Western Honshu Research Articles

Phylogeography and genetic population structure of the endangered bitterling Acheilognathus tabira tabira Jordan & Thompson, 1914 (Cyprinidae) in western Honshu, Japan, inferred from mitochondrial DNA sequences

Phylogeography and genetic population structure of the endangered bitterling Acheilognathus tabira tabira Jordan & Thompson, 1914 (Cyprinidae) in western Honshu, Japan, inferred from mitochondrial DNA sequences

Trentepohlia brevicellulis comb. et stat. nov. (Trentepohliaceae, Ulvophyceae) found in Japan

SUMMARYThe family Trentepohliaceae contains many common aerial algae, most widely distributed, particularly in tropical and subtropical regions. Eight species of the genus Trentepohlia have been reported in Japan. We report another taxon, Trentepohlia brevicellulis (Cribb) S. Handa and H. Tsubota comb. et stat. nov., growing on bark in western Honshu, Japan. This alga was previously described as Trentepohlia bosseae var. brevicellulis Cribb. However, the relationship between the bosseae and brevicellulis varieties of T. bosseae could not be ascertained owing to the lack of genetic information for brevicellulis. Therefore, we aimed to examine the detailed morphological characteristics of brevicellulis in wild samples and cultured strains and to review the taxonomy, including systematic information obtained by genetic analysis. Its phylogenetic position was resolved based on 18S rDNA sequence data. It differs from T. bosseae and its variety samoensis in exhibiting a warty zoosporangium surface, an unthickened septum with no central pit field, and a non‐rusty‐brown cell wall. The four key characteristics of T. brevicellulis include a warty layer on the inner surface of the non‐bent side of the suffultory cell wall, an ostiole located near the base of the zoosporangium, curved tapering filaments with thickened cell walls, and globular vegetative spores in the basal portion of the filament. Transmission electron microscopy revealed a pit field wherein simple plasmodesmata were present in the septum. Phylogenetic analysis suggested that this alga and T. bosseae form distinct clades and that T. brevicellulis is separate from T. bosseae. Thus, our study helped redefine the accurate taxonomic position of the species under study as Trentepohlia brevicellulis (Cribb) S. Handa and H. Tsubota comb. et stat. nov., a clade distinct from T. bosseae and reported for the first time in Japan.

Lathrobium motonari, a new soil-inhabiting species of the genus Lathrobium (Coleoptera: Staphylinidae: Paederinae) from western Honshu, Japan

Lathrobium motonari sp. nov. is described from northeastern area of Hiroshima Prefecture, western Honshu, Japan, with figures of male and female genital organ including the structures of endophallus in a fully everted condition.

Phylogeography of alpine and subalpine adapted Pseudostenophylax caddisflies (Limnephilidae: Trichoptera): a strong relationship with mountain formation

Abstract Organisms that inhabit the alpine zone tend to have distribution areas that are isolated and scattered in patches, in effect ‘sky islands’. We focused on Pseudostenophylax caddisflies, a typical alpine aquatic insect group. Phylogenetic analyses were conducted on all eight Japanese species, with the monophyletic lineage of each strongly supported. The traditional classification system dividing Pseudostenophylax into ‘ondakensis’ and ‘adlimitans’ species groups was also strongly supported. For the first time, the existence of a cryptic species in Hokkaido was revealed in this study. Two species of the adlimitans species group live in western Honshu, Shikoku and Kyushu, but those distribution areas are difficult to explain in terms of the current geography. The phylogenetic analyses results also closely reflected the related geological history and palaeogeography. Interestingly, Pseudostenophylax amurensis, recently recorded on the Korean Peninsula, was positioned within the Japanese lineage of the ondakensis species group. Thus, some Japanese lineages may have reversely dispersed to the Korean Peninsula. Many interesting insights can be gained from the close relationship between the genetic structure of aquatic insects adapted to alpine and subalpine regions and their palaeogeographical history.

