Porities+lutea

// Porites lutea // (Figure 1) is hard coral from the family Poritidae that can be easily found around the tropical reefs of the world. They are practically impossible to identify without close examination but has been categorised under “large boulder-shaped (massive) colonies” for the ease of fulfilling public interests [1].
 * Introduction **


 * [[image:Fig 1 porites sp18, 21.jpg width="1038" height="397"]] ||
 * Figure 1. //Porites lutea// found in Cyrene Reef, Singapore. A shows a specimen submerged in shallow waters, while B shows a specimen half exposed and also with a strange shape. ||

**Distribution ** //__Habitat __// It occurs commonly with other //Porites// species, growing on the back of reef margins, fringing reefs and lagoons [2]. It is also common to see them appear near shore during low tide, they are known to survive short durations of exposure [1, 2, 3].

//__Local Distribution __// Locally, it can be found easily along remaining coral reefs and along shores during low tide. A few notable areas where it can be found includes Raffles Lighthouse, Pulau Semakau, Pulau Jong, Sisters Island, Pulau Hantu, St. John’s Island, Kusu Island and Cyrene Reefs (Map 1) [3, 4]. Additionally, unconfirmed sightings also possibly place these species along the northern shores [1].

media type="custom" key="29435561" Map 1.

//__World Distribution __// The coral inhabits reefs across the tropics, stretching from the Red Sea, Western Indian Ocean to the French Polynesian Islands [2, 5].

**Biology **

**Coral anatomy **
Basic coral anatomy can be seen in Figure 2. Most of the identifying features of the genus //Porites// can be seen from the calice. Key differences between species is from septa arrangements, presence and structure of paliform lobes (or pali) and structure of the columella. These are important key words that will be used throughout parts dealing with morphology.



Figure 2. General anatomy of hard corals, showing both skeletal features and polyp features. http://coral.biota.biodiv.tw/book/export/html/403

The general structure and coral anatomy can be seen from Figure 2. The massive structure we usually see, as observed from Figure 1, are mostly made up of the skeleton. The living part of the coral is usually only at the surface which contains the polyp.

**Feeding **
<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Corals feed using two ways, as seen in Video 1. The main method with which they feed and get most of their energy from is through a symbiotic relationship with <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">zooxanthellae [6, 7]. The corals provide a home and shelter these zooxanthellae, whom in return, provide glucose, glycerol and amino acids through photosynthesis for the coral [6, 7]. The coral uses these to produce proteins, fats, carbohydrates and calcium carbonates which form the skeleton [8, 9, 10, 11, 12].

media type="youtube" key="tZuxZdG6TfM" width="560" height="315" Video 1. Feeding process of corals. (Copyright © 2015 Khaled bin Sultan Living Oceans Foundation)

<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">The second method is through food capture using their tentacles which has nematocysts [6, 7]. This usually occurs at night. Nematocysts are cells that contain a secretory organelle containing toxins which is used for prey capture and defence [13], they are able to fire upon contact and pierce through soft tissue [13], as seen in Video 2.

media type="youtube" key="IJidAI1WASo" width="560" height="315" Youtube Video 2. Stinging cells of nematocysts in slow motion. (Copyright © 2014 Smart Everyday)

**<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Reproduction **
<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Corals are able to reproduce both asexually and sexually. Asexual reproduction occurs through the budding of a colonial polyps from the parent polyps [12]. This usually occurs only after the main colony or parent polyp grows to a certain size, after which, it is a continual process throughout the polyp’s life [9].

