Integrative species delimitation and phylogeny of the branchiate wormBranchiodrilus(Clitellata, Naididae)

Characterization of four novel actinospore types of fish parasitic myxozoans and the occurrence of Branchiodrilus hortensis and Ophidonais serpentina from fish farms of Hungary

Six distinct actinospore types were identified in the intestinal epithelium of oligochaetes collected from the Szigetbecse and Makád fish farms of Ráckeve Danube Arm Fishing Association, in Hungary. Four new types: triactinomyxon type, raabeia type, aurantiactinomyxon type 1, and aurantiactinomyxon type 2, were described morphologically and molecularly from three invertebrate host species: Limnodrilus hoffmeisteri, Ophidonais serpentina, and Tubifex tubifex. The 18S ribosomal DNA (rDNA) analysis revealed that these new types of actinospores did not match any myxospore sequences available in GenBank. Phylogenetic analysis placed the triactinomyxon type within the Myxobolus clade that parasitizes cyprinid fish, while the raabeia type and aurantiactinomyxon type 2 were both placed within the Myxobolus clade associated with Perciformes fish. Aurantiactinomyxon type 1 was clustered in a clade containing gill-infecting Henneguya spp. from Esociformes fish. However, no myxospores have been found yet to link to the newly sequenced actinospores reported in this survey. This study also reports the first occurrence of two oligochaetes species, Branchiodrilus hortensis and Ophidonais serpentina in Hungary, specifically in fish farms of Ráckeve Danube Arm Fishing Association. Moreover, this is the first report on the involvement of Ophidonais serpentina in the life cycle of myxozoans.

Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview

Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.

Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation

BACKGROUND

Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species.

RESULTS

A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species.

CONCLUSION

We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.

On the identity and phylogenetic position of Dero indica (Clitellata: Naididae)

The identity and validity of the freshwater worm Dero indica (Clitellata: Naididae; Naidinae) has been debated, and it has been suggested that it is likely to be identical with D. digitata. In this study we combine a newly generated COI sequence of D. indica with available sequences from GenBank, to estimate the phylogeny of Dero using both Bayesian Inference and Maximum Likelihood. The trees show that D. indica is well separated from D. digitata, instead it is closest to D. vaga, but with low support. Furthermore, the analyses confirm the close relationship between Dero and Branchiodrilus found in previous studies, and indicates the presence of cryptic species in D. furcata and D. digitata.

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.