Population genetic patterns across the native and invasive range of a widely distributed seagrass: Phylogeographic structure, invasive history and conservation implications.

Aim: The seagrass Zostera japonica is a dramatically declined endemic species in the Northwestern Pacific from the (sub)tropical to temperate areas, however, it is also an introduced species along the Pacific coast of North America from British Columbia to northern California. Understanding the population's genetic patterns can inform the conservation and management of this species. Location: North Pacific. Methods: We used sequences of the nuclear rDNA internal transcribed spacer (ITS) and chloroplast trnK intron maturase (matK), and 24 microsatellite loci to survey 34 native and nonnative populations (>1000 individuals) of Z. japonica throughout the entire biogeographic range. We analysed the phylogeographic relationship, population genetic structure and genetic diversity of all populations and inferred possible origins and invasion pathways of the nonnative ones. Results: All markers revealed a surprising and significant deep divergence between northern and southern populations of Z. japonica in the native region separated by a well-established biogeographical boundary. A secondary contact zone was found along the coasts of South Korea and Japan. Nonnative populations were found to originate from the central Pacific coast of Japan with multiple introductions from at least two different source populations, and secondary spread was likely aided by waterfowl. Main Conclusions: The divergence of the two distinct clades was likely due to the combined effects of historical isolation, adaptation to distinct environments and a contemporary physical barrier created by the Yangtze River, and the warm northward Kuroshio Current led to secondary contact after glacial separation. Existing exchanges among the nonnative populations indicate the potential for persistence and further expansion. This study not only helps to understand the underlying evolutionary potential of a widespread seagrass species following global climate change but also provides valuable insights for conservation and restoration.

Tidal Variations of Fish Larvae Measured Using a 15-Day Continuous Ichthyoplankton Survey in Subei Shoal: Management Implications for the Red-Crowned Crane (Grus japonensis) Population in Yancheng Nature Reserve.

The National Yancheng Rare Birds Nature Reserve is a vitally important staging habitat for the wild population of red-crowned cranes (Grus japonensis) in China. The population relies on local high-protein food sources, such as fish juveniles, to fuel their migratory journeys. However, little is known about the ecology of the fish larvae and juveniles that migrate to the inshore area via tidal rhythm in Subei Shoal, which is adjacent to the reserve. Therefore, we used a fixed study station (32°55'1.2″ N, 121°19'58.8″ E) to conduct a continuous 15-day ichthyoplankton survey at 2 h intervals beginning at 05:00 on 25 April and ending at 03:00 on 10 May 2019. We identified the tidal variations in the number of fish larvae and juveniles and the number at various developmental stages and assessed how they were related to environmental variables such as sea surface temperature, salinity, turbidity, and tidal height in the Dafeng Sea area of Subei Shoal. We found that the number of species and larval individuals were highest and lowest, respectively, at the highest and lowest tidal height, and they obviously increased and decreased with the rising and ebb tide, respectively. Our findings indicate that the variation in numbers of the larvae and juveniles depends on species and developmental stage. The species Acanthogobius ommaturus, Pholis fangi, Cynoglossus joyneri, Liza haematocheila, and Lateolabrax japonicus and the total number of larvae were most influenced by tidal height. These results provide a better understanding of the habitat of prey species of the red-crowned crane wild population as well as scientific data that can be applied to manage the wild population in the reserve sustainably.

Seasonal variations in the diversity and benthic community structure of subtidal artificial oyster reefs adjacent to the Luanhe River Estuary, Bohai Sea.

