20

Table 7. ANOVA test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005……………………………………………………....…20

Table 8. Tukey test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005…………………………………………………...…….21

Table 9. Levene test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002………………………………………………….….…..26

Table 10. Kruskal-Wallis test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002……………………………………….….…..26

Table 11. ANOVA test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002……………………………………………………..…..26

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Page Table 12. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003…………………………………………………………27

Table 13. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003……………………………..…….…..27

Table 14. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003…………………………………………………………28

Table 15. Tukey test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003………………………………………………………....28

Table 16. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004…………………………………………………………29

Table 17. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004……………………………………..…29

Table 18. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004………………………………………………………....29

Table 19. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005……………………………………………………....…30

Table 20. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005…………………………………………….…30

Table 21. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005…………………………………………………………31 . Table 22. Tukey test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005………………………………………………………....32

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Page Table 23. Percent coverage by category for random photographic method on shallow reef zone at Rancho Pedro Paila in 2001 and 2005……….…………………………………….....39

Table 24. Percent coverage by category for repetitive photographic method on shallow reef zone at Rancho Pedro Paila from 2003 to 2005……………………………………………….40

Table 25. Percent coverage by category for random photographic method on mid reef zone at Rancho Pedro Paila in 2001 and 2005………………………………………………………….41

Table 26. Percent coverage by category for repetitive photographic method on mid reef zone at Rancho Pedro Paila from 2003 to 2005……………………………………………….42

Table 27. Percent coverage by category for random photographic method on deep reef zone at Rancho Pedro Paila in 2001 and 2005………………………………………………...43

Table 28. Percent coverage by category for repetitive photographic method on deep reef zone at Rancho Pedro Paila from 2003 to 2005……………………………………………….43

Table 29. Percent hard coral cover in Pez Maya from January to March of 2004 and 2005………………………………………..52

LIST OF APPENDICES

Page Appendix I. Coordinates of monitoring sites at Rancho Pedro Paila within the Sian Ka’an Biosphere Reserve, Quintana Roo, Mexico……………………………….……...60

Appendix II. Diagram of shallow-reef repetitive photographic stations at Rancho Pedro Paila……………………………..61

Appendix III. Diagram of mid-reef repetitive photographic stations at Rancho Pedro Paila…………………..…………………..62

Appendix IV. Diagram of deep-reef repetitive photographic stations at Rancho Pedro Paila………….……………………….….63

Appendix V. Photographic jigs used in this study at Rancho Pedro Paila…………….………………………………….…64

Appendix VI. Coral species list for random transects from Rancho Pedro Paila for 2001 and 2005……..……………….…..…65

Appendix VII. Coral species list for repetitive transects at Rancho Pedro Paila in 2001 through 2005…………..………….….66

Appendix VIII. Summary of random transects analyzed for this study from Rancho Pedro Paila for 2001 and 2005……….……67

Appendix IX. Summary table of Rancho Pedro Paila images available for analysis of repetitive stations for repetitive transects from 2002 to 2005…………………...68

ACKNOWLEDGMENTS

I would like to thank my committee members Dr. Wes Tunnell, Dr.

Quenton Dokken, and Dr. Roy Lehman for their time and patience. The field work portion of this project would have been impossible without the help of Jennifer Pearce, Leslie Smith, and Al Olswalt. Individuals donating to the Caribbean Connection are also thanked.

Dr. Kirk Cammarata is thanked for his help and guidance during the beginning of this project. Thanks are given to Dr. Kim Withers for her assistance with the statistics. Dr. Kevin Strycher and Ruth O’Brien are owed many thanks for listening to my rambling thought processes.

Kevin E. Kohler, with NOVA at Southeastern University

Oceanographic Center, is very much appreciated for all the assistance with issues dealing with Coral Point Count (CPC). More than one version was used, and issues, which took hours to deal with, were always dealt with and at some very strange hours. His assistance can not be thanked enough.

The person that needs to be thanked the most is my ever supporting wife, Kathy Haralson. Thanks also to my mother, Bonnie Haralson, for encouraging me to go back to school. I would also like to thank my late father, H.E. (Gene) Haralson, for listening patiently, while I discussed things I was studying. I was told after he passed away, that most of the time he had no idea what I was talking about, but was proud of my enthusiasm for learning.

INTRODUCTION

Coral reefs exist in waters which are usually considered to be oligotrophic, yet they continue to thrive (Wells, 1957). Their ability to

survive in this seemingly nutritionally poor environment has given rise to

the philosophy that they are self-sustaining ecosystems (Wells, 1957).

Their survival is largely due to the symbiotic relationship of

zooxanthellae which live within the coral polyps, and zooxanthellae are dependent upon the availability of light in order to achieve photosynthesis

(Titlyanov, 1981). The amount of light available for photosynthesis to occur is dependent upon water clarity (turbidity) and water depth

(Stoddart, 1969; Yentsch et al., 2002). This symbiosis is the basis of one of the most diverse and prolific ecosystems on earth, and the many factors involved in the success of this relationship are influenced by both natural and anthropogenic activities. Temperature, turbidity, wave action, and

pollution are just a few things having major affects upon coral reefs.

Scientist employ various field techniques to monitor the health and

status of particular reef systems, which may involve simple in situ counts

and measurements of particular taxa, or they may involve more

sophisticated use of still and video imaging. Texas A & M-Corpus Christi

(TAMUCC) began a long-term monitoring program at Rancho Pedro Paila

(RPP) in the Sian Ka’an Biosphere Reserve (SKBR), Quintana Roo,

1 2

Mexico, in 1996 to monitor the status of the Mesoamerican Barrier Reef

System (MBRS) in that locality. The purpose of this project is to review

this long-term coral reef monitoring program by comparing random (2001

and 2005) vs. repetitive (4 years) monitoring methods to see if one is

better than the other, and to note if any significant changes can be

detected.

Topography and weather have a major influence on the eastern

Yucatan Peninsula, with rainfall having little affect upon turbidity

because very little runoff occurs due to the karstic nature of the Yucatan

Peninsula (Ferre-D'Amare, 1985; Jordan-Dahlgren, 1989; Tunnell et al.,

1993). The Caribbean current system is the main source of oceanographic influence on the Atlantic reefs of Mexico (Jordan-Dahlgren and

Rodriguez-Martinez, 2003). The shoreline consists of a series of rocky outcrops or points, which act as sediment traps resulting in crescent shaped beaches in between (Tunnell et al., 1993). Bottom topography has such a gradual slope that sediments are deposited into deeper waters at a much slower rate than normal (Jordan et al., 1981). These factors have a large influence upon both the turbidity and sedimentation rate of the area.

The composition on the deep reef section consists of spur and groove formations oriented perpendicular to the wave action, allowing sand to be funneled down the grooves to the sandy plane below, and are typical of exposed windward reefs (Fenner, 1988). This serves as a method by which sandy sediment is transported through gravity, so as not

3 to suffocate the coral (Goreau, 1959; Goreau and Wells, 1967; Goreau et al., 1979). Undertows set up in the breaker zone help to eliminate sediment from more turbulent upper zones down the chutes to the fore reef (Goreau, 1959). “The most profuse coral growth generally occurs at the edges of steps where sediment drainage is most efficient, while the least growth occurs on level sites where sediments tend to accumulate”

(Goreau and Wells, 1967). Removal of accumulated sand is very important, because the gentle slope allows sand to be easily resuspended by the wave action created by tropical storms that frequent this area

(Jordan et al., 1981).

Gorgonian fauna varies greatly between the different zones of the coral reef (Jordan-Dahlgren, 1989). High density of the gorgonian fauna upon coral reefs of the eastern Yucatan Peninsula may be the result of the gentle slope of the region and wave action causing high levels of sand accumulation (Jordan-Dahlgren, 1989). High sand accumulation rate may also explain the dominance of the scleractinian corals, Montastraea cavernosa, Siderastrea siderea, and Diploria strigosa, recognized as being very efficient in shedding sedimentation (Jordan-Dahlgren, 1989).

Tropical storms and hurricanes are frequent visitors to the region and can have a major impact upon the structure of reefs along the eastern

Yucatan coastline, destroying in days what took decades or centuries to construct. Reef structures have an affect upon the coastline by acting as a buffer for the coastline from the affect of storm waves (Stoddart, 1969;

Milliman, 1973). It may take a reef 10 to 25 years to recover from damage caused by a single or series of hurricanes (Stoddart, 1969). On the other hand hurricanes through their destructive forces may be beneficial to coral reefs by creating disturbances, which allow new species to colonize areas that otherwise would not be available (Gray,

1997).