<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">For stony corals or hard corals, most are broadcast spawners, like //P. lutea//. This means they release a large number of sperm and eggs into the water to spread their young over broad areas [2]. They then form free-floating larvae known as planulae. This mass spawning is timed using environmental triggers such as lunar cues for short-term control, and temperature, day length and/or temperature change for long-term control [2, 9]. The mass spawning can be seen in Video 3.

media type="youtube" key="nbpH99AFtNM" width="560" height="315" Video 3. Mass spawning of corals. (Copyright © 2017 Ocean Today)

**<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Taxonomy **

**<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Morphological Taxonomy **
//__<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Description __//<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">(//Based off samples collected// [4]) <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Colonies hemispherical or helmet-shaped and large (Figure 1). Surface smooth and brown. Corallites small (1-1.5mm) with no coenosteum. All had the distinctive shorter dorsal directive and triplets fused to form trident (Figure 3.1, 3.2). Walls short but form a ridge like structure that forms a clear distinction between corallites, not present for all.

//__<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Holotype __//<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">: MNHM (Paris), Z. 191a
 * [[image:Porites lutea corallties.jpg]] || [[image:Calice.png]] ||
 * <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Figure 3.1. Image showing the identifying features of //P. lutea// using morphological differences in the calice. || <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Figure 3.2. Image showing an actual calice of //P. lutea//. A points towards the distinctively shorter dorsal directive/septum, while B shows the fused triplets forming a trident shape. ||

//__<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Original diagnosis & translation __// //__<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Diagnosis __//<span style="font-family: 'Times New Roman',serif; font-size: 12pt;"> [4] <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Colonies massive and form hemispherical shape that grow to 2m. The surface smooth with irregular humps across the colony. At coral edge, thick ledges seen forming, usually indicating end of living coral. Calices small (1.5mm) and shallow (Figure 3.2). Calices thin walls and perforated, walls grow out to form ridge structures that clearly divide corallites. Dorsal directive shorter than the rest and the ventral directive fuses to form trident (Figure 3.2). Fused ventral directive that forms a trident may not be seen throughout coralla and only forms at ends of septa. Five distinct pali, dorsal directive lacks one, the triplets form one and lateral pairs each have one. Columella weakly developed and absent in some, columella forms star shape connecting to 5 pali (Figure 3.2). Two synapticular rings observed, one outer and other palar.
 * [[image:original description.png width="786" height="258"]] || Polypier in convex and gibbous mass, with polygonal calices a little unequal, broad of 1 millimeter or 1 millimeter 1/2, very shallow, with distinct and distinct edges. In general, twelve poorly thin partitions, alternately a little unequal, very distinct from the pali. These are a little salient, usually five or six, very rarely more; and in the much narrowed central space which they leave between them, one sometimes notices a small, very small columella point. ||
 * <span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Figure 4. Original description from Edwards & Haime [14] || Translated using Google translator ||

**<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Phylogeny **
<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Kitano et al. [15] recent paper was the only attempt at looking to the phylogeny of Poritidae (Figure 4). The paper reveal interesting relationships between several genera of corals, including several taxonomical shifts [16, 17]. Even with all this new finding, however, support for species delimitation is not clear [15]. A major recent shift is the transfer of the genus //Alveopora// to Acroporidae [16]. Though morphologically, there were subtle differences between //Alveopora// and the other genera of Poritidae, particularly septal fusion present in //Porites// and //Goniopora// [5], the distinction on a genetic level was what led to its shift [17].

//<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Porites lutea //<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">is settled very strongly within the genus as seen in Figure 4, though a few new members were added in [15, 16]. It remains, however, that species identification is still heavily depended on morphological features [2, 5, 15, 16, 17]. <span style="font-family: Times New Roman,serif; font-size: 12pt;">Kitano et al. original figure description: Molecular phylogenetic relationships of the family Poritidae and related families based on mitochondrial COI sequences. Numbers on/below main branches show bootstrap values (.50%) in ML and NJ analyses, and Bayesian posterior probability (.0.8). Stars show specimens collected from the western Indian Ocean, and triangles show ones collected from Malacca Strait. Sample codes or accession numbers are shown after species names (see Table 1, Table S3). Grey in colour for Alveopora, green for Porites, purple for Stylaraea, blue for ‘Poritipora’, and orange for ‘Machadoporites’. Goniopora is shown by bars in black. Bernardpora is shown by the bar in red. doi:10.1371/journal.pone.0098406.g004 ||
 * [[image:taxo4254/Taxo tree.png width="1025" height="1362"]] ||
 * <span style="font-family: Times New Roman,serif; font-size: 12pt;">Figure 4. Phylogeny tree from Kitano et al. [15], //P. lutea// is underlined and pointed out in red.

