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Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation.

The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson’s theta was 31% overestimation on average. Thus, genetic diversities other than Watterson’s theta held good robustness under the spatial sampling.

Citizen science is an important approach to monitoring for biodiversity conservation because it allows for data acquisition or analysis on a scale that is not possible for researchers alone. In citizen science projects, the use of online training is increasing to improve such skills. However, the effectiveness of quiz-style online training, assumed to be efficient to enhance participants’ skills, has not been evaluated adequately on species identification for citizen science biodiversity monitoring projects. Memory mechanisms in adaptive learning were hypothesized to guide the development of quiz-based online training tools for learning birdsong identification and for improving interest in birds and natural environments. To examine the hypothesis, we developed a quiz-style online training tool called TORI-TORE. We experimentally applied TORI-TORE in Fukushima, Japan, and examined its effectiveness for bird identification training using test scores and questionnaires to determine participants’ attitudes in a randomized control trial. We obtained the following key results: (1) TORI-TORE had positive effects on test scores and trainees’ attitudes toward birds. (2) Adaptive training, in which questions focused preferentially on unmastered bird species based on the answer history of individual trainees inspired by adaptive learning, unexpectedly led to lower scores and satisfaction in TORI-TORE. (3) Focusing on species that are relatively easy to remember, short lag times between training and testing, and long question intervals positively affected scores. While there is room for improvement, we expect TORI-TORE to contribute to online capacity building and to increase interest in natural environments.

Although camera trapping has been effectively used for wildlife monitoring, its application to multihabitat insects (i.e., insects requiring terrestrial and aquatic ecosystems) is limited. Among such insects, perching dragonflies of the genus Sympetrum (darter dragonflies) are agroenvironmental indicators that substantially contribute to agricultural biodiversity. To examine whether custom-developed camera traps for perching dragonflies can be used to assess the relative population density of darter dragonflies, camera trapping, a line-transect survey of mature adult dragonflies, and a line-transect survey of exuviae were conducted for three years in rice paddy fields in Japan. The detection frequency of camera traps in autumn was significantly correlated with the density index of mature adults recorded during the transect surveys in the same season for both Sympetrum infuscatum and other darter species. In analyses of camera-detection frequency in autumn and exuviae in early summer, a significant correlation was observed between the camera-detection frequency of mature adults and the exuviae-density index in the following year for S. infuscatum; however, a similar correlation was not observed for other darter species. These results suggest that terrestrial camera trapping has the potential to be effective for monitoring the relative density of multihabitat users such as S. infuscatum, which shows frequent perching behavior and relatively short-distance dispersal.

Abstract Past land-use activity has massively altered the environment and vegetation over centuries, resulting in range contractions and expansions of species. When habitat recovery and species recolonization require a long time, the fingerprint of past land use can remain on the current distribution of species. To evaluate millennial-scale effects of land use in Japan, we explained the current ranges of 29 mammalian genera based on three types of archaeological land-use patterns (settlement, ironwork and kiln) considering potential confounding factors. The results indicate that archaeological human activity associated with ironwork and pottery production had severe negative effects on many genera of small and medium-sized mammals. Despite positive effects on some genera, the magnitudes were less than those of the negative effects. The relative importance of archaeological factors on small mammals was greater than those for medium- to-large mammals. The persistent imprint of past land-use patterns was non-negligible, explaining current mammalian diversity. Spatial ecological and archaeological information can provide meaningful insights into long-term socio-ecological processes, which are crucial for the development of sustainable societies in the Anthropocene.

Integrated weed management (IWM) is currently the most appropriate and effective method of agricultural weed control. To determine the most effective strategy, it is necessary to compare the effects of different control options and their rotation. Avena fatua (common wild oat) is one of the most common and economically threatening grass weed species of cereal crops worldwide. To examine the effects of non-chemical weed management options (farmland use, delayed sowing, and summer irrigation) on control of A. fatua, we recorded coverage levels and field conditions in 41 sites during the spring growing season of winter wheat for about 10 years. A transition matrix model was then constructed to project coverage levels of A. fatua under each management option using ordinal logistic regression. The results showed that farmland use had a remarkable effect on coverage; notably, planting of paddy rice and vegetables, which respectively eliminated the effect of coverage in the previous year and facilitated rapid convergence of coverage to 0%. Thus, although 90% of fields under continuous wheat cultivation were found to be at risk of A. fatua colonization, the risk was reduced to almost 0% with rotation of effective farmland use. As summer irrigation was also effective, more than 50% of wheat fields with the option continuously converged to no risk for A. fatua colonization. When the different management cycles were repeated, the effects were observed within 3 years, with a steady state reached in less than 10 years. Overall, these results suggest that simplified monitoring data could help decision-making on IWM, thereby helping to improve the efficiency of agricultural production.