Different morphs of the same coral species can occur at different depths. In deeper waters Acropora palmata grows in an unoriented fashion, while in shallower water, the branches are oriented into the waves, which may enable coral to better withstand the incoming wave action (Milliman, 1973).

Humans affect coral reefs through tourism, coastal development, over fishing, and pollution (Gray, 1997). Coastal development, to increase tourism, can have major negative affects upon natures’ protective mechanisms. Tourism-associated coastal development has generated multiple conflictive uses as well as threatened the well being of the reefs themselves (Jordan-Dahlgren and Rodriguez-Martinez, 2003). Mangrove forests, which dampen wave action, are destroyed to make room for new hotels, which may increase beach erosion and sedimentation rates, which may cause suffocation of the coral reef. Increased tourism can also negatively impact the reefs through increased incidental contact with the reef by the tourist and the locals trying to make a living from tourism.

Increased fishing pressure can result from tourists wanting to try the local

cuisine (Jordan-Dahlgren and Rodriguez-Martinez, 2003).

Damage to coral reefs can also be inflicted by anchors being tossed

onto the reef and increased pollution as a result of added load upon

wastewater systems and increased litter upon the beaches. Additional

tourism via cruise ships can have a devastating affect, resulting from the destruction of mangrove forests for docks and destruction of the reef itself by dredging (Sanchez et al., 2004). Dredging not only results in the immediate destruction of the reef, but continues to have an affect on the remaining reef through increased sedimentation and likely elevation in pollution by the cruise ship itself.

It is important to realize that we can not control weather events such as hurricanes or stop tourism to this area of the world, but we may be able to affect the degree in which they impact the area. By better understanding natures’ mechanisms for survival, we may lessen the anthropogenic impact to the area. Decreasing the destruction of the mangrove forests may help control beach erosion by stabilizing sedimentation rates. Stabilizing sedimentation rates should lead to healthier reefs and result in better survival rate of corals. Healthier coral reefs would result in better protection of the coastline from the storm surge produced by tropical storms and hurricanes. Man-made harbors and coastline protection are very expensive to construct, and usually provide less protection than do natural structures such as coral reefs. In order to

monitor natural and anthropogenic impacts, scientist and managers

employ various kinds of sampling techniques.

Sampling design is the foundation of any study and samples must be

collected in the least biased manner (Liddell and Ohlhorst, 1991), with

line transects, point quadrats, photo quadrats, photo transects, and video

transects commonly used. Important aspects to consider when choosing a

particular sampling method include spatial characteristics (reef site, reef

complexity, area, or region) and invasive intrusion. Sampling of benthic communities should be done as nondestructive as possible (Littler and

Littler, 1985).

Techniques used to study benthic communities on coral reefs have mainly been adapted from methods developed to study terrestrial plant communities (Loya, 1978; Chiappone and Sullivan, 1991; Krebs, 1999).

Laxton and Stablum (1974) determined that standardized photographic

techniques can produce images enabling one to identify reef corals, soft

corals, hydroids, and sponges to the species level. According to Loya

(1978), a comparison between photographic and in situ field transects

conducted in coral reef studies did not result in significantly different

data being collected.

Photographic methods have the advantage of allowing large amounts

of data to be gathered and stored into a permanent record and images can

then be analyzed in a controlled environment with access to references for

better identification of organisms (Bohnsack, 1979; Dodge et al., 1982;

Foster et al., 1991).

Line transects methods can be divided into intersected-length, quarter

point, and point transects (Dodge et al., 1982). Intersected-length

transects consist of a set length of line and the length of the sample, and

the species is noted for the entire length (Loya, 1978). Quarter point line

transects are conducted using a line divided into a set number of segments

noted by marks, with area and distance of specimens from these points

being noted. Point line transects use a set length of tape, line, or chain

with markings, under which subject is identified and noted, at set

distances along it.

The point quadrat method uses a Plexiglas sheet of a set dimension,

with adjustable legs for placement, and a series of holes through which a

sampling rod can be lowered onto an object. When this rod is lowered,

the object (species or substrate) it touches is identified (Foster et al.,

1991). This method is impractical in open water because it is time consuming and difficult to perform if any current is present.

The photo quadrat method uses a rectangular frame which is subdivided by monofilament line at set intervals. This frame is placed over the subject area and then photographed (Foster et al., 1991).

Rectangular quadrats tend to be better than square or circular quadrats at determining diversity of populations (Littler and Littler, 1985), and they

can be scaled to match the rectangular shape of a 35 mm transparency.

According to Foster et al. (1991), photo quadats are more precise in estimating cover than point quadrats. Photographs resulting from photo quadrat methods do present some difficulties, such as identifying species at points indicated, and typically underestimate total cover (Littler, 1971;

Foster et al., 1991).

The belt quadrat method uses a line as a guide, along which a continuous row of photographic quadrats are taken (Dodge et al., 1982).

The rectangular frame used is awkward and can be cumbersome to use on the uneven topography of a coral reef.

Photographic transects combine several earlier methods (line transect, photographic quadrat, and belt quadrat) to yield similar results.

The photographic transect method is a faster and easier method of sampling than collecting all of the data (identification of species) underwater (Littler, 1971; Bohnsack, 1979; Littler and Littler, 1985;

Chavez, 1997). This is an important factor while collecting information on the deep reef and in remote locations (Ohlhorst et al., 1988). On relatively flat reef sections, such as the top of a spur, one study determined that increasing distance between quadrats (random photographs) does not decrease accuracy (Laxton and Stablum, 1974).

This same study noted that accuracy can be affected if slope and depth increases greatly (Laxton and Stablum, 1974), so investigators need to be conscious of depth while doing benthic transects on coral reefs. The entire transect should be done at the same approximate depth to ensure

that recorded species diversity is not caused by change in vertical

zonation due to fluctuating depth.

The repetitive quadrat method involves placing permanently fixed

photographic stations on the coral reef so an image can be taken of that

precise location repeatedly over time. This requires securing numbered

plastic tags with stainless steel posts onto the coral reef in a number of

locations. Each photographic station is then photographed repetitively in a consistent predetermined manner to ensure the exact same area is recorded each time. These repetitive images are then overlaid to compare any changes in percent coverage of the species noted (Dokken et al.,

2001).

Video transects have also been used to examine benthic

communities on coral reefs. Video transects have an advantage of

supplying large numbers of images in a short period of time (Vogt, 1995).

Disadvantages of video transects when compared to still photography,

include images of lower quality, larger learning curve to produce

acceptable images, scale of images (due to continuously changing distance

from objects), and expense of equipment needed to transform video into

still digital frames for analysis (Jokiel et al., 2001).

Photographic slides of benthic subjects can be analyzed by several

methods. One involves overlaying a grid system onto the slide with a set

number of points. This method has an advantage over the photo quadrat

method because the number of points used for analysis can be changed.

Another method uses a computer program called Coral Point Count with

Excel extensions (CPCe), available from the National Coral Reef Institute

(Kohler and Gill, 2006). This latter method has the advantage of being

able to calculate percent coverage of a particular species. The CPCe

program is the latest version of PointCount99 referred to in much of the

literature (Jokiel et al., 2001; Kohler and Gill, 2006). Points can be

computer generated either randomly or in grid fashion, for identification

purposes and stored in an Excel file, and can be permanently set for later

reverification.

In earlier studies percent coverage was determined by weighing the

entire photograph, then cutting out the image of specimens, then using the

following formula to calculate percent coverage (Laxton and Stablum,

1974).

Weight of cut out image X 100 Weight of whole photograph

Later studies used area of the image to calculate percent coverage (Coles

et al., 2005). Here again, CPCe may be advantageous because an image

can be analyzed and saved, allowing re-analysis at a later time.

Scientists are not in agreement about which method is most suitable for the study of coral reefs, since they vary greatly between various

habitats, such as reef flat, reef crest, and reef slope (Gray, 1997). Issues

to consider in selecting a particular method include spatial issues, time

allotted for the study to be conducted, impact to the reef itself, and

physiological factors on divers (especially in the deeper zones). Another

challenge is that each method has advantages under certain conditions, but

not in all conditions encountered on a coral reef (Loya, 1978).

STUDY SITE

The Sian Ka’an Biosphere Reserve is located on the eastern shore of

the Yucatan Peninsula, Quintana Roo, Mexico (Figure 1). The reefs

studied are located just off shore at Rancho Pedro Paila (N 20˚02.593’, W

87˚28.835’).

Figure 1. Location map of Rancho Pedro Paila, Sian Ka’an Biosphere Reserve, Quintana Roo, Mexico (Reed, 2003).

