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Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem's biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.

Although there is high interest in realizing the great potential of applying eDNA methods to marine monitoring in the Northeast Atlantic, the implementation process has proven challenging. Researchers and stakeholders lack a common understanding about how eDNA methods can be used as well as a basis for discussing the various challenges and ambitions of both parties. The aim of the UNIFIeD project was to assess the current status of implementation; identifying these challenges and ambitions and provide a basis for enhanced communication between researchers and stakeholders. This report describes results from surveys addressing the key issues of eDNA application, standardization and implementation. In addition, the discussions and consensus from the following workshop is presented.

The Southern Ocean, in particular the southwest Atlantic sector, is experiencing rapid environmental changes. A long-term trend of density changes of key pelagic species has been noted over the last decades: Antarctic krill populations are declining whilst salps are on the rise and shifting their distribution poleward. A similar poleward expansion is anticipated for a third key player, the hyperiid amphipod crustacean Themisto gaudichaudii, leading to an increasing overlap of the distributions of these three species. Due to major knowledge gaps in the ecology, and genetic connectivity of T. gaudichaudii, the likelihood of this shift and its consequences for the pelagic food web structure remain largely unexplored. In this context, Themisto’s genetic and trophic connectivity as well as thermal response were investigated with state-of-the-art molecular methods. Phylogeographic analyses showed genetic homogeneity between localities in the Southern Ocean and Atlantic waters combined with high degree of phenotypic plasticity enabling different lineages to thrive in regions further south. Diet analyses using DNA metabarcoding were applied to characterize regional variation in diet. These analyses showed a diet predominantly composed of krill, in particular in the Antarctic Peninsula region, showing that Themisto’s poleward range expansion can further impact the already declining krill stocks. It also unexpectedly revealed ctenophores to be an important prey, despite their reputation as “trophic dead-end”. Transcriptome analyses were used to study the thermal response of Themisto individuals from different geographic populations that were experimentally exposed to heat and cold treatments. The analysis of differentially expressed genes showed that genetic lineages differ in thermal tolerances. It also revealed a wide range of molecular mechanisms in Themisto amphipods to cope with thermal stress. These findings contribute to better predict the impact of climate-driven rang

Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly, molecular approaches such as DNA metabarcoding are used in studying trophic relationships, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA metabarcoding with universal primers for cytochrome c oxidase I (COI) to study the diet composition of the northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40%–60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on stomach content analysis. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underlines the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.

Characterizing the extent of genetic differentiation among individuals and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. The Greenland Halibut is one of the main demersal fish species to be commercially exploited in Eastern Canada, and accurate information on geographic population structure and local adaptation is required to ensure the long-term presence of this species. We generated high-quality whole-genome sequencing data for 1,297 Greenland Halibut sampled across 32 locations throughout the Northwest Atlantic (from Arctic Canadian and Greenlandic coasts to the Gulf of St Lawrence). Population genetic structure was analyzed, revealing an absence of population differentiation between Canada and west Greenland but significant genetic differentiation between the Gulf of Saint Lawrence and the remainder of the Northwest Atlantic. Except for Gulf of Saint Lawrence, Greenland Halibut thus appear to be panmictic throughout the Northwest Atlantic. Environmental Association Analyses revealed that the environment explained up to 51 % might be replaced by 51% of the differentiation observed between the two stocks, with both ocean-bottom and surface variables (e.g., temperature and oxygen) involved in the observed genomic differentiation. Altogether, these results indicate that phenotypic differences previously observed between the Gulf of Saint Lawrence and the Northwest Atlantic likely resulted from functional adaptive divergence to their respective environmental conditions. Using coalescent simulations, we also assessed how high levels of migration between the two stocks would allow Greenland Halibut to potentially escape unfavorable environmental conditions in the Gulf of Saint Lawrence. In addition to supporting the management of this important exploited species, this work highlights the utility of using comprehensive genomic datasets to characterize the effects of climate change across a w

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome-wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (FST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome-wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto-nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre-glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.

1. The use of translocations to establish new or ‘refuge’ populations for species with high conservation value is controversial but widely used in conservation management. One of the risks of this approach is that an establishing population does not adequately capture the genetic diversity of the donor gene pool. This effect, rarely examined, is tested here. 2. In this study the genetic consequences of two conservation translocations after five generations (16 years) of the European whitefish, Coregonus lavaretus, were quantified. Both translocations were made using almost the same genetic groups and thus represent a partly replicated natural study. 3. Analysis of 12 informative microsatellites showed that expected heterozygosity, the mean number of alleles per locus and allelic richness did not differ between donor and translocated populations. There was also no loss of heterozygosity in the translocated populations, nor deviations from Hardy–Weinberg equilibrium expectations, nor signs of linkage disequilibrium. 4. All populations were genetically differentiated but pairwise FST values were low, indicating that the magnitude of divergence was small. 5. There was no evidence of inbreeding but there were significant differences in private allelic richness between donor and translocated populations. Of 50 alleles found in the donor population, 16% of the rarer alleles were lost in one translocated population and 8% in the other. 6. Allele loss without a reduction in heterozygosity strongly points to stochastic drift effects having occurred following translocation. The evidence indicates that alleles that were not detected in the donor population have arisen de novo in the translocated populations. 7. It is concluded that conservation translocations comprising even a modest number of propagules can successfully capture a high proportion of genetic variation of the host population, and that reduced genetic variation in the translocated population may be mitigated by th