Additional file 1: of Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

Table S1. Geographic distribution of the 106 haplotypes of C. aestuarii recorded at the 22 sampling sites within the Mediterranean Sea. (DOCX 44 kb

Case 3 of Table 1.

<p>This situation is a mix of case 1 and case 2. A taxonomic decision would simply lead to case 2, where supplementary data about the tempo of diversification would then be required (see text).</p

Case 1 of Table 1.

<p>A set of species is paraphyletic (blue) with a taxonomic entity embedded within (purple) it that is restricted to the area of reference (red circle): A simple taxonomic decision could fulfill the two criteria of monophyly and endemicity. Indeed the taxonomic decision would render the whole set of species monophyletic (purple becomes blue).</p

Protocol to use the five criteria of Eastman and McCune [17] to detect and evaluate species flocks.

<p>The first three criteria (3 K) are the species diversity (« speciosity ») of the taxonomic component, its level of endemicity, and its monophyly. The two other criteria (2 K) are habitat dominance (in biomass) and ecological diversity. The modulation loop means that the geographical range and the taxonomic rank may have to be redefined in order to discover unsuspected flocks.</p

Case 2 of Table 1.

<p>The set of species under focus is monophyletic but contains an internal subpart that is secondarily « exported » outside the area of reference (red circle). See text for discussion.</p

Three situations for the taxon of reference (columns) are to be considered: it is monophyletic, paraphyletic or polyphyletic.

<p>There are also three situations to consider for the components of this taxon in the given area of reference (lines): monophyletic, paraphyletic or polyphyletic. To explain the table, we consider again the example of the non-notothenioid fish family Liparidae. It is monophyletic as a family (first column), however its components of the Antarctic shelf are polyphyletic because they are each related to Arctic liparids (bottom line). So the Antarctic liparid situation is the bottom left cell. Case 2 (when a taxon originating in the area of reference secondarily “exports” a part of its descent outside this area, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068787#pone-0068787-g004" target="_blank">Fig. 4</a>) is discussed in the text.</p