The Sian Ka’an Biosphere Reserve was established by the Mexican government, through presidential decree on January 20, 1986 (Wells,

1988; Harris, 1999). It was declared a World Heritage Site by UNESCO in 1987 (Harris, 1999). The Sian Ka’an Biosphere Reserve starts just south of Tulum and extends south for about 100 km. (Jordan-Dahlgren et al., 1994). The Reserve encompasses 4,500 km2 in total area, of which

1,200 km2 is marine environment (Wells, 1988; Jordan-Dahlgren et al.,

1994). The coastal wilderness of the Sian Ka’an Biosphere Reserve looks similar to the Florida Everglades National Park (Harris, 1999). “One- third of the reserve contains tropical forest, another third is savannah and mangrove jungle, and the rest is water, including the large bays, Bahia de la Ascension and Bahia del Espiritu Santo (Harris, 1999).” The crest and shallow fore reef consists of a fringing-barrier reef that is predominately made up of Acropora palmata (Jordan-Dahlgren et al., 1994). The reef, which lies off Sian Ka’an is part of the Mesoamerican Barrier Reef

System, stretches for 320 km along the entire length of Quintana Roo state from Cancun, through Belize, to the coast of Honduras (Wood,

1997).

MATERIALS AND METHODS

Monitoring programs compared in this study have been in place for several years and consist of two different monitoring methods. Collection of field data was conducted yearly in late May. The first method, a

random photographic transect method, was established in 1996. A second

method, a repetitive, fixed-location photographic data collection protocol,

was established in 2001(Done, 1981; Reed, 2003). The reef was divided

into four distinct zones consisting of the patch reef (<10m), shallow reef

(10-15m), mid-reef (15-20m), and deep reef (>20m) (Appendix I). The

patch reef was excluded from the fixed-location “repetitive” photographic

method due to difficulty related to swallow depth of that zone.

All four zones were studied by using the random photographic

transect method in May 2001(Ledford, 2003; Reed, 2003). Photographic

images were taken starting at randomly chosen points at approximately 1

meter intervals along a chosen compass heading. Ledford (2003) took the

photographic images in 2001 on the patch and shallow zones to use in his thesis and Reed (2003) took the 2001 photographic images of the mid and deep zones.

The repetitive photographic method was carried out annually beginning in 2002, in each of the reef zones (excluding the patch reef). In

2001, permanent mooring bolts were installed on the shallow, mid, and deep reef zones. Near each of these permanent mooring bolts, four fixed photographic locations were established by attaching numbered yellow plastic tags to stainless steel rod driven into the substrate. Locating these

tagged locations was achieved by the use of diagrams for each mooring

site (Appendixes II, III, and IV). Repetitive sites were photographed

using a Nikonos V camera fitted with a 15 mm lens and two Nikonos SB

105 strobes attached to a metal T-bar 1 meter in length (Appendix V-B).

This method resulted in a coverage area of 4.63 m². The T-bar was fitted with a level and a compass and all photographs were taken with the compass pointing North and the bubble centered in the level.

All photographic images for both random and repetitive photographic transects were collected in May 2005. The random patch reef transects were taken on the windward side (southeastern) at three separate depths as a method of obtaining three line transects. The camera was maintained at a constant depth of 2.44 meters, 3.05 meters and 3.66 meters during each photographic transect and the photographic images were taken perpendicular to the substrate. Three transects were collected from the shallow reef, mid-reef, and deep reef by using a photographic point line transect method, starting at fixed locations and laid out on a continuous compass heading. Photographic images were taken at one meter intervals measured by a meter tape laid out along the approximate apex of each spur of the reef studied. This was done to eliminate variances in populations, due to changing depth, from the top of the reef zone as compared to the sides of the reef zones.

The random photographic transects taken in May 2001 and May

2005 were obtained by using a Nikonos V underwater camera with a 35 mm lens and a Nikonos SB 105 strobe. This assemblage was attached to a metal jig (87 cm in length) with a 5 cm standard attached to the end. The jig used for the random photographic transects was changed between 2001

and 2005 (Appendix V-A&B). The stainless steel rod was changed to an

aluminum angle rod. Length and 5 cm standard remained the same. The

resultant image yielded an area of 0.26 m².

Photographic images from 2001 were digitized using a Nikon Super

Coolscan 5000. Photographic images from 2005 were digitized by the

film developing company, but some were also scanned using the same

Nikon Super Coolscan 5000. The “random” digitized pictures were

overlaid with a grid of 49 points assigned by CPCe 3.3. These points

were used to mark the organisms to be identified and analyzed to describe

the benthic community. The “repetitive” digitized images were analyzed

using CPCe 3.4 to determine area which was used to determine percent

coverage.

Data was stored in Excel files and then later statistically analyzed

by using SPSS. Levene test were carried out on all data to test for

homogeneity of variances and in most cases there were a few departures from the assumption of homogeneity of variances. Because of these departures the Kruskal-Wallis tests (non-parametric equivalent of the one- way ANOVA) were performed. Analyses of variance (ANOVA) were done to compare with Kruskal-Wallis and for ease of running post hoc test.

According to McKillip (2006), ANOVA is relatively robust in terms of departures from homoscedasticity, therefore should be considered a valid comparison tool in the study of this data. Kruskal-Wallis and ANOVA test only tells us if there are variances in populations, but it does not show

were those differences are. In order to determine where these occur, a

post hoc test such as a Tukey test need to be carried out, and it is often

used since it has both good power and tight control over Type I error rate

(Sokal and Rohlf, 2003; Field, 2005). Tukey tests were done to determine

where the differences in the populations between the zones noted as 1

(patch), 2 (shallow), 3 (mid), and 4 (deep).

RESULTS

Results are divided into four sections. Part A is the comparison of

random photographic method conducted at Rancho Pedro Paila in May

2001 and 2005 only. Part B is the comparison of the repetitive

photographic method conducted at Rancho Pedro Paila in May 2002, 2003,

2004, and 2005. Part C is the comparison of random versus repetitive

photographic methods conducted at Rancho Pedro Paila in May 2005 only.

The final section of the results (Part D) is a comparison of the methods to

examine if one method is better at detecting change of the benthic community of this coral reef by zones.

Identification data was divided into several categories. Categories

were made up of hard corals, octocorals, sponges, macroalgae, and jig.

The hard corals category includes Scleractinia and Millipora while the

octocoral category includes Gorgonia and Alcyonaria.

PART A. Comparison of Random Method in Four Reef Zones.

According to the Levene test (Table 1) conducted on the random method data from RPP in May 2001, there are significant departures from the assumptions of homogeneity of variance in the categories of octocorals, sponges, and jig.

The Kruskal-Wallis test (Table 2) indicates differences between zones in the sponge category, while analysis of variance (ANOVA) test

(Table 3) indicates that there are significant differences between the zones in sponge and macroalgae categories. Both analytical tests were conducted using an α = 0.05 level of significance.

Tukey tests (Table 4 a) indicates a significant difference in sponges between patch (1) and shallow (2) reef zones, when compared to the mid

(3) and deep (4) reef zones. A significant difference in the macroalgae

(Table 4 b) is noted between the shallow and deep reef zones.

Table 1. Levene test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001.

Levene Statistic df1 df2 Significance Hard Corals 3.476 3 7 0.079 Octocorals 7.073 3 7 0.016 Sponges 5.911 3 7 0.025 Macroalgae 1.467 3 7 0.304 Jig 8.269 3 7 0.011

Table 2. Kruskal-Wallis test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square 4.033 4.015 8.158 6.379 2.379 df 3 3 3 3 3 Asymp. Sig 0.258 0.260 0.043 0.095 0.498

Table 3. ANOVA test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001.

df F Significance Between zones 3 Hard Corals Within population 7 1.521 0.291 Total 10 Between zones 3 Octocorals Within population 7 1.386 0.324 Total 10 Between zones 3 Sponges Within population 7 11.042 0.005 Total 10 Between zones 3 Macroalgae Within population 7 6.969 0.017 Total 10 Between zones 3 Jig Within population 7 1.053 0.427 Total 10

The Levene test (Table 5) conducted on the random photographic

method data from RPP in May 2005 indicates that all categories meet the

assumption of homogeneity of variance.

Both the Kruskal-Wallis (Table 6) and the ANOVA test (Table 7)

detect differences in zones of both hard coral and octocoral categories.

Tukey test (Table 8a) showed a significant difference between hard coral

populations of the shallow and deep reef zones. Octocoral (Table 8b) data

indicates significant differences in populations between the patch reef and all other reef zones.

