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28 results for “Japanese Archipelago”
Data from: An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago
The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 combinations of interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74 % of the taxa, and an rbcL sequence dataset covering 97.9 % of the taxa. Distribution of diversity was visualized by species richness and phylogenetic diversity. Apomixis was observed in 11.0 % of the native taxa whose reproductive modes are known. The number of sexually reproducing polyploid taxa (n = 199) is less than sexual diploids (n = 241), and 30 of them are evidently allopolyploid, in contrast with the low number of possible autopolyploids (n = 4). A morphological character dataset in Lucid format is provided for taxonomic identification of the native taxa.
Fig. 3 in First Japanese Record of Uropterygius fasciolatus (Muraenidae: Uropterygiinae) Collected from Yonaguni-jima Island, Ryukyu Archipelago
Fig. 3. Illustration of teeth on maxilla (left) and mandible (right) in Uropterygius fasciolatus (KAUM–I. 88910, 441.4 mm TL) collect- ed from Yonaguni-jima island, Japan.
Fig. 1 in First Japanese Record of Uropterygius fasciolatus (Muraenidae: Uropterygiinae) Collected from Yonaguni-jima Island, Ryukyu Archipelago
Fig. 1. Fresh specimen of Uropterygius fasciolatus (upper: KAUM–I. 88909, 304.0 mm TL; middle: KAUM–I. 88910, 441.4 mm TL) collect- ed from Yonaguni-jima island, Japan, and holotype (lower: BMNH 1877.2.24.84, 304.0 mm TL) collected from Atafu in the Tokelau Islands.
Fig. 2 in First Japanese records of Anguilla luzonensis (Osteichthyes: Anguilliformes: Anguillidae) glass eels from Okinawa-jima Island, Ryukyu Archipelago, Japan
Fig. 2. Caudal fin and caudal pigmentation pattern of Anguilla luzonensis glass eel (fresh specimens), KYUM-PI-05434.
Fig. 3 in First Japanese records of Anguilla luzonensis (Osteichthyes: Anguilliformes: Anguillidae) glass eels from Okinawa-jima Island, Ryukyu Archipelago, Japan
Fig. 3. Neighbor-joining phylogenetic tree of species of Anguilla in the Indo-Pacific waters based on partial 16S rRNA sequences. The numbers beside internal branches indicate bootstrap probabilities for 1,000 replicates.
Fig. 3 in First Japanese Record of Muraenichthys gymnopterus (Anguilliformes, Ophichthidae) from Ishigaki-jima Island, Ryukyu Archipelago
Fig. 3. Sensory pores on the head (A), teeth on the maxilla and palatal areas (B), and teeth on the lower jaw (C) of Muraenichthys gymnopterus (WMNH-PIS12244; 174.5 mm total length) collected from Nagura Amparu in Ishigaki-jima Island, Japan. IMT, intermaxillary teeth; IO, infraorbital pores; LL, lateral-line pores; POM, preoperculomandibular pores; SO, supraorbital pores; UJT, upper-jaw teeth; VT, vomerine teeth. Arrows indicate the locations of interorbital and median supratemporal pores.
Fig. 1 in First Japanese Record of Muraenichthys gymnopterus (Anguilliformes, Ophichthidae) from Ishigaki-jima Island, Ryukyu Archipelago
Fig. 1. Map of the sampling site at which the Muraenichthys gymnopterus specimen was collected in Nagura Amparu, Ishigaki-jima Island, Japan (A); photograph of the sampling site at low tide just before we collected a specimen of M. gymnopterus on 29 October 2020 (B).
Data from: An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago
Open the record for dataset details and reuse information.
