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Callicarpa subpubescens is endemic to the oceanic Ogasawara Islands, and multiple ecotypes have been suggested to exist within southern part of this group, the Hahajima Islands, each associated with unique localized habitats. We determined the habitat characteristics of each ecotype, the presence or absence of pre- and post-mating isolation, the amount of gene flow among ecotypes in adult trees and naturally pollinated seeds using EST-SSR markers, and discussed how ecotypes are maintained in this species. There were four ecotypes in the Hahajima Islands, one of which presumed to be derived from hybridization of the remaining two ecotypes. The spatial distribution and habitat of each ecotype showed distribution which have depended on the suitable environment for each ecotype, i.e. local adaptation. The leaf morphology and size distribution of each ecotype also indicated the appropriate forms for each habitat. Flowering times more or less overlap among the ecotypes, indicating that pre-mating isolation is not perfect. Artificial cross-pollination showed that no post-mating isolation exists between ecotypes. Hybridization rates in adult trees and naturally pollinated seeds were 37.2% and 26.4%, respectively, and most of the hybrids were backcrosses and few F1. The hybridization rates of each ecotype and paternal correlation indicated that the flowering synchrony and spatial distribution of ecotypes contributed to hybridization among ecotypes. The reversion to the original ecotype which adapted to the environment through backcrossing would contribute to the maintenance of the ecotypes.

The COVID-19 Registry Japan (COVIREGI-JP), a registry of patients hospitalized with coronavirus disease (COVID-19), contains the largest national COVID-19 inpatient population. Since COVIREGI- JP invites voluntary participation by facilities, selection bias is inevitable. The current study examined the representativeness of COVIREGI-JP data in comparison to open-source national data. The number of infections and deaths among hospitalized COVID-19 patients in COVIREGI-JP were compared to those in national data recorded during the six waves of the COVID-19 epidemic until March 6, 2022. During the period studied, patients in COVIREGI-JP represented 1% of the total COVID-19 cases according to national data; the proportion was high during the first wave (32.7%) and tended to decrease, especially after the fourth wave. The overall proportion of patients from each region varied from 0.8% to 2.5%, but case fatality rates in COVIREGI-JP tended to be higher than those in the national data, with the exception of a few waves, in several regions. The difference was smallest during the first wave. Although COVIREGI-JP consistently registered cases from all regions of the country, the proportion tended to decline after the beginning of the epidemic. Given the epidemiological persistence and the ever-changing epidemiology of COVID-19, continued case registration and data utilization in COVIREGI-JP is desirable, although selection bias in COVIREGI-JP registration of cases should be carefully interpreted.

Background Several studies have investigated whether pregnancy is a risk factor for developing severe COVID-19; however, the results remain controversial. In addition, the information regarding risk factors for developing severe COVID-19 in pregnant women is limited. Methods A retrospective cohort study analyzing the data from the nationwide COVID-19 registry in Japan was conducted. Propensity score matched analysis was performed to compare COVID-19 severity between pregnant and nonpregnant women. Multivariate analysis was also conducted to evaluate risk factors for developing moderate-to-severe COVID-19 in pregnant women. Results During the study period, 254 pregnant and 3752 nonpregnant women of reproductive age were identified. After propensity score matching, 187 pregnant women and 935 nonpregnant women were selected. A composite outcome of moderate-to-severe COVID-19 was more frequently observed in pregnant women than that of nonpregnant women (n=18, 9.6% vs. n=46, 4.9%; P=0.0155). In multivariate analysis, the presence of underlying diseases and being in the second-to-third trimester of pregnancy were recognized as risk factors for moderate-to-severe COVID-19 in pregnant women (odds ratio [95% confidence interval]: 5.295 [1.21-23.069] and 3.871 [1.201-12.477], respectively). Conclusions Pregnancy could be a risk factor for moderate-to-severe COVID-19 for women in Japan. In addition to the presence of comorbidities, advanced pregnancy stages may contribute to greater risks for developing moderate-to-severe COVID-19 in pregnant women.

Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers., ファイル公開：2020/11/01

Additional file 1: Table S1. Definition of the variables for confounding factors using multivariable analysis in Table 4.

Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers. Electronic supplementary material The online version of this article (10.1007/s10265-019-01134-6) contains supplementary material, which is available to authorized users.

Expressed sequence tagged (EST) microsatellite (SSR) markers were newly developed for Callicarpa subpubescens, a species endemic to the Bonin (Ogasawara) Islands of Japan, to investigate gene flow,...

PREMISE OF THE STUDY: Hybrid zones are areas where gene flow between related species is currently occurring, so information on the compatibility between related species and their hybrids is essential for predicting the dynamics of such zones generated by introgressive hybridization. In this study, we quantified the compatibility among Magnolia stellata, M. salicifolia, and their hybrids in a hybrid zone using gene dispersal modeling. METHODS: After determining the genealogical classes of adult trees in the hybrid zone, the paternity of 574 open-pollinated seeds from 37 known maternal trees was analyzed with microsatellite markers. A neighborhood-based Bayesian gene dispersal model developed by us for estimating compatibility was then applied to the paternity data. KEY RESULTS: When M. stellata or M. salicifolia were mothers, interspecific mating to produce F1 hybrids yielded significant incompatibility, but backcrossing with F1 hybrids did not. Furthermore, when F1 hybrids became mothers, no significant incompatibility resulted from backcrossing to parental species or intra-F1 mating to produce F2 hybrids. The estimated proportion of F1 hybrids in the outcrossed seeds (1.7%) in the hybrid zone was much lower than that in the adult trees (14.0%). CONCLUSIONS: While it is difficult to obtain F1 hybrids, their low incompatibility makes it easy to produce advanced generation hybrids, once they have been successfully obtained. Although the production of F1 seeds is rare, heterosis and/or weak selection pressure in an empty niche between the parental species’ niches may have contributed to the increased proportion of adult F1 hybrids in the hybrid zone.

Although the genetic structures of populations in several model organisms have been studied even at the genomic level, quite a few ecologically important or evolutionary interesting species, such as endemic species on oceanic islands, exist whose genetic variations have not yet been studied. Genetic studies of those species may add new insights to our knowledge of evolution, especially when accompanied with ecological and geological knowledge of the species. In this study, we analyzed the genetic variation of two related species of Hamamelidaceae, Distylium racemosum and Distylium lepidotum, living in different habitats and possessing distinctive morphological characteristics. Distylium racemosum is one of the dominant trees of broad-leaved evergreen forests in Japan, and D. lepidotum is a dominant shrub in dry scrub endemic to the Ogasawara Islands. We analyzed the nucleotide variation at 112 protein-coding loci in 95 samples for the two Distylium species and inferred population structure and demographic history on the basis of these data. Our results showed that the samples from two Distylium species were genetically clustered into the following three groups: D. racemosum, D. lepidotum in the Chichijima Island, and D. lepidotum in the Hahajima Island. Furthermore, D. racemosum appears to have diverged first approximately 10 million years ago (MYA), and, then, the split of two populations of D. lepidotum occurred around 1 MYA. Additionally, we detected a few candidate loci that may contribute to adaptation of the species or local populations by exploring the pattern of the variation within and between species using the FST-outlier approach.

Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is distributed on both the older Bonin and younger Volcano Islands. In this study, we conducted population genetic analyses of P. boninensis on these islands to examine the population diversity and structure across old and young islands, to assess potential differences in population demography with island age, and to collect any evidence of migration between old and young islands. We found that the genetic diversity of expressed sequence tag (EST)-based microsatellite (SSR) markers, the nucleotide diversity of nuclear DNA sequences, and the haplotype diversity of chloroplast DNA on young islands were lower than those on old islands. Clustering analyses of EST-SSR indicated that populations on old islands were strongly diverged from those on young islands. Approximate Bayesian computation analysis of EST-SSR suggested that population expansion occurred on old islands while population reduction occurred on young islands. We also found evidence of migration among old islands (mostly from south to north), while it appears that there have been very few migration events between old and young islands. These differences could be due to the fact that young islands tend to be geographically isolated and support smaller populations that began a shorter time ago from limited founders. The P. boninensis populations on the Volcano Islands are interesting from an evolutionary perspective as they constitute a classic example of the early stages of progressive colonization on oceanic islands with small effective population sizes and low genetic diversity.

