Honshu Research Articles

Life history traits of five ground beetle (Coleoptera: Carabidae) species common in Honshu Island, Japan

Ground beetles have been used as bioindicators for monitoring environmental changes. However, to interpret monitoring results, we need further information on their life history traits. We selected Harpalus griseus, H. eous, H. tridens, Synuchus cycloderus and Carabus procerulus, species common in Honshu Island, Japan. We examined their hind wings, flight muscles, gut contents and ovarian eggs to understand their flight activity, feeding traits and reproductive strategies. The three Harpalus species showed wing length / body length ratios (W/B) of 0.88 - 0.99. In H. tridens, the proportion of individuals with flight muscles and caught in aerial traps was lower than in the other two. S. cycloderus was macropterous with a W/B ratio of 0.75, but no individuals were caught in aerial traps, and none possessed flight muscles. C. procerulus was brachypterous. The three Harpalus species fed mainly on seeds and partly on arthropods. S. cycloderus was a generalist predator. Gut contents of C. procerulus consisted of amorphous fluid, suggesting extra-oral digestion. Egg type was categorized by the number and size of ovarian eggs. S. cycloderus had many-small eggs, while the other four had few but large eggs.

First report of an ambrosia beetle, Platypus quercivorus, vector of Japanese oak wilt, in Hokkaido, northern Japan

ABSTRACT An ambrosia beetle, Platypus quercivorus, is the vector of Japanese oak wilt, one of the most serious forest diseases in Japan. P. quercivorus is widely distributed in the main islands of Honshu, Kyushu and Shikoku, but there have been no records of P. quercivorus in Hokkaido, the northernmost main island in Japan. Because the mass mortality of oak trees caused by Japanese oak wilt is spreading northward in northern Honshu, we sampled P. quercivorus in 20 forest sites in the southernmost part of Hokkaido by using pheromone traps. Five P. quercivorus (two males and three females) were collected from four sites. Because oak species distributed in Hokkaido are all susceptible to Japanese oak wilt, monitoring and control measures will be needed to prevent the spread of Japanese oak wilt in Hokkaido.

Kampō medicine and Muro disease (Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex): Postscript and Historical Footnote.

Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-dementia Complex (ALS/PDC) is a disappearing neurodegenerative disease in three former high-incidence foci of the U.S. territory of Guam, Papua-Indonesia (New Guinea) and Kii Peninsula, Honshu Island, Japan (Muro disease). We report additional data that associate medicinal use of cycad seed to Muro disease in the southern Kozagawa focus of ALS/PDC. In the other two ALS/PDC-affected populations, cycad seed was used as a traditional topical medicine in New Guinea and Guam and, additionally, for food on Guam.

Estimating the spawning ground of Pacific saury Cololabis saira by using the distribution and geographical variation in maturation status of adult fish during the main spawning season

AbstractWe analyzed distribution and differences in body length, age, and maturation rate of Pacific saury Cololabis saira in the western North Pacific Ocean, during the main spawning season (winter), to locate its spawning ground. Sampling was conducted in the coastal area north of the Kuroshio axis (CA), the offshore area of the southern Japanese archipelago (SA), and the area east of the Honshu Island (EA) from 1996 to 2017. Higher densities of Pacific saury were widely observed on or just north (within 100–200 km) of the axis of the Kuroshio and the Kuroshio Extension currents. Body length, age composition, and sea‐surface temperature (SST) differed across the studied areas, with larger fish (>250 mm knob length, mainly age‐1) dominating at higher SST (16–21°C) in the SA and smaller fish (<250 mm knob length, age‐0) dominating at lower SST (14–16°C) in the EA. In the CA, both SST and body length values were in between those in the SA and EA. The area where matured Pacific saury were collected was broadly distributed in the study area, except for the CA and a part of the Transition zone where the SST was low and mean body length was short. This study suggests that the main spawning ground during winter, where the area of high density and high maturation rate overlap, is formed on or just north of the Kuroshio and the Kuroshio Extension axis.