Data from: Distribution patterns of lianas from subtropical to subboreal zones of the Japanese archipelago and the difference between climbing types
<p><strong>README</strong></p> <p>This dataset was used for the statistical analyses in the article: <a href="https://doi.org/10.1016/j.baae.2023.08.001">Kusakabe et al. (2023) Basic Appl. Ecol.</a> </p> <p> </p> <p><strong>Sub_plot_data_v2.csv</strong></p> <p>Liana abundances, environmental factors, and site information for each subplot in 19 study sites in the Japanese archipelago. Subplots are 400 m<sup>2</sup>(20 m × 20 m) quadrats.</p> <p> </p> <ul> <li> <p><strong>site_information</strong></p> <ul> <li><code>site_name</code> - Site_name.</li> <li><code>site_code</code> - Site_code.</li> <li><code>plot_code</code> - Subplot_code.</li> <li><code>longitude</code> - Longitude of each plot (°E).</li> <li><code>latitude</code> - Latitude of each plot (°N).</li> <li><code>altitude</code> - Altitude of each plot (m).</li> <li><code>forest_type</code> - Plots were classified into four types based on the composition of evergreen broadleaf, deciduous broadleaf, and evergreen coniferous trees. EC: evergreen coniferous forest, BC: mixed coniferous–broadleaf forest, BD: deciduous broadleaf forest, BE: evergreen broadleaf forest. The detailed definition of the forest type was described in Ishihara et al. (2011).</li> <li><code>forest_status</code> - Plots were also classified into three categories based on the age of the forests. old growth: ≥ 150 years old, old secondary: ≥ 100 years old, secondary: < 100 years old. The detailed definition of the forest status was described in Ishihara et al. (2011).</li> <li><code>x, y</code> - Coordinates of the point of origin of each subplot in the census plots (m).<br> </li> </ul> </li> <li> <p><strong>liana_stem_density & liana_basal_area</strong><br> Sum of liana stems (400 m<sup>-2</sup>) and basal area (cm<sup>2</sup>・400m<sup>-2</sup>) in each subplot.</p> <ul> <li><code>whole</code> - All lianas.</li> <li><code>twining</code> - Twining climbers.</li> <li><code>root</code> - Root climbers.</li> <li><code>tendril</code> - Tendril climbers.</li> <li><code>hook</code> - Hook climbers.</li> <li><code>scrambling</code> - Scrambling climbers.<br> </li> </ul> </li> <li> <p><strong>environmental_factors</strong><br> Environmental factors used in the analyses.</p> <ul> <li><code>MAT</code> - Mean annual temperature (°C).</li> <li><code>MAP</code> - Mean annual precipitation (mm).</li> <li><code>MSD</code> - Maximum snow depth (cm).</li> <li><code>SOCN</code> - Soil organic layer carbon:nitrogen ratio.</li> <li><code>SODM</code> - Soil organic matter dry mass (g・100 cm<sup>-2</sup>).</li> <li><code>TSD</code> - Tree stem density with a diameter of ≥ 5 cm at breast height (400 m<sup>-2</sup>).</li> <li><code>TBA</code> - Total basal area of trees with a diameter of ≥ 5 cm at breast height (cm<sup>2</sup>・400 m<sup>-2</sup>).</li> </ul> </li> </ul> <p>Values of latitude, longitude, altitude, SOCN, SODM, TSD, and TBA were derived from published articles (Ishihara et al. 2011, Niwa et al. 2016) and associated, updated datasets that are available on the website of the Biodiversity Center of Japan (<a href="https://www.biodic.go.jp/moni1000/findings/data/index.html">https://www.biodic.go.jp/moni1000/findings/data/index.html</a>). The definitions of forest type and status follow Ishihara et al. (2011). </p> <p>Values of MAT, MAP and MSD were derived from the Agro-Meteorological Grid Square Data, National Agriculture and Food Research Organization (Ohno et al. 2016).</p> <p> </p> <p><strong>References</strong></p> <p>Ishihara, M. I., Suzuki, S. N., Nakamura, M., Enoki, T., Fujiwara, A., Hiura, T., … Yoshida, Y. (2011). Forest stand structure, composition, and dynamics in 34 sites over Japan. _Ecological Research_, 26(6), 1007–1008. <a href="https://doi.org/10.1007/s11284-011-0847-y">https://doi.org/10.1007/s11284-011-0847-y</a></p> <p>Niwa, S., Toyota, A., Kishimoto, T., Sasakawa, K., Abe, S., Chishima, T., … Yoshida, T. (2016). Monitoring of the ground-dwelling beetle community and forest floor environment in 22 temperate forests across Japan. _Ecological Research_, 31(5), 607–608. <a href="https://doi.org/10.1007/s11284-016-1379-2">https://doi.org/10.1007/s11284-016-1379-2</a></p> <p>Ohno, H., Sasaki, K., Ohara, G., & Nakazono, K. (2016). Development of grid square air temperature and precipitation data compiled from observed, forecasted, and climatic normal data. _Climate in Biosphere_, 16, <a href="https://doi.org/10.2480/cib.J-16-028">https://doi.org/10.2480/cib.J-16-028</a></p> <p> </p> <p> </p>
Data from: Population genetic consequences of habitat fragmentation in ectomycorrhizal fungi with different dispersal mechanisms: Implications from ice-aged relict forests across the Japanese archipelago
Open the record for dataset details and reuse information.
