Five decades of monitoring data (1974-2022) at the acidified, acid-sensitive forested catchment of Langtjern in southern Norway document strong chemical recovery and browning of surface water, related to changes in sulfur (S) deposition. We used the process-oriented model MAGIC to simulate water chemistry from 1860 to 2100 using historical and projected deposition and climate. New in MAGIC is i) a solubility control of dissolved organic carbon (DOC) from S deposition, which allows inclusion of the changing role of organic acids in chemical recovery, and ii) climate-dependency of weathering rates. MAGIC successfully described measured chemical recovery and browning, and the change towards organic acid dominated acidification status. Hindcasts of pH suggested lower preindustrial pH than previously modelled with MAGIC, simulated without sulfate-dependency of DOC solubility. Climate scenarios indicated substantially wetter climate, leading to increased base cation losses and slight reacidification of the surface waters. A sensitivity analysis of weathering rates revealed that a doubling of weathering rates is needed to reach pre-industrial ANC in 2100, given that S deposition is expected to be reduced to a minimum. We conclude that impacts of climate change are most likely to lead to slight reacidification of surface waters, and that enhanced weathering rates could partly compensate this trend.

Excessive anthropogenic nitrogen fixation alters the nitrogen cycle and increases nitrogen deposition, leading to nitrogen saturation, which leads to forest decline and nitrate leakage into stream waters. Kureha Hill in Toyama Prefecture, Japan, is considered to be in nitrogen saturation, since many streams have contained high concentrations of nitrate for more than 20 years. This study verified the latest status of nitrogen saturation by comparing the latest data with 20-year observational data. Results showed that the current nitrate concentration in stream water is lower than that observed 20 years ago. However, the C/N ratio of the soil between 12 and 18, indicates that nitrogen saturation could take place. In addition, the net nitrogen mineralization and net nitrification rate showed no significant change from the past data. Based on the nitrogen leakage to the stream water, Kureha Hill’s nitrogen saturation was found to be less intense; however, its potential to produce nitrate has been unchanged for 20 years.

In recent years, there has been a growing interest in research on Ceratozamia cycads, which has resulted in a significant increase in our understanding of their diversity. However, species complexes that have been tackled through integrative methodologies have exhibited a bias towards morphology over genealogy. Thus, there arises the necessity to reevaluate the Ceratozamia mexicana species complex using phylogeographic tools. For this purpose, we have employed the integrative taxonomic protocol Schlick-Steiner et al. (2010) put forth. This protocol delineates species as testable hypotheses, incorporating lines of evidence within a reproducible and falsifiable framework. The evaluated data encompassed (i) phylogenetic and molecular variance analyses, (ii) multivariate morphometric analyses, and (iii) analysis of climatic niches. Out of the 196 individuals from 13 studied populations, seven monophyletic groups were recovered. These groups were substantiated by multivariate morphometric analysis, revealing significant differences, and were further validated by niche divergence. These results underscore a ‘whole agreement’ across the three disciplines, thus providing robust support for acknowledging the species as distinct lineages. The species delimited by these lineages, encompassing phylogenetic, morphological, and environmental factors, correspond to C. brevifrons, C. delucana, C. decumbens, C. mexicana, C. moretti, C. tenuis, and a novel cryptic species, sister to the latter. Finally, this genealogical characterization will offer utility in the future for uncovering the genetic identity of the holotype of the type species within the Ceratozamia genus.

Ecotypic divergence in tree taxa often occurs in sub-alpine habitats, where environmental conditions are more stressful than those in lower elevations. In the mountain oak species in Japan, Quercus crispula (Qc), the sub-alpine shrubby variety, Q. crispula var. horikawae (Qch), has been recognized in central and northern Honshu. Although Qch has different phenotypes from Qc, genetic divergence between Qc and Qch has not been examined yet. Pairs of Qc and Qch populations in eight locations and additional Qc and Qch populations around these locations were investigated. Leaf size of Qch was smaller than that of Qc. Chloroplast DNA haplotypes were shared between the Qc and Qch populations. In genotypes at 29 nuclear microsatellite loci, genetic diversity did not differ between the Qc and Qch populations. Principal component analysis and a neighbor-joining tree of populations based on microsatellite genotypes demonstrated that 13 Qc populations and eight Qch populations were grouped separately, except for three Qch populations that were grouped to Qc. Climatic conditions in the eight Qch populations were characterized by lower temperature and heavier snowfall than those in the 16 populations of the genetic group of Qc. These results suggest the genetic divergence between Qc and Qch associated with sub-alpine climatic conditions, irrespective of leaf size. The origin of the sub-alpine Qch lineage and the history of ecotypic divergence should be investigated in future genomic studies.