Although dragonflies are excellent environmental indicators for monitoring terrestrial water ecosystems, automatic monitoring techniques using digital tools are limited. We designed a novel camera trapping system with an original dragonfly detector based on the hypothesis that perching dragonflies can be automatically detected using inexpensive and energy-saving photosensors built in a perch-like structure. A trial version of the camera trap was developed and evaluated in a case study targeting red dragonflies (Sympetrum spp.) in Japan. During an approximately 2-month period, the detector successfully detected Sympetrum dragonflies while using extremely low power consumption (less than 5 mW). Furthermore, a short-term field experiment using time-lapse cameras for validation at three locations indicated that the detection accuracy was sufficient for practical applications. The frequency of false positive detection ranged from 17 to 51 over an approximately 2-day period. The detection sensitivities were 0.67 and 1.0 at two locations, where a time-lapse camera confirmed that Sympetrum dragonflies perched on the trap more than once. However, the correspondence between the detection frequency by the camera trap and the abundance of Sympetrum dragonflies determined by field observations conducted in parallel was low when the dragonfly density was relatively high. Despite the potential for improvements in our camera trap and its application to the quantitative monitoring of dragonflies, the low cost and low power consumption of the detector make it a promising tool.

In studies of habitat suitability at landscape scales, transferability of species-landscape associations among sites are likely to be critical because it is often impractical to collect datasets across various regions. However, limiting factors, such as prey availability, are not likely to be constant across scales because of the differences in species pools. This is particularly true for top predators that are often the target for conservation concern. Here we focus on gray-faced buzzards, apex predators of farmland-dominated landscapes in East Asia. We investigated context dependency of "buzzard-landscape relationship", using nest location datasets from five sites, each differing in landscape composition. Based on the similarities of prey items and landscape compositions across the sites, we determined several alternative ways of grouping the sites, and then examined whether buzzard-landscape relationship change among groups, which was conducted separately for each way of grouping. As a result, the model of study-sites grouping based on similarities in prey items showed the smallest ΔAICc. Because the terms of interaction between group IDs and areas of broad-leaved forests and grasslands were selected, buzzard-landscape relationship showed a context dependency, i.e., these two landscape elements strengthen the relationship in southern region. The difference in prey fauna, which is associated with the difference in climate, might generate regional differences in the buzzard-landscape associations.

Following the accident at the Fukushima Daiichi nuclear power plants in 2011, a large evacuation zone was imposed in an area where residents had historically managed forests and farmlands. Thus, the human activities that had maintained biodiversity and ecosystem services in the zone were discontinued. Such change can affect insects, a biodiversity component that is relatively tolerant to radiation exposure. In this study, we investigated flying insects, including pollinators, important ecosystem providers inside and outside the zone, using Malaise traps. The results showed that the number of individuals of Xylocopa appendiculata, the largest Apidae species in the region, was significantly lower inside the evacuation zone than outside it, whereas those of other insects were not lower significantly. Although we suggest that flying insects and their ecosystem services (i.e., benefits from them such as pollination) 3 years after the disaster were not critically impacted, it is important to monitor the long-term effects of the evacuation in the future.

The maintenance of mixed mating was studied in Shorea curtisii, a dominant and widely distributed dipterocarp species in Southeast Asia. Paternity and hierarchical Bayesian analyses were used to estimate the parameters of pollen dispersal kernel, male fecundity and self-pollen affinity. We hypothesized that partial self incompatibility and/or inbreeding depression reduce the number of selfed seeds if the mother trees receive sufficient pollen, whereas reproductive assurance increases the numbers of selfed seeds under low amounts of pollen. Comparison of estimated parameters of self-pollen affinity between high density undisturbed and low density selectively logged forests indicated that self-pollen was selectively excluded from mating in the former, probably due to partial self incompatibility or inbreeding depression until seed maturation. By estimating the self-pollen affinity of each mother tree in both forests, mother trees with higher amount of self-pollen indicated significance of self-pollen affinity with negative estimated value. The exclusion of self-fertilization and/or inbreeding depression during seed maturation occurred in the mother trees with large female fecundity, whereas reproductive assurance increased self-fertilization in the mother trees with lower female fecundity.