Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan

Understanding the structure and connectivity of coral populations is fundamental for developing marine conservation policies, especially in patchy environments such as archipelagos. The Nansei Islands, extending more than 1,000 km in southwestern Japan, are characterized by high levels of biodiversity and endemism, supported by coral reefs, although precise, detailed genetic attributes of corals are still largely unknown. In this study, we conducted population genomic analyses based on genome-wide, single-nucleotide polymorphisms (SNPs) of Acropora digitifera, a common species in the Nansei Islands, for which a complete genome is available. With ~24x sequencing coverage of entire genomes of 303 colonies collected at 21 locations, we identified more than four million genome-wide SNPs. While population structure analyses suggested weak genetic differentiation among sampled locations, the most southwestern location (the west end of the Yaeyama Islands) was genetically similar to the northernmost location (the Tanegashima Islands), separated by >1,000 km. Although examination of a migration network found a general tendency of northward migration along the Kuroshio Current, a substantial amount of southward migration was also detected, indicating important contributions of minor ocean currents to coral larval dispersal. Moreover, heterogeneity in the transition of effective population sizes among locations suggests different histories for individual subpopulations. The unexpected complexity of both past and present population dynamics in the Nansei Islands implies that heterogeneity of ocean currents and local environments, past and present, have influenced the population structure of this species, highlighting the importance of local scale assessments for effective coral restoration and management.

Variety of the drift pumice clasts from the 2021 Fukutoku-Oka-no-Ba eruption, Japan.

Pumice rafts that arrived at the Nansei Islands, Japan, provided a unique opportunity to investigate the Fukutoku-Oka-no-Ba (FOB) eruption of August 2021. Despite drifting for two months for >1300 km, the drift pumice raft had a large volume and contained a variety of pumice clasts, some of which were deposited during a high tide in a typhoon, while others were washed up on a sandy beach. Most of the drift pumice clasts are gray in color, vesicular, and have a groundmass containing black enclaves, which are similar to those collected in the ocean near FOB about one week after the eruption. Rare black pumice and the main gray pumice components have similar trachytic compositions, with SiO2 = 61–62 mass% and total alkalis = 8.6–10 mass% (on an anhydrous basis). Both pumice types contain clinopyroxene, plagioclase, and rare olivine phenocrysts. Thin-section observations show that the gray pumice has more elongated vesicles as compared with the black pumice that has spherical vesicles, even where the two types of pumice are in the same clast. The glass in the black pumice is transparent and brown in color, while that in the gray pumice is colorless. No micro or nano-crystals were observed during electron and optical microscopy in the brown domain. Raman spectra of the brown-colored glass exhibit a clear magnetite peak, suggesting magnetite nanolites cause the brown color. High-Mg (100 × Mg/[Mg+Fe] = 92) olivine in the black pumice has an equilibrium temperature of 1240 °C and a rim diffusion profile indicative of re-equilibration with the surrounding melt over a period of hours to days.The textural relationships between the gray and black pumice suggest that the black pumice had become black and viscous before the two types of pumice mixed. Therefore, crystallization of magnetite nanolites and a corresponding increase in melt viscosity were important in the eruption preparation process, which then resulted in a large-scale Plinian eruption.

A new species of Bestiolina (Copepoda, Calanoida, Paracalanidae) and complementary description of B. similis (Sewell, 1914) from the Nansei Islands, Japan

Two species of the calanoid copepod genus Bestiolina occurred in estuarine/coastal waters of the Nansei Islands, southernmost Japan. One of them is described herein as Bestiolina okinawae sp. nov., which is distinguished from known congeners by a combination of the following characteristics: 1) fifth pedigerous somite bearing groups of tiny spinules on the posterior end, 2) female mandible bearing a rod-shaped first gnathal tooth, 3) male left leg 5 with short apical spine on long terminal segment, and 4) legs 2–3 with endopodal segment 2 lacking spinules. The new species was the dominant zooplankter in oligohaline waters. The other species is morphologically identifiable to Bestiolina similis (Sewell, 1914). Genetic analysis using COI revealed that the two species differed by 9.9–10.0%, in contrast to small intra-specific genetic variation (0.0–1.5%). The two species were spatially segregated in low-salinity (2–30) estuaries and high-salinity (25–36) coastal waters, respectively, but co-occurred in some samples. Their body length decreased from the winter (around 20°C) to the summer (around 30°C) by 9.5–18.1%, depending on the species and sex. In both species, adult males, which lack mandibular gnathobase, were larger than the adult females.

Fine-scale horizontal distributions of multiple species of larval tuna off the Nansei Islands, Japan

To quantitatively evaluate the distribution of tuna larvae relative to oceanographic conditions, we conducted investigations off the Nansei Islands in the western North Pacific in June from 2015 to 2017. Five species, namely Pacific bluefin tuna Thunnus orientalis (PBF), yellowfin tuna T. albacares (YFT), skipjack tuna Katsuwonus pelamis (SKJ), frigate tuna Auxis thazard, and bullet tuna A. rochei (BT), were collected in each year. The most dominant species was BT throughout the 3 yr period, followed by SKJ in 2015 and YFT in 2016 and 2017. The horizontal larval distributions of the 5 species were largely influenced by the Kuroshio Current: larvae of the 2 Auxis species were distributed in the Kuroshio and the Kuroshio inshore waters, whereas those of the other species were found in the Kuroshio offshore waters. These differences are consistent with the differences in spawner distributions among the tunas. Generalized additive models (GAMs) indicated that the larval densities were affected by the sea surface height anomaly and that the larvae were not always amassed by horizontal transport. Sea surface temperature (SST) and salinity possibly influenced the larval physiology and survival, thereby determining their densities. In the GAMs, PBF and YFT showed similar responses to SST, and YFT and SKJ similarly responded to salinity. To avoid overlapping their ecological niches, the larvae of 3 species (PBF, YFT, and SKJ) are expected to differ in other ways, including their vertical distributions and feeding habits.