Overbrowsing by the explosively increasing deer has a huge impact on forest vegetation in the temperate zone. Although it was expected that, over the years, the decline of forest floor vegetation would lead to a decrease in deer population, such a decline has not been observed. A dietary analysis of deer is necessary to establish the survival mechanisms of deer populations in forests with degraded understory vegetation. This study explores the foraging strategy of sika deer, Cervus nippon, in Ashiu Research Forest, Kyoto, Japan, where the understory vegetation is severely degraded. A total of 177 fecal samples of sika deer were collected during each season and their food resources identified using DNA meta-barcoding technology and local plant DNA database. The results of the DNA meta-barcoding revealed that sika deer depended on non-preferred plants and preferred plants from early winter to spring. From summer to autumn, sika deer mainly feed on preferred plants. In all seasons, the percent cover of preferred plants for sika deer is also scarce in the forest floor. Biomass of preferred plants, such as litterfalls, play a significant role in maintaining the population density of sika deer when the understory vegetation is degraded in the forest habitat. Therefore, the degradation of the understory vegetation might not necessarily lead to a decrease in the population density of sika deer.

To ensure the persistence of populations and species that maintain unique biodiversity in suburban landscapes, it is necessary to establish an efficient management system for abandoned suburban secondary forests. Thinning operations seem to be an effective management approach to inhibiting the progress of forest succession, which could lower the level of species diversity. To evaluate the effect of thinning operations on the demographic performance (growth, survival, and sexual reproduction) of the rare subtree species Magnolia stellata, we set up a field experiment and monitored the population dynamics over 9 years. The results revealed that stem survival and flower production per genet showed a decreasing trend in the nonthinned site. However, thinning operations increased the demographic performance, in particular the stem growth and survival rates as well as flower and seed production. The findings suggested that thinning operations may decrease the extinction probability of not only the targeted local population but also the metapopulation, because the thinned population serves as a better seed source. Thus, the creation of well-lit sites by thinning operations would be a useful conservation strategy for M.stellata.

We studied the feeding ecology of the critically endangered Red-headed Wood Pigeon Columba janthina nitens, a subspecies endemic to a very remote and highly disturbed oceanic island chain, the Ogasawara Islands. An analysis based on high-throughput sequencing (HTS) was undertaken on 627 faecal samples collected over 2 years from two island habitats, and food availability and the nutrient composition of the major fruits were also estimated. The HTS diet analysis detected 122 food plant taxa and showed clear seasonal and inter-island variation in the diet of the Pigeons. The results indicated a preference for lipid-rich fruits, but the diet changed according to the availability of food resources, perhaps reflecting the foraging strategy of the Pigeons in isolated island habitats with poor food resources. Pigeons also frequently consumed introduced plants at certain times of year, perhaps compensating for the lack of preferred native food resources. However, the degree of dependence on introduced plants appeared to differ between the two island habitats, so the different impacts of introduced plant eradication on the foraging conditions for the Pigeons on each island should be considered. HTS diet analysis combined with field data may be useful for monitoring the foraging conditions of endangered species and may also inform an appropriate conservation strategy in oceanic island ecosystems with complicated food webs that include both native and introduced species.

Understanding the factors shaping rare species’ current genetic diversity and structure, particularly the impact of recent anthropogenic pressures, is important in order to develop appropriate conservation strategies based on robust predictions. Thus, we have genotyped all 585 surviving individuals of Magnolia stellata from six remnant populations and seven isolated tree sites in northern Mie Prefecture, Japan, using nuclear and chloroplast microsatellites. Three genetic clusters were detected by STRUCTURE analysis, with an oldest divergence time between pairs within 25 generations according to coalescent analysis. We attribute this recent divergence to recent anthropogenic environmental changes. Evidence of only one significant recent migration event between pairs of the six populations was detected, indicating that most of the remnant populations are isolated now. Their future genetic status was predicted using Monte Carlo simulations, under four scenarios. It declined more than twice as rapidly in a scenario assuming variations in fecundity among both female and male parents than in a scenario assuming no fecundity variations, but strongly improved in a scenario including promotion of migrations between adjacent pairs of populations. These predictions indicate that sexual reproduction of the species should be promoted by providing more suitable habitats and migration between populations should be enhanced by restoring remnant isolated tree sites and extinct populations. In addition, all the remnant populations should be conserved because they host current genetic variation that may be important for coping with future climate change, and they could provide important stepping-stones for gene flow.

