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BackgroundThe giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.FindingsWe present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.ConclusionsThis annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

Understanding how ecological, environmental and geographic features influence population genetic patterns provides crucial insights into a species' evolutionary history, as well as their vulnerability or resilience under climate change. In the Southern Ocean, population genetic variation is influenced across multiple spatial scales ranging from circum‐Antarctic, which encompasses the entire continent, to regional, with varying levels of geographic separation. However, comprehensive analyses testing the relative importance of different environmental and geographic variables on genomic variation across these scales are generally lacking in the Southern Ocean. Here, we examine genome‐wide single nucleotide polymorphisms of the Southern Ocean octopus Pareledone turqueti across the Scotia Sea and the Antarctic continental shelf, at depths between 102 and 1342 m, throughout most of this species' range. The circumpolar distribution of P. turqueti is biogeographically structured with a clear signature of isolation‐by‐geographical distance, but with long‐distance genetic connectivity also detected between East and West Antarctica. Genomic variation of P. turqueti was also associated with bottom water temperature at a circumpolar scale, driven by a genotype‐temperature association with the warmer sub‐Antarctic Shag Rocks and South Georgia. Within the Scotia Sea, geographic distance, oxygen and fine‐scale isolation‐by‐water depth were apparent drivers of genomic variation at regional scales. Putative positive selection of haemocyanin (oxygen transport protein), calcium ion transport and genes linked to RNA modification, detected within the Scotia Sea, suggest physiological adaptation to the regional sharp temperature gradient (~0–+2°C). Overall, we identified seascape drivers of genomic variation in the Southern Ocean at circumpolar and regional scales in P. turqueti and contextualised the role of environmental adaptations in the Southern Ocean. [ABSTRACT FROM AUTHOR]

Climate change is driving a pervasive global redistribution of the planet's species. Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach. Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges. We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems. Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change. Species redistributions present challenges for human well-being, environmental management and sustainable development. By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution. Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges. Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human-centred approaches. Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions.

Distributions of Earth's species are changing at accelerating rates, increasingly driven by human-mediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered by changes in species distribution. Consideration of these effects of biodiversity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation's Sustainable Development Goals.

Abalone (family Haliotidae) are an ecologically and economically significant group of marine gastropods that can be found in tropical and temperate waters. To date, only a few Haliotis genomes are available, all belonging to temperate species. Here, we provide the first chromosome-scale abalone genome assembly and the first reference genome of the tropical abalone Haliotis asinina. The combination of PacBio long-read HiFi sequencing and Dovetail's Omni-C sequencing allowed the chromosome-level assembly of this genome, while PacBio Isoform sequencing across five tissue types enabled the construction of high-quality gene models. This assembly resulted in 16 pseudo-chromosomes spanning over 1.12 Gb (98.1% of total scaffolds length), N50 of 67.09 Mb, the longest scaffold length of 105.96 Mb, and a BUSCO completeness score of 97.6%. This study identified 25,422 protein-coding genes and 61,149 transcripts. In an era of climate change and ocean warming, this genome of a heat-tolerant species can be used for comparative genomics with a focus on thermal resistance. This high-quality reference genome of H. asinina is a valuable resource for aquaculture, fisheries, and ecological studies. [ABSTRACT FROM AUTHOR]

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef‐building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein‐coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future. [ABSTRACT FROM AUTHOR]

The two‐toned pygmy squid (Idiosepius pygmaeus, Steenstrup, 1881) is a small, tropical cephalopod that inhabits seagrass meadows and is known to attach to blades of seagrass using a specialised adhesive organ. A global decline in seagrass habitat due to anthropogenic disturbances may threaten the species that rely on seagrass meadows for shelter, foraging and other crucial activities. It is unclear if I. pygmaeus can utilise alternative habitats in the absence of seagrass. Here, we test the effect of habitat type, material and composition type, and the presence of conspecifics on the settlement preferences of I. pygmaeus. Individuals each underwent three separate experiments: (1) testing the preference between their known habitat, Zostera muelleri subsp. Capricorni and potential substitute, Sargassum, (2) testing the preference to attach to a natural or artificial structure of similar shape and size, and (3) testing the preference of identical habitats, one with a conspecific adhered to and one without. We found that I. pygmaeus did not have a strong preference for either Zostera or Sargassum. However, a strong preference was found for attachment to the natural structure over the artificial one. There was also strong evidence for the use of conspecific cues in habitat choice, with 75% of individuals selecting the habitat that contained a conspecific. As habitat loss is the leading cause of species extinction, the knowledge of habitat preferences for I. pygmaeus is vital in order to assess their risk of population decline. The findings of this study suggest that I. pygmaeus could utilise an alternative habitat in the presence of seagrass meadow reduction, which is under threat from human activity. [ABSTRACT FROM AUTHOR]