Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure.

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.

Complex range shifts among forest functional types under the contemporary warming.

The direction and magnitude of species distribution shifts tend to differ among species and functional types (FTs). Quantifying functional trait variation and species interactions will improve our understanding of the complex mechanisms that govern ecosystem dynamics and their responses to climate change. Here, we analyzed differences in the juvenile and adult temperature ranges of Japanese tree species at the mean, colder edge, and warmer edge of their distributions to reveal how functional traits affect interactions between different FT groups (e.g., deciduous and evergreen broad-leaved trees), using linear models and permutation tests. Overall, juveniles preferred cooler sites, but with high variation. The variation among species was partly explained by the difference in seed mass where species with lighter seeds tend to colonize colder sites. On the other hand, the distribution range of FTs showed complex behavior at the ecotones of different FTs. Specifically, in three of eight ecotones, nonparallel range shifts between FTs were detected, which includes cold shifting in deciduous broad-leaved FT where a warm shift by subalpine FT happened, and cold shifting in subtropical FT where warm shifts by either the deciduous broad-leaved or the evergreen broad-leaved FTs happened. Our results suggest that past warming has caused a general cold shift at species level, whereas different mechanisms, such as light seeds disperse farther in distribution's colder edge and heavy seeds (e.g., evergreen broad-leaved) compete better in warmer edge, create nonparallel responses of FT distribution ranges leading to the observed homogenization at several ecotones among FTs. These complex range shifts at FT level have crucial implications for climate change mitigation and adaptation.

Current site planning of medium to large solar power systems accelerates the loss of the remaining semi-natural and agricultural habitats.

The global transition to renewable energy sources has accelerated to mitigate the effects of global climate change. Sudden increases in solar power facilities have caused the physical destruction of wildlife habitats, thereby resulting in the decline of biodiversity and ecosystem functions. However, previous assessments have been based on the environmental impact of large solar photovoltaics (PVs). The impact of medium-sized PV facilities (0.5-10 MW), which can alter small habitat patches through the accumulation of installations has not been assessed. Here, we quantified the amount of habitat loss directly related to the construction of PV facilities with different size classes and estimated their siting attributes using construction patterns in Japan and South Korea. We identified that a comparable amount of natural and semi-natural habitats were lost due to the recent installation of medium solar facilities (approximately 66.36 and 85.73% of the overall loss in Japan and South Korea, respectively). Compared to large solar PVs, medium PV installations resulted in a higher area loss of semi-natural habitats, including secondary/planted forests, secondary/artificial grasslands, and agricultural lands. The siting attributes of medium and large solar PV facilities indicated a preference for cost-based site selection rather than prioritizing habitat protection for biodiversity conservation. Moreover, even conservation areas were developed when economic and topological conditions were suitable for energy production. Our simulations indicate that increasing the construction of PVs in urban areas could help reduce the loss of natural and semi-natural habitats. To improve the renewable energy share while mitigating the impacts on biodiversity, our results stress the need for a proactive assessment to enforce sustainable site-selection criteria for solar PVs in renewable energy initiatives. The revised criteria should consider the cumulative impacts of varied size classes of solar power facilities, including medium PVs, and the diverse aspects of the ecological value of natural habitats.

Evaluation of the ecological niche model approach in spatial conservation prioritization.

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.

Crisis of Japanese vascular flora shown by quantifying extinction risks for 1618 taxa.

Although many people have expressed alarm that we are witnessing a mass extinction, few projections have been quantified, owing to limited availability of time-series data on threatened organisms, especially plants. To quantify the risk of extinction, we need to monitor changes in population size over time for as many species as possible. Here, we present the world's first quantitative projection of plant species loss at a national level, with stochastic simulations based on the results of population censuses of 1618 threatened plant taxa in 3574 map cells of ca. 100 km2. More than 500 lay botanists helped monitor those taxa in 1994-1995 and in 2003-2004. We projected that between 370 and 561 vascular plant taxa will go extinct in Japan during the next century if past trends of population decline continue. This extinction rate is approximately two to three times the global rate. Using time-series data, we show that existing national protected areas (PAs) covering ca. 7% of Japan will not adequately prevent population declines: even core PAs can protect at best <60% of local populations from decline. Thus, the Aichi Biodiversity Target to expand PAs to 17% of land (and inland water) areas, as committed to by many national governments, is not enough: only 29.2% of currently threatened species will become non-threatened under the assumption that probability of protection success by PAs is 0.5, which our assessment shows is realistic. In countries where volunteers can be organized to monitor threatened taxa, censuses using our method should be able to quantify how fast we are losing species and to assess how effective current conservation measures such as PAs are in preventing species extinction.

Gene flow and inbreeding depression inferred from fine-scale genetic structure in an endangered heterostylous perennial, Primula sieboldii.

We estimated the gene dispersal distance and the magnitude of inbreeding depression from the fine-scale genetic structure in the endangered heterostylous perennial Primula sieboldii. We indirectly estimated the neighbourhood size (Nb) and the standard deviation of gene dispersal distance (sigma(g)) from the detected genetic structure by using 10 microsatellite markers. We also estimated the fitness reduction in mating among neighbouring individuals caused by biparental inbreeding according to the genetic structure. We found clear fine-scale genetic structure (a significantly positive kinship coefficient within 42.3 m), and the indirect estimates of sigma(g) and Nb were 15.7 m and 50.9, respectively. These indirect estimates were similar to the direct estimates (18.4 m and 44.0). The slightly larger indirect estimate of Nb may reflect that inbreeding depression and genetic structure or rare long-distance dispersal that were overlooked in the direct estimate have elongated the long-term average of gene dispersal distance. P. sieboldii is also likely to suffer about 19% fitness reduction in progenies from mating among individuals 5 m apart. Our results suggest that biparental inbreeding and genetic structure can affect the range of gene dispersal and seed reproductive success in P. sieboldii.