Table 1.
List of dinoflagellate strains used in this study and whether sxtA1 and sxtA4 were PCR amplified.
Table 2.
Primers designed specifically for this study: Annealing site is an approximation and can vary slightly between species; Prorocentrum minimum was used as a reference.
Figure 1.
Phylogenetic tree of dinoflagellates inferred from rDNA.
Concatenated phylogeny, inferred from 18S+5.8S+28S rDNA (2900 characters). The tree is reconstructed with Bayesian inference (MrBayes). Numbers on the internal nodes represent posterior probability and bootstrap values (>50%) for MrBayes and RAxML (ordered; MrBayes/RAxML). Black circles indicate a posterior probability value of 1.00 and bootstrap >90%. N. scintilans is represented with a dashed branch as this taxon was excluded from the inference; alternatively its most “probable” placement was determined from a parallel Bayesian analysis. * Denotes taxa sequences generated from this study. See Table S2 for a full listing of accessions used.
Figure 2.
Phylogenetic tree of dinoflagellates inferred from rDNA and nuclear protein genes.
Concatenated phylogeny, inferred from 18S+5.8S+28S+actin+beta-tubulin+hsp90 (5626 characters). The tree is reconstructed with Bayesian inference (MrBayes). Numbers on the internal nodes represent posterior probability and bootstrap values (>50%) for MrBayes and RAxML (ordered; MrBayes/RAxML). Black circles indicate a posterior probability value of 1.00 and bootstrap >90%. N. scintilans is represented with a dashed branch as this taxon was excluded from the inference; alternatively its most “probable” placement was determined from a parallel Bayesian analysis. * Denotes taxa sequences generated from this study. See Table S2 for a full listing of accessions used. Non-ribosomal gene presence for each taxon is represented in brackets behind each species name (a: actin, b: beta-tubulin, h: hsp90).
Figure 3.
Phylogenetic tree of dinoflagellates inferred from rDNA, mitochondrial and nuclear protein genes.
Concatenated phylogeny, inferred from 18S+5.8S+28S+cob+cox1+actin+beta-tubulin+hsp90 (7138 characters). The tree is reconstructed with Bayesian inference (MrBayes). Numbers on the internal nodes represent posterior probability and bootstrap values (>50%) for MrBayes and RAxML (ordered; MrBayes/RAxML). Black circles indicate a posterior probability value of 1.00 and bootstrap >90%. N. scintilans is represented with a dashed branch as this taxon was excluded from the inference; alternatively its most “probable” placement was determined from a parallel Bayesian analysis. The cytochrome genes cob and cox1 for H. triquetra were excluded from the inference, a parallel phylogeny including these genes for this taxon can be seen in Figure S1. * Denotes taxa sequences generated from this study. See Table S2 for a full listing of accessions used. Red font indicates sxtA presence and blue font indicates no sxtA detection. Non-ribosomal gene presence for each taxon is represented in brackets behind each species name (a: actin, b: beta-tubulin, c1: cox1, cb: cob, h: hsp90). The phylogenetic support for the thecate/athecate split is highlighted with bold type.
Figure 4.
Phylogenetic tree of dinoflagellates inferred from rDNA, mitochondrial and nuclear protein genes (reduced phylogeny).
Concatenated phylogeny, inferred from 18S+5.8S+28S+cob+cox1+actin+beta-tubulin+hsp90 (7138 characters). This phylogeny was inferred excluding taxa with only rDNA signal; done to evaluate effects of missing characters and taxon sampling on the inference shown in Fig. 3. The tree is reconstructed with Bayesian inference (MrBayes). Numbers on the internal nodes represent posterior probability and bootstrap values (>50%) for MrBayes and RAxML (ordered; MrBayes/RAxML). Black circles indicate a posterior probability value of 1.00 and bootstrap >90%. N. scintilans is represented with a dashed branch as this taxon was excluded from the inference; alternatively its most “probable” placement was determined from a parallel Bayesian analysis. The cytochrome genes cob and cox1 for H. triquetra were excluded from the inference. * Denotes taxa sequences generated from this study. See Table S2 for a full listing of accessions used. Red font indicates sxtA presence and blue font indicates no sxtA detection. Non-ribosomal gene presence for each taxon is represented in brackets behind each species name (a: actin, b: beta-tubulin, c1: cox1, cb: cob, h: hsp90). The phylogenetic support for the thecate/athecate split is highlighted with bold type.
Table 3.
Comparison of the phylogenetic support (Posterior probability and bootstrap) received for the dinoflagellate orders, major lineages, clades and nodes in the inferences of Fig. 1, 2, 3, 4 (ordered; MrBayes/RAxML).