Exceptional reefs of Palawan: Anthropogenic extinction, reef refuge areas under climate change, and priority species for conservation

The National Assessment of Coral Reef Environments (NACRE) Program reported that one-third of the reefs in the Philippines declined in the past decade. As human activities and climate change effects intensify, there is still a lack of systematic prioritization of species and reef areas that should be protected to ensure the preservation of coral diversity in the country, particularly in Palawan province which has its richest reefs. The objectives of this study are 1) to identify coral species that are evolutionarily distinct and vulnerable to anthropogenic impacts and climate change that should be prioritized for protection; and 2) to identify reef areas that are possible refuges under the worst climate scenario. This study made use of species richness, phylogenetic diversity, and index of rarity to determine priority species and reef areas in Palawan that are vulnerable to anthropogenic impacts. This study proposes 30 evolutionarily distinct and locally endangered species and 88 globally rare species. These species include the eight IUCN endangered and globally rare species (Cantharellus noumeae, Alveopora minuta, Alveopora excelsa, Porites ornata, Hydnophora bonsai, Pectinia maxima, Anacropora spinosa, and Lobophyllia serrata). El Nido was found to have the highest species richness and phylogenetic diversity, while the Calamianes has the highest index of rarity in the whole of Palawan. Ecological Niche Model (ENM), a machine learning tool, was used to project future potential refugia in Palawan under the stabilized emissions scenario of RCP 4.5 and the high emissions scenario of RCP 8.5. Ecological niche models reveal three range shift patterns: habitat loss, west and east coast shift, and the deeper range shift. The average habitat reduction in Palawan across 75 species is 4% (SD ±17%) in the RCP 8.5 scenario and 3% (SD ±14%) in the RCP 4.5 scenario. At the national level, models trained in Type 1 coral communities of the country exhibit a habitat loss of \u3e 36% under RCP 4.5 and \u3e45% under RCP 8.5. On the other hand, models trained in Type 1 coral communities of Palawan showed an increase of 40% under RCP 4.5 and 87% under RCP 8.5. A Type 1 coral community is one out of seven coral community types in the Philippines. Type 1 coral communities are dominated by Acropora and massive Porites corals on upper reef slopes that face the southwest monsoon. The models show that well-developed coral reefs are potential refuge areas and should be prioritized for protection. Other potential refuge reefs include upwelling sites in the Philippines and the atolls of Cagayancillo and Tubbataha. Palawan reefs and other Type 1 coral communities of the country like those in the Bicol Shelf, Bohol, Visayan Sea, and Tawi-Tawi and the shallow reefs of the Sunda Shelf, which includes Sabah, Malaysia and the Riau Islands, Bangka-Belitung, and North and West Sumatra in Indonesia were found to be the best conditioned and well-adapted reef areas for the worst-case high emissions scenario of future climate

New records of scleractinian coral in the Philippines: Euphyllia paraglabrescens

Euphyllia paraglabrescens Veron, 1990, is one of the eight Euphyllia species and one of the 14 members of the Family Euphyllidae. Veron (2000) reports Tanegashima, Japan as the exclusive biogeographic range of the species and his latest inventory of Philippine corals (Veron and Fenner 2000) did not list its occurrence here. Moreover, it is uncommon in the inshore reefs of Talim Bay, Lian, Batangas, and hence the species is hereby described

Spatial diversity of coral reef communities in Sulu Sea marine corridors

Most protected coral reefs and coral communities in the Philippines are in small fishery reserves chosen for their coral cover and fish biomass, rather than their biodiversity conservation value. In an effort to improve criteria for designing these small reserves, spatial arrangement, particularly patch sizes of the reef benthos, was examined using semivariograms computed from DCA ordination scores of raw data. The data were generated from reef photos taken at one-meter intervals along I 00m transect lines, deployed along depth contours at 27 reef sites in three locations in the Sulu Sea. These locations are along the Cagayan Ridge (including Cagayancillo, and the Tubattaha National Marine Park), and reefs in Balabac Islands, southern Palawan that lie in a strait connecting the Sulu Sea with the South China Sea. Three basic community types were discerned - Type I communities are made up mostly by sand, rubble, and macroalgae as typically encountered in reef flats and backreef areas; Type 2 communities are a mix of different forms of various coral genera (except Acropora); and Type 3 communities are made up mostly of Acropora, either in tabulate or branching form. These community types are typically seen as mosaics, but their relative proportions vary with depth and exposure to monsoon winds, and appear to indicate disturbance history of a site. Type I and Type 3 communities are typically large patches, with the latter at shallow sites, and the former at deep or sheltered ones. Community mosaics dominated by both types have low diversity, but the latter also has the highest coral cover. Type 2 communities, on the other hand, have small mosaic patches and steep species area curves. These are typically found at intermediate depths

