Natural History Museum and Institute, Chiba
Recent publications
We examined the chemical constitution of the red alga Laurencia saitoi Perestenko, collected from Katsuura, Boso Peninsula, Chiba Prefecture, Japan. This specimen produced a new polyhalogenated acetogenin, named katsuurallene ( 1 ), which structure was determined by the spectral methods, along with known diterpene, deoxyparguerol ( 2 ) and triterpene, thyrsiferol ( 3 ). In this paper we describe the structural elucidation of katsuurallene together with some biological activities.
Seven isolated eggshell fragments and six eggshell impressions were collected from the Okurodani Formation (Hauterivian to Barremian) in Shokawa, Takayama City, Gifu Prefecture, Japan. To date, these specimens represent the oldest fossil eggshells in the country. Microscopic observations classified the eggshells into Testudoolithidae indet., Ramoprismatoolithus okurai oogen. et oosp. nov. and indeterminate type. For Testudoolithidae indet., the eggshell microstructure and estimated egg size suggest that they could be laid by any of the cryptodiran turtles reported by skeletal remains from the formation: Trionychoidea, Xinjiangchelyidae and Sinemydidae. Ramoprismatoolithus okurai bears prismatic microstructure and ramifying ridges on the outer surface, the combination of which is unusual for prismatoolithid eggshells. Based on morphological observations and phylogenetic analyses, Ramoprismatoolithus was ascribed to troodontid or closely related non-avian maniraptorans. The remaining specimens consist of eggshell surface impressions without original fragments, for which oospecies and taxonomic affinity are indeterminate. These findings demonstrate that eggshell fragments shed light on small-bodied taxa that are poorly represented by skeletal remains in the region. While the fossil record of small maniraptoran species from the early Early Cretaceous is relatively scarce worldwide, Ramoprismatoolithus adds to this record and extends the confirmed geographic range of this clade. urn:
Betula davurica is a relict species in Japan of which distribution is influenced by topography at local scale. This species may also be dependent on disturbance for regeneration. However, no studies found that estimate and compare the effects of topography and human disturbance on abundance of this species. Focusing on abandoned charcoal kilns and charcoals in the surface soil as proxies for historical disturbance, we assessed the status of B. davurica in a secondary deciduous broad-leaved stand in central Japan. Although B. davurica was once a dominant species in the study area, its regeneration has stagnated after decline of charcoal production. The oldest individual was 90 years of age, suggesting that the current-day population established following a period of grassland dominance 100 years ago. We found multiple abandoned kilns, as well as widespread charcoal fragments in the surface soils of the study area. Both individuals, that had established prior to and following the decline of charcoal production, tended to be distributed at sites with other tree species with smaller DBH and at gentle slope. Location of charcoal kilns did not significantly affect the distribution of this species. It is possible that B. davurica prefers to gentle slope at the sites where historical logging for charcoal production and fire disturbance had influenced at the whole. Cessation of logging and fire disturbance have likely inhibited the regeneration of B. davurica. Logging of other tree species around at gentle slope may be necessary for the survival of this species.
An isolated theropod tooth was found in the HauterivianBarremian Itsuki Formation of the Tetori Group in the Kuzuryu district, Ono City, Fukui Prefecture, central Japan. The present specimen, OMFJ V-1, shows a thick lanceolate basal cross-section and small mesial and distal denticles. A cladistic analysis based on the dental characters suggested that OMFJ V-1 be classified as belonging to Allosauroidea or Tyrannosauroidea. Principal component and linear discriminant analyses also suggested that OMFJ V-1 belongs to either of these two theropod clades. The posterior probabilities obtained in the linear discriminant analyses indicated that the confidence of the classification as Allosauroidea is slightly higher than that for Tyrannosauridae. However, because these analyses also supported possibilities of OMFJ V-1 belonging to other theropod clades to lesser extents, its taxonomic referral remains ambiguous. If OMFJ V-1 belongs to Tyrannosauroidea, it would indicate that a medium-sized tyrannosauroid already appeared in central Japan during the HauterivianBarremian age. On the other hand, if OMFJ V-1 belongs to Allosauroidea, it would indicate that at least two medium-to-large-sized theropods, allosaurids and tyrannosaurids, lived almost coevally in this region. The third possibility is that OMFJ V-1 belongs to Megaraptora. If such affinities are established, it would represent the oldest record of this clade of theropods.
