Table 1.
Species and sample data, along with Genbank accession numbers, of ITS2 and16S rRNAs gene sequences (Genbank accession numbers of COI and28S rRNA sequences are reported in Figure S1 and S2, respectively).
Figure 1.
ITS2 secondary structure models for Ostreidae, Gryphaeidae and Pteridae.
(A) ITS2 secondary structure model for Ostreidae showing the typical four domain folding (exemplified in the type-species Ostrea edulis). DI–IV, stem-loops domains. Conserved sequences are boxed, see text for definition. (B) secondary structure models of Domain I and II. Conserved sequences are boxed with different colors indicating differences among taxa. See text for explanation. Acronyms are: Cgi, Crassostrea gigas; Cvi, Crassostrea virginica; Hhy, Hyotissa hyotis; Oed, Ostrea edulis; Pma, Pinctada imbricate; Ssc, Saccostrea scyphophilla.
Figure 2.
Phylogeny of the Ostreidae derived from mitochondrial 16S rRNA and COI, and nuclear ITS2 rRNA and 28S rRNA gene sequence datasets using Hyotissa hyotis and Neopycnodonte cochlear (Gryphaeidae) as outgroup.
(A–B) Maximum-Likelihood phylogenetic trees based on the 16S rRNA (A) and ITS2 rRNA (B) gene fragments. Above the nodes are reported bootstrap values (BP) ≥70 of the Maximum-Likelihood phylogenetic analyses based on primary sequence (ML) and on sequence-structure alignments (MLseq-str) (BPML/BPMLseq-str); below the nodes are reported Bayesian posterior probabilities values (BPP) ≥0.9 of the Bayesian phylogenetic analyses. See Table 1 for details on sequence used and acronyms (BA). (C–D) Bayesian phylogenetic trees based on the 16S+COI (C) and ITS2+28S (D) combined sequence datasets. Above the nodes are reported BPP values ≥0.9 of the Bayesian analyses; below the nodes are reported BP≥70 of the Maximum-Likelihood analyses. See Table 1 and Figure S1 and S2 for details on sequence used and acronyms.
Figure 3.
Phylogenetic and systematic relationships of the Ostreidae species derived from Bayesian and Maximum-likelihood analyses combining 16S rRNA, COI, ITS2 rRNA, and 28S rRNA gene sequence datasets using Hyotissa hyotis and Neopycnodonte cochlear (Gryphaeidae) as outgroup.
(A) Bayesian tree based on the concatenated analysis of the gene sequence datasets with Bayesian posterior probabilities (BPP) ≥0.9 reported above the nodes. Below the nodes are reported the BPP ≥0.9 of the Bayesian analyses performed implementing a multi-species coalescent model in the *BEAST software. (B) Maximum-likelihood tree based on the concatenated analysis of the gene sequence datasets with bootstrap values ≥70 reported in correspondence of the nodes.