CoenoGuides: Scleractinian identification guides

Coeno - Greek koinos, meaning common. The CoenoGuide, a series of electronic (pelf) form identification guides to families under Phylum Cnidaria, Order Scleractinia, are introduced. They are one of the products that will be made available for free in Coenomap (http://coenomap.philreefs.org/), a web site that was designed to encourage and facilitate the identification of coral species and the mapping of their distributions in the Philippines. AH the guides feature many images of the coral species, either of the living coral, or both the Jiving coral and its skeleton. AH guides, initially, are location specific, following J.E.N. Veron\u27s dictum that species boundaries for valid species may blur at larger geographic scales. They will also be family-specific, to keep the file sizes to manageable levels and make them accessible to those with poor internet connections or limited bandwidth. Most authors are also not consistently reliable across families, so users should be able to choose from possible alternative CoenoGuides for a given family. Since the CoenoGuides are electronic, new versions can easily be made and distributed to reflect corrections, taxonomic revisions, and improvements in the images and information contained. More importantly, CoenoGuides can be the vehicle to move coral taxonomy (at least in the Philippines) farther from a slow-changing, expert-based discipline to one that is more dynamic and consensus-based. Where consensus cannot be achieved, alternative schemes may eventually be made available in Coenomap. The schemes that work best will likely be downloaded more than others or will have more favorable comments in associated blogs. Everyone is thus encouraged to collaborate and develop CoenoGuides, or improve existing ones, and be recognized as a contributor or author, and advance coral research and monitoring in the countr

Optimizing DNA extraction and PCR amplification conditions for establishing phylogenetic relationships of bubble corals (family Euphyllidae)

Coral taxonomy traditionally relies on skeletal morphology, a fact, which does not hold true in the case of the family Euphyllidae. Most of the 14 bubble coral species under this family are identified in a far more subjective way of visually inspecting their soft tissue features while in their live form. This creates a number of taxonomic issues within the family which may be resolved with information from both molecular techniques and skeletal features. Phylogenetic relationships among species in the family may be clarified in this initial attempt towards applying molecular tools on bubble coral taxonomy particularly on Euphyllia yaeyamaensis ana Euphy/lia ancora. These were initially preserved and kept in Chaotropic buffer solution (CHAOS) upon collection. Viogene Extraction kJt and primer pairs 15 and 255, ITS4 and A18S, previously identified to deliver considerable results in other molecular studies, were tested on the samples. The cost-efficiency of the Viogene Kit is its major advantage over the Phenol chloroform method, which is less likely to yield DNA products after all the tedious and time-consuming steps. Extraction procedure from the Viogene Kit was specifically modified for coral DNA. Gel electrophoresis showed presence of DNA in all the samples. PCR conditions are currently undergoing several modifications to satisfy the requirements that will produce the desired fragments for sequencing

Morphological and DNA sequence analysis of the Cytochrome oxidase (cox1) of a new record of Acropora in Lian, Batangas and Bolinao, Pangasinan

Colonies of Acropora, first spotted at Talim Bay, Lian, Batangas, is suspected to be a new record for the Philippines. Conventional taxonomic identification of the coral reveals that it may be Acropara abrotanoides or Acropora robusta. The probability of these suggested species was confirmed through DNA sequencing. The mitochondrial control region cytochrome oxidase 1 (cruel) is known to be a very conserved gene region. Amplified sequences of cox1 were analyzed and revealed a 98% to100% likelihood of being Acropora tenuis, a species that is very morphologically di

Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa)

Use of universal primers designed from a public DNA database can accelerate characterization of mitochondrial (mt) genomes for targeted taxa by polymerase chain reaction (PCR) amplification and direct DNA sequencing. This approach can obtain large amounts of mt information for phylogenetic inferences at lower costs and in less time. In this study, 88 primers were designed from 13 published scleractinian mt genomes, and these were tested on Euphyllia ancora, Galaxea fascicularis, Fungiacyathus stephanus, Porites okinawensis, Goniopora columna, Tubastraea coccinea, Pavona venosa, Oulastrea crispata, and Polycyathus sp., representing 7 families of complex and robust corals. Seventy-four of the 88 primers (84.1%) successfully amplified completed mt genomes of these 9 corals. Several unique features were identified, including a group I intron insertion in the cytochrome oxidase subunit I (COI) genes of Por. okinawensis, Gon. columna, T. coccinea, and F. stephanus and an extended length of the 3'-end of the COI gene of E. ancora. Preliminary tests using a subset of primers successfully obtained the COI 3'-end of Euphyllia representatives, and the resulting species phylogeny is in agreement with corallite characters and tentacle shapes. The universal primers provided herein effectively decoded scleractinian mt genomes, and can be used to reveal different levels of molecular phylogenetic inferences in scleractinian corals

