As a consequence of the decline of numerous commercial fish populations, an ecosystem‐based approach to fisheries management, which includes the protection of essential fish habitat (EFH), has emerged. Cold‐water coral (CWC) sites are recognized as biodiversity hotspots, but numerous examples of CWC destruction and degradation as a result of anthropogenic activities are well documented. However, although functional connections between CWCs and fish stocks are suspected, based on correlative evidence, proof of any close or direct relationship identifying CWCs as EFH is still lacking. Here, we provide evidence of the utilization of CWCs by fish larvae, mainly those of redfish (Sebastes spp). In multiyear surveys, fish larvae were consistently found closely associated with five species of sea pen (Octocorallia: Pennatulacea) in April and May. Prevalence and/or yields of fish larvae varied with coral host species, depth, location, and colony size. Evidence of the role of CWCs in the early life history of some fish species provides the strongest argument yet for the categorization of CWCs as EFH in the design of management programs.

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs. Echinoderms, ubiquitous in the marine environment, are important from evolutionary, ecological, and socioeconomic perspectives. Together with chordates and hemichordates, they form the deuterostome clade, making them a crucial node in the study of chordate ancestry. Within echinoderms, class Holothuroidea is unique; its members (the sea cucumbers) display remarkable regenerative abilities and play key roles as sediment bioturbators and symbiotic hosts, and many are prized in the seafood and pharmaceutical industries. The sea cucumber genome therefore has the potential to significantly contribute to our understanding of important evolutionary and biological processes and help enhance aquaculture programs. Here we present a high-quality genome sequence for the economically important species Apostichopus japonicus. Through comparative analyses, we identified 763 echinoderm-specific gene families enriched in genes encoding membrane proteins, ion channels, and signal transduction proteins. Marker genes associated with the notochord and gill slits were also found, providing valuable insight into the origin of chordates. The reduced number and low expression levels of biomineralization genes reflect the skeletal degeneration seen in sea cucumbers. Importantly, 2 gene families appeared to be expanded in A. japonicus and may play crucial roles in its heightened regenerative potential. Together, findings from the sea cucumber genome provide important and novel insights into echinoderm and deuterostome biology.

Population connectivity refers to the exchange of individuals among populations: it affects gene flow, regulates population size and function, and mitigates recovery from natural or anthropogenic disturbances. Many populations in the deep sea are spatially fragmented, and will become more so with increasing resource exploitation. Understanding population connectivity is critical for spatial management. For most benthic species, connectivity is achieved by the planktonic larval stage, and larval dispersal is, in turn, regulated by complex interactions between biological and oceanographic processes. Coupled biophysical models, incorporating ocean circulation and biological traits, such as planktonic larval duration (PLD), have been used to estimate population connectivity and generate spatial management plans in coastal and shallow waters. In the deep sea, knowledge gaps in both the physical and biological components are delaying the effective use of this approach. Here, we review the current efforts in conservation in the deep sea and evaluate (1) the relevance of using larval dispersal in the design of marine protected areas and (2) the application of biophysical models in the study of population connectivity. Within biophysical models, PLD can be used to estimate dispersal distance. We propose that a PLD that guarantees a minimum dispersal distance for a wide range of species should be used in the planning of marine protected areas in the deep sea. Based on a review of data on species found at depths >200 m, a PLD of 35 and 69 days ensures a minimum distance for 50 and 75%, respectively, of eurybathic and deep-sea species. We note that more data are required to enhance accuracy and address the high variability in PLD between and within taxonomic groups, limiting generalizations that are often appealing to decision-makers. Given the imminent expansion of resource exploitation in the deep sea, data relevant to spatial management are needed urgently.