Phylogeographic analysis of the Japanese wild boar (<I>Sus scrofa leucomystax</I>)

The Japanese wild boar (Sus scrofa leucomystax) is an indigenous subspecies of the wild boar, which is distributed in Honshu, Shikoku, Kyushu, and other smaller islands of Japan. The distribution area of the Japanese wild boar has in the last 40 years expanded by 1.9-fold due to improved suitable survival conditions, such as global warming which has decreased snowfall, increased abandoned farmland, and decreased hunting pressure. As a result, the negative impacts of this population increase on humans continue to spread. In this study, 1,251 Japanese wild boars were sampled from 32 prefectures which nearly cover the entire expanded distribution area in Japan, and phylogeographical analysis was performed using 30 Measurement of Domestic Animal Diversity recommended microsatellite markers. Both neighbor-joining (NJ) phylogenetic trees constructed using Nei's DA genetic distance matrix and population genetic structure analysis classified Japanese wild boar into six phylogeographical subpopulations, including northern Honshu, eastern Honshu, central Honshu, western Honshu, Shikoku, and Kyushu. The six identified genetic subpopulations were speculated to form as a result of several factors, including human activity between the northern and eastern Honshu, occurrence of three mountain ranges of 3,000-meter height between the eastern and central Honshu, the inland sea between western Honshu and Shikoku, and the presence of strait between western Honshu and Kyushu. Interestingly, some individual wild boars from Gunma, Tochigi, and Miyazaki areas formed distinct and separate subpopulations, with animals within these subgroups exhibiting traits such as low genetic differentiation and high diversity, which likely suggested gene influx from domestic pigs or other sources.

Systematic headwater sampling of white‐spotted charr reveals stream capture events across dynamic topography

AbstractAimRiver system rearrangements such as stream capture play a crucial role in determining range expansion and gene flow of stream organisms between different watersheds. However, it is challenging to clarify the role of stream capture in dynamic landscapes where frequent connections and disconnections occur in stream networks. We hypothesized that fine‐scale sampling with genome‐wide analysis could reveal the effect of stream capture on the range expansion of stream fish and detect unidentified river rearrangement of headwater streams in a highly heterogeneous landscape.LocationHonshu Island, Japan.Taxon Salvelinus leucomaenis. MethodsTo identify stream capture events from biological evidence, a sampling strategy was designed with fish collected from multiple pairs of adjacent headwater streams. This included a ‘typical site’ where the occurrence of a stream capture event has been confirmed with geological evidence. The genetic population structure was analysed using genome‐wide single nucleotide polymorphism (SNP) data using MIG‐seq, followed by a Bayesian clustering approach.ResultsEvidence was found for historical dispersal across watersheds, including a typical stream capture site. This cross‐drainage dispersal promoted gene flow among the three genetic groups of focal fish inhabiting western Honshu Island. The likelihood of past stream capture increased substantially when the inter‐headwater distance was less than 2000 m, or the altitudinal difference was less than 200 m in the current topography.Main ConclusionsIn highly dynamic areas, such as the study site, which is surrounded by active faults, stream capture may be frequent, and aids inter‐drainage dispersal of freshwater organisms, where large‐scale range expansions would otherwise be impossible. Systematic pairwise headwater sampling, together with genome‐wide SNP analysis, provides biological evidence for the history of water system rearrangements and enables the identification of geological events.

Dependence of flower-bearing on trunk size and trunk origin in four tree species of the subgenus Quercus

ABSTRACT We investigated the flower-bearing properties of four sympatric oak species in the subgenus Quercus commonly grown in semi-natural forests in western Honshu Island, Japan. Quercus variabilis and Quercus acutissima belong to the section Cerris and Quercus serrata and Quercus aliena belong to the section Quercus. The timing and pattern of flower-bearing varied among the four oaks, but were synchronized between the male and female inflorescences within each species. Trunk size was the primary factor affecting the flower-bearing properties; more flowers were borne on thicker trunks. Threshold trunk sizes for flower-bearing, below which no flowers were borne, were identified in the two Cerris section oak species; in contrast, the two Quercus section oak species bore flowers even on the smallest trunks. The smallest flower-bearing trunk sizes of the Quercus section oaks were extremely small compared with the other tall tree species distributed in the temperate zone of Honshu Island. The flowering probability was not clearly influenced by whether the stem originated from a seedling or a sprout, except for the male inflorescences of Q. aliena, which rather showed a positive relationship between sprout-origin and flower-bearing. Thus, no trade-off relationship between sprouting and flowering was observed.

