If we assume, however, that Archaea is a derived lineage from gram-positive bacteria [ 36, 37], then HTPG proteins originated before the origin of Archaea, but were subsequently lost in this lineage.
If the latter, it is possible that N. jurassica is a derived lineage within the genus or, conversely, that the genus originated in a warm temperate climate and later radiated into the tropics.
Because zebrafish are representatives of a derived lineage, it has been suggested repeatedly in the literature that a basal ray-finned fish, such as the paddlefish, must be examined to confirm this hypothesis.
Alternatively, the biparental inheritance of the chloroplast that we have observed in O. tauri may be a derived state from a lineage with uniparental chloroplast transmission.
Finally, node G represents the common ancestor of the sordidus species group, which is a derived, monophyletic lineage that evolved within Australia (Table 1, Fig. 1).
In short, although Zygnematophyceae are the most diverse of the charophyte groups (∼3,000 species), they possess few macroscopic morphological similarities with land plants, hence they are a highly derived lineage of freshwater algae that appear to have retained few macromorphological characters that were present in their immediate ancestor with land plants.
The alternative interpretation posed was that the condition in N. scintillans was a derived state in this lineage: "The ancestral system may have had two genes, which fused in Noctiluca".
Based on the phylogenetic analyses reported in Figure 2 and also comparative analyses of the NifU protein (not shown) it appears that truncation of nifU in spheroid bodies is a derived feature of the endosymbiont lineage.
In contrast, an intact reading frame for fdxN is conserved in all other close free-living cyanobacterial relatives, indicating formation of the pseudogene is a derived feature of the spheroid body lineage.
