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Ecological niche models (ENMs) are widely used in spatial prioritization for biodiversity conservation (e.g. selecting conservation areas). However, it is unclear whether ENMs are always beneficial for such purposes. We quantified the benefit of using ENMs in conservation prioritization, comparing the numbers of species covered by conservation areas selected on the basis of probabilities estimated by ENMs (ENM approach) and those selected on the basis of raw observation data (raw-data approach), while controlling survey range, survey bias, and target size of conservation area. We evaluated three ENM algorithms (GLM, GAM, and random forests). We used virtual community data generated by simulation for the evaluation. ENM approach was effective when survey bias is strong, survey range is narrow, and target size of conservation area is moderate. The percentage of cases in which the ENM approach outperformed the raw-data approach ranged from 0.0 to 33% (GLM), 31% (GAM), and 75% (random forests) depending on conditions. The number of rare species (< 20 presence records) included in the conservation area based on the ENM approach was less than, or the same as, that of the raw-data approach. The unexpectedly limited cases in which the ENM approach was effective in the present research may depend on the conservation target we used (to cover as many species as possible in conservation area). Our results highlight urgent need for evaluating ENM's effectiveness under other conservation targets for wise use of ENM in conservation prioritization.

SecSel, a protected-area prioritization tool, has been developed to help design areas that efficiently protect multiple features, including conservation of biodiversity and use of ecosystem services. The prioritization by SecSel is based on evaluation of the local units of each feature. The evaluation metrics should be quantitative but need not be ratio scale. The minimum requirement of the input data is that they are ordinal. The conservation target is the number of local units with high values of each feature to be protected in the area. SecSel can handle conflicts among features, including conflicts between conservation and utilization of land or specific ecosystem functions. Before the selection procedure, one of a conflicting pair of features in a site is discarded. That decision is based on the dispensability of the local unit to fulfilling the conservation target of each feature. SecSel also considers the cost of including each site in the protected area and the compactness of the area in terms of total boundary length or the distance to the nearest site. To demonstrate the functionality of Secsel, we used it to design land use in an alpine region of northern Japan where conservation of alpine vegetation and its recreational use are important considerations.

Elucidating biodiversity patterns and their background processes is critical in biodiversity science. Dissimilarity, which is calculated based on multivariate biological quantities, is a major component of biodiversity. As spatial and temporal biodiversity information availability increases, the scope of dissimilarity studies has been expanded to cover various levels and types of spatiotemporal biodiversity facets (e.g. gene, community and ecosystem function), and diverse pairwise dissimilarity indices have been developed. However, further development of the dissimilarity concept is required in comparative studies on spatiotemporal structures of biodiversity compositional patterns, such as those exploring commonalities of biogeographical boundaries among taxa, compared to the conventional ones to consider higher dimensions of dissimilarity: dissimilarity of dissimilarity structures. This study proposes a novel and general concept, higher‐order dissimilarity (HOD), for quantitatively evaluating the dissimilarities of spatial or temporal dissimilarity structures among different datasets, proposes specific implementations of HOD as operational indices, and illustrates the potential resolution of scientific and practical questions through HOD. We further demonstrate the advantages of the HOD concept by applying it to actual patterns, such as long‐term and/or large‐spatial hypothetical monitoring datasets. Our conceptual framework on HOD extends the existing framework of biodiversity science and is versatile, with many potential applications in acquiring more valuable information from ever‐increasing biodiversity data. 要旨 生物多様性のパターンとその背後に存在するプロセスを解明することは、生物多様性科学において極めて重要である。多変量の生物学的な数量に基づいて計算される非類似度は、生物多様性の主要な要素の一つである。空間的・時間的な生物多様性情報の入手可能性が高まるにつれて、非類似度研究の範囲は、様々なレベルや種類の時空間的生物多様性の側面(例えば、遺伝子、群集、生態系機能)を対象とするように拡大し、多種多様なペアワイズ非類似度指標が開発されてきた。しかしながら、生物多様性の組成パターンの時空間的構造に関する比較研究、例えば分類群間の生物地理学的境界の共通性を探る研究においては、従来よりも高次元の非類似度、すなわち非類似度構造の非類似度を考慮するために、非類似度概念のさらなる発展が求められている。 本研究では、異なるデータセット間の空間的・時間的非類似度構造の非類似度を定量的に評価するための新規かつ一般的な概念である高次非類似度を提案し、実用指標としての高次非類似度の具体的な実装を提案し、高次非類似度による科学的・実用的問題の解決の可能性を示す。 さらに、高次非類似度の概念を、仮想の長期的および/または大規模空間的なモニタリングデータセットのような実際のパターンに適用することで、その利点を実証する。 高次非類似度に関する本研究で提案する概念的枠組みは、生物多様性科学の既存の枠組みを拡張し、非常に多くの応用可能性があり、増え続ける生物多様性データからより価値のある情報を取得するのに様々な場面で役立つだろう。