Lanternfish otoliths (Myctophidae, Teleostei) from the Miocene of Japan

Lanternfishes (Myctophidae) are one of the most common groups of fishes in the mesopelagic zone of the world ocean, and their otoliths have been dominant in pelagic sediments since at least Miocene times. Many species have a wide geographic distribution, with several being circumglobal. This wide distribution makes myctophid otoliths potentially useful for supraregional stratigraphic purposes. The Sea of Japan and the Northwest Pacific is an important region for investigations into the diversity and evolution of the Myctophidae. Here, we describe a large collection of myctophid otoliths from the late early to early middle Miocene (late Burdigalian to early Langhian) from six localities on western and central Honshu, which were under warm water influence during that time. A total of 22 species are recognized, of which eight are new. In the order in which they are described, the new species are Bolinichthys higashibesshoensissp. nov., Ceratoscopelus brevissp. nov., Lampadena eximasp. nov., Lampanyctus lenticularissp. nov., Lampanyctus tsuyamaensissp. nov., Stenobrachius ohashiisp. nov., Diaphus epipedussp. nov., and Diaphus watatsumisp. nov. At least nine species are also known from coeval sediments outside of Japan, most notably New Zealand and Europe. This distribution reflects the extraordinary geographic spread of myctophid species already in the early Miocene and indicates the potential for their future use for biostratigraphic purposes. The paleoecological and paleobiogeographical implications of the studied myctophid otolith assemblages are discussed. Furthermore, the stratigraphic ranges of the observed species are discussed and compared with data from other regions of the world in an attempt to outline the potential future application of myctophid otoliths for supraregional biostratigraphic purposes.

Cinusa nippon n. sp. (Isopoda: Cymothoidae) Parasitic in the Buccal Cavity of Coastal Puffers (Tetraodontiformes: Tetraodontidae) from Japan, with the First Specimen-Based Record of the Isopod Genus from the Pacific Region.

Cinusa nippon n. sp. is described as the second species of the genus from ovigerous females and adult males found in the buccal cavity of three species of coastal puffers [vermiculated puffer, Takifugu snyderi (Abe, 1989) (type host); panther puffer, Takifugu pardalis (Temminck and Schlegel, 1850); and fine patterned puffer, Takifugu flavipterus Matsuura, 2017], in the southern Sea of Japan off western Honshu, Japan. The female of the new species is distinguished from that of its single congener, Cinusa tetrodontis Schioedte and Meinert, 1884, by the shape of pereonite 1 (straight lateral margins with slightly produced anterolateral angles in the new species vs. rounded anterolateral sides and angles in C. tetrodontis). The number of recurved robust setae on the female's maxilliped article 3 is also different between the two species: C. nippon n. sp. has two robust setae, while C. tetrodontis has three robust setae. Moreover, the male of the new species is differentiated from that of C. tetrodontis in the number of antennal articles and recurved robust setae on the maxilla and maxilliped. Cinusa nippon n. sp. represents the first specimen-based record of the genus from the Pacific region. An amended diagnosis of the genus is provided.

Nihonella gen. nov., a new troglophilic genus of dwarf spiders from Japan with a discussion on its phylogenetic position within the subfamily Erigoninae (Araneae, Linyphiidae)

A new monospecific genus belonging to the family Linyphiidae Blackwell, 1859, Nihonella gen. nov., is described using an integrative taxonomic approach based on the species N. chika gen. et sp. nov. The new genus is endemic to Western Honshu, Japan, and it shows distinctive genitalic and somatic characters of other genera of the subfamily Erigoninae Emerton, 1882. Nihonella gen. nov. is found only in the twilight and transition zones of caves in Okayama and Nara Prefectures. The phylogenetic position of Nihonella gen. nov. within the subfamily Erigoninae, and its relationship as a sister clade of the species of the group of Savignia Blackwell, 1833 (sensu Millidge 1977), is discussed on the basis of both, morphological and molecular evidence.

Genetic structure analysis of cultivated and wild chestnut populations reveals gene flow from cultivars to natural stands

Japanese chestnut (Castanea crenata Sieb. et Zucc.), the only fruit tree species domesticated in Japan, has been cultivated alongside natural stands since prehistorical times. Understanding the genetic diversity of this species and the relationships between cultivated and wild chestnut is important for clarifying its breeding history and determining conservation strategies. We assessed 3 chestnut cultivar populations and 29 wild chestnut populations (618 accessions). Genetic distance analysis revealed that wild populations in the Kyushu region are genetically distant from other populations, whereas other wild and cultivar populations are comparatively similar. Assignment tests suggested that cultivars were relatively similar to populations from central to western Honshu. Bayesian structure analyses showed that wild individuals were roughly classified according to geographical distribution along the Japanese archipelago, except that some wild individuals carried the genetic cluster prevalent in cultivars. Parentage analyses between cultivars and wild individuals identified 26 wild individuals presumed to have a parent–offspring relationship with a cultivar. These results suggested that the genetic structure of some wild individuals in natural stands was influenced by gene flow from cultivars. To conserve wild individuals carrying true “wild” genetic clusters, these individuals should be collected and preserved by ex situ conservation programs.