Artificial oyster reefs provide important spawning and nursery grounds for a variety of fishes and large mobile crustaceans. Between July 2016 and May 2017, seasonal surveys of species composition and community structure were performed in the artificial oyster reef area and control area adjacent to the Luanhe River Estuary in China. During the survey year, 56 species belonging to 50 genera, 45 families, and 19 orders were recorded. The dominant economically important fish and mobile crustaceans were Hexagrammos otakii, Pholis fangi, Sebastes schlegelii, Charybdis japonica, and Oratosquilla oratoria. Resident fishes belonged to the Cynoglossidae, Paralichthyidae, Pleuronectidae, and Gobiidae families. Seasonally important fish species included Lateolabrax japonicus, Konosirus punctatus, Thryssa kammalensis, Hexagrammos agrammus, and Acanthopagrus schlegelii. The ranges of H' values among stations were 1.18-2.16, 0.65-1.75, 1.18-2.06, and 0.62-1.92 in spring, summer, autumn, and winter, respectively. The benthic organisms present in the community of artificial oyster reef areas can be classified into groups according to month and season. The abundance biomass curves showed that the oyster reef area in spring, autumn, and winter experienced low disturbance, whereas the community structure in summer was subject to large variations from external disturbance. We also found that as the age of the oyster reefs increased, the percentage of oysters in the low shell height group (< 40 mm) decreased. The oyster density was 324 ind/m2 for the reef created in 2016, 724 ind/m2 for the reef created in 2015, and 364 ind/m2 for the reef created in 2013. These findings can be used to develop suitable management strategies for the sustainable maintenance of artificial oyster reef ecosystems.

Phylogeographic heterogeneity of the brown macroalga Sargassum horneri (Fucaceae) in the northwestern Pacific in relation to late Pleistocene glaciation and tectonic configurations.

Pleistocene glacial oscillations and associated tectonic processes are believed to have influenced the historical abundances and distribution of organisms in the Asia Northwest Pacific (ANP). Accumulating evidence indicates that factors shaping tempospatial population dynamics and distribution patterns of marine taxa vary with biogeographical latitude, pelagic behaviour and oceanographic regimes. To detect what kinds of historical and contemporary factors affected genetic connectivity, phylogeographic profiles of littoral macroalga Sargassum horneri in the ANP were analysed based on mitochondrial (Cox3) and chloroplast (rbcL) data sets. Five distinct clades were recovered. A strong signature of biogeographical structure was revealed (Φ(CT) = 0.487, P < 0.0001) derived from remarkable differentiation in clade distribution, as clade I is restricted to Chinese marginal seas (Yellow-Bohai Sea, East China Sea and South China Sea), whereas clades II-V are discontinuously scattered around the main Islands of Japan. Furthermore, two secondary contact regions were identified along the south Japan-Pacific coastline. This significant differentiation between the two basins may reflect historical glacial isolation in the northwestern Pacific, which is congruent with the estimates of clade divergence and demographic expansion during the late Quaternary low sea levels. Analysis of molecular variance and the population-pair statistic F(ST) also revealed significant genetic structural differences between Chinese marginal seas and the Japanese basin. This exceptional phylogeographic architecture in S. horneri, initially shaped by historical geographic isolation during the late Pleistocene ice age and physical biogeographical barriers, can be complicated by oceanographic regimes (ocean surface currents) and relocating behaviour such as oceanic drifting.

Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters.

BACKGROUND: Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. METHODS: We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. RESULTS: In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to a raft, which was applied to half of the oyster culture rafts to improve oyster growth. The area of seagrass meadows has been expanding since 2013. Although the lagoon had experienced frequent oyster mass mortality events in summer before the tsunami, these events have not occurred since 2011. The 2011 earthquake and tsunami deepened the sill depth and widened the entrance to enhance water exchange and improve water quality in the lagoon. These changes brought the expansion of seagrass meadows and reduction of mass mortality events to allow sustainable oyster culture in the lagoon. Mapping and monitoring of seagrass meadows and aquaculture facilities via satellite remote sensing can provide clear visualization of their temporal changes. This can in turn facilitate effective aquaculture management and conservation of coastal ecosystems, which are crucial for the sustainable development of coastal waters.

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation.

We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.

Revealing the deposition of macrophytes transported offshore: Evidence of their long-distance dispersal and seasonal aggregation to the deep sea.

The role of coastal macrophyte beds as a carbon sink is under debate. Various studies have provided global estimates of the carbon sequestration and stocks of macrophyte beds; however, the final fate of macrophyte debris exported from coastal beds remains uncertain, and must be determined in order to fully clarify the role of coastal vegetation as a carbon sink. Here we conducted bottom-trawl surveys to investigate the extensive and seasonal aggregation of exported macrophytes on the continental shelf and slope seafloor (40-1,800 m). Sunken macrophytes showed a clear seasonal trend with highest biomasses in summer. This was mainly caused by the most collected macrophyte species Sargassum horneri. Furthermore, we used numerical simulations to verify the link between sea-surface hydrographic condition and seafloor distribution of sunken macrophytes. Our results showed that S. horneri accumulated beneath the Kuroshio Extension current, which is the western boundary current of the North Pacific subtropical gyre. Overall, floating macrophytes that became transported offshore by a stable sea-surface current, such as the western boundary current, constitute an organic carbon pathway from coastal waters to the deep sea. Our findings suggest that these buoyant macrophytes can act as a biological pump to enhance oceanic carbon sequestration.

