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Abstract:
We explored the 18S rDNA sequences of Pseudo-nitzschia and its close relatives, together with their individual secondary structure information to reconstruct phylogenies. Forty-eight taxa classified in the Bacillariaceae and Achnanthaceae were analyzed by character-based (maximum parsimony and maximum likelihood) and distance-based (neighbour-joining) methods. Three raphid diatoms from the Eunotiaceae were used as out-groups. The sequence-structure alignment was generated by 4SALE (i.e. a one-letter encoded alignment that contained the individual secondary structure information) and applied to the character-based phylogeny reconstruction. All analyses highly support Pseudo-nitzschia + Fragilariopsis as monophyletic. The Pseudo-nitzschia/Fragilariopsis clade is further divided into three subclades. One clade comprises members in the P. seriata and P. americana complexes and species of Fragilariopsis; the second and third clades constitute members in P. pseudodelicatissima and P. delicatissima complexes. Among all analyses, the distance-based method yielded a more highly resolved phylogenetic framework for the Pseudo-nitzschia/Fragilariopsis clade than did the character-based analyses. Other than those currently known genetic markers, 18S rDNA was also useful in exploring the intrageneric relationships.
ACKNOWLEDGEMENTS
The authors are grateful to Dr Stephen S. Bates (Fisheries and Oceans Canada) for his reviewed comments and English revision. This work was supported by the Malaysian government through the Ministry of Education under JSPS/COMSEA Matching Fund (GA002-2014) and Higher Institution Centre of Excellence Research Grant (IOES-2014C) and by the University of Malaya under UMRP (RU006A/B-2014, RU009B-2015).