Table 4. Tukey test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2001.

a. Sponges

Subset for alpha = .05 Zone N 1 2 Tukey HSD 2 3 0.9313 1 3 1.4253 4 2 3.9350 3 3 4.2767 Sig. 0.907 0.966

b. Macroalgae

Subset for alpha = .05 Zone N 1 2 Tukey HSD 4 2 38.0300 1 3 43.540043.5400 3 3 48.548048.5480 2 3 59.6513 Sig. 0.051

Table 5. Levene test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005.

Levene Statistic df1 df2 Significance Hard Corals 2.448 3 9 0.130 Octocorals 2.174 3 9 0.161 Sponges 0.274 3 9 0.843 Macroalgae 3.066 3 9 0.084 Jig 0.882 3 9 0.486

Table 6. Kruskal-Wallis test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square 9.165 8.478 2.775 4.346 3.978 df 3 3 3 3 3 Asymp. Sig 0.027 0.037 0.428 0.428 0.264

Table 7. ANOVA test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005.

df F Significance Between zones 3 Hard Corals Within population 9 5.634 0.019 Total 12 Between zones 3 Octocorals Within population 9 14.002 0.001 Total 12 Between zones 3 Sponges Within population 9 0.696 0.578 Total 12 Between zones 3 Macroalgae Within population 9 1.737 0.229 Total 12 Between zones 3 Jig Within population 9 1.664 0.243 Total 12

The random photographic method data from 2001 and 2005 were

compared, to test if the method was consistent and to test if adding the

measuring tape to this method improved results. The Levene test for 2001

(Table 1) random method data indicated that the population was not

representative of a normally distributed population, while 2005 (Table 5)

did represent a normally distributed population. Results from the Kruskal-

Wallis (Table 2) test for 2001 differed from the ANOVA for 2001, while

both 2005 tests (Tables 6 and 7) showed hard coral and octocoral

21 categories had differing populations in different zones. Comparison of data analyzed by ANOVA for the random photographic method in both

2001 (Table 3) and 2005 (Table 7) indicated that there were differences between the zones. Tukey test were able to determine differences in category population by zones, 2001(Table 4a-b) and 2005 (Table 8a-b).

Table 8. Tukey test results of data collected by the random method on four reef zones at Rancho Pedro Paila in May 2005.

a. Hard corals

Subset for alpha = .05 Zone N 1 2 Tukey HSD 4 4 4.7528 3 3 5.82005.8200 1 3 10.854310.8543 2 3 11.8430 Sig. 0.077 0.081

b. Octocorals

Subset for alpha = .05 Zone N 1 2 Tukey HSD 2 3 8.8237 3 3 10.6833 4 4 11.5348 1 3 20.8187 Sig. 0.542 1

Figures 2 through 6 give a visual comparison (2001 vs 2005) of percent coverage by category divided by zone and year, showing similar results for both 2001 and 2005 except for the jig category. This may be

22 explained by a change from a stainless steel rod used in 2001 to an aluminum angle jig in 2005.

A comparison of hard coral percent coverage showed similar results in 2001 and 2005 (Figure 2), except for a notable decrease in percent coverage in all reef zones, especially in the mid and deep reef zones.

Percent coverage of octocoral (Figure 3) for both 2001 and 2005 yielded similar results, with error bars in 2001 being more pronounced in the patch reef zone than in 2005. In the sponge category (Figure 4) percentage variation between zones was noticeable, with the greatest difference occurring in the shallow reef zone. Random method yielded consistent results for macroalgae (Figure 5) in both 2001 and 2005, with some variations between reef zones. Percent macroalgae coverage has a trend of decreasing with increased depth except for the patch reef zone of 2001.

The most pronounced difference in data, when comparing the random method, was for the jig (Figure 6) category, which showed significant percentage differences between 2001 and 2005. The percent coverage in the shallow reef zone and error bars were more pronounced in 2001 than in 2005.

Zone 15.00 Patch Shallow Mid Deep 12.00

9.00

6.00 % Hard Coral coverage% Hard Coral

3.00

0.00 2001 2005 Year Error bars: +/- 1.00 SE

Figure 2. Comparison of mean hard coral percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila. ZoneZone 25.00 Patch Shallow Mid Deep 20.00

15.00

10.00 % Octocoral coverage % Octocoral

5.00

0.00 2001 2005 Year Error bars: +/- 1.00 SE

Figure 3. Comparison of mean octocoral percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila.

Zone 6.00 Patch Shallow Mid Deep 5.00

4.00

3.00

2.00 % Sponge coverage % Sponge

1.00

0.00 2001 2005 Year Error bars: +/- 1.00 SE

Figure 4. Comparison of mean sponge percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila.

Zone

70.00 Patch Shallow Mid 60.00 Deep

50.00

40.00

30.00

20.00

% Macroalgae coverage % Macroalgae 10.00

0.00 2001 2005 Year Error bars: +/- 1.00 SE

Figure 5. Comparison of mean macroalgae percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila.

Zone 8.00 Patch Shallow Mid Deep

6.00

4.00 % Jig coverage % Jig

2.00

0.00 2001 2005 Year Error bars: +/- 1.00 SE

Figure 6. Comparison of mean jig percentage for the random method by zone in 2001 and 2005 at Rancho Pedro Paila.

PART B. Comparison of Repetitive Method in Three Reef Zones.

There was a departure from the assumption of homogeneity in the sponge category in the Levene test (Table 9) conducted on the repetitive method data from RPP in May 2002. The Kruskal-Wallis test (Table 10) noted differences between zones in both the sponge and jig category; while the ANOVA test (Table 11) indicated a significant difference between the zones in the jig category only. No post hoc test could be performed in 2002 because there are fewer than three groups (zones).

Slides for the shallow reef zone could not be located for the year 2002.

Table 9. Levene test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002.

Levene Statistic df1 df2 Significance Hard Corals 3.609 1 5 0.116 Octocorals 2.827 1 5 0.154 Sponges 12.316 1 4 0.025 Macroalgae 4.794 1 4 0.094 Jig 0.312 1 5 0.600

Table 10. Kruskal-Wallis test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square .000 0.125 3.857 0.000 4.5 df 1 1 1 1 1 Asymp. Sig 1.000 0.724 0.050 1.000 0.034

Table 11. ANOVA test results of data collected by the repetitive method on two reef zones at Rancho Pedro Paila in May 2002.

df F Significance Between zones 1 Hard Corals Within population 5 0.332 0.590 Total 6 Between zones 1 Octocorals Within population 5 0.042 0.845 Total 6 Between zones 1 Sponges Within population 4 2.732 0.174 Total 5 Between zones 1 Macroalgae Within population 4 0.125 0.741 Total 5 Between zones 1 Jig Within population 5 85.086 0.000 Total 6

The Levene test (Table 12) conducted on the repetitive method data

from RPP in May 2003 showed a departure from the assumption of

homogeneity for the macroalgae category. Categories of sponges,

macroalgae and jig differed by zone according to the Kruskal-Wallis test

(Table 13), while the ANOVA test (Table 14) indicated differences

between the zones in the macroalgae and jig categories. Tukey test for

macroalgae (Table 15a) showed differences between the shallow (2) and

deep (4) reef zones, while the jig category (Table 15b) showed differences

between the shallow (2) and mid (3) reefs zones compared to the deep (4)

reef zone.

Table 12. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003.

Levene Statistic df1 df2 Significance

1.922 2 9 0.202 Octocorals 1.723 2 9 0.232 Sponges 4.315 2 7 0.060 Macroalgae 7.566 2 7 0.018 Jig 0.105 2 9 0.901

Table 13. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square 3.5 0.3577 7.855 6.545 7.499 df 2 2 2 2 2 Asymp. Sig 0.174 0.167 0.020 0.038 0.024

Categories for sponges and macroalgae showed departures from the assumption of homogeneity by the Levene test (Table 16) conducted on

28 the repetitive method data from RPP in May 2004. Results from the

Kruskal-Wallis test (Table 17) and ANOVA test (Table 18) did not show differences between the zones in any category. Tukey tests did not detect any significant difference in any category.

Table 14. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003.

df F Significance Between zones 2 Hard Corals Within populaton 9 1.131 0.365 Total 11 Between zones 2 Octocorals Within populaton 9 1.839 0.214 Total 11 Between zones 2 Sponges Within populaton 7 2.062 0.198 Total 9 Between zones 2 Macroalgae Within populaton 7 6.687 0.024 Total 9 Between zones 2 Jig Within populaton 9 12.568 0.002 Total 11

Table 15. Tukey test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2003.

a. Macroalgae

Subset for alpha = .05 Zone N 1 2 Tukey HSD 2 4 1.9625 3 2 2.49502.4950 4 4 5.4110 Sig. 0.888 0.085

b. Jig

Subset for alpha = .05 Zone N 1 2 Tukey HSD 3 4 4.2993 2 4 4.3100

4 4 4.6698 Sig. 0.991 1.000 Table 16. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004.

