Phylogenetic analyses of <i>Mnemiopsis leidyi</i>.

<p>Phylogenetic and network relationship between the 17 haplotypes identified in the alignment of COI (A) Neighbor joining phylogenetic tree based on nucleotide divergence calculated using Tamura-Nei model. (B) Network relationships among haplotypes for native and introduced populations, inferred by statistical parsimony. Pie charts correspond to sampled haplotypes described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081067#pone-0081067-g001" target="_blank">Figure 1</a>. The size of the charts corresponds to the frequency of the haplotype among all samples. Black circles indicate missing haplotypes and each line represents a single mutation step. Colours show different locations for recovered haplotypes: green: native region, blue: Northern Europe, red: Ponto-Caspian region, and yellow: Mediterranean Sea.</p

Conceptual model of the functioning of <i>Posidonia oceanica</i> seagrass ecosystem.

<p>For functional compartments and box numbers, see text. Primary producers are in green; filter-feeders, suspension-feeders, litter, detritus feeders, Dissolved Organic Carbon (DOC) and microbial loops are in orange; predators (including herbivores) are in yellow. The width of the arrows roughly represents the importance of the carbon flow. The proper <i>P. oceanica</i> ecosystem is included within the red rectangle. MPO: Multicellular Photosynthetic Organisms. POM: Particulate Organic Matter. From C.F. Boudouresque, unpublished.</p

Robustness of the quality index (EBQI) with regard to the weighting of compartments (boxes).

<p>The 17 sites are arranged from left to right according to their growing EBQI (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098994#pone-0098994-t004" target="_blank">Table 4</a>) and ecological status (bad through high). Deep red = bad, orange = poor, green = moderate, light blue = good, deep blue = high. In order to test the effect of the weighting of the compartments (boxes) on the EBQI (robustness), weighting values have been randomly perturbed (above, ±1; below, ±2). 1000 iterations were performed. The change of the ecological status (bad through high) of a site, for a given iteration, is shown by the color of the new class within which it falls.</p

Robustness (index of similarity) of the quality index (EBQI) to the weighting of compartments (boxes).

<p>Percentage of times the ecological status of each site was unaltered by random perturbation of the weighting of the boxes (1,000 iterations) by ±1 through ±4. The similarity is equal to 100% when the class of the site is never changed after perturbation and 0% if it is always changed.</p

Comparison of EBQI with Ecological Quality Ratios (EQRs) based mainly upon <i>P. oceanica</i> (the organism itself) and aimed at establishing the ecological status of the seawater body.

a<p>The metrics of PREI are: shoot density, shoot leaf surface area, ratio between epibiota biomass and leaf biomass, depth of the lower limit and type of this limit <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098994#pone.0098994-Gobert1" target="_blank">[14]</a>.</p>b<p>The metrics of POMI are: shoot density, meadow cover, percentage of plagiotropic rhizomes, shoot leaf surface area, percentage of foliar necrosis, P, N and sucrose content in rhizomes, δ¹⁵N and δ³⁴S isotopic ratio in rhizomes, N content in epiphytes, Cu, Pb and Zn content in rhizomes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098994#pone.0098994-Romero1" target="_blank">[12]</a>.</p>c<p>The metrics of BiPo are: shoot density, shoot leaf surface area, lower depth limit and lower limit type <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098994#pone.0098994-LopezyRoyo1" target="_blank">[15]</a>.</p><p>PREI, POMI and BiPo indices are based upon distinct but similar metrics and range from 0 (lowest ecological status) to 1 (highest ecological status).</p