Figure 1.
Proportion of successfully barcoded strains in our dataset for selected taxa.
Numbers on X-axis are percentages. Gym/Gyr denote strains called Gymnodinium or Gyrodinium. 335 sequences failed at the amplification step (65%), 132 failed at the sequence stage whilst 47 (8%) failed due to the presence of paralogues or contaminants. The Pfiesteriaceae and Alexandrium taxa were proportionately worse at amplification compared to other genera.
Figure 2.
Comparison of ITS versus COI DNA barcodes in species–level identification.
Panel A and B refer to ITS and COI respectively. Dark grey shading indicates intraspecific distances whereas light grey interspecific distances. Y axis shows percentage of named species and genera that fall into pairwise distance categories (X-axis). Both A and B share same X-axis. Although both ITS and CO1 barcodes fall within the 0–0.02% range, note how ITS has a sizeable gap in genetic distance within species compared to between species, that is lacking for COI marker. In this study 2% or less PWD between strains was used as a species cut off, which encompassed 94% of strains. Abbreviations: Sym: Symbiodinium and Sym gp. A? refers to unknown group A Symbiodinium sp.; Karl.: Karlodinium; K. ven.: Karlodinium veneficum; C.sp.: Cryptoperidiniopsis sp.; Scr.: Scrippsiella; S.troch.: Scrippsiella trochoidea.
Figure 3.
Neighbour-joining phylogenetic analysis of ITS DNA barcodes for all dinoflagellates from culture collections in this study and from GenBank.
Using uncorrected p-distances. Most species could be accurately identified with ITS which showed cryptic speciation in Scrippsiella, Heterocapsa, Oxyrrhis and Karlodinium. Strain labels were removed for clarity but are available in Figure S1 and also listed in Table S1. Abbreviations: S. sp. : Scrippsiella species; Sym: Symbiodinium. Brackets represent species groups as identified using criteria described in methods and results. GB indicates a genbank deposited strain.
Table 1.
Summary of Clonal strain variation of dinoflagellate ITS sequences from public databases.
Table 2.
Strain synonym variation in dinoflagellate ITS barcodes.
Figure 4.
Light Micrographs of Heterocapsa group 1, CCMP1322 (A), CCMP2770 (B) and 103238 (C), revealing different morphologies.
This genus showed one of the highest levels of strain name incongruities. 103238 and a third strain 103248 (D), were both putatively identified as Katodinium asymmetricum but ITS-barcoding showed the latter was unrelated to this or any other dinoflagellate studied here. Note pigments of 103238 and 103248 belong to cryptophytes food and these strains are heterotrophic.