Mamos, T. | bioRxiv Science

bioRxiv2023

Distribution, diversity and diversification from a DNA barcoding perspective: the case of Gammarus radiation in Europe`s oldest inland waterbody - the ancient Lake Ohrid

AimA detailed, comparative DNA-barcoding and morphospecies based overview of the vertical and horizontal distribution of Lake Ohrid endemic Gammarus species-flock. Re-evaluation of the origin of the species-flock dating, identification of events that putatively influenced diversification patterns in the species-flock. LocationLake Ohrid: a deep and ancient lake of tectonic origin, biosphere reserve, UNESCO World Heritage Site, located on the Macedonia/Albania border. TaxonGammarus species-flock (Amphipoda, Crustacea) MethodsExtensive sampling and DNA barcoding of 600 individuals were carried out. DNA sequences were analysed using species delimitation methods, haplotype network reconstructions, Bayesian molecular dating and demographic analysis. The COI-based delimitation results were validated with nuclear 28S RNA data. ResultsThe species flock distribution has weak horizontal but clear vertical structure. The diversity across bathymetric gradients correlates with temperature and salinity; and the highest diversity with sublittoral and springs of lakes shore. Two new MOTUs representing putatively new species are revealed and supported also by the nuclear marker. The time of flock radiation overlaps with the time of lake formation. The COI gene shows signs of positive selection and an acceleration in substitution rate. The demographic changes of the flock happened during the last ky. Main conclusionsDistribution of the Gammarus species-flock is vertically structured, reflecting habitat zonation. Parapatric speciation as one of the mechanisms in flocks diversification is suggested. Detection of new MOTU suggests that the flocks diversity is still not fully revealed. Nevertheless, failure to recover three other MOTUs suggests the loss of gammarid diversity in the lake. This represents,together with the current threats to the lake ecosystem (i.e. climate changes, development of tourism), a clear call for conservation efforts. The speciation events and demographic changes within the flock relate presumably to glacial and postglacial water level changes and to colonisation of new depth ranges and the associated springs.

molecular biology↗

bioRxiv2019

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. 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 utilization of metabarcoding in aquatic biomonitoring.

ecology↗