Sargassum horneri C. Agardh space capacity estimation reveals that thallus surface area varies with wet weight.

Sargassum horneri C. Agardh is an important commercial edible seaweed species in east Asia. Benthic beds and floating rafts in coastal areas make excellent habitats for marine organisms to feed, hide, and spawn. Many commercially important fish species such as Japanese anchovy (Engraulis japonicus), yellowtail (Seriola quinqueradiata), and Japanese horse mackerel (Trachurus japonicus) live in seaweed beds. Chinese and Japanese fisherman rely on S. horneri beds as productive fish harvest areas. The Zhejiang government in China set a total allowable catch standard, to preserve the Ma'an Islands ecosystem, which is a marine protected area. In this study we analysed the association between weight and one-sided surface area of S. horneri beds, and calculated the ratio of one-sided surface area to change in wet weight over time. We collected samples from December 2014 to May 2015. Approximately 1 g of S. horneri biomass provided ~15 cm2 of one-sided surface area available to marine organisms. These calculations can be used as a reference regarding potential space to improve total allowable catch standard management in S. horneri beds, through the estimation of space capacity of seaweed beds.

Effect of maternal foraging habitat on offspring quality in the loggerhead sea turtle (Caretta caretta).

Exploring a trade-off between quantity and quality of offspring allows differences in the fitness between alternative life histories to be accurately evaluated. We addressed the mechanism that maintains alternative life histories (small oceanic planktivores vs. large neritic benthivores) observed in a loggerhead sea turtle (Caretta caretta) population, which has been suggested to be environmental, based on the lack of genetic structure and a large difference in reproductive output. We examined whether maternal foraging habitat affects offspring quality, by measuring the morphology, emergence success, and righting response of hatchlings following incubation in a common open sand area over the whole nesting season at Yakushima Island, Japan, and by recording early growth and survival of offspring that were reared in a common environment at a Japanese aquarium. Furthermore, we tested whether sea turtles adjust egg size in response to temporal shifts of the incubation environment. There were no significant differences in any hatchling traits between oceanic and neritic foragers (which were classified by stable isotope ratios), except for clutches laid during the warmest period of the nesting season. There were also no significant differences in the growth and survival of offspring originating from the two foragers. The size of eggs from both foragers significantly increased as the season progressed, even though the rookery had heavy rainfall, negating the need to counteract heat-related reduction in hatchling morphology. In comparison, the sizes of adult body and clutches from both foragers did not vary significantly. The results further support our previous suggestions that the size-related foraging dichotomy exhibited by adult sea turtles does not have a genetic basis, but derives from phenotypic plasticity. Adjustment in reproductive investment may be associated with: (1) predation avoidance, (2) founder effect, and/or (3) annual variation in egg size.

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.

Hidden heat transfer in equilibrium states implies directed motion in nonequilibrium states.

We study a class of heat engines including Feynman's ratchet, which exhibits a directed motion of a particle in nonequilibrium steady states maintained by two heat baths. We measure heat transfer from each heat bath separately, and average them using a careful procedure that reveals the nature of the heat transfer associated with directed steps of the particle. Remarkably we find that steps are associated with nonvanishing heat transfer even in equilibrium, and there is a quantitative relation between this hidden heat transfer and the directed motion of the particle. This relation is clearly understood in terms of the principle of heat transfer enhancement, which is expected to apply to a large class of highly nonequilibrium systems.

Attachment strength of the subtidal seaweed Sargassum horneri (Turner) C. Agardh varies among development stages and depths.

