Principal Coordinates Analysis (PCoA) carried out on the 70 species using standardized functional distances.

<p>The 15 dominant species are represented by circles of sizes that are proportional to their mean relative biomass when they occur. Their percentages of occurrence over the 810 samples are given in parentheses. The other 55 species are plotted with grey crosses. Codes for dominant species names are: Af = <i>Ariopsis felis</i>, Ar = <i>Archosargus rhomboidalis</i>, Bc = <i>Bairdiella chrysoura</i>, Bm = <i>Bagre marinus</i>, Br = <i>Bairdiella ronchus</i>, Ca = <i>Cynoscion arenarius</i>, Cf = <i>Chaetodipteurs faber</i>, Cm = <i>Cathorops melanopus</i>, Cn = <i>Cynoscion nothus</i>, Ma = <i>Menticirrhus americanus</i>, Mu = <i>Micropogonias undulatus</i>, Po = <i>Polydactylus octonemus</i>, Sl = <i>Stellifer lanceolatus</i>, Sp = <i>Symphurus plagiusa</i>, St = <i>Sphoeroides testudineus</i>. Bold names are for species belonging to the sea-catfishes group (a group on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040679#pone-0040679-g006" target="_blank">Figure 6</a>) while names underlined or in italics correspond to species from the two sciaenid groups (respectively b and d groups on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040679#pone-0040679-g006" target="_blank">Figure 6</a>). The center part of the PCoA plane is blown up in the top left corner.</p

Appendix B. Computation of the functional diversity indices.

Computation of the functional diversity indices

Location of the study area and of the 37 sampled stations (UTM coordinates).

<p>Location of the study area and of the 37 sampled stations (UTM coordinates).</p

Taxonomic and functional diversity at local and regional scale.

<p>Local (mean α) and regional (γ) components are expressed as equivalent number of species (mean±SD), of taxonomic (circles) and functional (squares) diversities computed on community composition (white) or abundance structure (black) for temporal and spatial strata. The grey triangles represent species richness.</p

Statistics obtained under the four null-models (Figure 2) for the taxonomic <i>ß_TA</i> and functional <i>ß</i>-diversity indices (<i>ß_FC</i> and <i>ß_FA</i>).

<p>Values represent the percentage of strata in which p-values indicate that the observed <i>ß</i>-diversity is significantly lower (−), not significantly (ns) different and significantly higher (+) than expected under the corresponding null hypothesis.</p

Supplement 1. R script for computation of functional diversity and functional specialization indices.

<h2>File List</h2><blockquote> <p><a href="FDind.R">FDind.R</a> -- R source code for indices computation </p> </blockquote><h2>Description</h2><blockquote> <p>The FDind.R R program computes the 3 functional diversity indices presented in Villéger et al. 2008 (Ecology 89:2290–2301), and the functional specialization index proposed by Bellwood et al. 2006 (Proc. R. Soc. B. 273:101–107). </p> <p>Computation requires R libraries « ape » and « geometry » and two matrices as inputs:</p> <ul> <li> <p>« traits » (S*T): T traits values for the S species (at least 2 quantitative continuous traits, i.e., numeric values)</p> </li> <li> <p>« abundances » (C*S) : abundances for the S species in C communities (NA allowed)</p> </li> </ul> <p>The function returns a dataframe (C*5) with Species richness (Nbsp), functional richness (FRic), functional evenness (FEve), functional divergence (FDiv) and functional specialization (FSpe) values for each of the C communities. </p> <p>A basic example is provided at the end of the script.</p> <p>Details on indices computation are presented in <a href="appendix-B.htm">Appendix B</a>.</p> </blockquote

Appendix C. Summary of data analysis and randomization procedure.

Summary of data analysis and randomization procedure

Appendix D. Dominant fish species in the northern part of the Terminos lagoon.

Dominant fish species in the northern part of the Terminos lagoon

Appendix A. Functional characterization of fishes.

Functional characterization of fishes

Taxonomic and functional <i>ß</i>-diversity.

<p>Taxonomic (circles) and functional (squares) <i>ß</i>-diversity values, based on community composition (white) or abundance structure (black), for the two scales of interest (mean±SE).</p