eDNA based bycatch assessment in pelagic fish catches.

Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.

Comparative genomics and signatures of selection in North Atlantic eels.

Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the FST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events.

Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic.

Monitoring the distribution of marine nonindigenous species is a challenging task. To support this monitoring, we developed and validated the specificity of 12 primer-probe assays for detection of environmental DNA (eDNA) from marine species, all nonindigenous to Europe. The species include sturgeons, a Pacific red algae, oyster thief, a freshwater hydroid from the Black Sea, Chinese mitten crab, Pacific oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout and North American mud crab. We tested all assays in the laboratory, on DNA extracted from both the target and non-target species to ensure that they only amplified DNA from the intended species. Subsequently, all assays were used to analyse water samples collected at 16 different harbours across two different seasons during 2017. We also included six previously published assays targeting eDNA from goldfish, European carp, two species of dinoflagellates of the genera Karenia and Prorocentrum, two species of the heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside eDNA sampling but with only one sampling event over the one year. Because eDNA was relatively fast and easy to collect compared to conventional sampling, we sampled eDNA twice during 2017, which showed seasonal changes in the distribution of nonindigenous species. Comparing eDNA levels with salinity gradients did not show any correlation. A significant correlation was observed between number of species detected with conventional monitoring methods and number of species found using eDNA at each location. This supports the use of eDNA for surveillance of the distribution of marine nonindigenous species, where the speed and relative easy sampling in the field combined with fast molecular analysis may provide advantages compared to conventional monitoring methods. Prior validation of assays increases taxonomic precision, and laboratorial setup facilitates analysis of multiple samples simultaneously. The specific eDNA assays presented here can be implemented directly in monitoring programmes across Europe and potentially worldwide to infer a more precise picture of the dynamics in the distribution of marine nonindigenous species.