Data from: Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times—based on three molecular clock node calibrations—using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades—that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
Subspecies and Distribution. M.f.fuscataBlyth,1875—JapaneseArchipelagoSoftheTsugaruStrait(41°30°N),inHonsu,Shikoku,andKyushuIs,andtheclose-lyingKojima(=Koshima),Kashima,Awajishima,Shodoshima,andKinkazanislets. M. f. yakui Kuroda, 1941 — Japanese Archipelago (Yakushima I, ¢.60 km S of Kyushu). in Cercopithecidae
Subspecies and Distribution. M.f.fuscataBlyth,1875—JapaneseArchipelagoSoftheTsugaruStrait(41°30°N),inHonsu,Shikoku,andKyushuIs,andtheclose-lyingKojima(=Koshima),Kashima,Awajishima,Shodoshima,andKinkazanislets. M. f. yakui Kuroda, 1941 — Japanese Archipelago (Yakushima I, ¢.60 km S of Kyushu).
Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago
<p><span>This study aimed to reveal the evolutionary timescale and processes underlying the diversity of <em>Rubus</em> in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, <em>R. chamaemorus</em>, <em>R. pedatus</em>, <em>R. vernus</em>, <em>R. pseudojaponicus</em>, and <em>R. ikenoensis</em>, were found to belong to anciently diverged lineages; in particular, <em>R. ikenoensis</em> formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. <em>Malachobatus</em>, <em>Chamaebatus</em>, and sects. <em>Pungentes</em>, <em>Idaeanthi</em>, and <em>Parvifolii</em> (subg. <em>Idaeobatus</em>), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, <em>R. sieboldii</em> has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. <em>Microphylli</em>, <em>Corchorifolii</em>, <em>Peltati</em>, and <em>Rosifolii</em> (subg. <em>Idaeobatus</em>), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, <em>R. sumatranus</em>, <em>R. peltatus</em>, <em>R. corchorifolius</em>, and <em>R. chingii</em>, was incongruent among gene trees. At the lower taxonomic levels, <em>R. illecebrosus</em>, <em>R. grayanus</em>, and the thornless species of sect. <em>Microphylli</em> showed earlier divergence.</span></p>
FIGURE 6 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 6. Skulls of the newly describing Barbastella species: a—Barbastella pacifica sp. nov., holotype BSI 168-07, adult male, Kunashir Island; b—Barbastella pacifica sp. nov., NSMT M-8774, female, Honshu, Saitama; c—B. leucomelas, NMP PB2883, adult male, Egypt, Sinai; d—B. cf. darjelingensis, ZMMU S-186685, adult male, Vietnam, Lao Cai. Scale bar 5 mm.
FIGURE 4 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 4. Bivariate scatter plot for the First and Second Canonical Variances calculated in Discriminant Function analysis for 18 cranial and dental measurements of 117 Barbastella specimens.
FIGURE 3 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 3. Bivariate scatter plots for the PC analyses of putative and accepted Barbastella species; Factors (Principal Components) are calculated from the 17 cranial and dental measurements in total for 117 specimens; analyzes were performed independently for each pair of species.
