Japoshvili, B. | Search bioRxiv

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↗

bioRxiv2018

Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae)

The phylogenetic relationships and the phylogeography of seven species of Caucasian barbels of the genus Barbus s. str. were studied based on extended geographic coverage and the use of mtDNA and nDNA markers. Based on the 26 species studied, matrilineal phylogeny of the genus Barbus is composed of two clades: a) West European clade, and b) Central and East European clade. The latter comprises two subclades: b1) Balkanian subclade, and b2) Ponto-Caspian subclade, which includes 11 lineages mainly from Black and Caspian Sea drainages. Caucasian barbels are not monophyletic and are subdivided into two groups. The Black Sea group encompasses species from tributaries of the Black Sea, including the reinstalled B. rionicus, except for B. kubanicus. The Caspian group includes B. ciscaucasicus, B. cyri (with B. goktschaicus, which might be synonymized with B. cyri), B. lacerta from the Tigris-Euphrates basin and B. kubanicus from the Kuban basin. The genetic structure of Black Sea barbels was influenced by glaciation-deglaciation periods accompanied by freshwater phases, periods of migration and the colonization of Black Sea tributaries. Intra- and intergeneric hybridization among Caucasian barbines was revealed for the first time. In the present study, we report the discovery of B. escherichii in the Kuban basin, where only B. kubanicus was known to inhabit. Hybrids of these two species were detected based on both mtDNA and nDNA markers. Remarkably, the Kuban population of B. escherichii is distant to closely located conspecific populations, and we consider it as a relic. We reveal the intergeneric hybridization between evolutionary tetraploid (2n=100) B. goktschaicus and evolutionary hexaploid (2n=150) Capoeta sevangi in Lake Sevan.

evolutionary biology↗