Background As populations age and pandemics continue, grief disrupts the health and productivity of increasingly bereaved populations. While funerals can reconnect old friends and relations to provide psycho-social support, and satisfying funeral participation reportedly reduces such psychiatric complications of grief, the psychological effects of recent restrictions on funerals remains unclear. This first English report of open-ended responses to a Japan-wide survey sheds some light on this by looking at Japanese psychological reflections on their funerals. Objectives To determine what aspects of funerals the Japanese bereaved feel psycho-socially valuable or conversely problematic, and for what reasons. Setting Data were collected using anonymized all-Japan postal surveys from 2019 to 2020. Participants 288 recently-bereaved chief mourners submitted 353 open-ended responses discussing their experiences and feelings about the funerals they conducted. Method Anonymized data were divided into positive, regrets, vacillations, and negative comments about the subjects most frequently cited. Results Most commonly cited were funeral directors (64), attendees (56), ritual/ceremony (49), and the need for (pre-)planning (40). Respondents profoundly appreciated funeral directors' support, and regretted not having planned better or invited more people to the funeral. Dissatisfaction tended to focus on unexplained expenses and mistakes or offenses in rituals. Many also criticized their doctors for not realistically forecasting their loved ones' demise. Conclusions Responses validated that responsive funeral directors can significantly support their clients through early acute grief, and that inviting more celebrants to a full funeral facilitates psycho-social support and may obviate future regrets. Rituals too provide memorable means to help survivors deal with grief. Medical professionals should psychologically encourage terminal patients' families to communicate while patients are still coherent; families are strongly advised to discuss funeral plans with their elders before the end of life.
There are many cases where eutrophication has become a common in irrigation pond, remarkable in ponds because the use of agricultural land irrigation has been abolished and it is operated as a park pond. Regular water drying is no longer carried out in these park ponds. Ecological disturbances such as water level fluctuation has disappeared in these ponds, and overgrowth of certain alien species is observed. Artificial water level disturbances were revived in these ponds, increasing predation pressure by birds on invasive crayfish Procambarus clarkii and bullfrog Rana catesbeiana. As a result, low density management of invasive crayfish and bullfrog was successful. The overgrown area of aquatic plants has expanded, and the population density of zooplankton such as Cladocera has increased. The effect spread widely to the biota through the food web, and the effect on water environment conservation was confirmed.
Promoting the use of renewable energy and conserving biodiversity are conflicting issues that need addressing. While the development of offshore wind facilities/turbines is accelerating, many seabirds have been exposed to collisions with wind turbines. We must identify high collision areas and avoid the construction of wind turbines in these spaces to reduce these conflicts. One solution is to develop useful finer scale sensitivity maps. In this study, we created a fine-scale map of collision risk by spatial modelling using information from bird flights at sea and explored the relative importance of each geographic variable relevant to the risk. Between 2016 and 2019, we collected 3D-location data from 117 black-tailed gulls (Larus crassirostris) of three colonies in two areas and 21 slaty-backed gulls (L. schistisagus) of four colonies in one area of northern Hokkaido, Japan. The spatial models that explain the occurrence of M-zone flight, which is the flight within the heights of high collision risk (20–140 m height), were constructed at a 1 km mesh using a random forest algorithm, a machine-learning tool. The model satisfactory predicted the spatial distribution of M-zone flights using geographic variables and species (correlation coefficient: 0.57–0.94), although data had some degrees of variation between species, years, colonies, and areas. Our model can be applied to other regions, as long as we have general topological information and the locations of colonies and harbors. The distance to the breeding colony and the nearest harbors were important, and the collision risk was 6–7 times higher within 15 km from the colonies and 5 km from harbors. Black-tailed gulls used different sites for foraging and commuting between years, whereas slaty-backed gulls used relatively consistent sites. These variations between species and among years suggest that collecting bird data over multiple years is necessary and effective for creating a generally applicable sensitivity map.
