Marine Pollution Bulletin 114 (2017) 1135–1140 Contents lists available at ScienceDirect Marine Pollution Bulletin journal homepage: www.elsevier.com/locate/marpolbul Baseline Coral benchmarks in the center of biodiversity W.Y. Licuanan a,b,⁎, R. Robles a, M. Dygico c, A. Songco d, R. van Woesik e a Br. Alfred Shields FSC Ocean Research Center, De La Salle University Manila, Philippines Biology Department, De La Salle University Manila, Philippines c World Wide Fund of Nature – Philippines, Puerto Princesa City, Palawan, Philippines d Tubbataha Management Ofﬁce, Puerto Princesa City, Palawan, Philippines e Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA b a r t i c l e i n f o Article history: Received 18 July 2016 Received in revised form 22 September 2016 Accepted 5 October 2016 Available online 19 October 2016 Keywords: Benchmarks Hard coral cover Generic diversity Philippines Hierarchical sampling a b s t r a c t There is an urgent need to quantify coral reef benchmarks that assess changes and recovery rates through time and serve as goals for management. Yet, few studies have identiﬁed benchmarks for hard coral cover and diversity in the center of marine diversity. In this study, we estimated coral cover and generic diversity benchmarks on the Tubbataha reefs, the largest and best-enforced no-take marine protected area in the Philippines. The shallow (2–6 m) reef slopes of Tubbataha were monitored annually, from 2012 to 2015, using hierarchical sampling. Mean coral cover was 34% (σ ± 1.7) and generic diversity was 18 (σ ± 0.9) per 75 m by 25 m station. The southeastern leeward slopes supported on average 56% coral cover, whereas the northeastern windward slopes supported 30%, and the western slopes supported 18% coral cover. Generic diversity was more spatially homogeneous than coral cover. © 2016 Elsevier Ltd. All rights reserved. Coral reefs are important to many tropical countries because they support ﬁsheries and tourism (Mumby et al., 2004), and protect shorelines from storm waves (Ferrario et al., 2014). Unfortunately, coral reefs are declining at an alarming rate, with an estimated 75% of global reefs under threat from local human pollution, and most reefs under threat from climate-change-induced thermal stress (Burke et al., 2011). Already, approximately 19% of the world's coral reefs have been effectively lost, and another 15% may be lost in the next 10–20 years (Wilkinson, 2008). Even the iconic and well-managed Great Barrier Reef has lost half of its coral cover from 1998 to 2012 (De'ath et al., 2012; but see also Sweatman et al., 2011; Hughes et al., 2011; Osborne et al., 2011). Without corals, coral reefs will lose the major framework builders, along with the architectural complexity needed to support ﬁshes and other reef-associated organisms (Graham et al., 2006), and will lose their capacity to grow and keep up with sea-level rise (van Woesik and Done, 1997; Perry et al., 2013). Benchmarks for common metrics, such as hard coral cover and diversity, are needed to assess the well-being of reef systems, and to determine management efﬁcacy. Such benchmarks can: (i) provide insights into background variability across reefs through time (Murdoch and Aronson, 1999), (ii) determine what levels of change can be effectively ignored, and (iii) suggest what levels of change are indicative of signiﬁcant departures from normal states. Such knowledge can be used to determine expected rates of recovery for different coral ⁎ Corresponding author. E-mail address: firstname.lastname@example.org (W.Y. Licuanan). http://dx.doi.org/10.1016/j.marpolbul.2016.10.017 0025-326X/© 2016 Elsevier Ltd. All rights reserved. reef habitats (van Woesik, 2013), and used to improve the detectability of adverse effects of different human activities. Information on the variability of these metrics, across habitats, reefs, and regions, may even help reﬁne appropriate scales of management for various human impacts. This knowledge could also provide a basis for evaluating the sensitivity of various assessment methodologies, and determine the adequacy of sampling designs used in describing and monitoring coral reefs. The aim of the present study is to provide new benchmarks for coral cover and generic diversity (i.e., number of coral genera) using data from the Tubbataha Reefs Natural Park, the largest and bestenforced no-take marine protected area in the Philippines (Dygico et al., 2013). Strict enforcement has been in place at Tubbataha since 2001. The marine park is located in the Sulu Sea, which has been considered among the most diverse regions of the Coral Triangle, which itself is the center of global marine diversity (Veron et al., 2009; Sanciangco et al., 2013). Annual monitoring of the