Sargassum horneri is one of the most important contributors to the rafts of floating seaweed in the waters off the coasts of northeastern Asia. These rafts serve as spawning and nursery grounds for many marine organisms, including Japanese saury and yellowtail. Thus, the details of the attachment/detachment mechanisms of S. horneri are of commercial significance for the aquaculture industry. Here, we describe variations in the attachment strength of S. horneri as it relates to its developmental stage and depth along a bottom gradient. We measured the attachment strength/dislodgement force of S. horneri samples with holdfast detachment in Shidagaura Cove, Shimoda, Japan, from December 2014 to May 2015. After we had determined the dislodgement forces required to detach thalli from the substratum (using a spring scale device) in the field, we transferred released individuals to the laboratory and measured selected morphological traits. Attachment strength was linearly related to the holdfast basal area when thalli were immature (prior to mid-March), but not when they were mature (mid-March to May). Thus, attachment strength was maintained through the reproductive phase and declined thereafter, allowing released thalli to join the drifting raft community. Rafting may be a mechanism by which the species expands its distribution range, as floating thalli continuing to shed germlings that are able to recruit when suitable habitat is encountered. Attachment strengths were greater in the shallows than in deeper water, reflecting the differences in wave forces experienced at different depths.

Impacts by heavy-oil spill from the Russian tanker Nakhodka on intertidal ecosystems: recovery of animal community.

The impact of a heavy-oil spill from the Nakhodka on an intertidal animal community, and the recovery process of animals from the damage were surveyed from the autumn of 1997 to the spring of 2001. The field study was carried out in the rocky coast of Imago-Ura Cove, located along the Sea of Japan, where clean-up operations for oil pollution had been conducted less intensely than in other polluted areas. We have examined individual number of each animal taxon by continuously placing a quadrat of 5 m width along the entire intertidal zone of the cove. A total of 76 invertebrate taxa including 57 species of mollusks, 10 species of crustaceans were observed during the survey. The number of taxa increased from 1998 to 1999 in areas where the initial oil pollution was intense. Total individual number of benthic animals continued to increase from 1998 to 2000 in the polluted areas. The impact of oil on benthic animals was different from species to species. Some species such as Cellana toreuma and Monodonta labio confusa increased rapidly after the oil spill, whereas other species such as Patelloida saccharina lanx and Septifer virgatus did not show any apparent temporal tendencies. Population size structure of P. saccharina lanx varied greatly among years, however that of M. labio confusa did not. For P. saccharina lanx, recruitment was unsuccessful in 1997, possibly due to the effect of oil pollution. These differences in responses to oil pollution among benthic animals are considered to be caused by the differences in habitat use, susceptibility to heavy-oil, life history and migration ability. The findings suggest that it took at least 2-3 years for the intertidal animal community to recover to its original level after the oil spill.

Possible change in distribution of seaweed, Sargassum horneri, in northeast Asia under A2 scenario of global warming and consequent effect on some fish.

Global warming effects on seaweed beds are already perceptible. Their geographical distributions greatly depend on water temperatures. To predict future geographical distributions of brown alga, Sargassum horneri, forming large beds in the northwestern Pacific, we referred to future monthly surface water temperatures at about 1.1° of longitude and 0.6° of latitude in February and August in 2050 and 2100 simulated by 12 organizations under an A2 scenario of global warming. The southern limit of S. horneri distribution is expected to keep moving northward such that it may broadly disappear from Honshu Island, the Chinese coast, and Korean Peninsula in 2100, when tropical Sargassum species such as Sargassum tenuifolium may not completely replace S. horneri. Thus, their forests in 2100 do not substitute those of S. horneri in 2000. Fishes using the beds and seaweed rafts consisting of S. horneri in East China Sea suffer these disappearances.

Unusual distribution of floating seaweeds in the East China Sea in the early spring of 2012.

Floating seaweeds play important ecological roles in offshore waters. Recently, large amounts of rafting seaweed have been observed in the East China Sea. In early spring, juveniles of commercially important fish such as yellowtail accompany these seaweed rafts. Because the spatial distributions of seaweed rafts in the spring are poorly understood, research cruises were undertaken to investigate them in 2010, 2011, and 2012. Floating seaweed samples collected from the East China Sea during the three surveys contained only Sargassum horneri. In 2010 and 2011, seaweed rafts were distributed only in the continental shelf and the Kuroshio Front because they had become trapped in the convergence zone of the Kuroshio Front. However, in 2012, seaweed was also distributed in the Kuroshio Current and its outer waters, and massive strandings of seaweed rafts were observed on the northern coast of Taiwan and on Tarama Island in the Ryukyu Archipelago. Environmental data (wind, currents, and sea surface height) were compared among the surveys of 2010, 2011, and 2012. Two factors are speculated to have caused the unusual distribution in 2012. First, a continuous strong north wind produced an Ekman drift current that transported seaweed southwestward to the continental shelf and eventually stranded seaweed rafts on the coast of Taiwan. Second, an anticyclonic eddy covering northeast Taiwan and the Kuroshio Current west of Taiwan generated a geostrophic current that crossed the Kuroshio Current and transported the rafts to the Kuroshio Current and its outer waters. Such unusual seaweed distributions may influence the distribution of fauna accompanying the rafts.

