Invasion history of Cardamine hirsuta in Japan inferred from genetic analyses of herbarium specimens and current populations

The Japanese Archipelago hosts a rich butterfly fauna, and elucidating the genetic structures of multiple species is necessary to clarify their formation processes. This study aimed to reveal the genetic structure and distribution formation process of Parnassius citrinarius, which is widely distributed across the Japanese Archipelago from Hokkaido to Shikoku, through phylogeographic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Thirty haplotypes were revealed from 311 individuals from 47 sites, indicating significant differences in the genetic structures between the eastern and western parts of the Japanese Archipelago. In Eastern Japan, multiple genetic clusters were found, with some sites harboring two clusters. The divergence times among populations in Eastern Japan were relatively recent, and no genetic differentiation was observed between regions, including between Hokkaido and Honshu, which are separated by a narrow strait. In contrast, in Western Japan, including Shikoku, unique genetic clusters were observed in each region. The phylogenetic relationships among populations were regionally clustered, and the divergence times were relatively ancient. The distribution and genetic structure of P. citrinarius in the Japanese Archipelago have been significantly influenced by temperature fluctuations and the presence of geographical barriers during the Pleistocene glacial-interglacial cycles, including the potential formation of refugia in Western Japan.

The onset, dispersal and crop preferences of early agriculture in the Japanese archipelago as derived from seed impressions in pottery

Salmonella infections represent a leading cause of foodborne illnesses; resistance to third-generation cephalosporins (TGCs), which are a first-choice antimicrobial for treating human Salmonella enteritis, has become a serious public health concern worldwide. Because the consumption of undercooked chicken meat products is a major cause of foodborne salmonellosis in Japan, we conducted three surveys at different periods between 2017 and 2022, with the cooperation of four abattoirs (two in Eastern and two in Western Japan). The first survey was conducted at abattoir A, which is located in Eastern Japan. Salmonella was detected in 84.4% of broiler flocks tested (27/32); among them, all the TGC-resistant isolates obtained from one farm (farm FA) were identified as S. Infantis. Salmonella was recovered from 62.5% of breast meat samples (20/32), with one case suggesting cross-contamination. The second survey was conducted at three other abattoirs to examine the prevalence of TGC-resistant Salmonella, in both Western (abattoirs B and C) and Eastern (abattoir D) Japan. Salmonella was detected in 90.6% of broiler flocks examined (29/32). TGC-resistant S. Infantis was isolated from 2 flocks until 2018 and not thereafter. Subsequently, isolates were identified as TGC-susceptible S. Schwarzengrund in both regions. The third survey was performed at abattoir A to elucidate whether there were changes in the phenotypes. Of the 11 broiler flocks introduced from farm FA, 10 were positive for Salmonella (90.9%); all the isolates were S. Schwarzengrund susceptible to TGC. This study shows that TGC-susceptible S. Schwarzengrund has replaced the resistant phenotypes among broiler flocks in both Eastern and Western Japan. Although chicken meat products could be cross-contaminated with Salmonella during the slaughtering process, reducing the prevalence of Salmonella in broiler flocks remains important to decrease Salmonella enteritis in humans.

The Japanese Archipelago consists of a series of isolated yet interconnected islands off the Eurasian continent. The linear topography of the archipelago presents a unique biogeographic context for the dispersal of organisms from the continent. In this study, mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP) variation were employed to elucidate the dispersal history of the Japanese clouded butterfly (Parnassius glacialis) across the Japanese Archipelago, including the northern island (Hokkaido), the main island (Honshu), and Shikoku Island. Network analysis of 1192bp of mtDNA (cytochrome oxidase I and II) regions revealed 49 haplotypes and three distinct haplotype groups, which correspond geographically to Eastern Japan, Western Japan, and Chugoku-Shikoku. The Chugoku-Shikoku group is the most ancient lineage. Divergence time estimates using whole-genome sequencing of mtDNA suggest that the Japanese lineage diverged from the continental P. glacialis approximately 3.08 million years ago (Ma). Subsequently, the Eastern Japan and Western Japan lineages diverged from the Chugoku-Shikoku lineage around 1.06Ma, with subsequent divergence of the Eastern and Western Japan lineages at approximately 0.62Ma. P. glacialis is estimated to have expanded its distribution via a land bridge that once connected China and the Japanese Archipelago. Population structure analysis based on 3067 SNP genotypes revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. Through mtDNA and SNP variation analyses, four primary genetic barriers were identified: between Hokkaido and Honshu, between Eastern and Central Japan, within the Kansai region, and in the Chugoku region. The first three barriers correspond to notable geographical features, the Blakiston Line, a line parallel to the Itoigawa-Shizuoka Tectonic Line, and a boundary crossing Lake Biwa. These findings suggest that Japanese P. glacialis diverged from the continental P. glacialis and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.

