Figure 1.
Phylogenetic relationships within the cnidarian Class Anthozoa according to the “naked corals” (nc) hypothesis (modified from [24]).
Table 1.
Mitochondrial genome sequence data included in the present analyses
Figure 2.
Nucleotide (upper) and amino acid (lower) content of the protein coding genes in the mitochondrial genomes of hexacorallians.
The data shown are averages across the “Robust” corals (n = 14), basal and “Complex” corals (n = 17), corallimorpharians (n = 12) and other hexacorallians (n = 4).
Table 2.
Compositional biases of the mitochondrial genomes of the anthozoan Orders included in the present analysis.
Figure 3.
Phylogenetic analyses based on (a) the nucleotide sequences of the mitochondrial genes encoding proteins and (b) the amino acid sequences of the proteins encoded by the mitochondrial genomes.
Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses. Dashed lines indicate the corallimorpharian clade. Light grey blocks identify the scleractinian clades. (I) Octocorallia used as outgroup; (II) Actiniaria; (III) Zoanthidea; (IV) Antipatharia; (V) Corallimorpharia; (VI) “Basal” Scleractinia; (VII) “Robust” Scleractinia; (VIII) “Complex” Scleractinia.
Figure 4.
Codon-based phylogenetic analyses inferred using CodonPhyml – Yap et al. model [52] for Maximum Likelihood – and MrBayes – GTR substitution model and three categories of non-synonymous/synonymous ratios (M3 model).
Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses.
Table 3.
Comparison of the two competing topologies (scleractinian monophyly, SM, and “naked coral”, NC) using the Approximately Unbiased (AU), Kishino-Hasegawa (KH) and Shimodaira-Hasegawa (SH) tests for a variety of tree reconstruction methods.
Figure 5.
Phylogenetic analyses of the mitochondrial sequences encoding stable RNAs (12S rRNA, 16S rRNA, trnM, and trnW).
Values on the nodes indicate the non-parametric SH test and bootstrap replicates (ML), and posterior probability (BI) support respectively. Where no values are shown on a node, that edge was fully supported under all analyses. Large boxes indicate the Corallimorpharia (dark-gray) and Scleractinia (light-gray) clades. Note that deep-water azooxanthellate species (Corallimorphus profundus and Gardineria hawaiiensis) represent the earliest diverging branches for Corallimorpharia and Scleractinia respectively.
Figure 6.
Codon usage in hexacorallian anthozoans.
CodonW [73] was used to estimate codon usage biases; default settings were used in calculation of the codon adaptation index. NC: effective codon number. CAI: codon adaptation index. Colour coding and taxon choice is as shown in Figure 2.
Table 4.
Posterior probability of the topologies recovered by different models using Phylobayes (SM: scleractinian monophyly, NC: naked coral).