Tubbataha reefs (Fig. 1) followed a hierarchical sampling design (Green et al., 2011). The hierarchical levels were transects nested within stations, which were nested within study sites. Two sites each were established in the north and south atolls of the Tubbataha reefs. The sites were 6–28 km apart, and each site supported two stations about 250–600 m apart (electronic supplementary material). Five 50-m transect lines were randomly placed within each station. Each station was approximately 25 m × 75 m, and was located at 2–6 m depth. The transects were re-randomized for every sampling period (following Green et al., 2011). Monitoring involved photographing sections of the reef beneath each transect line, at 1-m intervals, using a 1136 W.Y. Licuanan et al. / Marine Pollution Bulletin 114 (2017) 1135–1140 Fig. 1. Map of the Tubbataha Reefs Natural Park showing the study stations monitored. digital camera mounted on aluminum monopods. The camera was contained in Ikelite® underwater housing, ﬁtted with an Inon wide angle (100o ﬁeld of view) lens to allow each photograph to cover one square meter of reef. Digital images from 160 transects, sampled from 2012–2015 were processed in the laboratory using Coral Point Count with Excel extensions (CPCe; Kohler and Gil, 2006). Ten points were randomly placed on every 1 × 1 m digital image, and the corals under each point were identiﬁed to genus. Some genera were also identiﬁed to growth form, therefore in this paper taxa are occasionally referred to as Taxonomic Amalgamation Units (electronic supplementary material). A two-level analysis of variance using repeated measures (ANOVAR) was used to examine the changes in percentage coral cover and generic diversity that occurred across sites and through time. Post-hoc Tukey tests were performed to specify which years and which sites signiﬁcantly differed from each other. A two-level nested analysis of variance (ANOVA) was also applied to both coral cover and generic diversity data, collected in 2015, to compare the means and variances across sites and stations. The program R (R Core Team, 2015), version 3.1.0, was used to perform the ANOVAR and ANOVA tests. Power analysis for a one-sample t-test (Zar, 2010; p. 117) was used to compute the minimum detectable change in coral cover, and to compute the change in generic diversity through time at the station, site, and location levels. The alpha and beta values were arbitrarily set at 5% and 20%, respectively. From 2012 to 2015, the average coral cover and average generic diversity on the Tubbataha reefs were 34% (σ ± 1.7) and 18 (σ ± 0.9), respectively. Site 2, along the western slope, had the lowest coral cover at 18% (σ ± 5.3) and the lowest number of genera (15, σ ± 1.9), whereas Site 3, on the southeastern slope, had the highest coral cover at 56% (σ ± 4.1) (Fig. 2). Site 1, on the northeastern windward slope, supported the highest number of genera at 20 (σ ± 0.5) (Fig. 3). At the station level, coral cover ranged from 14% to 57%, and the average number of genera ranged from 15 to 22. From 2012 to 2015, there were no signiﬁcant changes in hard coral cover (location level ANOVAR, p = 0.484) (Table 1), and no signiﬁcant changes in number of genera (location level ANOVAR, p = 0.299) on the Tubbataha reefs (Table 1; Fig. 2). There were also no signiﬁcant changes in coral cover and generic diversity at the site level (p = 0.31 for hard coral cover, and p = 0.67 for generic diversity) (Fig. 3). Coral cover was unchanged despite two thermal stress events — one in 2013, and the other in 2015 (Fig. 4). The power analysis indicated that annual changes in coral cover as small as 3% were detectable at the location level (Table 2), suggesting that the current sampling protocol is adequate at Tubbataha reefs to detect changes in coral cover, should any changes occur. However, the minimum detectable change was approximately 7% cover at the site level, and 9% at the station level (Table 2). Sampling for the number of genera also appeared adequate, at least at the location level. The power analysis indicated that changes as small as two genera were detectable at the location level, and changes of three genera were detectable at the site and station levels (Table 2). There were highly signiﬁcant differences in coral cover across sites, but only marginally signiﬁcant differences in coral cover among stations (Table 3, Fig. 2). Indeed, the greatest variance in coral cover was apparent among sites (10 km), at 71%, with only 9% variance in coral cover among stations (Fig. 5). There were no signiﬁcant differences in the number of genera among sites and among stations (Table 3, Fig. 3), although most of the variance in the number of genera was apparent among stations (25%), rather than among sites (13%) (Fig. 5). Ship groundings, typhoons, and thermal stress events disturbed the reef slopes of Tubbataha during the four-year study period, yet the coral assemblages appeared resilient. In 2013, two ship groundings were monitored, one grounding occurred 1 km from Station 4A. From 2012 to 2015, ﬁve tropical storms passed within 350 km of the monitored reefs. In 2013, one severe tropical storm passed within 40 km of the reefs, and typhoon Haiyan, the strongest typhoon ever to hit land, was a Category 3 typhoon when it passed within 350 km of Tubbataha reefs. In addition, two thermal stress events, one in 2013 and the other in 2015 (Fig. 4), had no detectable effect on coral cover and diversity, even though 2014 and 2015 were respectively the second warmest and warmest years on record, globally (NOAA, 2015). Acroporids and pocilloporids, known for their thermal sensitivity (Marshall and Baird, 2000; Loya et al., 2001; van Woesik et al., 2011, Furby et al., 2013), remained among the most common genera on Tubbataha through the study period (electronic supplementary material). Examination of past data sets suggest no measureable changes have occurred to the Tubbataha reefs since the declines associated with the 1998-thermal stress event, from which the reef recovered rapidly (Ledesma and Mejia, 2002; Dygico et al., 2013). Statistical power of these earlier monitoring studies, however, was limited (unpublished data), even though the researchers surveyed some of the same stations used in the present study. W.Y. Licuanan et al. / Marine Pollution Bulletin 114 (2017) 1135–1140 1137 Fig. 2. Box and whiskers plot of coral cover for all Tubbataha stations monitored from 2012 to 2015. Plotted values are the median, the lower and upper quartiles (25% and 75%), and the minimum and maximum values (denoted by the whiskers). Fig. 3. Box and whiskers plot of generic diversity for all Tubbataha stations monitored from 2012 to 2015. Plotted values are the median, the lower and upper quartiles (25% and 75%), and the minimum and maximum values (denoted by the whiskers). Despite the lack of measureable change, Tubbataha had high spatial variability in both coral cover and number of coral genera. There was greatest variance among sites (10 km), than among transects (0.01 km) and stations (0.5 km) (Fig. 5). These results suggest that the reefs were broadly similar among habitats (0.5 km), but were patchy (0.01 km) within those habitats. The considerable spatial differences Table 1 Repeated measures ANOVA table for coral cover and generic diversity from 2012–2015, where p is the probability. Variable Source Degrees of freedom Sum of Squares Mean Square Coral cover YEAR SITE:YEAR Residuals YEAR SITE:YEAR Residuals 3 9 12 3 9 12 67.2 311.6 309.1 17.61 28.72 51.50 22.40 34.62 25.76 5.871 2.191 4.291 Generic diversity F-value p NF 0.870 1.344 0.484 0.310 1.368 0.744 0.299 0.666 in coral cover across sites is primarily a consequence of the culmination of differences in exposure to waves, currents, and light (Done, 1982; Storlazzi et al., 2005; DeVantier et al., 2006). In contrast, only 13% of the total variability in generic diversity was due to differences among sites, whereas 25% of the variability was due to differences among stations, and 62% was due to differences among transects (Fig. 5). This spatial pattern was consistent over time, except for a slight shift in variability in the number of genera from the site level to the transect level in 2013. Such spatial variability is expected when transects are re-randomized within stations every survey period (Green et al., 2011). The variability in coral cover, and especially the variability in number of genera among transects was likely because of small differences in (i) depth proﬁles, (ii) monospeciﬁc stands of Isopora brueggemanni, and (iii) the natural heterogeneity of reefs (Aronson and Precht, 1995; Storlazzi et al., 2005). The consistency in the number of genera across sites suggests that the corals in the different habitats were drawn from the same larval pool (Done et al., 1991; Melbourne-Thomas et al., 2011). 