<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Kitano et al. [15] phylogeny tree was made under the following methods:

<span style="font-family: 'Times New Roman',serif; font-size: 12pt;">Electropherograms and DNA sequences were checked and edited using Sequencher (Gene Code Co.) and SeeView 4.3.0. DNA sequences were aligned with MAFFT 7 using the L-INS-i option. Then, all sites with indels and several sites with alignment ambiguities were excluded manually from the subsequent analyses. Two aligned DNA datasets (COI and ITS) used in this study are shown in the supplementary information (Datasets S1, S2). Pairwise genetic distances were calculated as p-distance using MEGA 4.0.2. Phylogenetic trees were reconstructed by neighbour-joining (NJ) and maximum likelihood (ML). For NJ, PAUP* 4.0b10 was used to infer the topologies for both COI and the ITS markers using Kimura 2-parameter model and to conduct bootstrap analysis (1000 replicates). For ML, we assumed a model of nucleotide evolution obtained by using the Akaike Information Criterion (AIC) as implemented in MrModeltest 2.2. The most appropriate models of nucleotide evolution were TrN with invariant (I) and gamma (G) parameters (TrN+I+G) for the COI marker, and TrNef +I+G for ITS marker. PAUP* was used to reconstruct a best ML tree using a heuristic search and the tree-bisection-reconnection branch swapping method. GARLI (Genetic Algorithm for Rapid Likelihood Inference) 0.951 was preferred to PAUP* for the bootstrap estimation as the former is less time-consuming. Using GARLI, optimal ML topologies were searched with default setting using the models selected by MrModeltest (TrN+I+G for COI, TrNef +I+G for ITS) and bootstrap analyses (500 replicates) were conducted for each marker. MrBayes 3.2.2 was also used to conduct Bayesian analyses under the same models. Four parallel chains of 1–46106 generations were run for each marker. Trees were sampled every 100 generations, and the initial 25% of the total trees as burn-in were discarded. The remaining trees were pooled to produce a 50% majority rule consensus tree. The average standard deviation of split frequencies after 46106 generations was 0.002069 for COI, and ones after 2.46106 generations was 0.009967 for ITS.

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<span style="display: block; height: 1px; left: 0px; overflow: hidden; position: absolute; top: 386px; width: 1px;"> <span style="color: #212121; font-family: inherit,serif; font-size: 12pt;">Polypier in convex and gibbous mass, with polygonal calys a little unequal, broad of 1 millimeter or 1 millimeter 1/2, very shallow, with distinct and distinct edges. In general, twelve poorly thin partitions, alternately a little unequal, very distinct from the palis. These are a little salient, usually five or six, very rarely more; and in the very narrowed central space which they leave between them, one sometimes notices a small, very small columellar point. <span style="display: block; height: 1px; left: 0px; overflow: hidden; position: absolute; top: 1220.5px; width: 1px;">Polypier en masse convexe et gibbeuse, à calices polygonaux un peu inégaux, larges de 1 millimètre ou 1 millimètre 1/2, très peu profonds, à bords rninces et distincts. En général, douze cloisons médiocrement minces, alternativement un peu inégales, très distinctes des palis. Ceuxci sont un peu saillants, ordinairement au nombre de cinq ou six, très rarement plus; et, dans l'espace central très rétréci qu'ils laissent entre eux , on remarque quelquefois une petite pointe columellaire très grêle.” (Edwards & Haime, 1851: p 28)