Discrepancies between MICS-Asia III simulation and observation for surface ozone in the marine atmosphere over the northwestern Pacific Asian Rim region

Abstract. In order to identify the causes of overestimate of the surface-level O3 mixing ratio simulated by three regional chemical-transport models, NAQPMS v.3 (abbreviated as NAQM in this paper), CMAQ v.5.0.2, and CMAQ v.4.7.1, compared to the EANET observational data at a marine remote site at Oki in July 2010, analyses of hourly O3 mixing ratios and net ozone production were made in the context of MICS-Asia III. In addition to Oki, model-simulated and observational data for two other EANET marine sites, Hedo and Ogasawara, were also examined. Three factors, i.e., long-range transport from the continent, in situ photochemical formation, and dry deposition of O3 on seawater, have been identified as contributing to the overestimate by these regional models at Oki. The calculated O3 mixing ratios during long-range transport from the continent were much higher for all three models than those of the observation. In situ photochemical formation, demonstrated by a distinct diurnal variation which was not discerned in the observational data, was seen in the simulated data of all three models and ascribed to the virtual transport of NOx from the southern urban areas of the main island of Japan. The overestimate of the O3 mixing ratio in the background oceanic air mass has been discussed referring to dry deposition velocity (Vd) of O3 over oceanic water. Sensitivity analysis of the dry deposition velocity to the concentration of O3 was made for Oki in July. An increase in Vd from 0.0005 to 0.001 cm s−1 used in the standard runs for CMAQ by a factor of 10 decreases the O3 mixing ratio by more than 20 ppbv on an event basis in certain periods of time and by ca. 4.9 ppbv as a monthly mean in July. The dry deposition velocity of O3 in Bohai Bay and the Yellow Sea has been assumed to be comparable to that of the open ocean in all three models, which could have resulted in the overestimate of O3 mixing ratios in this area and also in the long-range transport of O3 from the continent to Oki. A higher value of dry deposition velocity in this marine area is expected considering the higher content of organics in the surface sea layer brought by rivers and atmospheric wet deposition. Empirical measurements of the mixing ratios and dry deposition flux of O3 in this area are highly recommended, since they would affect the simulated mixing ratios in the downwind region in the Pacific Rim region.

Structural Elements of the Sea of Japan’s Basin and Adjacent Continental and Island Dry Land, According to Data from Space-Based Geological Investigations

A representative system of fault and block dislocations in the Sea of Japan segment of the continent–ocean transition zone, identified using space-based geological data and a set of available geomorphological, geological, and geophysical materials, allow the eponymous Late Paleozoic mega-arch to be constructed. The ring form, duration, and scales of basite, acidic magmatism, and the presence of geological and geophysical signs of mantle diapirism associate the main features of its structure and development with plume activity. The geological prehistory, plume tectonics, and periodic inversions of the geodynamic regime determined the direction and character of destructive transformations of the continental margin in the Early Mesozoic and Middle and Late Cenozoic, and the specific character of the region evolution in general. Features of the inherited development of the structural plan include the preservation of the granite core of the mega-arch, associated with the underwater Yamato rise having a continental type of crust, in the geometric center of the Sea of Japan basin; the presence of radial-concentric hypsometric and structural-magmatic zonation; and the relict nature of many other underwater rises. The absence of compensatory collision–accretion dislocations in the east of Honshu Island and on the island arc slope of the adjacent deep-sea trench, the weak variability of strikes of dry land–sea tectonic marks through faults in satellite images, the preservation of the paleoarch structural elements, and other data contradict ideas about large horizontal movements of lithospheric blocks within the Sea of Japan segment of the Eurasia–Pacific Ocean transition zone.