FIGURE 5 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 5. Penial bones of barbastelles: a–c—B. barbastellus (a, b—Russia, Krasnodar territory, ZMMU S-169241, S- 169265; c—Czech Republic, n/n); d–e—B. caspica, (d—Tajikistan, ZMMU S-169301; e—Kirghizstan, CUP CT84/253); f—B. leucomelas, Egypt, Sinai, NMP 90521; g—B. darjelingensis, Nepal, Annapurna Himalaya, ZMMU S-164496; h—B. cf. darjelingensis, Vietnam, Lao Cai province, ZMMU S-186685; i–k—B. pacifica sp. nov. (i, j—Japan, Nagano prefecture, NSMT M-52949, 52944; k—Japan, Hokkaido, NSMT M-18559); c, e and f adopted from Benda et al. 2008; k—from Yoshiyuki 1989; others—original. Scale bar 1 mm.
FIGURE 2 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 2. Phylogenetic relationships of Barbastella sp. n. based on A) ND1 sequences (929bp), B) partial cytb (609bp) sequences and C) COI (523bp) sequences. The scale indicates genetic distance estimated by the Kimura 2-parameter method on the NJ tree. The bootstrap values derived from 1000 replication for NJ tree / maximum likelihood probabilities. Specimens of Plecotus auritus (ND1 HM164052; COI JF443099) or P. sacrimontis (Cytb OCUM5351) were used as an outgroup. The sample numbers correspond to those in the Appendix (Tables A1, A2).
FIGURE 1 in Taxonomic status of the barbastelles (Chiroptera: Vespertilionidae: Barbastella) from the Japanese archipelago and Kunashir Island
FIGURE 1. Distribution of barbastelles (adopted from the IUCN Red List (www.iucnredlist.org); with additions from Smith & Xie 2008; Benda et al. 2012; 2015; Fukui 2015). Red—Barbastella barbastellus, dark blue—B. caspica, light blue—B. leucomelas, magenta—B. darjelingensis sensu stricto, green—B. cf. darjelingensis, light brown—B. n. sp. Full symbols mark material genotyped by at least one gene; open symbols—specimens included into morphological study only. Type localities of named taxa: 1—darjelingensis Hodgson, 1855; 2—caspica Satunin, 1908; 3—walteri Bianchi, 1916; 4—leucomelas Cretzschmar, 1826; 5—beijingensis Zang et al., 2008; 6—barbastellus Schreber, 1774; 7—guanchae Trujillo, Ibáñez and Juste, 2002.
Migration-tracking integrated phylogeography supports long-distance dispersal-driven divergence for a migratory bird species in the Japanese archipelago
<p>Previous phylogeographic studies of migratory bird species have not discriminated long-distance dispersal (LDD) from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). We used the Brown Shrike as a model species, and we conducted molecular phylogenetics, species distribution models (SDMs) and migration tracking. We assessed whether the LDD hypothesis is applicable to the divergence history of the Japanese subspecies of the Brown Shrike.</p> <p>The datasets include three zipped files, namely DataS1.zip, DataS2.zip, and DataS3.zip. See the READ ME (AOKI_et_al_2021_DATASET_README.txt) for how each of the folder and files contained in them can be used to reproduce our results.</p> <p>DataS1.zip inlcudes an xml file to conduct the BEAST analysis. Molecular data, which include nucleotide sequences obtained for cytochrome b (cytb), cytochrome oxidase c subunit I (COI), myoglobin intron-2 (MB) and transforming growth factor beta 2 intron-5 (TGFb2), have been all reposited to DDBJ international nucleotide sequence database, and accession numbers have been already given to them. Accession numbers are provided in the appendix attached to the main manuscript.</p> <p>DataS2.zip includes several data that are related to produce occurrence data of the Brown Shrike used in the analysis and an R code to reproduce the SDMs. Explanatory climatic variables are all available at WorldClim v.1.4 (Hijmans et al., 2005), which are processed in the R code.</p> <p>DataS3.zip includes migratory route analyses using light-level geolocator data are available as the original light-level data and R codes. Sensitivity analyses were also conducted in these analyses, but their codes and results are seperately provided here.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.