Rotifers are ubiquitous freshwater animals for which many complexes of cryptic species (i.e. distinct species that are morphologically difficult to distinguish) are described. Keratella cochlearis occurs globally and shows a wide phenotypic diversity indicating the potential presence of a species complex. We sampled lakes of the Trentino-South Tyrol region (Italy) and investigated mitochondrial genetic diversity in K. cochlearis in relation to detailed lorica measurements. We sequenced the mitochondrial cytochrome c oxidase subunit I and used the generalised mixed Yule coalescent approach, Poisson tree process model and automatic barcode gap discovery to delimit mitochondrial groups, associated with putative evolutionary significant units (ESUs). Based on 248 sequences, eight putative ESUs were indicated that could only partially be delimited by lorica morphology. Specifically, several morphological characteristics (i.e. spinelets, bended median ridge, and posterior spine) were found in specimens of different putative ESUs, and thus, these characters seem to be of poor discriminatory value. Furthermore, different putative ESUs of K. cochlearis were found in the same lake. We conclude that the high mitochondrial genetic diversity may be linked to tolerance of K. cochlearis to varying environmental conditions.

Discordance between mitochondrial and nuclear phylogenies is being increasingly recognized in animals and may confound DNA-based taxonomy. This is especially relevant for taxa whose microscopic size often challenges any effort to distinguish between cryptic species without the assistance of molecular data. Regarding mitonuclear discordance, two strikingly contrasting scenarios have been recently demonstrated in the monogonont rotifers of the genus Brachionus. While strict mitonuclear concordance was observed in the marine B. plicatilis species complex, widespread hybridization-driven mitonuclear discordance was revealed in the freshwater B. calyciflorus species complex. Here, we investigated the frequency of occurrence and the potential drivers of mitonuclear discordance in three additional freshwater monogonont rotifer taxa, and assessed its potential impact on the reliability of DNA taxonomy results based on commonly used single markers. We studied the cryptic species complexes of Keratella cochlearis, Polyarthra dolichoptera and Synchaeta pectinata.Phylogenetic reconstructions were based on the mitochondrial barcoding marker cytochrome c oxidase subunit I gene and the nuclear internal transcribed spacer 1 locus, which currently represent the two most typical genetic markers used in rotifer DNA taxonomy. Species were delimited according to each marker separately using a combination of tree-based coalescent, distance-based and allele-sharing-based approaches. Mitonuclear discordance was observed in all species complexes with incomplete lineage sorting and unresolved phylogenetic reconstructions recognized as the likely drivers. Evidence from additional sources, such as morphology and ecology, is thus advisable for deciding between often contrasting mitochondrial and nuclear species scenarios in these organisms.

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A recent study based on DNA taxonomy indicated that the widespread rotifer Keratella cochlearis comprises several evolutionarily significant units (ESUs). Identification of ESUs based on DNA taxonomy alone is problematic and usually requires morphological, demographic, and/or ecological evidence. We isolated three haplotypes belonging to two ESUs of K. cochlearis and conducted life table experiments to investigate if this genetic diversity is reflected in demography. We found significant differences between haplotypes in life history traits (average lifespan, number of offspring, and percent of rejected eggs) and in demographic parameters (instantaneous growth rate, generation time, and net reproductive rate of the populations). During the experiments, all the haplotypes produced abnormal females with a deformed lorica, which was never reported before in K. cochlearis. We also report the first case of an amphoteric female (producing both females and males) in K. cochlearis. We hypothesize that K. cochlearis haplotypes and thus ESUs may exhibit niche differentiation through their different life histories. The link between demographic parameters of K. cochlearis and niche utilization requires further research.