Predictive model outcomes of impacts on coral cover on atolls.

<p>Four columns represent lagoonal and ocean-facing coral populations of branching and encrusting and massive corals. Models use recruitment values of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036921#pone-0036921-g005" target="_blank">Fig. 5</a>, and size distributions of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036921#pone-0036921-g003" target="_blank">Fig. 3</a> multiplied by matrices of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036921#pone-0036921-g002" target="_blank">Fig. 2</a>. This is the general model that was verified by hindcasting dynamics between 1998 and 2006. First row: trajectory of coral cover under annual recruitment reduction of one percent ( = 50% cumulatively over 50 model years). Thick/dotted lines = scenario without/with recruitment reductions, red dots = final degraded coral cover value after 50 model years. Second row: trajectory of coral cover with/without (thick/dotted lines) recruitment reduction (1% annually cumulative over 50 years) and 75% mortality in non-recruit size classes every eight years. Third row: Synergistic effects of recruitment reduction and repeat mortality of non-recruit size classes (2–5) on coral cover. Color coded value is percent of cover remaining relative to completely undisturbed scenario.</p

Summary of annual recruitment level ( = number of spat) between 1998 and 2006 required to obtain size distributions as observed in 2006, based on model runs.

<p>Matrices show color-coded modal values of number of spat for each year (x-axis) and each depth zone (y-axis). Highest recruitment levels are orange, lowest black. Overall, higher values of recruitment (more orange cells) were predicted for inside the lagoons.</p

Human impacts in coral reef lagoons.

<p>Human impacts in coral reef lagoons.</p

Size distribution of corals in the Chagos.

<p>Branching, encrusting and arborescent corals are pooled, since arboresecent corals only occur in specific environments. Values are based on sums of all measured corals in all transects in each environment. The fifth size-class used in models is spat, which cannot be adequately counted in phototransects.</p

Location of the Chagos archipelago (a) and sampling sites in lagoons an on ocean-facing reefs (b–d).

<p>ADCP current measurements are shown as small insets. Current speed is color-coded (see color bar). Black dots show sampling sites.</p

Mean matrices A (upper row) and corresponding elasticity matrices (lower row) for all three growth forms calculated from 10000 Monte-Carlo trials sampling model life tables in five stages.

<p>Upper row: The 25 entries of the 5×5 matrix are arranged in column-order. Transitions of settled recruits (A_1,1…A_5,1) first, then small corals (A_1,2…A_5,2) and so on. A new size class begins at each multiple of 5 (recruits are at positions 1–5, corals <5 cm at positions 6–10, corals 5–10 cm at positions 10–15, etc). Lower row: Elasticity matrices based on transition matrix including variable recruitment. Expressed as means and standard deviations of all elasticity values obtained by substituting all possible combinations of (1, 10, 100, 1000, 10000) into <b>A</b>_1,4 and <b>A</b>_1,5.</p

Live coverage of branching and encrusting as well as massive growth forms at sample sites on ocean-facing reefs and in lagoons of the Chagos archipelago.

<p>Arborescent forms are included with branching and encrusting forms since they covered significant space mainly in shallow and deep lagoons, but not the other habitats. Error bars are standard deviation.</p

Location of sampling sites in the Red Sea.

<p>Red stars = transect surveys 2006, 2008, 2009; blue crosses = transect surveys 1988, 1989, 1997; green crosses = squares of 1997. Sites in Egypt from the Gulf of Suez to Ras Banas from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-Riegl1" target="_blank">[5]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-Riegl3" target="_blank">[18]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-Riegl5" target="_blank">[20]</a>; Sites in Sudan (purple circles) from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-Mergner1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-Edwards1" target="_blank">[17]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone.0038396-DeVantier2" target="_blank">[26]</a> were used to compare validity of results.</p

(a) Variation of recorded species richness among sites.

<p>(b) Abundance distribution (log) of the 21 most common (>1% of total species occurrences) species encountered in all transects ranked by their relative contribution to total intercept. The species constributing most to total intercept was <i>Porites lutea</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038396#pone-0038396-t001" target="_blank">Table 1</a>). No significant differences (X² = 2.6, df = 15, p>0.25) (c) Size distribution of individual intercepts. No significant differences (X² = 0.14, df = 18, p>0.25).</p

Grouping of transects based on species presence/absence.

<p>All clusters include transects from all geographic locations. Euclidian distance with Ward's method of linkage.</p