Поселенческие комплексы среднего дзё:мона региона Тохоку: общие черты, локальные особенности и основные термины

Over the past decade, the data on the archaeological cultures of the Japanese archipelago, from the Paleolithic to the Kofun period, have been actively introduced into the Russian archaeology. These materials concern various aspects of the subsistence life of local tribal formations. This study discusses features of the internal structure of the Middle Jōmon settlements from the Tohoku region. The article presents the data from archaeological reports of the most significant sites of this period. Some materials about Middle Jōmon sites (such as Sannai Maruyama, Goshono) were previously published in Russian periodicals, however, the overwhelming majority of data have been presented for the first time. The main attention is paid to the description of the site location, the characteristics of pit-dwellings and raised-floor buildings, household and ritual objects, their location relative to each other, with a short mention of the discovered artifacts. The article was based on materials of the author’s PhD dissertation research “The Middle Jōmon period of Honshu island (5–4 thousand years ago): general characteristics and local features” [Ivanova, 2018].

Taxonomic status of genera Nodularia, Middendorffinaia and Inversiunio (Bivalvia: Unionidae) from South-East Asia: morphometric, genetic and GenBank data

Recent investigations of East Asian freshwater mussel genera Nodularia, Middendorffinaia and Inversiunio confirmed validity of the taxa, while their composition and taxonomic uncertainty concerning classification of these genera within a specific subfamily are still in question. The aim of the present study is to clarify the taxonomy and systematics of Nodularia and Middendorffinaia genera from the Russian Far East and Inversiunio from Japan, using a multiple dataset approach that combines morphology of glochidia, detailed conchological analyses with morphometry of adult and glochidial shells, and a molecular technique involving COI barcoding marker. As a result, three genetically distinct and highly divergent lineages were recognized confirming the existence of three distinct genera. The existence of five Nodularia species in Southeast Asia is shown. One of the sequences is shown to be incorrectly assigned to N. jourdyi, while in fact it also represents N. douglasiae, according to the BIN system. Existence of a single Nodularia species, namely N. douglasiae, and a single Middendorffinaia species, namely M. mongolica, in the Russian Far East is supported. We conclude that so-called comparatory species Nodularia amurensis, N. schrencki, and N. vladivostokensis are junior synonyms of the species Nodularia douglasiae; the comparatory species Middendorffinaia ussuriensis and M. dulkeitiana are junior synonyms of the species Middendorffinaia mongolica. Within Inversiunio specimens from Japan four species were recognized based on types of glochidial microsculpture of shells and genetic data. Gene sequences of Inversiunio verrucosus, endemic to the Seomjingang River basin in South Korea, and I. yanagawensis from Kyushu Island in Japan are very similar and they can be regarded as the same species, with Inversiunio verrucosus as a junior synonym of Inversiunio yanagawensis. Mussels from Honshu Island first referred to I. yanagawensis are shown to be a separate species.

Bioelectricity generation and remediation of contaminated intertidal zone of Yamaguchi Bay, Japan

This study explores the use of sediment microbial fuel cells (SMFCs) to generate a safe, stable, and efficient supply of bioelectricity to sensors and simultaneously improve sediment quality. Supplying energy to geoenvironmental monitoring sensors remains a challenge as traditional batteries and solar cells are limited by the need to recharge and the erratic weather condition, respectively. Four different sediments from the Yamaguchi bay located in south part of the Honshu island, Japan were experimented on. The acid volatile sulfide (AVS) was the main source of contamination in the intertidal zone and was, hence, used as an indicator for possible bioremediation. Various factors have been studied for its effect on voltage generation. Voltage generation was dependent on the microbes in and grain size distribution of the sediment. It was found that voltage values showed almost twice when two anodes were used instead of a single anode. As the temperature reached optimum temperature of the enzymes of the Geobacteria, the increased activity lead to higher voltage. SMFC was effective in reducing the AVS value of the sediment. SMFCs in the field exhibited greater voltage generation compared to SMFCs of the same size in the laboratory. A positive correlation between voltage generation and AVS reduction was demonstrated.