To clarify the environmental distribution of Vibrio vulnificus, sea water, sea mud, and oysters were examined at 13 sites, i.e. 4 sites in the Tokyo Bay (eastern Japan) and 9 sites (5 sites for oysters) in Tokushima Prefecture (western Japan). 1. V. vulnificus was isolated from 80 (54.8%) of the 146 samples of sea water examined. It was isolated from 19 (41.3%) of the 46 samples from western Japan and 61 (61.0%) of the 100 samples from eastern Japan. 2. It was isolated from 40 (40.8%) of the 98 samples of sea mud obtained in eastern Japan. 3. It was isolated from 655 (30.3%) of the 2,165 samples of oysters. They were 30 (9.7%) of 309 samples from western Japan and 625 (33.7%) of 1,856 samples from eastern Japan. 4. The density of V. vulnificus was 0.3-1.1 x 10(6) MPN/L in seawater, 0.3-1.1 x 10(5) MPN/100 g in sea mud, and 0.3-1.1 x 10(7) MPN/100 g in oysters. 5. Seasonally, V. vulnificus was isolated from 44 (6.2%) of the 713 samples in spring, 450 (72.6%) of the 620 samples in summer, 264 (51.8%) of the 510 samples in fall, and 17 (3.0%) of the 56 samples in winter. Thus, the isolation rates of V. vulnificus from sea water and oysters tended to be higher in eastern Japan than in western Japan and to be highest in summer, then, in fall.

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.

During the last 11 years of 1951-61, there were 54 typhoons which attacked the Japanese Archipelago bringing about heavy rains and severe damages.. The geographical distribution of heavy rains in connection with these typhoons were illustrated on about 200 daily isohyetal maps of Japan. And their distribution patterns and hourly changes of rainfall intensities were checked and analyzed. Then, the following four distuibution patterns were identified: 1) Orographic rain-band pattern 2) Frontal rain pattern 3) Coastal rain pattern 4) Scattered rain pattern 1) Orographic rain-band patternA) This was the most frequently occurring and the most characteristic pattern. It occurred on 65% occasions of typhoon rains in Japan (Tab. 1). Amount of areal rainfall for whole Japan brought by one typhoon of this pattern was much larger than those by the other patterns of rains and often exceeed 25×109 tons.B) Locations of rain-bands were restricted geographically to the following 8 regions. The more distinctive ones were designated by asterisk: 1) Boso Peninsula (Eastern Japan) 2)* Izu-Tanzawa-Ashio Mts. (Eastern Japan) 3) Akaishi-Kusatsu Mts. (Central Japan) 4) Mikawa-Kiso Mts. (Central Japan) 5)* Kii-Suzuka-Ibuki Mts. (Western Central Japan) 6) Eastern Shikoku-Osaka (Western Japan) 7) Western Shikoku (Western Japan) 8)* Eastern Kyushu (Southern Japan)C) Band structures were mainly constructed on the eastern side of the typhoon path. Therefore the afore-mentioned 8 rain-bands were not always constructed by every typhoon, irrespective of the path of the center. 1) When a large and strong typhoon passed along the western coast of Kyushu Island, the 8 band structures were observed together frequently.-Fig. 1, TY 5609 & TY 5612. 2) When a typhoon landed on Shikoku Island, the western-most band in Kyushu was not formed. -TY 5817. 3) When a typhoon hit and traversed central Japan, only eastern band structures appeared remark-ably.-TY 5915.D) At the southern tip of each rain-band, there is a high mountain of more than 1, 000 m in elevation facing to open sea and/or flat lands of its eastern side.E) The axis of each band structure did not always run parallel with the direction of the mountain range starting from the aforementioned southern high mountain. The axis often stretched from SSW to NNE.F) The average width of the rain-bands was rather narrow and only about 30 km, but their maximum length often reached more than 300 km. However, they did not pass beyond the central back-bone mountains of Japan mostly.G) The rainfall of this pattern is not a typical orographic rain along the upslope of a mountain range, as is taught in textbooks of meteorology. Numerical calculations of orographic rainfall at various locations in Eastern Japan were done and the amounts of theoretically expected orographic rains on each cross point of 15 km mesh on the 1: 200, 000 topographic sheets covering the area were evaluated. The calculations were made by different wind directions of each 20° difference and the wind speeds were assumed always to be 20 m/s. The results were plotted on the maps and isohyets were drawn by wind directions. Thus, 18 isohyetal maps of orographic rains in Eastern Japan were constructed and the distribution patterns of orographic rains were illustrated by various wind directions. A similar pattern to the above-mentioned band-type distribution was recongnized with that of orographic rains by prevailling wind of 140° directions as are shown in Figs. 2 & 5. However, the directions of the prevailing wind above the area during rains were about 200° up to at least 10 km and its speeds were about 20 m/s as a shown in Figs. 3, 4, 8 & 10.