Initial findings of the nationwide assessment of Philippine coral reefs

The Philippine archipelago is well known for its species-rich coral reefs, yet updated information on the present status of its coral reefs at the national level is lacking. Hence, a nationwide assessment was initiated in 2014 to update the information on the status of coral reefs in the Philippines. Reefs sampled were randomly selected from around the country, with the number of assessment stations for each of six biogeographic regions stratified by the total area of reefs in each of these regions. Five 50 m transects were randomly deployed in each assessment station. The initial data gathered from 2015 up to 2017 included a total of 166 stations (108 in Luzon, 31 in Visayas, and 27 in Mindanao), sampled across 31 provinces. None of these stations were classified in the excellent category based on live coral cover, and more than 90% of the same stations were in the poor and fair categories. Their average hard coral cover, weighted by the reef area of each biogeographic zone, was 22% (95% confidence intervals: 19.4, 24.9). These values indicate a marked decline in the condition of local reefs over the last four decades, thereby revealing the urgent need for the revision and update of conservation and management policies. © 2017, Science and Technology Information Institute. All rights reserved

Resurrecting a subgenus to genus: Molecular phylogeny of Euphyllia and Fimbriaphyllia (order Scleractinia; family Euphyllidae; clade V)

Background. The corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among scleractinian genera, the Euphyllia, with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution. Multiple genetic markers were used to construct the phylogeny of six Euphyllia species, namely E. ancora, E. divisa, E. glabrescens, E. paraancora, E. paradivisa, and E. yaeyamaensis. The phylogeny guided the inferences on the contributions of the colony structure, polyp morphology, and life history traits to the systematics of the largest genus in Euphyllidae (clade V) and, by extension, to the rest of clade V. Results. Analyses of cytochrome oxidase 1 (cox1), cytochrome b (cytb), and β- tubulin genes of 36 colonies representing Euphyllia and a confamilial species, Galaxea fascicularis, reveal two distinct groups in the Euphyllia that originated from different ancestors. Euphyllia glabrescens formed a separate group. Euphyllia ancora, E. divisa, E. paraancora, E. paradivisa, and E. yaeyamaensis clustered together and diverged from the same ancestor as G. fascicularis. The 30-end of the cox1 gene of Euphyllia was able to distinguish morphospecies. Discussion. Species of Euphyllia were traditionally classified into two subgenera, Euphyllia and Fimbriaphyllia, which represented a dichotomy on colony structure. The paraphyletic groups retained the original members of the subgenera providing a strong basis for recognizing Fimbriaphyllia as a genus. However, colony structure was found to be a convergent trait between Euphyllia and Fimbriaphyllia, while polyp shape and length, sexuality, and reproductive mode defined the dichotomy better. Species in a genus are distinguished by combining polyp morphology and colony form. The cluster of E. glabrescens of the Euphyllia group is a hermaphroditic brooder with long, tubular tentacles with knob-like tips, and a phaceloid colony structure. The Fimbriaphyllia group, with F. paraancora, F. paradivisa, F. ancora, F. divisa, and F. yaeyamaensis, are gonochoric broadcast spawners with short polyps, mixed types of tentacle shapes, and a phaceloid or flabello-meandroid skeleton. Soft-tissue morphology of G. fascicularis and Ctenella chagius were found to be consistent with the dichotomy. Conclusions. The paraphyly of the original members of the previous subgenera justify recognizing Fimbriaphyllia as a genus. The integrated approach demonstrates that combining polyp features, reproductive traits, and skeletal morphology is of high systematic value not just to Euphyllia and Fimbriaphyllia but also to clade V; thus, laying the groundwork for resolving the phylogeny of clade V. © 2017 Luzon et al

Nuclear and mtDNA genes suggest polyphyletic origin of species in the genus Euphyllidae

Veron (2000) devised a scheme to identify species in the family Euphyllidae that deviates from the traditional approach to coral taxonomy. For this family, soft tissue features were defined to be more crucial than corallum features in species identification. Polyp morphology, however, may not be sufficient to distinguish species particularly because the problem is further confounded by the occurrence of natural hybrids within this group. In this work, the phylogeny of the genus Euphyllia, the largest genus under the family Euphyllidae, was examined together with Nemenzophyllia turbida and Catalaphyllia jardinei. Nuclear and mitochondrial markers, particularly beta-tubulin and cytochrome oxidase 1 in Euphyllia species divide the genus into two distinct groups suggesting that the genus is polyphyletic. Neighbor-joining trees drawn with Kimura 2 parameter of 500 replicates clusters Euphyllia paradivisa and Euphyllia glabrescens together and separate from Euphyllia paraancora, E.paraglabrescens, E.ancora, and E divisa. Nemenzophyllia turbida and Catalaphyllia jardinei individually separates from the two Euphyllia clusters and the outgroup Galaxeafascicularis. These results suggest other characters are needed to resolve the species, at least, of Euphyllia and that revision of the family may be required