Filtration is required during the collection of trace amounts of environmental DNA (eDNA) from water samples to achieve a concentration sufficient for downstream molecular experiments. To date, collected water samples have been filtered by humans or electric power using various instruments. We developed a simple gravity filtration system that does not need for an external force. The system comprises a plastic bag filled with a water sample (1 L), a filter cartridge, and a long plastic tube (e.g., 2 m). When hung at a height equal to the tube length, this filtration unit can enable power-free collection and concentration of eDNA at any remote location within a reasonable time (10–60 min). • A simple, rapid, power-free, practical filtration system for environmental DNA analysis is reported. • If there is a place to hang the filtration system, filtration can be performed anywhere. • The filtration speed increased when the system was hung higher.
A small pufferfish, Torquigener albomaculosus, is known to construct an elaborate geometric circular structure, which has been referred to as a “mystery circle,” with a diameter of ~2 m in the sand of the seabed. We reconstructed a 3D model of this structure for the first time using a “structure from motion” (SfM) algorithm. The mystery circle constructed by the pufferfish may have potential applications for biomimetics similar to the structures constructed by termites and prairie dogs. To support the significance of its structural characteristics, it was observed that the water passing through the valley upstream always gathers in the center of the structure, regardless of the direction of water flow. Furthermore, it has the function of extracting fine-grained sand particles from the valleys and directing these to the center. Computational fluid analysis can be performed immediately using the quantified 3D data, and the structural features of the mystery circle is expected to be applied in a wide range of fields, such as architecture and engineering, via biomimetics.
The Yokozuna Slickhead Narcetes shonanmaruae is a recently described deep-sea fish species and an active-swimming, relatively large top predator in Suruga Bay, Japan. Its only known habitat is the deepest part of the bay (>2,000 m); six individuals have been collected thus far (up to 138 cm in total length). During our monitoring survey of faunal diversity on seamounts within marine protected areas in Japanese waters, environmental DNA (eDNA) metabarcoding revealed the Yokozuna Slickhead 12S ribosomal RNA gene sequence on/around three seamounts belonging to the Nishi-Shichito Ridge (at depths of around 2,000 m) located 400–600 km south of the known locality. A baited camera system deployed at the foot of one of the three seamounts at a depth of 2,091 m captured a Yokozuna Slickhead individual that was over 250 cm in total length, threatening Pacific Grenadiers Coryphaenoides acrolepis around the bait and attacking the bait cage. A combination of eDNA metabarcoding and baited camera observation represents a powerful tool for the detection of rare predatory fish species and the study of their ecology even in the deep sea, thus helping to better understand vulnerable marine ecosystems and reveal the impact of the rapidly changing global ocean.
Fire regimes in North American forests are diverse and modern fire records are often too short to capture important patterns, trends, feedbacks, and drivers of variability. Tree‐ring fire scars provide valuable perspectives on fire regimes, including centuries‐long records of fire year, season, frequency, severity, and size. Here, we introduce the newly compiled North American tree‐ring fire‐scar network (NAFSN), which contains 2562 sites, >37,000 fire‐scarred trees, and covers large parts of North America. We investigate the NAFSN in terms of geography, sample depth, vegetation, topography, climate, and human land use. Fire scars are found in most ecoregions, from boreal forests in northern Alaska and Canada to subtropical forests in southern Florida and Mexico. The network includes 91 tree species, but is dominated by gymnosperms in the genus Pinus. Fire scars are found from sea level to >4000‐m elevation and across a range of topographic settings that vary by ecoregion. Multiple regions are densely sampled (e.g., >1000 fire‐scarred trees), enabling new spatial analyses such as reconstructions of area burned. To demonstrate the potential of the network, we compared the climate space of the NAFSN to those of modern fires and forests; the NAFSN spans a climate space largely representative of the forested areas in North America, with notable gaps in warmer tropical climates. Modern fires are burning in similar climate spaces as historical fires, but disproportionately in warmer regions compared to the historical record, possibly related to under‐sampling of warm subtropical forests or supporting observations of changing fire regimes. The historical influence of Indigenous and non‐Indigenous human land use on fire regimes varies in space and time. A 20th century fire deficit associated with human activities is evident in many regions, yet fire regimes characterized by frequent surface fires are still active in some areas (e.g., Mexico and the southeastern United States). These analyses provide a foundation and framework for future studies using the hundreds of thousands of annually‐ to sub‐annually‐resolved tree‐ring records of fire spanning centuries, which will further advance our understanding of the interactions among fire, climate, topography, vegetation, and humans across North America.