Levene Statistic df1 df2 Significance Hard Corals 3.384 2 9 0.080 Octocorals 2.888 2 9 0.107 Sponges 69.107 2 7 0.000 Macroalgae 4.313 2 9 0.049 Jig 0.929 2 9 0.430

Table 17. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square 2.000 5.115 5.455 1.500 0.731 df 2 2 2 2 2 Asymp. Sig 0.368 0.077 0.065 0.472 0.694

Table 18. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2004.

df F Significance Between zones 2 Hard Corals Within population 9 0.757 0.497 Total 11 Between zones 2 Octocorals Within population 9 3.501 0.075 Total 11 Between zones 2 Sponges Within population 7 2.435 0.157 Total 9 Between zones 2 Macroalgae Within population 9 0.358 0.709 Total 11 Between zones 2 Jig Within population 9 0.565 0.587 Total 11

The Levene test (Table 19) conducted on the repetitive method data

from RPP in May 2005 showed departures for the assumption of

homogeneity in both the hard coral and sponge category. The Kruskal-

Wallis test (Table 20) showed no differences between zones for any

category, while ANOVA test (Table 21) showed questionable differences

between the zones in the jig category with a (0.050) value. The jig

category according to the Tukey test (Table 22a) showed a significant difference between the mid (3) and deep (4) reef zones.

Table 19. Levene test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005.

Levene Statistic df1 df2 Significance Hard Corals 9.382 2 8 0.008 Octocorals 0.624 2 8 0.560 Sponges 19.624 2 6 0.002 Macroalgae 2.644 2 8 0.131 Jig 0.524 2 8 0.611

Table 20. Kruskal-Wallis test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005.

Hard Corals Octocorals Sponges Macroalgae Jig Chi-Square 1.076 0.848 2.944 2.227 4.806 df 2 2 2 2 2 Asymp. Sig 0.584 0.654 0.229 0.328 0.090

Comparison of percent coverage for hard coral (Figure 7) was

consistent, increasing with depth, for all four years using the repetitive

method. Error bars were consistently more significant in the deep zone.

Octocoral (Figure 8) percent coverage was consistent for all four years,

31 typically increasing with depth. Error bars were significant in every zone each year with a few exceptions. Sponge (Figure 9) percent coverage consistently noted a greater percentage in the mid reef zone, but also had the largest error bars variance. Macroalgae (Figure 10) category fluctuated over the four years, and had significantly larger error bars in

2002, 2003, and 2004 than those recorded for 2005. The repetitive photographic method produced very consistent results over the four year period for the jig (Figure 11) percent coverage. There was a noticeable dip in 2003 in percentage, but error bars had little variance between any zone and year.

Table 21. ANOVA test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005.

df F Significance Between zones 2 Hard Corals Within Population 8 1.301 0.324 Total 10 Between zones 2 Octocorals Within Population 8 0.412 0.676 Total 10 Between zones 2 Sponges Within Population 6 1.871 0.234 Total 8 Between zones 2 Macroalgae Within Population 8 0.986 0.414 Total 10 Between zones 2 Jig Within Population 8 4.459 0.050 Total 10

Table 22. Tukey test results of data collected by the repetitive method on three reef zones at Rancho Pedro Paila in May 2005.

a. Jig

Subset for alpha = .05 Zone N 1 2 Tukey HSD 3 4 5.8375 2 4 5.98505.9850 4 3 6.0710 Sig. 0.207 0.544

Zone 10.00 Shallow Mid Deep

8.00

6.00

4.00

% Hard Coral coverage% Hard Coral 2.00

0.00 200 2003 2004 2005 2 Year

Error bars: +/- 1.00 SE

Figure 7. Comparison of mean hard coral percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila.

Zone 25.00 Shallow Mid Deep

20.00

15.00

10.00

% Octocoral coverage % Octocoral 5.00

0.00 2002 2003 2004 2005 Year

Error bars: +/- 1.00 SE

Figure 8. Comparison of mean octocoral percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila.

Zone 12.00 Shallow Mid Deep 10.00

8.00

6.00

4.00 % Sponge coverage % Sponge

2.00

0.00 2002 2003 2004 2005 Year Error bars: +/- 1.00 SE

Figure 9. Comparison of mean sponge percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila.

Zone 14.00 Shallow Mid Deep 12.00

10.00

8.00

6.00

4.00 % MacroalgaeCoverage

2.00

0.00 2002 2003 2004 2005 Year Error bars: +/- 1.00 SE

Figure 10. Comparison of mean macroalgae percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila.

Zone 7.0 0 Shallow Mid Deep 6.0 0

5.0 0

4.0 0

3.0 0

2.0

% Jig coverage % Jig 0

1.0 0

0.0 0 2002 200 2004 2005 3 Year Error bars: +/- 1.00 SE

Figure 11. Comparison of mean jig percentage for repetitive method for years 2002-2005 by zone at Rancho Pedro Paila.

PART C. Comparison of Random versus Repetitive

The Levene test (Table 5) conducted on the random method data

from RPP in May 2005 indicates no significant differences in any

category, while the repetitive method (Table 17) departs from the

assumption of homogeneity for both the hard coral and sponge categories.

Both the Kruskal-Wallis test (Table 6) and the ANOVA test (Table

7) showed significant differences between the zones in categories of hard

corals and octocorals, while neither test for the repetitive method (Tables

20 and 21) indicated a significant difference between the zones in any category except the jig category with the ANOVA, which was border line.

Tukey test (Table 8 a) for the random method indicates that there is a significant difference in hard coral between the shallow (2) and deep (4) reef zones. Tukey test for octocorals (Table 8b) shows a significant difference in populations between the patch (1) reef and all other zones.

The repetitive method Tukey test (Table 22a) detected a difference in the jig category between the mid (3) and deep (4) reef zones.

In the comparison of random versus repetitive methods (Figure 12),

note the difference in hard coral percent coverage in the shallow zones

acquired by each method and the extreme error bar associated with the

repetitive method deep zone. Percent octocoral coverage (Figure 13)

showed increasing percent coverage, with increasing depth, but the error

bars were more pronounced with the repetitive method. The shallow and

deep zones of the sponge (Figure 14) population varied greatly between

the two methods, with error bars in the mid reef zone being more

pronounced in the repetitive method. Macroalgae percentage coverage

differences (Figure 15) had the largest disparity in results than any other

category, with the repetitive method doing a very poor job of representing this category. Jig category (Figure 16) yielded similar results by both methods. Larger error bars by the random method are most likely related to the analysis of images by point ID, while repetitive method always included entire jig area.

Zone 14.00 Patch Shallow Mid 12.00 Deep

10.00

8.00

6.00

4.00 % Hard Coral coverage% Hard Coral

2.00

0.00 Random Repetitive Method Error bars: +/- 1.00 SE

Figure 12. Mean hard coral percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method.

Zone

25.00 Patch Shallow Mid Deep 20.00

15.00

10.00 % Octocoral coverage % Octocoral 5.00

0.00 Random Repetitive Method Error bars: +/- 1.00 SE

Figure 13. Mean octocoral percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method.

Zone 6.00 Patch Shallow Mid 5.00 Deep

4.00

3.00

2.00 % Sponge Coverage Coverage % Sponge

1.00

0.00 Random Repetitive Method Error bars: +/- 1.00 SE

Figure 14. Mean sponge percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method.

Zone

60.00 Patch Shallow Mid 50.00 Deep

40.00

30.00

20.00 % Macroalgae coverage % Macroalgae

10.00

0.00 Random Repetitive Method Error bars: +/- 1.00 SE

Figure 15. Mean macroalgae percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method.

Zone 8.00 Patch Shallow Mid Deep

6.00

4.00 % Jig coverage % Jig 2.00

0.00 Random Repetitive Method Error bars: +/- 1.00 SE

Figure 16. Mean jig percentage at Rancho Pedro Paila for May 2005 by zone by comparing random versus repetitive method.

Part D. Comparison in methods to detect change.

Data collected from RPP was separated by zone and method to see if noticeable differences in a zone could be detected when comparing the random photographic method (2001 and 2005) to the repetitive photographic method 2002-2005). The patch reef was excluded from this section since the repetitive photographic method was not conducted upon that zone.

Comparing methods on the shallow reef zone by the random method

(Table 23 and Figure 17) to the repetitive method (Table 24 and Figure

18) for percent coverage by category is greater for macroalgae with the random method, while octocorals is the higher with the repetitive method.

