Data sources and historical analyses.

<div><p>a) Number of papers (each quadrat is one document) per decade on the coralligenous assemblages of Mesco Reef, according to the year of publication.</p> <p>Grey quadrats represent descriptive ‘natural history’ reports (including species lists and/or environmental information); black quadrats represent studies based on quantitative (cover) data. b) Change with time in the occurrence of a number of selected species mentioned in both qualitative and quantitative studies on the coralligenous assemblages of Mesco Reef. In the lower panel, continuous lines indicate the presumed persistence of a species, with thicker lines representing an increase in abundance or frequency and thinner lines a decrease, as perceived by the different authors. In the upper panel, diamonds represent the cumulative numbers of perceived changes, while the smoothed line indicates the general trend with time.</p></div

Study area.

<p>a) Geographical setting in the Ligurian Sea. b) Three-dimensional reconstruction of the Mesco Reef based on multibeam data from Regione Liguria. c) Bathymetric map of Mesco Reef, with study sites (capital letters).</p

Decision flow-chart for implementing EBM and choosing effective monitoring design in coastal zones to be protected.

<p>White boxes: steps required for ecosystem based evaluation of relevant pressures; grey boxes: policy consequences of ecosystem-based analysis.</p

Quantitative historical analysis.

<p>a) Kite diagrams of the change in cover over time (as estimated from photoquadrats) of four categories of species: winners, losers, commuters, constants (see text). b) Average (± se) Euclidean distance among photoquadrats and their coefficient of variability from 1961 to 2008.</p

Ordination plot on the first three axes (Roman numerals) from Correspondence Analysis of the cover data matrix for the coralligenous assemblages of Mesco Reef, from 1961 to 2008.

<p>The upper left panel depicts the plot of all species points (crosses) and photoquadrat points (dots) to show the overall geometry of the ordination model. Details for each site are illustrated separately for the sake of clarity in the subsequent five panels, clockwise: trajectory and species of the assemblage at site B; trajectory and species of the assemblage at site C; trajectory and species of the assemblage at site D; trajectory and species of the assemblage at site F; trajectory and species of the assemblage at site I; position in 1961 and species of the assemblage at site P; trajectory and species of the assemblage at site S. Codes refer to the name of the species as showed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118581#pone.0118581.t001" target="_blank">Table 1</a>.</p

Cover of three dimensional categories for each sites in 1993 (white) and 2008 (grey).

<p><b>a</b>): high; <b>b</b>) medium-high; <b>c</b>) medium; <b>d</b>) medium-low; <b>e</b>) low. Note that scales on Y axis are different. The vertical dotted line separates the sampling sites within the MPA (black characters) from those outside (grey characters).</p

Data sources and historical analyses.

<div><p>a) Number of papers (each quadrat is one document) per decade on the coralligenous assemblages of Mesco Reef, according to the year of publication.</p> <p>Grey quadrats represent descriptive ‘natural history’ reports (including species lists and/or environmental information); black quadrats represent studies based on quantitative (cover) data. b) Change with time in the occurrence of a number of selected species mentioned in both qualitative and quantitative studies on the coralligenous assemblages of Mesco Reef. In the lower panel, continuous lines indicate the presumed persistence of a species, with thicker lines representing an increase in abundance or frequency and thinner lines a decrease, as perceived by the different authors. In the upper panel, diamonds represent the cumulative numbers of perceived changes, while the smoothed line indicates the general trend with time.</p></div

Change in reef community at Portofino, in the vicinity of sampling site J: a) <i>Sargassum vulgare</i> and <i>Dictyopteris polypodioides</i> canopy in 1981; b) <i>Sarpa salpa</i> grazing in a turf-dominated environment in 2009.

<p>Change in reef community at Portofino, in the vicinity of sampling site J: a) <i>Sargassum vulgare</i> and <i>Dictyopteris polypodioides</i> canopy in 1981; b) <i>Sarpa salpa</i> grazing in a turf-dominated environment in 2009.</p

Total list of the species found in the photoquadrats, ordered according to their codes as used in Fig. 5, and their time trend. A ‘winner’ is a species whose cover has increased between 1961 and 2008, vice versa for a ‘loser’; a ‘commuter’ showed a change in the 1990s, while for a ‘constant’ species little or no change in cover was observed.

<p>Total list of the species found in the photoquadrats, ordered according to their codes as used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118581#pone.0118581.g005" target="_blank">Fig. 5</a>, and their time trend. A ‘winner’ is a species whose cover has increased between 1961 and 2008, vice versa for a ‘loser’; a ‘commuter’ showed a change in the 1990s, while for a ‘constant’ species little or no change in cover was observed.</p

Results of PERMANOVA analyses on individual taxa and three-dimensional categories.

<p>Bold numbers indicate significant results.</p