Effect of translate speed of typhoon on wind waves

Quantitative assessments on the effect of translate speed of typhoons on wind waves were carried out. A WRF-SWAN coupled model that used observed meteorological data was applied to eight different typhoons in the vicinity of Shiono-Misaki, on the pacific side of Honshu Island, Japan. The authors proposed a new methodology to modify the translate speed and wind field of tropical cyclones using an empirical model in which the gross wind speed is expressed as the summation of two different types of wind generation. Two different trends of the relationship between the significant wave height ( $$H_{{\text{s}}}$$ ) and translate speed ( $$V$$ ) were found, describing the most dominant parameter. Typhoons with a modest intensity and size (for the case of Japan) generally showed a positive correlation between the change in the maximum $$H_{{\text{s}}}$$ and $$V$$ , which means translation wind speed was the dominant parameter. In contrast, stronger typhoons were less sensitive to the change in $$V$$ and could maintain high waves even when almost stationary. With reference to the results, it is important to raise awareness of the future problems that could be caused by large storms that stall for prolonged periods of time.

GEBCO GRIDDED BATHYMETRIC DATASETS FOR MAPPING JAPAN TRENCH GEOMORPHOLOGY BY MEANS OF GMT SCRIPTING TOOLSET

The study investigated geomorphology of the Japan Trench located east of Japan, Pacific Ocean. A high-resolution GEBCO Gridded Bathymetric Dataset was used for modeling, mapping and visualization. The study aimed to compare and analyse variations in the geomorphic structures of the two parts of the trench and to visualize variations in the geological, geophysical and bathymetric settings. Technically, the cartographic work was performed using scripting based on the Generic Mapping Toolset (GMT). Modelled cross-sectioning orthogonal profiles transecting the trench in a perpendicular direction were automatically digitized and graphed in the two segments. The results of the bathymetric analysis shown that the southern part is shallower: with deeper values in absolute (139 samples between –7000 to –8000 m) and statistical records (the most frequent values are within –5500 to –5800 m) comparing to the northern segment (–5300 to –5500 m). The geomorphological analysis shows a more complicated relief in the northern part of the trench, which has a higher seismic activity. The southern part has a gentler slope on the Honshu island side. The geoid modeling along the trench ranges in 0–20 mGal. The highest values are recorded by the Honshu Island (>40 mGal). The rest of the area has rather moderate undulations (20–40 mGal). The free-air marine gravity of the Sea of Japan is <40 mGal. The results include 2D and 3D graphical models, thematic cartographic maps, spatial and statistical analysis of the Japan Trench geomorphology. Tested GMT functionality can be applied to future regional bathymetric modeling of the ocean trenches. All presented maps and graphs are made using GMT scripting toolset.

Preliminary results of monitoring of Rhododendron brachycarpum D. Don ex G. Don fil. in Kunashir island (Sakhalin Region)

The study presents preliminary data on monitoring of Rhododendron brachycarpum D. Don ex G. Don fil.,a rare species of the Kunashir island flora. Comparative morphological and molecular phylogenetic analyses were carriedout with samples of R. brachycarpum and R. fauriei Franch from the island of Kunashir, the Sikhote-Alin Nature Reserve,and Japan (Honshu and Hokkaido islands). R. brachycarpum and R. fauriei are species with fuzzy boundaries concerningsystematics. The internal transcribed spacers (ITS1-5.8S-ITS2) in nrDNA were chosen as molecular markers. Preliminaryresults support the consideration that R. fauriei and R. brachycarpum are two separate species.

Isolation and characterization of microsatellites from a cicada, Yezoterpnosia nigricosta (Hemiptera: Cicadidae), distributed in subarctic and cool temperate forests.