We explored the genetic diversity and population genetic structure of an invasive alien species, the raccoon Procyon lotor, which was introduced into the Shikoku Island of Japan, using sequences of the mitochondrial control region and 10 polymorphic microsatellite loci. In 80 individuals examined, we detected two genetically divergent haplotypes, indicating that two maternal lineages had been introduced into Shikoku Island. Population clustering analysis suggested the nonexistence of genetic structure in the area. The relatedness network showed that the raccoon population in Shikoku Island consisted of closely related individuals. The genetic diversity of the Shikoku raccoon population was lower than that in the native range. These results and a prior report indicate that the Shikoku raccoon population is likely to have expanded from small numbers of founders originating from an initial invasive population. Raccoon captures outside Kagawa are decreasing, although past expansions into Tokushima and Ehime suggest that there are no geographical barriers among these areas. Therefore, action should be taken to prevent any re-expansion of the raccoon population in Kagawa. Intensive monitoring and the elimination of dispersers from Kagawa, as well as effort to eradicate potential source populations for expansion in Kagawa, are needed.
Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.
Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57–35 and 37–14 ka, respectively, followed by interpopulation hybridization.
Here we describe Stylobates calcifer sp. nov. (Cnidaria, Actiniaria, Actiniidae), a new carcinoecium-forming sea anemone from the deep-sea floor of Japan. Stylobates produces a carcinoecium that thinly covers the snail shells inhabited by host hermit crabs Pagurodofleinia doederleini. The new species is distinct from other species by the shape of the marginal sphincter muscle, the distribution of cnidae, the direction of the oral disk, and host association. The species’ novelty is supported by the data of its mitochondrial genes 12S, 16S, and COIII and nuclear genes 18S and 28S. Also, we conducted behavioral observation of this new species, focusing on the feeding behavior and interaction with the specific host hermit crab. Our observations suggest that this sea anemone potentially feeds on the suspended particulate organic matter from the water column or the food residuals of hermit crabs. When the host’s shell changed, intensive manipulation for transference of S. calcifer sp. nov. was recorded. However, although the hermit crab detached and transferred the sea anemone to the new shell after shell change, the sea anemone did not exhibit active or cooperative participation. Our data suggest that the sea anemone may not produce a carcinoecium synchronously to its host’s growth, contrary to the anecdotal assumption about carcinoecium-forming sea anemones. Conversely, the host hermit crab’s growth may not depend entirely on the carcinoecium produced by the sea anemone. This study is perhaps the first observation of the behavioral interaction of the rarely studied carcinoecium-forming mutualism in the deep sea.
In this review, the phytogeography and history of Japanese beech (Fagus crenata Blume and F. japonica Maxim.) forests are re‐examined in light of recent phytogeographical and palaeobotanical research advances. I explain the floristics and the climatic and geological contrasts between Japanese beech forests on the Sea of Japan side and the Pacific side of the Japanese archipelago. We also review recent studies on the origin of dwarf evergreen shrub species occurring along the Sea of Japan. The old scenario that these dwarf evergreen shrub species diverged directly from counterpart species occurring on the Pacific coast of Japan is no longer supported. We propose more intricate speciation processes, including phylogenetic relations to extant Chinese species and inter‐species hybridization. We also review the results of recent palaeobotanical studies of forests on the Japanese islands in the Quaternary. The long persistence of beech forests through glacial/interglacial cycles of the Quaternary—with repeated spread and contraction of the geographical range—is confirmed. In addition, we briefly explain the phytosociological classification system of the Japanese beech forest and the geographical ranges of each vegetation type. We review studies of the geographic distribution of F. crenata and F. japonica at the population level, highlighting the need for further ecological and genetic studies of population dynamics near the range limits to understand historic migration processes better. The phytogeography and history of Japanese beech (Fagus crenata Blume and F. japonica Maxim.) forests are re‐examined in light of recent phytogeographical and palaeobotanical research advances. We briefly explain the phytosociological classification system of the Japanese beech forest and the geographical ranges of each vegetation type. We review studies of the geographic distribution of F. crenata and F. japonica at the population level, highlighting the need for further ecological and genetic studies of population dynamics near the range limits to understand historic migration processes better.
