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The genetic diversity and structure of Pulsatilla cernua, a continental‐grassland relict, were investigated using variations in chloroplast DNA (cpDNA) and microsatellites of nuclear DNA. In the analyses of three cpDNA regions, 17 haplotypes were found in 24 populations of P. cernua from Japan, Korea, and Russia. Although the route and time of migration between the continent of Asia and Japan could not be well resolved, the cpDNA haplotype network suggests the existence of several ancient lineages in Japan and a recent secondary migration from Japan to the continent. Microsatellite analyses did not indicate genetic structure among the Japanese populations, indicating the existence of gene flow across the distribution area until recently. These results indicate that the present fragmentation of P. cernua in Japan may reflect a rapid, recent reduction from a previously large, continuous distribution.

In four probe sensing for measurement of voltage-current curve of superconducting layer-coated tapes, it has been reported that, when a large accidental defect is included in the region between the voltage probes, the critical current value estimated with the one micro-volt/cm criterion is low when the voltage probe spacing is small but it becomes higher when the spacing is larger. In the present work, a simulation study was carried out to reproduce the feature stated above and to describe the dependence of critical current value on the voltage probe spacing under the co-existence of a large crack and multiple small cracks. In simulation, the current shunting model at cracks and a Monte Carlo simulation method were applied to a model superconducting tape, which was composed of one local section with a large crack and multiple local sections with small cracks of different size from each other. The experimentally observed increase in critical current with increasing voltage probe spacing in the large defect included tape was reproduced well by the present simulation. Then, it was shown that the increase in critical current of the large crack-included region with increasing voltage probe spacing is caused by the increase in the ligament part-transported current and shunting current at the large crack due to the increase in critical voltage for determination of critical current. Furthermore, it was shown that the upper and lower bounds of the critical current of the region, in which a large crack and multiple small cracks exist, can be derived from the voltage-current curve of the section with a large crack, and the critical current of the region is given by the upper bound for a given size of the largest crack when the difference in size between the large crack and multiple small cracks is large.

Background Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. Results Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9563 contigs. A total of 4510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from − 0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. Conclusions The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability. Electronic supplementary material The online version of this article (10.1186/s12870-018-1621-x) contains supplementary material, which is available to authorized users.

To elucidate the origin and migration history of the “Mansen elements,” a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.

To accurately estimate the damage of soil-structure systems during earthquakes, reliable analytical methods and appropriate modeling of soils and structures are necessary. Herein seismic response analyses are performed on an embankment, a caisson-type composite breakwater, and a caisson-type quay wall to verify the applicability of the strain space multiple mechanism model, where both the total and updated Lagrangian (TL/UL) formulations are introduced based on the large deformation (finite strain) theory. Both infinitesimal and large deformation analyses are performed to examine the effect of geometrical nonlinearity. All of the computed results (e.g., deformation and excess pore pressure ratio) indicate that the TL and UL formulations are theoretically and numerically equivalent, validating the computer program for large deformation analysis. In addition, the large deformation analyses decrease the amount of deformations compared to the infinitesimal deformation analysis in these three cases. This tendency becomes more significant as the amplitude of the input ground motions increases. We also perform a centrifuge model test to investigate the large deformation mechanism of liquefiable sloping ground and compare the experimental results with numerical simulations. The comparison indicates that the large deformation analysis by the UL formulation reasonably simulates the experiment, whereas the infinitesimal deformation analysis overestimates the deformation.