The cicada Yezoterpnosia nigricosta (Hemiptera: Cicadidae) is distributed in subarctic and cool temperate forests in Japan, China and the Russian Far East. Due to its limited and isolated distribution at higher altitudes in cool temperate forests on the main island of Japan, especially in the central and southern areas, this species is listed as a threatened or near-threatened species on the Red List of 12 prefectures in Japan. Moreover, there are concerns about the impacts of climate change on the species' distribution and population demography. In this study, seventeen microsatellite markers were developed for Y. nigricosta, and marker suitability was evaluated using 32 individuals from two populations in Nagano prefecture (central Japan) and Hokkaido, a northern island of Japan. The number of alleles, expected heterozygosity and fixation index at each locus were 1-15 (mean = 4.294), 0.000-0.914 (mean = 0.519) and -0.225-0.456 (mean = 0.108), respectively. Furthermore, there was moderate genetic differentiation between the two populations (FST = 0.111, F'ST = 0.237). These markers will be useful to evaluate the genetic structure and to infer population demographic history of Y. nigricosta populations, which can contribute to population genetics studies of this species.

Host-parasite relationships between seabirds and the haemadipsid leech Chtonobdella palmyrae (Annelida: Clitellata) inhabiting oceanic islands in the Pacific Ocean.

The duognathous haemadipsid leeches of the genus Chtonobdella show a trans-oceanic distribution throughout the Indo-Pacific region. Although passive long-distance dispersal (LDD) of Chtonobdella leeches by birds has been suggested, little is known about the host-parasite relationships between avian hosts and Chtonobdella leeches. In the current study, we investigated Chtonobdella leech infestations of the eyes and other mucus membranes of migratory procellariiform seabirds, Pterodroma hypoleuca and Oceanodroma tristrami, captured at six locations in the Bonin Islands, Honshu and Okinawa Island, Japan. Analyses of the partial sequences of 18S rRNA, 28S rRNA, and mitochondrial cytochrome c oxidase subunit I (COI) and morphological examination of the specimens demonstrated that the Chtonobdella leeches belonged to Chtonobdella palmyrae, which is indigenous to Palmyra Atoll in the Northern Line Islands. A dominant COI sequence type was observed in samples from all six sites; therefore, C. palmyrae almost surely dispersed approximately 1000 km by infesting the eyes and mucus membranes of procellariiform seabirds. The host-parasite relationships between procellariiform seabirds and C. palmyrae provide explicit evidence of the LDD of duognathous haemadipsid leeches. The taxonomic status of Haemadipsa zeylanica ivosimae from the Volcano Islands is also briefly discussed.

A Neogene bristlemouth of the genus Cyclothone (Stomiiformes: Gonostomatidae) from South Korea

ABSTRACT A fossil specimen of bristlemouth fish of the genus Cyclothone is reported for the first time from the marine deposits of the middle Miocene Duho Formation, South Korea, and described as new species Cyclothone duhoensis, sp. nov. This is the second stomiiform fish discovered there. It represents the oldest nominal species of its genus, and the third and southernmost record of fossil bristlemouth from the ancient Eastern Sea (Sea of Japan) basin after the findings in the Sakhalin (Russia) and Honshu (Japan) islands. The new Miocene bristlemouth is very similar to the Recent congeners. Nevertheless, it can be separated from them by the presence of more than 15 photophores in the AC series, of which at least four photophores are behind the anal-fin base, and by a peculiar upper jaw dentition. The biological features of the Recent bristlemouths along with this unique finding hint at shallow-water conditions during the Duho Formation sedimentation.

Contrast across a boundary: Differing histories of two eelpout populations on a continuous continental slope

