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  • 1
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2017-04-11)
    Abstract: Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids ( Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid ( Harmothoe imbricata ). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2615211-3
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  • 2
    In: Zoologica Scripta, Wiley, Vol. 49, No. 4 ( 2020-07), p. 458-472
    Abstract: Higher systematics and evolutionary history of Protobranchia, a subclass of Bivalvia, have long been controversial due to paucity of prominent shell characters and difficulties in collecting live material for diverse taxa. Here, we evaluate the reliability of shell microstructure for protobranch higher systematics by reconstructing a molecular phylogeny of the subclass. Relationships were assessed using the nuclear (18S rRNA, 28S rRNA and histone H3) and mitochondrial (16S rRNA and cytochrome c oxidase subunit 1) gene sequences from 89 in‐group species. Maximum likelihood reconstruction with the nuclear markers recognized five superfamilies (Nuculoidea, Solemyoidea, Manzanelloidea, Nuculanoidea and Sareptoidea) as the in‐group clades of the monophyletic Protobranchia. Sareptoidea is herein redefined to comprise Sarepta and Setigloma in the sole family Sareptidae, whereas Pristigloma and its monotypic Pristiglomidae are transferred from this superfamily to Nuculanoidea, both in the order Nuculanida. Mapping of shell microstructure characters on the tree confirmed their conservativeness at superfamily level when only living species were taken into account. The Nuculoidea have shells with the outer prismatic and middle/inner nacreous structures; Solemyoidea are characterized by either the radially elongate simple prismatic structure or the reticulate structure in the outer shell layer; Manzanelloidea, Nuculanoidea and Sareptoidea have shells of homogeneous, fibrous prismatic and/or fine complex crossed lamellar structures, all of which lack large structural units. Our Bayesian time calibration, on the contrary, suggested frequent loss of nacre in the Paleozoic and Mesozoic history of Protobranchia, at least once each in Nuculoidea, Manzanelloidea, Solemyoidea and Sareptoidea in the Paleozoic, and perhaps multiple times in Nuculanoidea by the Mesozoic.
    Type of Medium: Online Resource
    ISSN: 0300-3256 , 1463-6409
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2022109-5
    detail.hit.zdb_id: 121103-1
    SSG: 12
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  • 3
    In: Journal of Crustacean Biology, Oxford University Press (OUP), Vol. 40, No. 5 ( 2020-09-16), p. 556-562
    Abstract: Genetic connectivity provides a basis for evaluating the resilience of animal communities by elucidating gene flow and serves as a proxy for realized dispersal through planktonic larval dispersal, settlement, and reproductive success. Gandalfus yunohana (Takeda, Hashimoto & Ohta, 2000) is a brachyuran crab endemic to deep-sea hydrothermal vents in the northwestern Pacific. Although an iconic and often dominant species, the connectivity among its populations is yet to be examined. We obtained barcoding sequences of the mitochondrial COI gene of G. yunohana from four vent fields including two on the Izu Arc, one on the northern Mariana Arc, and one in the Okinawa Trough. Genetic diversity of populations on the Izu and northern Mariana arcs were similar and shared the dominant haplotypes, showing no genetic subdivision regardless of the habitat depth. The Okinawa Trough population, for which only one specimen was available, was not genetically different from specimens from the Izu/Mariana arc populations. Estimation of the number of immigrants among populations suggests that the migration from north to south is higher than in the reverse direction. Our results resonate with previous laboratory-culture experiments, suggesting a high dispersal capability for G. yunohana. Visual observations and sampling, however, suggest that G. yunohana is exceedingly rare in the Okinawa Trough. This perhaps results from a lack of sufficient larval supply from the Izu-Bonin-Mariana Arc vents, and there may not be a reproductive population in the Okinawa Trough.