Thermal transistor utilizing gas-liquid transition.

We propose a simple thermal transistor, a device to control heat current. In order to effectively change the current, we utilize the gas-liquid transition of the heat-conducting medium (fluid) because the gas region can act as a good thermal insulator. The three terminals of the transistor are located at both ends and the center of the system, and are put into contact with distinct heat baths. The key idea is a special arrangement of the three terminals. The temperature at one end (the gate temperature) is used as an input signal to control the heat current between the center (source, hot) and another end (drain, cold). Simulating the nanoscale systems of this transistor, control of heat current is demonstrated. The heat current is effectively cut off when the gate temperature is cold and it flows normally when it is hot. By using an extended version of this transistor, we also simulate a primitive application for an inverter.

Thermal diode utilizing asymmetric contacts to heat baths.

We propose a simple thermal diode passively acting as a rectifier of heat current. The key design of the diode is the size asymmetry of the areas in contact with two distinct heat baths. The heat-conducting medium is liquid, inside of which gaslike regions are induced depending on the applied conditions. Simulating nanoscale systems of this diode, the rectification of heat current is demonstrated. If the packing density of the medium and the working regime of temperature are properly chosen, the heat current is effectively cut off when the heat bath with narrow contact is hotter, but it flows normally under opposite temperature conditions. In the former case, the gaslike region is induced in the system and it acts as a thermal insulator because it covers the entire narrow area of contact with the bath.

Physical and topographic factors affecting suspended particulate matter composition in a shallow tropical estuary.

To better understand topography-dependent characteristics of suspended particulate matter (SPM) in a tropical shallow estuary during dry season, the physical factors causing an increase in SPM and the sources of SPM were investigated at the western coast of Thailand. Single and multiple regression analyses using physical parameters as independent variables indicated that periodic tidal current-driven resuspension, episodic wind-driven resuspension, and river-borne inputs were the most important factors controlling SPM increases in areas surrounded by sand bars, areas directly facing the ocean, and areas close to the river mouth, respectively. The assessment of the origin of increased SPM over the background levels estimated from the chemical signatures (delta(13)C and C/N ratio) at all investigated locations and for each event responsible for an increase in SPM confirmed the results of the multiple regression analyses. The results suggested that specific characteristics of SPM at each location were highly contributed by sedimentary materials and could be rather consistent through the season under similar weather conditions.

Expression for the stationary distribution in nonequilibrium steady states.

We study the nonequilibrium steady state realized in a general stochastic system attached to multiple heat baths. Starting from the detailed fluctuation theorem, we derive concise and suggestive expressions for the corresponding stationary distribution which are correct up to the second order in thermodynamic forces. The probability of a microstate eta is proportional to exp[Phi(eta)] where Phi(eta)=-[under summation operator]kbeta_{k}E_{k}(eta) is the excess entropy change. Here, E_{k}(eta) is the difference between two kinds of conditioned path ensemble averages of excess heat transfer from the kth heat bath whose inverse temperature is beta_{k}. This result can be easily extended to steady states maintained with other sources, e.g., particle current driven by an external force. Our expression may be verified experimentally in nonequilibrium states realized, for example, in mesoscopic systems.

Steady-state thermodynamics for heat conduction: microscopic derivation.

Starting from microscopic mechanics, we derive thermodynamic relations for heat conducting nonequilibrium steady states. The extended Clausius relation enables one to experimentally determine nonequilibrium entropy to the second order in the heat current. The associated Shannon-like microscopic expression of the entropy is suggestive. When the heat current is fixed, the extended Gibbs relation provides a unified treatment of thermodynamic forces in the linear nonequilibrium regime.