Japan is considered a global hot spot of biodiversity. With regard to species diversity, insects are no exception. To date, more than 32,000 insect species have been identified in Japan, while around 100,000 species of insects are estimated to inhabit this country. In this paper, we outline background factors having contributed to diversification of Japanese insects. Of course, the high degree of Japanese insect diversity is the result of many complex factors. In addition to the humid Asian monsoon climate and the extensive latitudinal gradient of habitats, the extremely complex geological history has contributed as an important factor to generate and maintain the high species diversity and endemism. In particular, the independent origins of northeastern and southwestern Japan from the Eurasian continent have greatly contributed to the diverse composition of Japanese insect fauna. To highlight the importance of this process, we introduce some case studies and previously published papers focusing on several insect groups with low dispersal ability. Those cases indicate that the geological history of Japan has played an important role in the differentiation of Japanese insect species. Besides such geological factors, climatic and ecological factors in combination have contributed to the formation of Japanese insect fauna in complicated ways and produced its particularly high degree of biodiversity. The knowledge compiled here will provide useful information for future studies aiming to understand more deeply the processes of speciation and faunal formation of Japanese insects.

In the Tohoku Medical Megabank project, genome and omics analyses of participants in two cohort studies were performed. A part of the data is available at the Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp) as a web-based database, as reported in our previous manuscript published in Nucleic Acid Research in 2018. At that time, jMorp mainly consisted of metabolome data; however, now genome, methylome, and transcriptome data have been integrated in addition to the enhancement of the number of samples for the metabolome data. For genomic data, jMorp provides a Japanese reference sequence obtained using de novo assembly of sequences from three Japanese individuals and allele frequencies obtained using whole-genome sequencing of 8,380 Japanese individuals. In addition, the omics data include methylome and transcriptome data from ∼300 samples and distribution of concentrations of more than 755 metabolites obtained using high-throughput nuclear magnetic resonance and high-sensitivity mass spectrometry. In summary, jMorp now provides four different kinds of omics data (genome, methylome, transcriptome, and metabolome), with a user-friendly web interface. This will be a useful scientific data resource on the general population for the discovery of disease biomarkers and personalized disease prevention and early diagnosis.

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.

Aim Pelophylax frogs in East Asia provide an opportunity to explore the impact of glacial cycling on demographic and genetic dynamics, because it has been suggested that they experienced distribution shifts and subsequent mtDNA introgression from Pelophylax plancyi to Pelophylax nigromaculatus in association with climatic oscillations. However, their evolutionary history, including the pattern of introgression, is incompletely understood. We used phylogenetic analyses based on multiple markers to address their evolutionary history, and palaeodistribution modelling to test whether the predicted distribution can explain the pattern of introgression suggested by molecular phylogenetics.Location East Asia, including far-eastern Russia, mainland China, the Japanese archipelago, the Korean Peninsula and Taiwan.Methods Ninety-nine samples of the Pelophylax nigromaculatus species complex were collected from 75 localities throughout the distributional range of each species. Phylogenetic analyses were performed with the mitochondrial cytochrome b (cytb) gene and six nuclear genes using two European Pelophylax frogs as outgroups. Additionally, palaeodistributions of P. nigromaculatus and P. plancyi were predicted using bioclimatic variables.Results Differences were observed between the mitochondrial and nuclear DNA trees in the phylogenetic position of P. plancyi. Similar phylogenetic discordance was also observed within P. nigromaculatus. Distribution modelling suggested that a considerable distributional shift of P. nigromaculatus occurred in association with glacial cycling and that the distributional range of P. plancyi was relatively narrow during glacial periods. Main conclusionsThe analyses detected five historical mtDNA introgression events and determined their directions, none of which had been deduced in previous studies. In association with glacial cycling, the distributional ranges of P. nigromaculatus and P. plancyi appear to have shifted repeatedly, resulting in multiple complex introgressions. By combining phylogenetic analyses with palaeodistribution modelling, our results supported the hypothesis that the history of mtDNA introgression among Pelophylax frogs was shaped by glacial cycling.