AMS-dated archaeobotanical assemblages from hearth deposits of Middle Yayoi (fourth century bce–first century ce) cultural layers of the Maenakanishi site (36°09′N, 139°24′E) in northern Saitama Prefecture demonstrate that besides rice, foxtail and broomcorn millet were the most important staple crops during the second and first centuries bce. The reliance on less demanding dry-field crops at Maenakanishi and other Early to Middle Yayoi settlements in north-western Kanto and the Central Highlands in eastern central Japan contrasts with concurrent agricultural production in western and north-eastern (Tohoku) Japan, where rice cultivation generally dominated and millets apparently played a minor role. Two factors, which likely influenced this pattern, are the uneven density distribution and the cultural heterogeneity of indigenous non-agricultural Jomon populations during the formation and spread of the Yayoi culture (tenth/fourth century bce–250 ce) brought to the Japanese islands by farmers from the Asian mainland. In western Japan the spread of rice cultivation was likely promoted by low Jomon population densities. The higher importance of foxtail and broomcorn millet at Maenakanishi may be explained by cultural influence from the northern Central Highlands. Early agricultural communities in this region appear to have preferred these newcomer crops that required less labour and organisational efforts.

In recent years, the impact of tourism on socioeconomic structures has attracted the attention of the Japanese government. To plan and implement effective tourism policies and strategies, it is important to understand the basic characteristics of tourism resources in a given region. Tourism resources have been regarded as one of the most important indices for evaluating the tourism potential of a region and analyzing tourism phenomena. However, previous studies on tourism regions in Japan were based on limited resources and analyses have been largely qualitative. Therefore, this study focuses on a statistical analysis of substantial data, such as the distribution of tourism resources, to clarify the regional characteristics of tourism resources in Japan. First, the number of tourism resources, which are assigned a weighted value on the basis of an evaluation ranking determined by the Japan Travel Bureau Foundation, is calculated for each prefecture. The results of the statistical dispersion show that, among prefectures, there are great differences in the quantities of each type of tourism resource. Next, the prefectures are classified into four regional clusters based on similarities of location quotients. The first cluster is abundant in natural landforms and is mainly located in eastern Japan. The second cluster predominantly consists of elements concerning surface water such as lake water and river water and is composed of prefectures at various locations around the country. The third cluster, composed of prefectures in the metropolitan areas of both eastern and western Japan, has extensive urban cultural resources. The fourth cluster primarily contains important natural and cultural components, which are closely located along the Seto Inland Sea and in south-west Japan, including Okinawa. Finally, to analyze the regional attractiveness of each prefecture, the coefficient of specialization and the weighted number of the resources are compared to ranking data on tourist arrivals and projected destinations of domestic tours. The results show that popular tourist destinations have high values in the dimension of the number of tourism resources, and these regions are divided into two types with high or low specialization. In conclusion, the distribution of tourism resources determines the characteristics of each prefecture as a tourism region and makes a difference in the regional attractiveness of prefectures. The comprehensive analysis of a wide variety of tourism resources is effective for identifying the regional differences of tourism resources and reinforcing the findings of classifications of Japan's tourism regions provided by prior studies.