The macroalgae category had the greatest differences in percent coverage when comparing both methods. Each method showed relatively consistent results when data from different years was compared by category, but percent coverage varied greatly between methods. An example, comparing percent coverage of hard coral by the random method (Table

23) remained at approximately 13.25, while by the repetitive method

(Table 24) the average value was about 3.74.

Table 23. Percent coverage by category for random photographic method on shallow reef zone at Rancho Pedro Paila in 2001 and 2005.

Random Shallow 2001 Shallow 2005 Hard Corals 13.27 13.19 Octocorals 9.82 9.65 Sponges 0.95 3.21 Macroalgae 61.13 49.17 Jig 2.31 5.73

70 60 50 40 Shallow 2001 30 Shallow 2005 20 10 % coverage coverage % 0 Jig Sponges Octocorals Octocorals Macroalgae Macroalgae Hard Corals Hard Corals Figure 17. Percent coverage by category for random photographic method on shallow reef zone at Rancho Pedro Paila in 2001 and 2005.

Table 24. Percent coverage by category for repetitive photographic method on shallow reef zone at Rancho Pedro Paila from 2003 to 2005.

Repetitive Shallow 2003 Shallow 2004 Shallow 2005 Hard Corals 3.78 3.78 3.67 Octocorals 12.16 11.24 11.49 Sponges 0.07 0.14 0.39 Macroalgae 1.96 7.48 3.64 Jig 4.31 5.68 5.98

14 12 10 Shallow 2003 8 Shallow 2004 6 4 Shallow 2005

% coverage coverage % 2 0 Jig Sponges Octocorals Macroalgae Macroalgae Hard Corals Hard Corals

Figure 18. Percent coverage by category for repetitive photographic method on shallow reef zone at Rancho Pedro Paila from 2003 to 2005.

Comparing the random photographic method on the mid reef (Table

25 and Figure 19) and the repetitive photographic method (Table 26 and

Figure 20) again showed percent coverage being higher for magcroalgae category by the random method and octocoral being greater by the repetitive method. In the mid reef zone the random photographic method showed more stable percent coverage by category as compared to the fluctuating percent coverage by the repetitive photographic method. The random method had a significant change in percent coverage in the jig category between 2001 and 2005.

Table 25. Percent coverage by category for random photographic method on mid reef zone at Rancho Pedro Paila in 2001 and 2005.

Random Mid 2001 Mid 2005 Hard Corals 9.32 6.43 Octocorals 11.81 11.89 Sponges 4.35 2.90 Macroalgae 49.57 46.83 Jig 0.61 6.32

60 50 40 Mid 2001 30 20 Mid 2005 10

% coverage coverage % 0 Jig Sponges Octocorals Macroalgae Macroalgae Hard Corals Hard Corals

Figure 19. Percent coverage by category for random photographic method on mid reef zone at Rancho Pedro Paila in 2001 and 2005.

Table 26. Percent coverage by category for repetitive photographic method on mid reef zone at Rancho Pedro Paila from 2002 to 2005.

Repetitive Mid 2002Mid 2003 Mid 2004 Mid 2005 Hard Corals 5.28 6.03 5.25 3.69 Octocorals 14.93 14.14 18.65 10.60 Sponges 3.03 7.34 1.84 3.67 Macroalgae 2.40 1.25 6.34 2.18 Jig 6.00 4.30 5.72 5.84

20 15 Mid 2002 10 Mid 2003 Mid 2004 5 Mid 2005 %coverage 0 Jig Sponges Octocorals Macroalgae Hard Corals

Figure 20. Percent coverage by category for repetitive photographic method on mid reef zone at Rancho Pedro Paila from 2002 to 2005.

Comparing the deep reef zone by the random method (Table 27 and

Figure 21) and the repetitive method (Table 28 and Figure 22) the same trend of the random method having a greater percent coverage in the macroalgae category, while the repetitive method had an elevated octocoral percent coverage. The random method again had a large variance in percent coverage in the jig category. Both methods showed larger differences between categories in the deep reef zone than in the other two zones.

Table 27. Percent coverage by category for random photographic method of deep reef zone at Rancho Pedro Paila in 2001 and 2005.

Random Deep 2001 Deep 2005 Hard Corals 10.11 5.19 Octocorals 11.79 13.38 Sponges 4.04 2.42 Macroalgae 38.89 46.85 Jig 0.47 7.41

50 40 Deep 2001 30 20 Deep 2005 10

% coverage 0 Jig Sponges Octocorals Macroalgae Hard Corals

Figure 21. Percent coverage by category for random photographic method of deep reef zone at Rancho Pedro Paila in 2001 and 2005.

Table 28. Percent coverage by category for repetitive photographic method for deep reef zone at Rancho Pedro Paila from 2002 to 2005.

Repetitive Deep 2002Deep 2003 Deep 2004 Deep 2005 Hard Corals 7.48 7.30 6.20 6.07 Octocorals 15.97 20.29 15.76 16.27 Sponges 0.05 0.37 0.15 1.08 Macroalgae 2.12 5.41 3.13 1.57 Jig 6.54 4.67 5.78 6.07

25 20 Deep 2002 15 Deep 2003 10 Deep 2004 5 Deep 2005 %coverage %coverage 0 Jig Sponges Octocorals Hard Corals Macroalgae Macroalgae

Figure 22. Percent coverage by category for repetitive photographic method for deep reef zone at Rancho Pedro Paila from 2002 to 2005.

DISCUSSION

Random vs. Repetitive

This study looks at two basic photographic methods used to study the benthic community associated with coral reefs in order to see if one is better than the other (more efficient, effective) and to see if either could detect changes in the coral community over time. Photographic transects have an added advantage over visual surveys since they can be archived and studied later if questions about analysis ever arise (Nadon and

Stirling, 2006). Photographic images used in this comparison were acquired by random and repetitive methods. A limitation of how comparisons were set up was governed by availability of photographic images from previous research. These included, having only one year

(2001) with three random photographic transects per zone (due to thesis

projects by Ledford 2003 and Reed 2003), one year with only two zones

of repetitive images (2002), and not having repetitive images for 2001.

Methods used in image analysis for each field method was determined by

methods already in place by previous researchers. Population is defined

as entire reef population unless otherwise stated.

Discussion will focus on the two methods in 2005 (from Part C of results), since that year represents the most complete and consistent data set. For any method to be truly beneficial, it must be representative of the entire reef population, and if either method does not achieve this, then it should not be used as such (Porter and Meier, 1992).

Comparison of data acquired by the random photographic method versus the repetitive photographic method indicates that the random method does a better job of assessing populations on coral reefs overall.

Using both the Kruskal-Wallis tests (Tables 6 and 20) and ANOVA tests results (Tables 7 and 21), the random method detected differences in populations between reef zones in both hard corals and octocorals, which the repetitive method did not. Changes in populations between reef zones is something that is expected to take place (Goreau, 1959; Goreau and

Wells, 1967; Jordan-Dahlgren, 1989; Tunnell et al., 1993; Jordan-

Dahlgren et al., 1994). The random method Tukey test (Table 8a) for hard corals showed a difference between the shallow and deep reef zones, while the octocoral Tukey test (Table 8b) indicated differences between the patch reef zone and all other zones of the reef. The Tukey test for the

46 repetitive method (Table 22a) noted differences in jig categories between the mid and deep reef zones, which is contrary to the visual representation of the jig percent coverage in Figure 16. All test run on 2005 data,

Levene, Kruskal-Wallis, ANOVA and Tukey, clearly indicate that the random method is the better of the two methods in that particular year.

Also the conclusions from Part A and Part B of the results indicate that the random method is the more reliable method.

Field Logistic Considerations

Another aspect of this and any other study is the logistics of collecting the field data, and photography provides a way of sampling large areas underwater (Aronson et al., 1994). Collection of reliable reef data is essential in the development and testing of any model (Ohlhorst et al., 1988) to be used in the future management of coral reefs through out the world. It is important to recognize that complex sampling designs may be self defeating, if they are difficult to carry out in the field and tiring for the researchers to utilize or implement (Krebs, 1999). In most field oriented research simplicity is an asset, but this is especially true when done in remote locations. Research on coral reefs is usually conducted in remote locations and diving adds safety concerns to the equation, especially on deep water surveys (Ohlhorst et al., 1988). Field photographic image collection by both photographic methods examined in this study can be performed in a very short period of time and with

minimal support staff, with the repetitive method being the more time

consuming of the two.