Environmental DNA reveals cryptic diversity within the subterranean amphipod genus Pseudocrangonyx Akatsuka & Komai, 1922 (Amphipoda: Crangonyctoidea: Pseudocrangonyctidae) from central Japan

Abstract An environmental DNA (eDNA) detection method confirms the presence of the subterranean amphipod genus PseudocrangonyxAkatsuka & Komai, 1922 in the city of Kyoto, Honshu, Japan for the first time in more than 90 years. Phylogenetic trees using partial sequences of the 16S rRNA gene of eDNA samples from Kyoto and specimens collected from various locations in Japan and Korea highlight that two genetically distinct taxonomic units inhabit Kyoto’s subterranean environments. Results reveal that the ranges of distinct phylogroups of Pseudocrangonyx widely overlap with each other around Lake Biwa in central western Honshu. The eDNA results increase our understanding of the species richness and complicated evolutionary history of these stygobitic amphipods.

A Phylogenetically Distinct Group of Glandirana rugosa Found in Kyushu, Japan.

The Japanese wrinkled frog Glandirana rugosa is separated into five genetically different groups. One group in western Japan is further divided into three subgroups, found in Kyushu, Shikoku, and western Honshu. We collected G. rugosa frogs at 39 sites in Kyushu and determined nucleotide sequences of the mitochondrial 12S and 16S rRNA genes for phylogenetic analysis. Unexpectedly, we found a group of frogs in southeastern Kyushu that did not cluster with any of the pre-existing five groups of G. rugosa on the phylogenetic trees. The frogs in the new group and G. rugosa in Kyushu were externally similar, but there were a few significant differences in morphological features between the two populations. In addition, we observed significant differences in the frogs' calls . Thus, the group of the frogs in southeastern Kyushu may represent a new candidate species in the genus Glandirana. We discuss the possibility of a new species.

A new species of the genus Pseudocrangonyx (Crustacea: Amphipoda: Pseudocrangonyctidae) from Simbok Cave, Korea.

A new subterranean species of pseudocrangonyctid amphipod, Pseudocrangonyx joolaei, is described from the groundwater of a cave in South Korea. Pseudocrangonyx joolaei sp. nov. can be distinguished from its congeners by the number of sternal gills as well as a combination of the antennal sinus, the accessory flagellum of antenna 1, and the terminal article of uropod 3. Molecular phylogenetic analyses based on nuclear 28S rRNA and histone H3, and mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed that P. joolaei sp. nov. formed a clade with P. akatsukai Tomikawa Nakano, 2018 that inhabits limestone caves in the western Honshu island, Japan.

Delineating management units for Pacific cod (Gadus macrocephalus) in the Sea of Japan

Advances in population genetics have brought about the use of management units (MUs) for the assessment and management of marine resources. Some marine species with an apparently continuous distribution actually have local genetically distinct populations across their range, so careful consideration is required in the delineation of MUs. To delineate MUs for Pacific cod (Gadus macrocephalus) in the coastal area of the Sea of Japan, we studied the geographic distribution and genetic variation of the species. Two geographically separate groups were identified based on the analysis of trawl survey data. A spatially explicit clustering analysis of 309 sequences of the mitochondrial NADH dehydrogenase 2 gene identified two groups of samples: one in the central to northern Sea of Japan (NJ) and another in the westernmost shelf area around the Tsushima Strait (WJ). The population structure was further confirmed by analysis of molecular variance and a significant pairwise Φst value between the two groups. The NJ population had experienced a post-glacial population expansion, whereas the WJ population size remained stable, probably reflecting different oceanographic conditions in the two regions. The two populations diverged from each other during the last glacial period, likely due to habitat discontinuity. Finally, based on the species’ genetic population structure and the geographic distributions, we parsimoniously propose that a single boundary be set along the coast of western Honshu Island to divide MUs in the Sea of Japan.

