Indices used to express rarity and diversity of habitats and fishes.

<p>Hk is the Shannon-Weaver index of entity k.</p><p>Ni and Nj : Number of stations where the corresponding fish/habitat is absent.</p><p>Ai: Abundance of fish specie i.</p><p>Atot: Total abundance of all species.</p><p>Sj: Surface of habitat j.</p><p>Stot: Total surface of all habitats.</p

Criteria used to characterize habitats in this study.

<p>The first six characterizations consider only one criterion at time. The five last use various combinations of the six criteria.</p

Discrepancies between habitat surface areas present on the area and habitat surface areas sampled.

<p>The figure displays a specific example, considering a 250 m neighborhood size and a characterization of habitats based on medium geomorphology. On the x-axis, habitats are ranked from the least (on the left) to the most (on the right) represented on the overall map. Some well represented habitats on the overall map (e.g. habitats “14” and “15”) appear under-sampled.</p

Characteristics of fish sampling stations.

<p>Panel <b>A</b> localizes sampling stations in Port-Bouquet bay in New-Caledonia. Black dots indicate fish census stations. Panel <b>B</b> indicates the number of overlaps between fish census’ 5000 m neighborhoods. For a specific area, the higher the number of overlaps (1 to more than 10), the higher is the bias of habitats’ rarity index. Panels <b>C–H</b> present habitat characterization around fish sampling stations 1, 2 and 3, based upon coarse geomorphology (C), a combination of coarse, medium, and fine geomorphology (D), and a combination of coarse, medium, fine geomorphology, rugosity, and benthic components (D). (F), (G) and (H) show habitats characterizing the three fish census stations when various grains are considered (respectively 250 m, 500 m, and 750 m).</p

Effect of removing stations on SAI results and comparison with all stations results (Wilcoxon’s test).

<p>For all scenario tested (1 to 5 stations randomly removed from the initial dataset) we evaluated the proportion of SAI results significantly different from results obtained with the overall dataset. We also compared mean (SD) of SAI results when all neighborhood sizes and habitat characterizations are confounded.</p

Accumulation curves of two contrasted examples of surrogacy effectiveness. A

<p>shows good surrogacy effectiveness obtained for functional rarity with a characterization of habitats based on medium geomorphology and considering a 500 m neighborhood size; <b>B</b> shows poor surrogacy effectiveness obtained for functional richness with a characterization of habitats based on topography and considering a 5000 m neighborhood size.</p

Map of New Caledonia with sampling sites for microchemistry (yellow circles) and underwater visual censuses (UVC, green circles).

<p>Polygons indicate the different lagoons, remote reefs and islands for which UVC data were collected; numbers indicate the number of UVC transects.</p

Relationship between <i>L. fulviflamma</i> density and mangrove area.

<p>Spearman-rank correlation between standardized mangrove area and density of <i>L. fulviflamma</i> in the different lagoons, reefs and islands of the archipelago of New Caledonia (see map on Fig. 1) is given.</p

PCA biplot of otolith elemental concentrations from mangroves and reefs.

<p>Green and blue dots indicate the 37 fishes collected in mangroves (M) and the 159 fishes collected in reefs (R), respectively. Only concentrations of Rb, Sn and Mn in otoliths were used in the PCA.</p

Results of factorial ANOVA testing for the effect of biotope (d.f = 3), fishing pressure (hereafter “fishing”, d.f. = 2) and their interaction (d.f. = 6) on coral reef benthic and fish communities in New Caledonia.

<p>Only significant effects are reported for clarity, but see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060564#pone.0060564.s001" target="_blank">Appendix S1c</a> for a complete report, including all relationships tested with corresponding post-hoc tests for the effect of fishing pressure. Groups of herbivorous fish are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060564#pone.0060564.s001" target="_blank">Appendix S1a</a>. “****”: <i>P</i><0.001, “***”: <i>P</i><0.005, “**”: <i>P</i><0.01, “*”: <i>P</i><0.05.</p