Totally random photographic transect lines, like those utilized in

this study from 2001; require a minimum of three people, including one

boat sitter. The diving buddy team can take random photographic

transects very rapidly by starting at a random point and continuing along

a constant compass heading. Photographic images can be taken at

approximately equal distances of separation by many simple methods, but

photographic images collected using approximate distances can introduce

unintentional bias (Ohlhorst et al., 1988). This bias can be hard to

overcome due to the human eye being attracted to colorful and strange

objects, i.e. coral heads or sponges.

Random photographic line transects with a measuring tape, like

those conducted in this study in 2005, requires four people, including a

boat sitter. A dive team consisting of three people is needed to perform

this method, with two people stretching out and holding the ends of the

meter tape, while the third diver takes the photographic images. By

adding the measuring tape you may eliminate the introduction of

unintentional bias. According to Krebs (1999), “In field ecology,

systematic samples are easier to apply and seem to be the equivalent of random samples in many field situations.” This method could be modified by installing permanent end points, between which the tape could be stretched. This modified method would result in repetitive photographic

line transects. One researcher determined that line transects using a one

meter-square grid, resulted in the most effective technique of acquiring

the best quantitative data for characterizing spatial patterns on patch reefs

(Chiappone and Sullivan, 1991).

The repetitive photographic sites can be preformed with a minimum

of three people, including a boat sitter. This is the most labor intensive field method looked at in this study, due to the extensive time required in relocating the repetitive photographic stations. After an extended absence, fouling overgrowth can make the marker tags relocation difficult.

Errors in site diagrams (Appendix II –IV) can also create difficulties in locating markers. The repetitive photographic method could be enhanced

by leaving more of the rod (10 to 15 cm) exposed to expedite the

relocation process and by increasing the number of permanent photographic stations.

Comparing the experiences of collecting field data for both random versus repetitive methods, the random method (with or without the measuring tape) can be done in less time. Locating repetitive photographic stations can be very time consuming. Time could be better spent on gathering more random transects to increase the size of the data base. Increasing the number of transects to at least five and up to twenty per site, according to some literature (Aronson et al., 1994; Nadon and

Stirling, 2006), should increase accuracy, precision, and statistical power

of the data collected. The random method also had the advantage, because

it produced better resolution of small taxa (Bohnsack, 1979; Ohlhorst et

al., 1988), because less area was covered by each photographic image.

Image Analysis

Field data collection can be very expensive and photographic

surveys can save money by decreasing underwater time. After field data

has been collected it must be analyzed, with image analysis being

somewhat time consuming (Vogt, 1995). This study compared percent

coverage by point analysis (random method) and area analysis (repetitive method) and comments on comparative analysis times are noted. Both percent coverage analysis from the raw photographic images were performed on the computer program Coral Point Count with Excel

extensions (CPCe) (Kohler and Gill, 2006).

The random photographic transects were easily analyzed using both

CPCe 3.3 and 3.4. Point analysis is fundamentally identical in both

versions. Although for this study the grid data point method was chosen

to determine percent coverage, these programs also have the ability to

assign points randomly. The random point assigning feature on CPCe would be an excellent way to introduce randomness to a long term study using permanent repetitive photographic stations or adding additional randomness to random photographic line transects.

The repetitive photographic transects analyzed by area are more time consuming and require more computer memory than the point data method used on the random photographic transects. Area analysis appears

50 to over estimate octocoral coverage (Figure 13), and under estimate algae coverage (Figure 15). This could be explained because when a three dimensional surface is projected onto a two dimensional plane, such as a photographic image, overestimation of surface area occurs with objects closer to the lens (octocorals) and underestimates object farthest away from the lens (macroalgae) (Porter and Meier, 1992). This problem is magnified through the use of the 15mm lens on the repetitive method, because short focal length lenses steepen perspective, magnifying the foreground compared to the background (Coute and Green, 1989). It is imperative that all photographic images be taken orthogonal to the substrate (Laxton and Stablum, 1974) in order not to exaggerate this problem further. Small rare coral colonies are often difficult to detect in flat photographic images (Nadon and Stirling, 2006), and this is especially true if the area covered by the image is rather large like the image (4.63 m2 ) taken by the repetitive method. The area measuring feature of CPCe 3.4 is an excellent program and would be very useful in determining changes in coral species coverage or looking at coral disease over time, but it should be done with a narrower angle lens than the 15 mm lens to decrease area covered and eliminate other problems inherent to wide angle lens.

Change Through Time

Comparison of data from the random and repetitive photographic methods used at Rancho Pedro Paila did not give a clear indication if

51 either method was better at detecting change. In order to improve chances of detecting changes in reef fauna, data from both methods were divided by zones, shallow (Tables 23-24 and Figures 17-18), mid (Tables 25-26 and Figures 19-20), and deep (Tables 27-28 and Figures 21-22). Changes in category percent coverage were detected by both photographic methods, but greater differences were noted between methods (Part C of results).

Ecosystems, such as coral reefs, are in a constant state of flux and changes should be expected (Boyce and Haney, 1997). Ohlhorst (1988) stated that intensive sampling of a few small areas may be inappropriate for the study of coral reef populations. Inherited limitations of this study did not allow for a decisive answer to be reached.

Time is a critical issue with any research project and the point analysis method was the less time consuming than the area method.

Analyzing four repetitive photographic images by area took approximately the same amount of time to analyze thirty six images of a random photographic transect by point analysis. The random method, using point analysis, resulted in much larger data sets and was stronger statistically.

Adjacent Comparative Study

Global Vision International (GVI) at Pez Maya has a long term monitoring program located several kilometers south of Rancho Pedro

Paila. Both facilities are located within the Sian Ka’an Biosphere

Reserve. Pez Maya has implemented the Mesoamerican Barrier Reef

System (MBRS) Synoptic Monitoring Programme (SMP) as their

52 monitoring method (Almada-Villela et al., 2003; Woods-Ballard et al.,

2005). One of the main objectives of the MBRS program is to develop and implement a Regional Environmental Monitoring and Information

System (Almada-Villela et al., 2003). Four countries consisting of Belize,

Guatemala, Honduras, and Mexico have adopted the MBRS program as a standard, so regional data may be compared (Almada-Villela et al., 2003).

Percent cover is determined by using a point intercept method, recording every 25 cm. Five replicate transects (30 meter line transects) per site are recorded (Almada-Villela et al., 2003). GVI monitors hard coral at depths of 5 meters, 10 meters, and 20 meters (Woods-Ballard et al., 2005). Pez

Maya data, in (Table 29), on hard corals coincides nicely with the data on hard corals obtained in this study by the random method in 2005 (Figure

2).

Table 29. Percent hard coral cover in Pez Maya from January to March of 2004 and 2005 (Woods-Ballard et al., 2005).

5 meters 10 meters 20 meters Overall 8.03% 11.95% 6.99% 9.23%

The method used by GVI is dependent upon knowledge of personnel and the five-person trained groups who conduct these transects (Woods-

Ballard et al., 2005). Volunteers go through an extensive training program and stay at Pez Maya for six weeks at a time (Woods-Ballard et al., 2005).

The Pez Maya field method requires extensive knowledge of fauna

and divers that can perform these tasks using scuba. Their system also

requires a commitment of approximately six weeks in the field to collect

their data. Reliance on trained volunteers working for six weeks and

living in primitive conditions is a difficult challenge for this program, but

it appears to be generating significant and useful information.

Analysis of this study at RPP, indicates that the random

photographic method using a measuring tape and image analysis through

point analysis gives the best data sets. This is also achieved with the

least amount of field collection time, and larger data sets are gathered in

the same time required to analyze fewer repetitive photographic images.

CONCLUSIONS AND RECOMMENDATIONS

After completing this study and reviewing the Pez Maya’s report,

the author feels that random photographic transects using a meter tape is

the best method examined for monitoring coral reefs. Photographic

images can be rapidly collected using a minimal amount of equipment.

Skills needed to collect data would also be minimal. The research team would only need to know how to dive, understand the correct procedures

for collecting the data, and have knowledge about operating an underwater

camera. Identification and analysis could be done after returning home.

Analysis of random single transects done by students from Texas

A & M-Corpus Christi on the annual Coral Reef Ecology field trip to RPP,

which were excluded in this study, should be done to help develop a better

overall picture of the typical benthic community of Rancho Pedro Paila.

Instead of expanding the number of repetitive photographic stations

at Rancho Pedro Paila, the author would change to repetitive photographic

line transects with meter tapes and increase the number of transects done

yearly. End point markers could rise above the substrate for easier

relocation and equipment needed would be limited to a meter tape and

underwater camera with jig. This would result in images taken over the

same area of the reef annually, and it would increase the amount of data

collected yearly many times over.