This article reviews the essential role of mathematical models in understanding and combatting the pandemic of novel coronaviruses, in particular focusing the advance in the use of mathematical models in disease control in Japan. Highlighting the integral role of mathematical models in public health, the article introduces a model that factors in the heterogeneity of infectious contacts, concentrating on the effectiveness of testing and isolation, alongside a model that involves economic losses. The models exhibit how, given such heterogeneity, milder behavioral restrictions can still achieve suppression, rigorous testing and isolation can effectively curb the spread, and containment measures can mitigate economic losses. These models aid in grasping the complicated dynamics of disease transmission and optimizing interventions. The knowledge of population ecology is also considered effective for public health in statistical analysis, organizing concepts using dynamic mathematical models, which lead to policy proposals and deepen understanding. Evolution theory may help the understanding of virulence subject to change. However, effective prevention necessitates not only models but also the practical implementation of efficacious measures. The cooperation of various disciplines is particularly crucial in achieving a balance between health measures, economic interests, and human rights. Moreover, the article acknowledges the limitations of models and underscores the significance of real-world execution. Overall, the article advocates for a broader outlook to tackle future pandemics and related challenges, underscoring the importance of ongoing academic cooperation and global governance to effectively address emerging infectious diseases and their far-reaching implications.

Adaptive introgression has been proposed in oaks (genus Quercus). In northern Japan, Q. mongolica var. crispula (Qc) is common in inland habitats, and Q. dentata (Qd) occurs in coastal habitats. At the northern distributional limit of Qd, Q. × angustilepidota (Qa), a hybrid taxon between Qc and Qd, occurs in coastal habitats. The three taxa, Qc, Qa, and Qd, were transplanted to inland and coastal common gardens (sites). Genotypes at 27495 loci, phenotypes of eight traits of leaves and shoots, and 30-year-old tree size were measured for 224 individuals in both sites. Genotypic variation revealed a hybrid zone between Qc and Qd, including both northern-edge Qd admixed with Qc and coastal Qa backcrossed to Qc. Phenotypes of Qa trees were intermediate between those of Qc and Qd trees. Size of Qa and Qd trees was smaller than that of Qc trees in the inland site but was larger in the coastal site, suggesting adaptation of Qa and Qd to coastal environment. Local ancestry was estimated from phased genotypes of admixed trees using reference genotypes of 47 Qc and 25 Qd trees, indicating heterogeneous ancestry along chromosomes. Association mapping of genotypes and admixture mapping of ancestry suggested that some loci potentially associated with four traits were related to stress response and were located at introgressed genomic regions. Further studies are necessary to show the genetic basis of adaptive introgression resulting in Qd-like phenotypes of Qa in coastal habitats.

Tetraploid Ficaria verna is a common spring geophyte that forms large populations in central Europe and is considered invasive in northern USA and Canada. It is considered an almost seed-sterile taxon, relying on vegetative reproduction by underground tubers and aerial bulbils. Recent studies have revealed high levels of population genetic diversity in F. verna, raising the question of how genetic diversity is maintained and which factors may be responsible for the observed patterns. Polymorphic nuclear microsatellite markers were established to define multi-locus genotypes (MLGs), to analyze fine-scale spatial genetic structure (SGS) using grid and cross sampling schemes, and to quantify genetic diversity within and between nine populations with different disturbance regimes in central Germany. 115 MLGs were identified among a total of 347 samples. The G/N ratio varied between 0.16 and 0.70 among populations, and in each population a number of unique MLGs occurred. Genotypes were highly intermingled within populations, suggesting a ‘guerrilla’ dispersal strategy. Significant negative SGS was found in five out of nine populations in fine-scale cross sampling (up to 4 m) and in only one population in grid sampling (up to 14.6 m). No single MLG was found in more than one population, while many alleles were shared between populations. Within-population genetic diversity increased with greater exposure to both anthropogenic and natural disturbances. Regular gap openings, facilitated propagule establishment (vegetative and sexual), and propagule dispersal by water and mowing machines are likely important factors explaining the positive effects of disturbance on local genetic diversity of F. verna.

COVID-19, caused by the novel coronavirus (SARS-CoV-2), is an emerging infectious disease (EID) with a relatively high infectivity and mortality rate. During the state of emergency announced by the Japanese government in the spring of 2020, citizens were requested to stay home, the number of infected people was drastically reduced without a legally-binding lockdown. It is well-acknowledged that there is a trade-off between maintaining economic activity and preventing the spread of infectious diseases. We aimed to reduce the total loss caused by the epidemic of an EID like COVID-19 in the present study. We focused on early and late stages of the epidemic and proposed a framework to reduce the total loss resulted from the damage by infection and the cost for the countermeasure. Mathematical epidemic models were used to estimate the effect of interventions on the number of deaths by infection. The total loss was converted into the monetary base and different policies were compared. In the early stage, we calculated the damage by infection when behavioral restrictions were implemented. The favorable intensity of the intervention depended on the basic reproduction number, infection fatality rate, and the economic impact. In the late stage, we calculated indicators and showed it depended on the ratio of the cost to maintain the hospitalization system to the monetary loss per deaths by infection which strategies should be adopted.

