Phylogenetic patterns
We observed some phylogenetic structure within the data, such as highest
similarities between certain congener pairs and an overall resemblance
of congeneric species. Consistently, only very small deviations in
proteomic pattern have been reported in cryptic species complexes
(Müller et al., 2013, Dieme et al., 2014), specifically those with only
recent speciation (Maasz et al., 2020, Paulus et al., 2022). However,
when including all six calanoid genera with congeners in the analysis,
similarity was not consistently related to phylogenetic distance and was
partly higher between non-congeners than between congeners. Phylogenetic
relationships have successfully been identified using proteomic
composition (Telleria et al., 2010, Maltseva et al., 2020) and it was
suggested that proteomic fingerprints may describe phylogenetic
relationships (Zurita et al., 2019). However, our data indicate that
proteomic fingerprints are not suitable to address phylogenetic
questions in calanoid copepods. This makes sense as proteomic
fingerprints are a potpourri of around 300 mainly cytosolic molecules
with genes of quite different mutation rates behind them, also
influenced by various physiological processes.
For most genera the higher similarity between congeners was not
influencing species identification success and is therefore probably not
of practical relevance. However, the strongest misidentification while
testing library robustness against regionality (i.e., the library did
not include specimens from the respective region, but only from other
regions), derived from the highly similar congener pairs from the same
sub-genus A. danae and A. negligens , as well as C.
typicus und C. chierchiae. This misidentification was not
resolvable by the post-hoc test, which has been shown to detect false
positives quite reliably (Rossel & Martinez Arbizu, 2018a). Since this
only occurred when a non-region-specific library was used, this problem
may only be relevant to monitoring studies in which a rare species in
the habitat or a neobiota of a very similar congener pair is not
included in the library used. We have demonstrated here that the
composition of the reference library can have a significant impact on
the identification of closely related species and therefore needs to be
thoroughly tested.