4.1 | Phylogenetic analyses
Newly-designed primers combined with a few existing primer pairs enabled
us to amplify ~700-1000 base pairs of the mitochondrialCOI fragment for 66 MOTUs from all groups of ctenophores (Figure
2). The COI phylogeny illuminated a great deal of species-level
diversity that was not evident for the 18S fragment, within and
between groups. However, the levels of divergence and saturation for
mitochondrial genes among ctenophores are some of the highest in the
Metazoa (Lavrov & Pett 2016). Despite high levels of mitochondrial
variation, within-species diversity of ctenophores rarely exceeded 4%
(Figure 3b). Saturation within the phylum, especially at third codon
positions, obscured many higher-level relationships and resulted in
basal polytomies. Curiously, we found a higher proportion of transitions
than transversions for the COI fragment among ctenophores (Figure
3a). For protein-coding loci, transitions are often more common than
transversions because they usually result in synonymous mutations and
involve the exchange of bases of similar shapes (Xia et al. 1996). It is
plausible that the proportion of transitions within our data were overly
saturated and additional mutations were obscured. The mitochondrial
genomes of ctenophores are enriched with A/T residues, which also could
contribute to a greater incidence of transversions (purines⇄pyrimidines)
than transitions. Plots of other mitochondrial loci also revealed the
same pattern, where transitions saturated quickly, often at
~20% GTR distance, and there were higher proportions of
transversions (Figure S1). Despite high levels of saturation, closely
related species and groups were well supported, especially within the
Lobata (Figure 4b). Although saturation among divergent taxa resulted in
poor phylogenetic resolution, and it was difficult to make strong
conclusions based on the COI fragment alone, COI sequences
were easily attributable to MOTUs, and proved useful for species
delimitation.