The benthic pennate diatom Nitzschia navis-varingica is known to produce domoic acid (DA) and its isomers. The species is widely distributed in the Western Pacific (WP) region. To investigate the genetic differentiation and gene flow patterns among the populations in the WP region, two nuclear-encoded rDNA loci, the large subunit rDNA (LSU rDNA) and the internal transcribed spacer 2 (ITS2), were used to analyze the genetic diversity of 354 strains of N. navis-varingica. The frustule morphological characteristics of N. navis-varingica were examined using transmission electron microscopy (TEM), and the frustule morphometrics of the strains were compared. With sequence divergences of less than 0.9%, the LSU rDNA phylogeny revealed a monophyletic lineage of all strains tested and showed no distinct geographical structuring. Nonetheless, in the ITS2 inferences, eight distinct clades (designated as haplogroups A to H) with moderate to high genetic heterogeneity ranging from 0.5 to 19.7% were identified. Low genetic differentiations among the geographically separated populations (Ф_ST of 0.48) were observed, which suggested high gene flow and lack of spatial genetic structuring. Molecular clock analysis of the ITS2 phylogeny traced the evolutionary history of Nitzschia back to the Cenozoic era, indicating that the dispersal of this species in the WP was likely influenced by historical events during the late Pleistocene, contributing to its homogenous distributions in the region. Additionally, environmental and ecological selections during the Quaternary Period most likely played a role in the observed genetic homogeneity.

amnesic shellfish poisoning, diatom, frustule, harmful algal bloom, second internal transcribed spacer, transmission electron microscopy