Source, path, and site effects for subduction and crustal earthquakes in eastern and western Japan were estimated by spectral inversion analyses using about 10,000 strong motion records observed at 895 sites in Japan. Flat level of acceleration source spectra for the Tottori-ken Seibu earthquake were half of that for the Hyogo-ken Nanbu earthquake. Stress drops for crustal earthquakes were less than those for subduction earthquakes. Stress drops for subduction earthquakes in eastern Japan were bigger than those for subduction earthquake in Hyuganada region. It was found that stress drops for big crustal earthquakes were larger than the other small- and middle-sized crustal earthquakes.

<p>   In East Asia, a significant subtropical front called the Baiu/Meiyu front appears just before midsummer and brings the huge rainfall there, greatly influenced by the Asian summer monsoon. However, large-scale atmospheric features and rainfall characteristics (such as convective or stratiform rain) as well as the total rainfall amount around the front show rather great differences between the western and eastern portions. For example, in the western part of the Japan Islands (especially around Kyushu District, the most western part) and the Changjiang River Basin in Central China, the more frequent appearance of the heavy rainfall events due to the organized deep convective clouds than in the eastern Japan results in the larger climatological precipitation amount there. This is greatly related to the larger moisture transport toward the western part of the Baiu front than toward the eastern part. On the other hand, the rainfall characteristics around the front in the eastern Japan tend to be largely influenced by the cool Okhotsk air mass with rather stable stratification. Furthermore, their year-to-year, intraseasonal and short-period variations including the diversity of the “heavy rainfall types” are also very large.</p><p>The extreme events in association with the Baiu/Meiyu activity are greatly reflected by the above variability of the frontal activity. Inversely, it would be also important viewpoint that detailed examination of some extreme events could lead to the better understanding of the “dynamic climatological features” of the Baiu/Meiyu system itself.</p><p>In such concept, the present study will examine the frontal-scale rainfall features and the atmospheric conditions for the extremely heavy rainfall event around the Baiu front in western to central Japan during 5-7 July 2018. Although it is the common feature for the Baiu frontal rainfall heavy in western Japan that the frequent appearance of the meso-scale intense rain bands results in the huge total rainfall amount there, it is noted that the extremely large total rainfall area was distributed much more widely up to the central Japan with also considerable contribution of the long-persistent “not-so-intense rain” there, as often found in the heavy rainfall in the eastern Japan. Our analyses of the atmospheric fields suggest that this extreme event seems to be characterized by the strong mixture both of the large-scale factors for activating the “western Japan Baiu” and the “eastern Japan Baiu”.</p><p>As for the precipitation analyses, the 10-minute precipitation data at many meteorological stations in the Japan Islands area were used to discuss on the frontal-scale “rainfall characteristics” as well as the total rainfall amounts.</p>

We analyzed the home range of deer in western Japan. We collected data on 120 GPS-collared deer from Kinki, Shikoku, and Kyushu. The home range size in western Japan was smaller than that of deer in eastern and northern Japan. The percentage of individuals that made seasonal movements in western Japan was 20%. The percentage of seasonal migrants in collared deer varied regionally. The proportion of seasonal migrants was higher in areas with more snow accumulation. As the period during which the snow depth exceeded 50 cm became longer, the proportion of seasonal migrants increased. The migration distance ranged from 1.9 to 14.3 km, which was shorter than those in eastern and northern Japan. Further, individuals that use deciduous broad-leaved forests as their summer habitat tended to migrate seasonally, while deer who used evergreen broad-leaved forests tended to be more sedentary. Vegetation and topography in western Japan differ significantly from those in eastern and northern Japan, and deer behavior is also characteristic and unique to western Japan.

