Table 1.
Morphological diagnostic characters used to discriminate the 11 species of Oncaeidae present in the Gulf of Naples (*measured using traditional method).
The species investigated in the present work are indicated in bold. List of characters [11]: 1 = body size ≥ 1mm; 2 = body size < 1mm; 3 = exoskeleton moderately chitinised; 4 = exoskeleton heavily chitinised; 5 = leg 4 endopod with distal conical process; 6 = leg 4 endopod without distal conical process; 7 = prosome with conspicuous dorso-posterior projection in lateral view; 8 = prosome without conspicuous dorso-posterior projection in lateral view; 9 = prosome to urosome ratio; 10 = genital double-somite length to width ratio; 11 = anal somite length to width ratio; 12 = caudal ramus length to width ratio.
Table 2.
List of all the sequences used for phylogenetic analyses.
Sequences produced in this study are reported in bold. Species name reported in GenBank entry, voucher number or isolate name and GenBank accession number are reported for each COI, ITS and ITS1 entries. The last nine rows contain information for the COI outgroup sequences.
Fig 1.
COI phylogeny (split frequency σ = 0.002).
Posterior Probability (PP) is reported at each node. Branch colour represents PP; colour code for PP is reported in the figure. Scale bar represents 0.02 substitutions per site. GenBank accession numbers are reported, followed by the genus and species names. If a branch was condensed, the genus and species names are reported followed by the number of sequences contained in each branch. The uncondensed Bayesian tree is reported in S3 Fig. Torquoise and cyan shades indicate the Triconia/Oncaea s. s. clade. The pink shade indicates the Sapphirina clades. The lilac shade indicates outgroups. GoN = Gulf of Naples, i.e. sequences produced in the present work.
Fig 2.
a. ITS1-5.8S-ITS2 (split frequency σ = 0.003) and b. ITS1 (split frequency σ = 0.003) phylogenetic trees reconstructed by Bayesian inference. Posterior Probability (PP) is reported at each node. Thickness of branches represents PP. Scale bar represents 0.2 substitutions per site. The species name and the GenBank identification number of the corresponding sequence are reported. GoN = Gulf of Naples, i.e. sequences produced in the present work.
Table 3.
Length in base pair of the ITS2 regions inferred from secondary structure predictions.
Species reported in bold were produced in the present study.
Fig 3.
CBC analysis of ITS2 secondary structure for: a. Oncaea venusta and O. curta (O. venusta structure shown). b. O. media and O. venusta (O. media structure shown). c. O. mediterranea and O. curta (O. mediterranea structure shown).
Fig 4.
ITS2 stem phylogeny based on Bayesian inference (split frequency σ = 0.002).
Posterior Probability (PP) is reported at each node. Thickness of branches represents PP. Scale bar represents 0.2 substitutions per site. ITS2 secondary structure reconstructions are reported for each species. Full-size pictures of secondary structures are reported in S4 Fig.
Fig 5.
Interannual variability of abundance of a. Oncaea curta and b. Oncaea venusta recorded at LTER-MC. Thin line shows monthly raw-data (individual abundace) over the period 1984–2015; horizontal bold line represents the interannual monthly-averaged abundaces of the species.