1138 W.Y. Licuanan et al. / Marine Pollution Bulletin 114 (2017) 1135–1140 Fig. 4. Tubbataha sea surface temperature (SST) (°C) and degree heating weeks (DHW) data from January 2011 to January 2016 (data from NOAA Coral Reef Watch). The average coral cover on the Tubbataha reefs was higher than that currently found elsewhere in the Philippines, although coral cover was comparable to other well-managed reefs in the central Philippines (Stockwell et al., 2009), and on the relatively pristine reefs at Kingman and Palmyra atolls (Sandin et al., 2008). In particular, coral cover averaged around 24% for 79 reef sites that are part of an ongoing nationwide assessment in the Philippines (DM Licuanan personal communication). This estimate was derived using ﬁeld methods identical to that of the present work, following a stratiﬁed (by biogeographic zone) random sampling scheme. In comparison, Magdaong et al. (2014) reported a higher average coral cover of ~36% at 317 sites surveyed from 1981 to 2010 in the Philippines. The discrepancies between these two Philippine averages are potentially a consequence of: (i) the use of different methods, (ii) sampling at different depths, (iii) biases involved with sampling in protected areas. The same authors found coral cover was 5.8% higher in the protected areas in the Philippines than outside the protected areas. In addition, estimates of coral cover from Tubbataha are comparable with the 22% (95% conﬁdence intervals of 21% and 23%) coral cover reported in 2003 from 390 sites in the Indo-Paciﬁc (Bruno and Selig, 2007), and the 33% (± 0.6 SE) coral cover reported from 1996–2003 from 963 sites in the Indo-Paciﬁc (Bruno et al., 2009). Yet, Bruno and Selig (2007) estimated that coral cover in the Indo-Paciﬁc is at least 20% lower than the best estimates of historical Table 2 Minimum detectable changes in coral cover (delta in absolute percent coral cover) and generic diversity (number of TAUs) using power analysis at various hierarchical levels based on power analysis of 2012–2015 data; alpha = 5%, beta = 20%. Coral cover Location Site Station Tubbataha Site 1 Site 2 Site 3 Site 4 S1 A S1 B S2 A S2 B S3 A S3 B S4 A S4 B baselines. Thus, any new baseline proposed for coral cover can be already considered as ‘shifted’. The low levels of terrigenous inﬂuences and the open ocean setting produce coral assemblages on atolls, such as Tubbataha, that are different from assemblages on fringing reefs. For example, Acropora tends to be more common on offshore reefs than on nearshore fringing reefs (Licuanan et al., 2002; DeVantier et al., 2006). Monospeciﬁc stands of branching and corymbose Acropora frequently lead to high coral cover, but low generic diversity, on Tubbataha. Therefore, the benchmark for generic diversity may be on average lower on Tubbataha than elsewhere in the Philippines. This contrast is evident when comparing the work by Huang et al. (2014, 2016), who showed high diversities (398 coral species) in northern Palawan, and in western Luzon (433 coral species), with work by van Woesik (1996), who reported 260 coral species on Tubbataha. Note that the diversity presented in the present study are derived from quantitative sampling, within set areas (75 m × 25 m stations), and should not be directly compared with systematic searches for species over large extents of reef. The Tubbataha reefs are relatively undisturbed by local human populations, and are as close to pristine as is possible, for a modern reef in Asia (Nañola et al., 2011). Moreover, the reefs are under a high level of management, and are protected from ﬁshing pressure. Considering the diversity, and the high threat levels to Philippine reefs in general (Burke et al., 2011), coral cover on Tubbataha can serve as a useful benchmark for what is currently possible in the region. The relative geographic remoteness and high conservation status of Tubbataha also appear to provide relatively high resilience to regional stresses, at least for now, although a rapidly warming ocean will test that resilience. Generic diversity Variance Delta Variance Delta 2.8 8.01 28.2 16.91 10.01 6.71 18.46 16.72 64.04 78.05 15.96 25.94 3.39 3% 5% 9% 7% 6% 5% 8% 7% 14% 15% 7% 9% 4% 0.73 0.26 3.62 1.91 1.93 2.47 0.36 4.68 13.26 0.87 6.67 3.21 1.1 2 1 4 3 3 3 1 4 7 2 5 3 2 Table 3 Two-level nested ANOVA table for coral cover and generic diversity in 2015, where p is the probability. Variable Source Degrees of freedom Sum of Squares Mean Square F-Value p NF Coral Cover SITE STATION(SITE) Error Total SITE STATION(SITE) Error Total 3 4 32 39 3 4 32 39 6568 1051 2990 10,609 26.8 69.2 253.6 349.6 2189.4 262.8 93.4 23.43 2.81 b0.0001 0.0416 8.933 17.3 7.925 1.13 2.18 0.3527 0.0933 Generic Diversity W.Y. Licuanan et al. / Marine Pollution Bulletin 114 (2017) 1135–1140 1139 Fig. 5. Percentage variance in coral cover and in generic diversity per level of sampling, from 2012 to 2015. Acknowledgments We thank the editor and the anonymous reviewer for comments and suggestions that greatly improved the manuscript. This work was partially supported by the Department of Science and Technology and the respective organizations of the authors. Appendix A. Supplementary data Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.marpolbul.2016.10.017. References Aronson, R.B., Precht, W.F., 1995. 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