The most drastic change would be changing the 35mm lens to a 28

mm lens for the random photographic transects, and to decrease the length

of the jig to approximately 71 cm. The 28 mm lens is a better quality lens

and decreases the closest focusing distance to 0.6 m as compared to 0.8m

with the 35 mm lens (Coute and Green, 1989). Decreasing the jig length

would allow the area of the image to remain at 0.26 m2 ; allowing data

already collected to blend perfectly without having to modify data sets to

compensate for area change. Improved image quality would result from

the camera being closer (decreasing the water column) to the subject,

thereby increasing color and clarity, especially in turbid environments.

Another advantage of changing to the 28 mm lens is to improve quality of images (depth of field), especially between the end of the jig and camera

(Moody and Bates, 2006). Increasing the depth of field is very important in benthic studies, since the topography of coral reefs is varied.

The repetitive photographic stations are a good idea for studying changes of specific features, such as a diseased coral head or to measure growth of a specific coral head, but not the reef in its entirety. The computer program CPCe is excellent at determining area, but the repetitive photographic method may work better if the area covered by the images were not so large. The author would also recommend changing to a jig approximately 71 cm in length and using a 28 mm lens on the repetitive method for all the same reasons as mentioned previously for the random-repetitive stations. Instead of having two separate jigs and camera setups, modification of both jigs to a single system used for both methods seems to be most advantageous. Simplicity is advantageous in any field study, but especially in remote and difficult conditions that can happen when doing field work on coral reefs.

Digital cameras and underwater housings technology has been introduced in recent years and an examination of this new format should be conducted. Use of digital cameras would be beneficial because images could be examined for quality before leaving the field. Also the number of images taken per transect would not be limited by length of film and multiple transects could be taken using the same camera and jig, instead of having to carry multiple photographic setups. A concern with using the

56 new digital format is the method by which standardization of image area could be achieved.

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APPENDIXES

Appendix I. Coordinates of monitoring sites at Rancho Pedro Paila within the Sian Ka’an Biosphere Reserve, Quintana Roo, Mexico.

RPP Patch reef site N 20˚02.658’, W 87˚28.270’.

RPP Shallow reef site N 20˚02.613’, W 87˚27.985’.

RPP Mid reef site N 20˚02.729’, W 87˚27.658’.

RPP Deep reef site N 20˚02.783’, W 87˚27.528’.

Appendix II. Diagram of shallow reef repetitive photographic stations at Rancho Pedro Paila.

Appendix III. Diagram of mid-reef repetitive photographic stations at Rancho Pedro Paila.

Appendix IV. Diagram of deep reef repetitive photographic stations at Rancho Pedro Paila.

Appendix V. Photographic jigs used in this study at Rancho Pedro Paila (adapted from Reed 2003).

A. Jig used for 2001 Random transects

B. Jig used for 2005 Random transects

C. Jig used for all Repetitive transects

Appendix VI. Coral species list for random transects from Rancho Pedro Paila for 2001 and 2005 (Wood, 1983; Veron, 2000a; Veron, 2000b; Veron, 2000c).

Class Hydrozoa Owen, 1843 Order Hydrocorallina Family Milliporidae (Fleming, 1828) Millipora alcicornis (Linnaeus, 1758) Millipora complanata (Lamarack, 1816) Class Anthozoa Order Scleractinia (Bourne, 1900) Family Acroporidae (Verril, 1902) Acropora cervicornis (Lamarck, 1816) Acropora palmata (Lamarck, 1816) Family Agariciidae (Gray, 1847) Agaricia agaricites (Linnaeus, 1758) Agaricia fragilis (Dana, 1848) Agaricia humilis (Verrill, 1901) Agaricia lamarcki (Milne Edwards and Haime, 1851) Agaricia tenuifolia (Dana, 1848) Family Astrocoeniidae (Koby, 1890) Madracis decactis (Lyman, 1859) Madracis mirabilis (Lyman, 1859) Stephanocoenia intersepts (Lamarck, 1816) Stephanocoenia michelinii (Milne Edwards and Haime, 1848) Family Faviidae (Gregory, 1900) Colpophyllia natans (Houttuyn, 1772) Diploria clivosa (Ellis and Solander, 1786) Diploria labyrinthiformis (Linnaeus, 1758) Diploria strigosa (Dana, 1848) Manicina areolata (Linnaeus, 1758) Montastraea annularis (Ellis and Solander, 1786) Montastraea carvernosa (Linnaeus, 1766) Montastraea faveolata (Ellis and Solander, 1786) Montastraea franksi (Ellis and Solander, 1786) Solenastrea bournoni (Milne Edwards and Haime, 1849) Family Meandrinidae (Gray, 1847) Dichocoenia stokesi (Milne Edwards and Haime, 1848) Meandrina meandrites (Linnaeus, 1758) Family Mussidae (Ortmann, 1890) Isophyllia sinuosa (Ellis and Solander, 1786) Mussa angulosa (Pallas, 1766) Mycetophyllia aliciae (Wells, 1973) Mycetophyllia ferox (Wells, 1973) Mycetophyllia lamarckiana (Milne Edwards and Haime, 1848) Family Poritidae (Gray, 1842) Porites astreoides (Lamarck, 1816) Porites porites (Pallas, 1766) Family Siderastreidae (Vaughan and Wells, 1943) Siderastrea radians (Pallas, 1766) Siderastrea siderea (Ellis and Solander, 1786)

Appendix VII. Coral species list for repetitive transects at Rancho Pedro Paila in 2001 through 2005 (Wood, 1983; Veron, 2000a; Veron, 2000b; Veron, 2000c).

Class Hydrozoa Owen, 1843 Order Athecatae Family Milleporidae (Fleming, 1828) Millipora alcicornis (Linnaeus, 1758) Millipora complanata (Lamarack, 1816)

Class Anthozoa Order Scleractinia (Bourne, 1900) Family Acroporidae (Verril, 1902) Acropora cervicornis (Lamarck, 1816) Family Agariciidae (Gray, 1847) Agaricia humilis (Verrill, 1901) Family Faviidae (Gregory, 1900) Diploria clivosa (Ellis and Solander, 1786) Diploria labyrinthiformis (Linnaeus, 1758) Diploria strigosa (Dana, 1848) Montastraea annularis (Ellis and Solander, 1786) Montastraea carvernosa (Linnaeus, 1766) Family Meandrinidae (Gray, 1847) Dichocoenia stokesi (Milne Edwards and Haime, 1848) Meandrina meandrites (Linnaeus, 1758) Family Mussidae (Ortmann, 1890) Isophyllia sinuosa (Ellis and Solander, 1786) Mycetophyllia lamarckiana (Milne Edwards and Haime, 1848) Family Poritidae (Gray, 1842) Porites astreoides (Lamarck, 1816) Porites porites (Pallas, 1766) Family Siderastreidae (Vaughan and Wells, 1943) Siderastrea siderea (Ellis and Solander, 1786)

Appendix VIII. Summary of Random transects analyzed for this study from Rancho Pedro Paila for 2001 and 2005.

transect Random transects ID # images analyzed # points analyzed per image Patch 2001 P1B1 34 1666 P1F1 35 1715 P1M1 34 1666 Total 103 5047

Patch 2005 5033 38 1832 5034 35 1715 5037 37 1813 Total 110 5360

Shallow 2001 S1M1 34 1666 S1N1 34 1666 S1S1 35 1715 Total 103 5047

Shallow 2005 5035 36 1764 5036 30 1470 5039 35 1715 Total 101 4949

Mid 2001 1 35 1715 afa 37 1811 afb 34 1616 Total 106 5142

Mid 2005 5044 27 1321 5045 29 1421 5046 26 1274 Total 82 4016

Deep 2001 afa 34 1665 afb 32 1568 Total 66 3233

Deep 2005 5040 30 1450 5041 35 1715 5042 35 1715 5043 32 1421 Total 132 6301

Transect ID Column: Christopher Ledford (Ledford, 2003) used a letter/number sequence to differentiate between image transects. (P) = Patch and (S) = Shallow. Addie Reed (Reed, 2003) used 1, afa, and afb to denote separate photographic image transects. All 2005 image transects were assigned a four digit number by the development company and this assigned number was used to identify each transect.

Appendix IX. Summary table of Rancho Pedro Paila images available for analysis of repetitive stations for repetitive transects from 2002 to 2005.

Zone Year Station ID 2002 2003 2004 2005 Shallow 31 N/A YES YES YES 32 N/A YES YES YES 33 N/A YES YES YES 34 N/A YES YES YES Mid 41 N/A YES YES YES 42 YES YES YES YES 43 YES YES YES YES 44 YES YES YES YES Deep 51 YES YES YES YES 52 YES YES YES N/A 53 YES YES YES YES 54 YES YES YES YES