Multiple introductions can play a prominent role in explaining the success of biological invasions. One often cited mechanism is that multiple introductions of invasive species prevent genetic bottlenecks by parallel introductions of several distinct genotypes that, in turn, provide heritable variation necessary for local adaptation. Here, we show that the invasion of Aegilops triuncialis into California, USA, involved multiple introductions that may have facilitated invasion into serpentine habitats. Using microsatellite markers, we compared the polymorphism and genetic structure of populations of Ae.triuncialis invading serpentine soils in California to that of accessions from its native range. In a glasshouse study, we also compared phenotypic variation in phenological and fitness traits between invasive and native populations grown on loam soil and under serpentine edaphic conditions. Molecular analysis of invasive populations revealed that Californian populations cluster into three independent introductions (i.e. invasive lineages). Our glasshouse common garden experiment found that all Californian populations exhibited higher fitness under serpentine conditions. However, the three invasive lineages appear to represent independent pathways of adaptation to serpentine soil. Our results suggest that the rapid invasion of serpentine habitats in California may have been facilitated by the existence of colonizing Eurasian genotypes pre-adapted to serpentine soils.

Genji-firefly Luciola cruciata, a symbolic species in Japanese traditional agricultural landscapes, has recently been decreased. Therefore, conservation practices of this species have been tried in various parts of Japan. It was reported that the factors influencing the distribution of this species in eastern Japan differed from those in western Japan, and that the difference corresponded to topographical difference between the two regions. There are, however, few studies in which the difference is analyzed quantitatively. To compare factors influencing firefly distribution in eastern Japan with those in western Japan, we constructed regression models using firefly abundance as dependent variable and environmental measurement values as independent variables. Data were obtained from two areas: one was Ichikai Town, which is located in a hilly district in eastern Japan, and the other was Hagi City, which is located in a piedmont region in western Japan. The results showed that the dominance of gravel deposition covering riverbed and the abundance of freshwater snails Semisulcospira libertina were significant factors influencing firefly abundance in the both study areas, while such factors as the channel width, current velocity, dissolved oxygen and bank height did not performed as environmental factors constantly. We confirmed that we should be careful in applying an inductive model obtained in a study area to the other areas. It appears that regional comparison of environmental factors influencing abundance of target organisms to find the reasons that causes regional difference in environmental factors may be a way to construct models with higher universality.

In this study, LC-MS/MS was used to detect tetrodotoxin (TTX) in 47 commercially available bivalve molluscs (fifteen oysters, six clams, nine short-necked clams, three hard clams, three mussels, four corbiculae, and seven scallops) purchased from supermarkets and retail stores in Japan. In addition, eight preserved mussel samples collected from Osaka Bay in 2014–2015 for paralytic shellfish poisoning surveys were examined. TTX was detected in one oyster from western Japan and two scallops from eastern Japan (detection rate: 6.4%), with the highest TTX concentration detected in the oyster (20 µg/kg in the whole weight), followed by the scallops (8.2 and 17.6 µg/kg in the whole weight). These detected concentrations were below the EFSA-recommended threshold for total TTX concentration in bivalve molluscs (44 µg/kg). TTX had previously been detected only in scallops collected from eastern Japan; however, this study is the first to report TTX in oysters from western Japan. By contrast, TTX was not detected in mussels collected from Osaka Bay. This result contradicted a hypothesis that some paralytic-shellfish-toxin-producing plankton might produce TTX, so showed that no relationship exists between such plankton and the TTX content in bivalve molluscs.