Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used. The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri, P. likai, and P. apollonicus. For three species (P. strandjae, P. strymonicus, P. morella), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus, were supported as secondary species hypotheses. Finally, six of the primary species hypotheses (P. phoxinus, P. lumaireul, P. karsticus, P. septimanae, P. marsilii and P. csikii) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis. The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.

Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.

The common minnow species Cyprinus chrysoprasius, previously synonymised to Phoxinus phoxinus, was originally described from the Crimean Peninsula (Black Sea – Sea of Azov basin). A genetic analysis of the mitochondrial cytochrome oxydase 1 in the context of a phylogenetic study of European Phoxinus showed that it represents a distinct genetic clade and potentially a valid species. In the present study, we approach the issue following a broader, both genetic and morphological, study in order to check and support the validity of native Crimean Phoxinus under the earliest available name of the species: P. chrysoprasius. Our data demonstrate a reliable genetic distance of this minnow from geographically neighbouring clades and species, and a certain morphological distinctiveness. In order to determine the taxonomic concept of P. chrysoprasius, as a species involved in a genetically well-differentiated, but phenotypically poorly structured complex of east-European Phoxinus, a neotype for the species, based on topotypical material, is herein described and designated. The original type locality of the species is also clarified.

In light of recent technological advances – in fields such as computer science, imaging technologies, and molecular analysis methods – the possibilities for studying biological museum specimens and linking information across disciplines have expanded exponentially in recent years. In particular, scientific disciplines operating on the scale of so-called -omics technologies, originally developed in molecular biology, have found their way into the museum realm. This development has led to a proliferation of neologisms aimed at describing comprehensive approaches for analyzing museum specimens and collections with the help of large-scale datasets. Among these terms, “museomics” has become a frequently used, albeit rather loosely defined, synonym for a wide range of large-scale, integrative scientific approaches that are centered on, or incorporate, museum specimens. In this article, we aim to provide an overview of the most commonly used key terms, examine their conceptual interrelations, and present a literature-based survey of their usage. We advocate for using three terms at different hierarchical levels: (1) museomics for analytical approaches using biomolecules on museum specimen; (2) the extended specimen concept linking voucher specimens with diverse physical, digital, and contextual information; and (3) collectomics linking the data of the extended specimen with quantitative datasets from other domains of research. A key prerequisite for this linkage is the unambiguous assignment of data to the corresponding specimen using a Persistent Identifier (PID). Finally, we conclude the paper by reflecting on the current approaches and initiatives adopted at the Natural History Museum Vienna, emphasizing the importance of adopting a museum-wide strategy for developing extended specimen datasets using standardized data formats in accordance with Open Science principles.