Population panmixia of the pelagic shrimp Lucensosergia lucens between Japanese and Taiwanese waters in the western North Pacific

The pelagic shrimp Lucensosergia lucens is a commercially important species in Japan and Taiwan; however, a recent significant decline in L. lucens catch has been reported in Suruga Bay, Japan. In the present study, multiple molecular approaches were used to understand the population structure of L. lucens in Japanese and Taiwanese waters. Our analysis of mitochondrial cytochrome c oxidase subunit I and control region obtained by Sanger sequencing showed no evidence of different population structures, contrary to the previous study based on the control region. Genome-wide single-nucleotide polymorphism (SNP) analysis using multiplexed inter-simple sequence repeats genotyping by sequencing revealed panmixia in Japanese and Taiwanese populations. The contemporary migration rates estimated from the SNP data suggest that the Kuroshio Current plays a key role in L. lucens transportation from Taiwan to Japan. Additionally, mitogenome sequences obtained by genome skimming showed no region-specific genetic lineages in Japan or Taiwan. The results obtained by multiple molecular approaches suggested that L. lucens is widely distributed with a dispersal capacity in the Kuroshio and adjacent regions in the western North Pacific. Because apparent panmixia of L. lucens was observed in Japanese and Taiwanese waters, international cooperation is needed for the sustainable fishing of this shrimp.

The language of light: a review of bioluminescence in deep-sea decapod shrimps

In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.

Skimming genomes for systematics and DNA barcodes of corals

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory

Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.

Ecological Predictors and Functional Implications of Eye Size in Deep-Sea Shrimps

Constraints on energy resources and available light in the deep sea should place strong selection pressure on eye size, a fundamental determinant of visual ability. By examining eye size among 16 species (454 individuals) of deep-sea sergestid shrimps, we show significant differences in intraspecific eye growth rates and species eye-size averages that are correlated to different aspects of ecology and result in variable sighting distance thresholds of bioluminescence, one measure of visual performance. We used linear regressions modeling the lowest and highest bounds of phylogenetic signal to test for ecological correlates of relative and absolute eye size, which indicate the allocation of energetic resources toward eyes and an optical basis of visual capability, respectively. Of the ecological variables tested [mean depth, diel vertical migration (DVM) distance, habitat type, and light organ type], light organ type was the only significant correlate of both relative and absolute eye size, suggesting that bioluminescence plays a particularly important role in the evolution of sergestid vision and that these animals may be reliant on bioluminescent signaling. Our findings also suggest that the DVM imposes visual demands distinct from the average depths occupied by a species. While DVM distance correlated with relative eye size, mean depth correlated with absolute eye size, revealing that eye size increases with depth before 1,000 m, then decreases in bathypelagic (aphotic) zone. By applying measured eye sizes to models of visual performance, we estimated that sergestids can detect a bioluminescent point source from ≤3.77 m away, and that these sighting distance thresholds vary between species by a factor of three. In relative terms, however, all sergestids under the test conditions had a common detection threshold at ∼63.5 body lengths, suggesting that bioluminescence sighting distance is proportional among species and may be related to shared behaviors of swarming and copulation. By considering the effects of evolutionary history, light and nutrient availability, and the constraints of body size, our study reveals new patterns of deep-sea eye size evolution and provides new insights into the visual ecology of this diverse and important deep-sea group.