We satellite-tracked the eastern buzzard (Buteo japonicus) wintering in Japan to delineate both northward and southward migration routes, destinations, and stopover behavior. Twenty-two buzzards were captured and fitted with functional platform transmitter terminals. For these buzzards that departed from the capture sites, we observed a total of 65 northward migrations during 2008-2016 and a total of 55 southward migrations during 2008-2015. In spring, the eastern buzzards migrated eastward along the Seto Inland Sea in the Chugoku region or further inland. In eastern Honshu, they followed two different routes. One was to Hokkaido via the Tsugaru Peninsula from central or northern central Honshu northward along the side of the Sea of Japan in northern Honshu. The other was to Hokkaido via the Shimokita Peninsula, mainly from the Pacific Ocean side of northern Honshu, moving eastward through central Honshu. Of the 17 birds tracked, 10 summered in Sakhalin, three in Hokkaido, three in northern Honshu, and one unknown. In autumn, the buzzards retraced their northward migration routes. Of the 14 birds that were tracked the entire southward migration, 13 (92%) returned to their respective capture sites. One juvenile wintered in an area different from the capture site. Our study contributes to a deeper understanding of the distribution of breeding and wintering grounds and the migration routes of B. japonicus. In addition, the information on migration obtained in this study can contribute toward appropriate environmental impact assessment for wind power facilities in Japan.
Phoresy, the use of another organism for dispersal, is one of the most intriguing commensalistic interactions. The selection of a correct host is fundamental for phoretic organisms to ensure arrival to suitable habitats and to encounter potential mates. This study focuses on a group of phoretic mites in the genus Lasioseius (Acari: Blattisociidae). In La Selva Biological Station, a tropical wet forest in Costa Rica, Lasioseius mites feed on nematodes inside the scrolls formed by the young leaves of their hosts, plants in the order Zingiberales. When leaves expand and unfurl, mites disperse to another rolled leaf by clinging onto ‘rolled-leaf beetles’, a group of insect herbivores specialized on Zingiberales (genera Cephaloleia and Chelobasis; Coleoptera: Chrysomelidae). In this study, we determined whether Lasioseius mites associated with Cephaloleia belti Baly are specialized on this beetle species as a phoretic host. Mites may also be attracted to Chelobasis perplexa Baly, sharing the same host plant. Another possibility is that Lasioseius mites are opportunistic generalists and attach to rolled-leaf beetle species (e.g., Cephaloleia dorsalis Baly) that never share host plants with either C. belti or Ch. perplexa. In a laboratory setting, we tested whether mites preferred scents from and/or attached to particular beetle species. Scent attraction experiments showed that Lasioseius mites collected from C. belti were attracted to scents from C. belti and Ch. perplexa, but were not attracted to scents from C. dorsalis. Mites collected from C. belti attached to both C. belti and Ch. perplexa, but never to C. dorsalis. In conclusion, Lasioseius mites are not strict specialists, but are able to detect and attach to beetle species that inhabit their host plant.
Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations’ Sustainable Development Goal 14 for 2030. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see for revised estimates.
The complete chloroplast and mitochondrial genome sequences of Scopelophila cataractae (Pottiaceae, Bryophyta) are determined. The chloroplast genome is 122,290 bp with 118 genes and the mitochondrial genome is 105,607 bp with 67 genes, both genomes are circular. This study showed the S. cataractae plastome contains the smallest genome size, and a functional trnPGGG gene, relative to other pottiaceous species. Phylogenetic inferences support the sister relationship of S. cataractae to all other pottiaceous accessions.
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Chiba, Japan