Conservation biologists have a daunting task of understanding the causes of species decline associated with anthropogenic factors and predicting the extinction risk of a growing number of endangered species. By reducing variances of estimates with information on closely related species, phylogenetic information among species can bridge gaps in information on species with small range sizes when modelling large numbers of endangered species. However, modelling many species with the Gaussian process (GP), which underlies the evolutionary process of phylogenetic random effects, remains a challenge owing to the computational burden in estimating the large variance–covariance matrix. Here, we applied a phylogenetic generalised mixed model with random slopes and random intercepts to 1010 endangered vascular plant taxa in Japan following phylogenetic GPs implemented by nearest neighbour GP (NNGP) approximation. NNGP enables flexibility in changing the proximity on the phylogenetic tree of species from which information is borrowed to reduce the variances of estimates with a realistic computational burden. We evaluated the effectiveness of phylogenetic models by comparing the predictive performance and descriptive power of phylogenetic and non‐phylogenetic models and identified the anthropogenic factors contributing to the decline of each of the studied endangered species. We found that the model with phylogenetic information had better prediction performance than the model without phylogenetic information. The results showed that across all explanatory variables, the phylogenetic model could detect interspecific differences in response to environmental factors in a number of species more clearly. Combined with the phylogenetic signal results, we could also detect a phylogenetic bias in the species that could benefit from the positive effects of protected areas but reduce the local extinctions of 95% of all studied taxa. In conclusion, our model, considering phylogenetic information with NNGP , allows the elucidation of factors causing the decline of many endangered species. In future analyses, the estimation of extinction probability linked to environmental change might be applied to future climate–land use scenarios, advancing the comprehensive assessment of biodiversity degradation and threats to species at multiple scales.

The decline of wild bee populations causes the decline of bee-pollinated plant populations through the deterioration of pollination services. Since high bee species richness generally involves high functional group diversity, protecting areas of high bee species richness will help to maintain pollination services for plants. However, those areas do not always include the habitats of bee species with specialized functions that expand the range of plants being pollinated. To map important areas for protecting native bee species and their functions, we estimated the distributions and functional range of 13 bumble bee species and 1 honey bee species in Japan. The distributions were estimated from an ensemble of six species distribution models using bee occurrence data and environmental data. The functional range of bee species was estimated by combining the estimated distributions and proboscis length, which frequently corresponds to the floral shape of the plant species they pollinate. The estimated species richness was high in western Hokkaido and the estimated functional range was wide in central Honshu. Our method is useful to see whether areas important for high species richness of pollinators differ from those for rare species or their functions.

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.

Protected areas (PAs) spearhead global conservation efforts, but it has been repeatedly demonstrated that narrowly distributed species are more likely to be unrepresented in PAs. This means that where local extinctions are more likely outside PAs, a positive feedback loop could render PAs largely ineffective in decelerating extinctions, even where PAs effectively abate threats. Here we empirically test the elements of this feedback loop using distribution data for 1,572 threatened plants in Japan. Narrowly distributed species were indeed less likely to overlap PAs than widespread species, and local extinction rates for unprotected populations over 15 years were 1.5 times higher than those inside PAs. A simulation model showed that new PAs will substantially reduce extinction risk for widespread species, but not for narrowly distributed species, unless they are placed very precisely in the landscape. Our results suggest that a representation‐extinction feedback will limit the effectiveness of PAs in preventing extinctions unless PA placement is carefully targeted.

While many plant species are considered threatened under anthropogenic pressure, it remains uncertain how rapidly we are losing plant species diversity. To fill this gap, we propose a Global Legume Diversity Assessment (GLDA) as the first step of a global plant diversity assessment. Here we describe the concept of GLDA and its feasibility by reviewing relevant approaches and data availability. We conclude that Fabaceae is a good proxy for overall angiosperm diversity in many habitats and that much relevant data for GLDA are available. As indicators of states, we propose comparison of species richness with phylogenetic and functional diversity to obtain an integrated picture of diversity. As indicators of trends, species loss rate and extinction risks should be assessed. Specimen records and plot data provide key resources for assessing legume diversity at a global scale, and distribution modeling based on these records provide key methods for assessing states and trends of legume diversity. GLDA has started in Asia, and we call for a truly global legume diversity assessment by wider geographic collaborations among various scientists.

Question: Is a high-resolution remote-sensing system based on a radio-controlled helicopter (the 'Falcon-PARS system') an effective tool to obtain images that can be used to identify herbaceous species? Location: Watarase wetland, Japan. Methods: We applied the remote-sensing system to a wetland composed mainly of Phragmites australis and Miscanthus sacchariflorus. The aerial observation was performed in a 100 × 200 m area at a flying height of 30 m. From the obtained images, we tried to identify P. australis and M. sacchariflorus through visual interpretation. Results: We obtained images with a high spatial resolution (1 cm) and a positioning accuracy of finer than 1 m using this small and lightweight system, and confirmed that we could identify the above two species from the obtained images. Conclusion: Such a high-resolution system can be used to directly identify herbaceous species, and as a non-destructive alternative to ground surveys. This lightweight system can be carried to sites such as a high-altitude bog that cannot be reached by a motor vehicle. Because of the low flying height (below cloud level), aerial observation is possible even on cloudy days, thereby permitting observations in all seasons.