Two new species of Pseudogobio pike gudgeon (Cypriniformes: Cyprinidae: Gobioninae) from Japan, and redescription of P. esocinus (Temminck and Schlegel 1846)

Two new species of pike gudgeon, Pseudogobio agathonectris from western Honshu, Japan, and P. polysticta from eastern Honshu, Japan, are described, and P. esocinus (Temminck and Schlegel 1846) is redescribed. The two new species were previously considered to be P. esocinus, which had been only a nominal species of the genus from Japan. The two species are distinguishable from P. esocinus by following a combination of characters: tip of pectoral spiny soft ray not reaching that of 6th soft fin ray, and tip of outer edge of pectoral fin strongly curved posteriorly; long barbel (15.3–36.9% of HL in P. agathonectris, 16.9–34.8% in P. polysticta, respectively), with the tip commonly extending beyond vertical through anterior edge of eye; 10–14 (modally 13) and 12–14 (13) pectoral soft fin rays; long mouth (33.2–45.3% of HL and 29.6–42.0%); short length between anus and anal fin origin (16.5–21.4% of SL and 15.9–22.4%), with 11–14 (12) and 11–16 (12) scales; and small body size (at most 150 mm SL). Pseudogobio agathonectris is distinguishable from P. polysticta by the canonical discriminant functions based on five meristic and 25 morphometric characters, and distinct dark blotches and obscure black spots on dorsal and lateral body (vs. obscure blotches and many distinct spots).

Taxonomic revision of Eudesme (Ectocarpales s.l., Phaeophyceae) proposing a new species E. borealis sp. nov.

ABSTRACTMolecular phylogeny of Eudesme specimens collected from various localities in the Northern Hemisphere using mitochondrial cox1 and cox3 and chloroplast atpB, psaA, psbA and rbcL gene sequences revealed an undescribed species in the genus. In the analyses, three distinct clades (clades 1, 2 and 3) with high statistical supports were recognised. Specimens of clade 1 corresponded to the generitype E. virescens because the morphology agreed with the reported descriptions of the species, and the distribution (subboreal Europe) included the type locality. Clade 2 had a broad distribution in the Arctic Sea and coldwater regions of the northern Pacific and northern Atlantic. Specimens of clade 2 were morphologically distinguishable from E. virescens in having broader sporophytes. Specimens of clade 3 collected from western Honshu, Japan, had cox3 sequence identical to one of an old voucher specimen of E. shandongensis (63-519) described from the Yellow Sea. We propose the establishment of a new species, E. borealis, distributed in the Arctic, northern Pacific, and northern Atlantic regions.

The genus Setodes Rambur (Trichoptera, Leptoceridae) in Japan.

This report presents a revision of the Japanese species of the genus Setodes Rambur (Leptoceridae), and confirms 8 species. Among these are 3 new species: Setodes chirotheca sp. nov., distributed from Hokkaido to eastern Honshu; S. moritai sp. nov., distributed from central to western Honshu and Shikoku; and S. pseudofurcatulus sp. nov., from western Honshu. Additionally, several species are re-described: S. hinumaensis Katsuma 2009, S. ujiensis (Akagi 1960), S. minutus Tsuda 1942b, S. shirasensis Kobayashi 1984, and S. argentatus Matsumura 1907. One species, S. curviseta Kobayashi 1959 was originally described from Kyushu and is now synonymized with S. minutus. The larva, pupa, and case of S. hinumaensis are described for the first time.

THE ADMINISTRATIVE-TERRITORIAL REFORM OF YAMATO RULER – EMPEROR HOMUDA IN KIBI REGION

The current paper features the reasons and the content of the administrative-territorial reform introduced by Yamato ruler – emperor Homuda (Ōjin, 390 – late 414 / early 415 AD [of the corrected chronology]) in 411 AD [of the corrected chronology] in Kibi area (in western Honshu). The article contains the data obtained about the administrative-territorial units he organized and the local governors he appointed. It has been revealed that the elderly emperor delegated the rule to his three sons and retreated to Kibi area, which was the homeland of his younger wife E-hime. Upon his arrival, emperor Homuda undertook an administrative-territorial reform for the benefit of the hereditary owners of these lands, i.e. the Mitomo-wake clan. He established districts (Jap. agata) and appointed the “lords of districts” (Jap. agata-nushi). Besides, he appointed the “rulers of regions” (Jap. kuni-no miyatsuko) in the regions (Jap. kuni) of Bizen and Bicchū (in Near and Central Kibi). This reform resulted in the fact that emperor’s cousins-in-laws from his younger wife’s side rose to power in the regions (Jap. kuni) and in the newly- created districts (Jap. agata) of Near and Central Kibi.

A new record of the bump-head sunfish Mola alexandrini (Tetraodontiformes: Molidae) from Yamaguchi Prefecture, western Honshu, Japan

A new record of the bump-head sunfish Mola alexandrini (Tetraodontiformes: Molidae) from Yamaguchi Prefecture, western Honshu, Japan