Detecting drivers of population divergence across phylogeographic breaks is a major challenge in marine population genetics, partly due to uncertainties in molecular dating. Although the calibration of demographic transition (CDT) method is the most promising rate calibration technique for population-level events, there is a risk of making the false assumption that post-glacial population expansions coincided with global temperature rise. Further generalization of the technique is required to evaluate population histories of marine species whose abundance may be independent of changes in temperature. We explored the population history of a dwarf eelpout Petroschmidtia teraoi on Japanese continental slopes in the Sea of Japan and Sea of Okhotsk as a model organism for phylogeographic study. For rate calibration, we estimated historical stock sizes from a species distribution model and incorporated this data into the CDT method as a proxy for demographic transition (we term this combined method extended CDT, or eCDT). Our species distribution model showed that the range of P. teraoi is mainly determined by water depth and locality (i.e., latitude and longitude). Reconstructed historical stock sizes revealed contrasting demographic trends in the northern and western Sea of Japan on either side of the Noto peninsula, located at the midpoint of the Japanese mainland. We also found a sharp genetic break in the same location, and inferred contrasting demographic histories of local populations from the molecular data. The striking differences in the demographic histories of local populations even on apparently continuous continental slopes are most likely due to differences in available habitat area. eCDT appeared to work well as a rate calibration method for our temperature-independent study species, and our species distribution model revealed that local populations could have diverged due to discontinuities in available habitat. Finally, we assessed the strengths and weakness of the novel calibration method by analyzing simulated sequences.

Drosophila parasitoids (Hymenoptera) of Japan

AbstractThe Drosophila parasitoid system is an excellent model for the study of biological and ecological interactions. In Japan, extensive studies have been carried out on Drosophila parasitoids since the early 2000s. Here we provide up‐to‐date information on their diversity, distributions, host use and reproductive mode. Until now, 45 wasp species have been recorded. In addition, four genetically distinct groups (tentatively assigned as “races”) have been found in Ganaspis brasiliensis (Figitidae). Most of them are larvo‐pupal parasitoids belonging to the families Figitidae and Braconidae, and some are pupal parasitoids of the families Pteromalidae and Diapriidae. A species of Encyrtidae was also recorded. Their major hosts are indicated with information on the host's breeding sites. Except Ganaspis xanthopoda and two races of G. brasiliensis that are distributed both in tropical and temperate regions, they are divided into tropical and temperate species. The tropical species are mainly distributed in Southeast Asia, and their distributions in Japan are restricted to the Ryukyu islands, particularly Iriomote‐jima. The temperate species have been recorded from the main islands of Japan and surrounding islands but not from the Ryukyu islands, except two braconid species, Asobara japonica and Phaenocarpa sp. TK1. Some of the temperate species have also been recorded from Korea, China, Europe and/or North America. Among the 45 Japanese parasitoid species, at least seven are assumed to be thelytokous.

Genetic Diversity and Structure of Japanese Endemic Genus Thujopsis (Cupressaceae) Using EST-SSR Markers

The genus Thujopsis (Cupressaceae) comprises monoecious coniferous trees endemic to Japan. This genus includes two varieties: Thujopsis dolabrata (L.f.) Siebold et Zucc. var. dolabrata (southern variety, Td) and Thujopsis dolabrata (L.f.) Siebold et Zucc. var. hondae Makino (northern variety, Th). The aim of this study is to understand the phylogeographic and genetic population relationships of the genus Thujopsis for the conservation of genetic resources and future breeding. A total of 609 trees from 22 populations were sampled, including six populations from the Td distribution range and 16 populations from the Th distribution range. The genotyping results for 19 expressed sequence tag (EST)-based simple sequence repeat (SSR) markers, followed by a structure analysis, neighbor-joining tree creation, an analysis of molecular variance (AMOVA), and hierarchical F statistics, supported the existence of two genetic clusters related to the distribution regions of the Td and Th varieties. The two variants, Td and Th, could be defined by their provenance, in spite of the ambiguous morphological differences between the varieties. The distribution ranges of both variants, which have been defined from their morphology, was confirmed by genetic analysis. The Th populations exhibited relatively uniform genetic diversity, most likely because Th refugia in the glacial period were scattered throughout their current distribution area. On the other hand, there was a tendency for Td’s genetic diversity to decrease from central to southern Honshu island. Notably, the structure analysis and neighbor-joining tree suggest the hybridization of the two varieties in the contact zone. More detailed studies of the genetic structure of Td are required in future analyses.

The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific.

The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36–0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific.

Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population

Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.