<i>Echinometra</i> Bayesian inference phylogenetic reconstruction tree.

<p>Consensus tree of 170,000 trees (after burn-in) generated by MCMC analysis of 20 million generations. 544 bp long COI fragments of 189 <i>Echinometra</i> specimens were used in the analysis. 181 sequences were generated in the current study corresponding to five <i>Echinometra</i> species, and a novel <i>Echinometra</i> mitochondrial lineage. Sequences downloaded from GenBank represent the eight known species of <i>Echinometra</i> and are denoted <i>E</i>. sp. A, <i>E. mathaei</i>, <i>E</i>. sp. C and <i>E. oblonga</i>, <i>E. insularis</i>, <i>E. lucunter</i>, <i>E. viridis</i> and <i>E. vanbrunti</i> (accession numbers: AY262861, AY262940, AY262932, AY262886, AY262906; AF255471, AF255530 and AF255526, from Landry et al. [4] and McCartney et al. [7], respectively). <i>Heliocidaris crassispina</i> (Echinodermata, Echinoidea) (GenBank accession number: JN716400) was used as outgroup. The supporting > 50% values of 1,000 bootstrap replications of the ML analysis and the posterior probabilities of the BI analysis are shown above nodes respectively. Clades A-H are discussed in the text. </p

Spicule types of <i>Echinometra</i>.

<p>(A) Needle spicules in gonads of <i>E</i>. sp. EE. (B) Triradiate and 'figure-eight' shaped spicules in gonads of <i>E</i>. sp. C. (C) Triradiate spicules in tube feet of <i>E. oblonga</i>. (D) Bihamate spicules in tube feet of EE. Scale bars indicate 100 µm.</p

Collection sites of <i>Echinometra</i> specimens.

<p>(A) Map of the Indian Ocean and Eastern Pacific. Dots mark the three sampling sites: Okinawa, Zanzibar and Eilat. Detailed view of study sites: (B) Sesoko Isl., Okinawa, (C) Zanzibar, Western Indian Ocean, and (D) Eilat, Gulf of Aqaba/Eilat. Dots mark collection sites, scale bars indicate 1 km. Ca, Ba, Cu, Ki, Ja, Po, Mn, and Nu denote Changuu, Bawe, Chumbe, Kizimkazi, Jambiani, Pongwe, Mnemba and Nungwi, respectively. Ei and Ok denote Eilat and Okinawa, respectively.</p

Number of newly-infected corals (NICs).

<p>The red dots represent the number of NICs observed in the field along the studied year. The grey dots represent the median number of NICs as predicted by generating infections according to the SIS epidemic model based on <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004151#pcbi.1004151.e002" target="_blank">Eq 2</a> (see text), and the grey bars represent their 95% confidence interval.</p

Profile likelihood function <i>M</i>(<i>α</i>).

<p>The function is maximized at </p><p></p><p></p><p><mi>α</mi><mo>^</mo></p><p></p><p></p> = 1.9, giving the estimate of parameter <i>α</i>. The insert shows a close up of the 95% CI of <i>α</i> (represented by the red horizontal line).<p></p

Simulated future projections of the local coral community spanning 80 years.

<p>The future projections in panels <b>A</b>, <b>B</b> and <b>C</b> rely on the demographic scenario of constant influx of recruits (64 recruits per year). Panels <b>D</b>, <b>E</b> and <b>F</b> rely on the scenario of free-space regulation of recruitment (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004151#sec016" target="_blank">Material and Methods</a>). Panels <b>A</b> and <b>D</b> are based on the SST time-series measured between June 2006 and May 2007 recurrently from year to year in the corresponding months. Based on this time-series, we generate future projections by adding 0.5°C (panels <b>B</b> and <b>E</b>) and 1°C (panels <b>C</b> and <b>F</b>) to the SST of each month. In these simulations we allow each new recruit to settle randomly anywhere on the 10×10 m plane. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004151#pcbi.1004151.s004" target="_blank">S4 Fig</a> demonstrates robustness of these patterns under mild parameter variations.</p

Coral colonies from the genus Favia infected with WPD (white-plague disease).

<p><b>A</b>) Initiation of WPD—a thin zone of bleached tissue grading into exposed coral skeleton. <b>B</b>) A sharp boundary between apparently healthy tissue (‘H’) and freshly exposed skeleton (‘S’), with no build-up of microorganisms or necrotic tissue visible to the eye. With time, the exposed skeleton becomes colonized by algae (‘A’). <b>C</b>) An aggregation of corals infected with WPD.</p

part0

This data package contains all images and point annotations used in the present publication. To access the data download all parts, and then merge using the following command in a linux shell: cat data_package* > merged_data.zip. Then unzip the archive to access the data

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