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Additional file 1: Taxa list for the mixed prokaryote dataset.
Additional file 4: Taxa list for the gammaproteobacterial dataset II.
Additional file 6: Taxa list for the mixed eukaryotic dataset.
Additional file 2: Taxa list for the proteobacterial dataset.
Additional file 5: Taxa list for the fungi dataset.
From the above 106 taxa list, we selected 75 taxa, including 10 octocorals and 20 hexacorals, to build several codon alignments.
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An entire book could be written describing each and every point supporting the homologies of each muscle of each paired appendage of each of the three taxa listed on those tables.
The raw data of this analysis, i.e. taxa lists and abundances, are given in the Additional file 1.
To test the transferability of these newly designed microsatellite primers, two individuals of other 13 native taxa listed in Table 1, specifically 8 endemic species, were sampled from the field.
The 2006 to 2008 taxa lists and their abundance [22] were entered into the SPEAR web calculator (http://www.systemecology.eu/SPEAR/index.php, accessed 7 June 2010), whereas the 2014 macroinvertebrate data were analysed using the SPEAR calculator v0.9.0 (http://www.systemecology.eu/spearcalc/, accessed 6 November 2015, using family-level taxa, default traits and no recovery areas).
Alignments of DNA sequences were done using mafft v6.708b [47] for the taxa listed in Table S2.
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