Between 1925 – 1929, approximately 12 non-native mountain goats (Oreamnos americanus) were translocated from Alaska and British Columbia to the foothills of the Olympic Range, USA. By 1970, descendants of these goats had colonized the entire Olympic Range and concerns about the management of this introduced species developed as damage to alpine soil and vegetation occurred. A series of removals reduced the population from 1,175 in 1983 to 389 goats by 1990, followed by a period a stasis and growth indicated again in 2011 and 2016. We used empirical demographic and genetic data to parameterize a population genetics individual-based simulation model of the Olympic Range mountain goat population. We calibrated the model to simulate the population trajectory for Olympic mountain goats from establishment in 1925 through the 1983 census, and validated model dynamics by simulating the period from 1990 to 2016. Modeled population dispersal closely tracked anecdotal reports. However, observed heterozygosity did not align with published research, suggesting a process not accounted for within the simulation model, such as a bottleneck, founder effect, or population trajectory dynamics. Sensitivity analyses showed that changes in annual reproductive rate had the greatest influence on population trajectories, followed by juvenile mortality and adult female mortality, respectively. The modeled population showed that approximately 80% of the total animals removed during the 1980’s needed to be female in order for the observed population stasis to occur. This model has the potential to be used more widely with established or introduced mountain goat populations in other regions.

Although the amount of acidic deposition has recently decreased in Japan, acid deposition has deteriorated some forest ecosystems during the past few decades. We investigated the yearly variations in stream water chemistry for more than 20 years in two areas (Yusuhara and Taisho) in the Shmanto River Basin, southern Japan, where the effects of acidic deposition are considered to be modest. Stream water samples were collected monthly from three forest watersheds selected at each site. The annual means of the stream chemistry were predicted by multiple regression analysis. The sunlight hours were positively related with the potassium, magnesium, calcium, nitrate, sulfate, and bicarbonate concentrations in stream water. The results suggest that long sunlight hours boost the photosynthetic activities, thus promoting soil respiration and decomposition of soil organic matter; moreover, a higher carbonic acid concentration in the soil solution promotes cation weathering and carbonic acid dissociation to bicarbonate. The ammonium, nitrate, and sulfate concentrations in the bulk precipitation have decreased at Yusuhara and the sodium, magnesium, calcium, chloride, nitrate, and sulfate concentrations in the stream water have decreased in both areas. The nitrate and sulfate concentrations apparently responded to the decreasing input of acidic deposition. Given the decreasing trends in magnesium and calcium concentration with no change in bicarbonate concentration, we inferred that previous inputs of acidic deposition enhanced the rate of rock weathering.

Many ungulate species in Africa range in habitats that vary in type and quality over space and time, but ongoing environmental change is substantially altering their habitats. Identifying key environmental variables that regulate ungulate population densities can guide management actions for effective conservation. We studied the local population density responses of a community of sympatric ungulate species in the Tarangire Ecosystem of northern Tanzania, to a suite of environmental factors that vary over space and time, to quantify population trends, determine the primary environmental correlates of densities, and identify covariation in densities among species. We estimated seasonal densities of five commonly detected species (impala, dik-dik, Grant’s gazelle, eland, and waterbuck) based on 7 years of distance-sampling data from 41 replicate surveys of 237 line transects. We systematically analyzed the effects of spatial, seasonal, and annual environmental covariates on variation in transect species-specific densities across space and time. Despite large fluctuations in climatic factors, we documented more spatial than temporal variation in four of the five species, suggesting that spatial heterogeneity may provide some buffer against temporal variation in the environment. Protection of sufficient habitats and water sources should allow ungulates to respond to a temporally changing world by moving across space. Further, among-species covariation patterns identified two potential ungulate guilds (impala—dik-dik—waterbuck; eland—grant’s gazelle) that should aid in developing efficient and coordinated management actions.

There have been many attempts to understand population dynamics in fishery resources such as tuna species using an integrated-analysis model with multiple data sources. However, estimating the absolute abundance level in practical stock assessments remains challenging. The close-kin mark–recapture (CKMR) method provides information about the number of adults in a population utilizing close-kinship pairs (i.e., parent–offspring, full-sibling, or half-sibling pairs) identified based on statistical methods that employ genetic markers. To introduce the CKMR method into the stock assessment by integrated analysis, it is necessary to clarify the potential errors obtained from the uncertainties in the CKMR method and other data sources. In this paper, we applied three methods of kinship identification for samples from the wild Pacific bluefin tuna population using genome-wide DNA markers to determine the potential errors in statistical kinship estimates. Herein, one method used a random-forest classification algorithm called fraRF that employed pairwise identity-by-descent values. The other two methods were CKMRsim and COLONY. Comparisons among these three methods revealed differences in the numbers of inferred kinship pairs, especially for sibling relationships. The differences among the three methods seem to occur mainly from uncertainty of the kinship identification in the CKMR method. Therefore, this result provides an understanding of ways to incorporate the CKMR method into the integrated analysis model with the possible CKMR errors.