    Type of Medium: Online Resource
    ISSN: 0278-0372 , 1937-240X
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2173764-2
    SSG: 12
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  • 4
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 5 ( 2018-2-21)
    Type of Medium: Online Resource
    ISSN: 2296-7745
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2018
    detail.hit.zdb_id: 2757748-X
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2023
    In:  Zoological Journal of the Linnean Society Vol. 199, No. 1 ( 2023-09-01), p. 216-227
    In: Zoological Journal of the Linnean Society, Oxford University Press (OUP), Vol. 199, No. 1 ( 2023-09-01), p. 216-227
    Abstract: Merlionia zeeae , a new species belonging to a new genus, is described as a member of the cyclopoid family Anthessiidae (Copepoda), based on both sexes collected off the coast of Singapore. The new species was found in the gill cavities of the longnosed stargazer, Ichthyscopus lebeck (Actinopteri: Perciformes: Uranoscopidae), although almost all members of the family are associated with molluscan hosts. However, this copepod is not similar to other genera of the family Anthessiidae due to possessing the following characters: the curved hook-like antenna, which is similar to that of the family Chondracanthidae in both sexes; the distal portion of the maxilla covered with numerous spinules; and the lack of the maxilliped in the female. Both maximum likelihood and Bayesian inferences using partial SSU (18S) ribosomal RNA genes strongly supported a monophyletic clade formed by the new genus, and three anthessiid genera in this study. However, it was not supported that Anthessiidae and Chondracanthidae are closely related. Therefore, the new genus is considered to be a highly transformed member of the former, and the chondracanthid-form antenna might therefore be a product of convergent evolution attributable to the host-switching event from molluscs to fishes.
    Type of Medium: Online Resource
    ISSN: 0024-4082 , 1096-3642
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1471951-4
    SSG: 12
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  • 6
    In: Molecular Phylogenetics and Evolution, Elsevier BV, Vol. 125 ( 2018-08), p. 220-231
    Type of Medium: Online Resource
    ISSN: 1055-7903
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
    detail.hit.zdb_id: 1471402-4
    SSG: 12
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  • 7
    In: Evolutionary Applications, Wiley, Vol. 11, No. 10 ( 2018-12), p. 1915-1930
    Abstract: Studying population genetics of deep‐sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis‐based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6 , cox1 , and nad4 ) and 6,398 genomewide single nucleotide polymorphisms ( SNP s) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea ( SCS ) and three individuals in Sagami Bay ( SB ) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co‐occurrence of two cryptic semi‐isolated lineages. When using 125 outlier SNP s identified focusing on individuals in the Okinawa Trough ( OT ) and SB , a minor genetic subdivision was detected between individuals in the southern OT (S‐ OT ) and those in the middle OT (M‐ OT ) and SB . This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S‐ OT and the M‐ OT . Introgression analyses based on these outlier SNP s revealed that Hatoma Knoll in the S‐ OT represents a possible contact zone for individuals in the OT ‐ SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai‐yon Yonaguni Knoll in the S‐ OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2405496-3
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  • 8
    In: Nature Ecology & Evolution, Springer Science and Business Media LLC, Vol. 5, No. 3 ( 2020-11-25), p. 265-267
    Type of Medium: Online Resource
    ISSN: 2397-334X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2879715-2
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  • 9
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 8 ( 2022-04-26)
    Abstract: Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata , which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei . Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria . We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata , such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 10
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 7 ( 2020-11-25)
    Abstract: The ocean plays a crucial role in the functioning of the Earth System and in the provision of vital goods and services. The United Nations (UN) declared 2021–2030 as the UN Decade of Ocean Science for Sustainable Development. The Roadmap for the Ocean Decade aims to achieve six critical societal outcomes (SOs) by 2030, through the pursuit of four objectives (Os). It specifically recognizes the scarcity of biological data for deep-sea biomes, and challenges the global scientific community to conduct research to advance understanding of deep-sea ecosystems to inform sustainable management. In this paper, we map four key scientific questions identified by the academic community to the Ocean Decade SOs: (i) What is the diversity of life in the deep ocean? (ii) How are populations and habitats connected? (iii) What is the role of living organisms in ecosystem function and service provision? and (iv) How do species, communities, and ecosystems respond to disturbance? We then consider the design of a global-scale program to address these questions by reviewing key drivers of ecological pattern and process. We recommend using the following criteria to stratify a global survey design: biogeographic region, depth, horizontal distance, substrate type, high and low climate hazard, fished/unfished, near/far from sources of pollution, licensed/protected from industry activities. We consider both spatial and temporal surveys, and emphasize new biological data collection that prioritizes southern and polar latitudes, deeper ( & gt; 2000 m) depths, and midwater environments. We provide guidance on observational, experimental, and monitoring needs for different benthic and pelagic ecosystems. We then review recent efforts to standardize biological data and specimen collection and archiving, making “sampling design to knowledge application” recommendations in the context of a new global program. We also review and comment on needs, and recommend actions, to develop capacity in deep-sea research; and the role of inclusivity - from accessing indigenous and local knowledge to the sharing of technologies - as part of such a global program. We discuss the concept of a new global deep-sea biological research program ‘ Challenger 150 ,’ highlighting what it could deliver for the Ocean Decade and UN Sustainable Development Goal 14.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2757748-X
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