An apparent illegal introduction of Lepomis macrochirus macrochirus from Yokohama City, Kanagawa Prefecture, Japan, is reported based on a juvenile specimen and a photograph of two adults collected on 14 June 2015 and deposited in the Kangawa Prefectural Museum of Natural History. The specimens and photographs were initially reported on the internet-based social networking site, Twitter. Two specimens of Carassius auratus, including an aquarium form, were also reported at the same locality and date, suggesting that the illegal introductions originated from an aquarium release. Our report demonstrates an example of web data mining in the discipline of Citizen Science.
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
An ichthyofaunal list of bycatch species was compiled, the fish captured by bottom gill-nets set at approximately 300 m depth in the Uraga Suido Channel central Japan. Fragmentary ichthyofaunal lists are available for this area; these lists have focused on chondrichthyans or commercial actinopterygians, but voucher specimens have not been prepared for museum storage. An initial list of the fish fauna was compiled with vouchers, and seven species not previously recorded from the channel are reported. Most of these species belong to the Class Actinopterygii; Apristurus platyrhynchus (Tanaka, 1909), Beryx decadactylus Cuvier, 1829, Hoplostethus japonicus Hilgendorf, 1879, Sebastes iracundus (Jordan & Starks, 1904), Scalicus amiscus (Jordan & Starks, 1904), Atrobucca nibe (Jordan & Thompson, 1911), and an unidentified species of the eelpout family Zoarcidae. The taxonomic identity of the eelpout and the biogeography of the Uraga Suido Channel are considered. Further research is required to resolve outstanding faunistic issues, but live collections will likely end when the aging fishers who provide the specimens retire. At that point, existing museum collections will become increasingly important for future research. Examination of a collection that may have been previously deposited in the Chiba Prefectural Museum will be essential.
COI-based DNA barcoding could be an efficient tool for species identification of deep-sea fishes and could lead to the discovery of cryptic species diversity. However, the availability of reference sequences of deep-sea fishes for DNA barcoding is limited, especially for fishes in the northwestern Pacific Ocean. In this study, we performed DNA barcoding of mesopelagic and demersal fish species on the continental shelf and upper slope, collected from deepwater fisheries around Japan and southern Taiwan, to accumulate the reference sequences of deep-sea fishes in the northwestern Pacific Ocean. Overall, we obtained the COI sequences of 123 species from 50 families. Genetic diversity within each species for which COI sequences were obtained from multiple specimens was examined, and we found that Chimaera phantasma (Chimaeridae), Harpadon microchir (Synodontidae), and Pyramodon ventralis (Carapidae) showed high intraspecific genetic differentiation of more than 2% Kimura two-parameter distance. Moreover, for 19 widespread deep-sea fishes, a comparison between our data and previously acquired COI sequence data suggested a high level (more than 2% Kimura two-parameter distance) of genetic differentiation between the northwestern Pacific Ocean and other oceans in each widespread species. These results suggest that many cryptic species or regional populations have not yet been discovered in deep-sea fishes. Alternatively, genetic differentiation was not found worldwide for six species. These results indicate that many taxonomic and biogeographical issues remain for deep-sea fishes, and our DNA barcoding data would provide better understanding of these issues.
The numbers of deep-sea fish species and their genetic diversities are poorly understood because of taxonomic confusion and the lack of robust diagnostic features. However, DNA barcoding using mitochondrial DNA sequences may offer an effective approach to identifying cryptic species and characterizing their genetic diversities. To validate the genetic differentiation identified by DNA mitochondrial barcoding, it is necessary to show that these reflect variations present in nuclear genomic markers. Here, we performed DNA barcoding using cytochrome c oxidase subunit I (COI) sequences and also carried out multiplexed intersimple sequence repeat genotyping by sequencing (MIG-seq) for mesopelagic and demersal fish species from the continental shelf and upper slope of the northwestern Pacific Ocean. We obtained the COI sequences of 115 species from 48 families; the species were identified using the Barcode of Life Data System. Phylogenetic analyses using COI sequences showed high levels of intraspecific genetic differentiation (Kimura 2-parameter distances >2%) in 20 of 115 species, suggesting many cryptic species or intraspecific genetic differentiation previously unknown in these species. We performed phylogenetic and population genetic analyses using multiple single-nucleotide polymorphism loci obtained by MIG-seq of 3 species that showed high levels of intraspecific genetic differentiation in COI sequences. The nuclear markers confirmed the genetic differentiation in all 3 species identified by the COI sequences. The high concordance between these different genetic markers indicates the effectiveness of DNA barcoding for identifying cryptic deep-sea species and characterizing genetic differentiation in these species.
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