The Bonin Islands are endowed with endemic species. However, these species are at risk of extinction because of the exuberance of invasive alien plants. Therefore, native plant species should be revegetated after eradicating alien plants. We investigated the genetic variation of Terminalia catappa populations in the Bonin Islands by using nuclear (n) microsatellites (simple sequence repeats [SSRs]) and chloroplast (cp) DNA. No significant differences were observed in the genetic diversity of nSSRs among 22 populations. However, recent bottlenecks were detected in three populations on the Chichijima Island group. nSSR variation and cpDNA haplotypes suggested the presence of two genetically distinct groups in the Mukojima and Chichijima Island groups and the Hahajima Island group. A similar genetic structure was observed in plants and animals in the Bonin Islands. Populations on the three islands, which were separated from other islands in each island group when the water depth was 50-m lower than the present level, were dominated by unique nSSRs clusters, suggesting that historical changes in island connections during the Pleistocene era affected genetic substructuring. These results suggested that different factors contributed to the genetic structure of T. catappa on different geographic scales. At the whole-island level, the genetic structure was determined by long-distance seed dispersal by ocean currents. At the island-group level, the genetic structure was determined by historical changes in island connections caused by changes in the sea level due to glacial–interglacial transition. These findings would help in establishing transplantation zone borders for revegetating T. catappa on the Bonin Islands.

Twenty-six microsatellite loci were developed and characterized for Ligustrum micranthum, a species endemic to the Ogasawara Islands, Japan. The genetic structure of this species must be clarified in order to restore the island's ecosystem. A total of 8511 primer pairs were designed from de novo sequencing. Of the 48 primer pairs selected, amplification and polymorphisms were tested using one population each from the Chichijima and Hahajima Islands of the Ogasawara Islands. Twenty-six microsatellite loci were successfully amplified and the number of alleles for these loci ranged from five to 31 per locus, and the mean expected heterozygosities were 0.858 and 0.849, respectively. No significant deviation from the Hardy–Weinberg equilibrium was observed in either population, and no significant linkage disequilibrium was detected between any locus pair. The microsatellite loci reported in this study can be used in future studies to evaluate the genetic structure and mating system of L. micranthum.

To ensure the persistence of populations and species that maintain unique biodiversity in suburban landscapes, it is necessary to establish an efficient management system for abandoned suburban secondary forests. Thinning operations seem to be an effective management approach to inhibiting the progress of forest succession, which could lower the level of species diversity. To evaluate the effect of thinning operations on the demographic performance (growth, survival, and sexual reproduction) of the rare subtree species Magnolia stellata, we set up a field experiment and monitored the population dynamics over 9 years. The results revealed that stem survival and flower production per genet showed a decreasing trend in the nonthinned site. However, thinning operations increased the demographic performance, in particular the stem growth and survival rates as well as flower and seed production. The findings suggested that thinning operations may decrease the extinction probability of not only the targeted local population but also the metapopulation, because the thinned population serves as a better seed source. Thus, the creation of well-lit sites by thinning operations would be a useful conservation strategy for M. stellata.

Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. We investigated genetic structure using nuclear microsatellites and chloroplast DNA sequences and geographical variation in leaf morphological traits among Magnolia salicifolia populations across its entire range. Two distinct lineages, northern and southern, were detected genetically, and both lineages had substructure among populations. The width/length ratio and area of leaves showed latitudinal gradients, while the position of maximum leaf width exhibited a discontinuous change between the lineages. Approximate Bayesian computation detected exponential population growth and stable population size from the past to the present in the northern and southern lineages, respectively. Small migrations between the lineages were inferred. Divergence time between the lineages was estimated to be the early to middle Pleistocene. Ecological niche modelling revealed a single large potential area of distribution on the Sea of Japan side and multiple intermittent areas on the Pacific Ocean side during the Last Glacial Maximum. We suggest that these distinct evolutionary histories of the northern and southern lineages after diversification have influenced not only neutral markers but also genes controlling leaf morphological traits., ファイル公開日: 2019/11/01