Rare plant species identified in project areas where land is to be developed or altered may need to be extracted for ex-situ conservation under human control. During ex-situ conservation, it is important to minimize the impact of adverse factors including the potentially limited environmental adaptability of rare plants under cultivation and possible losses of genetic diversity due to inbreeding if the number of conserved individuals is low. Here we evaluate the conservation difficulty and genetic diversity of populations of the rare plant Violα raddeana at five sites based on harmful gene accumulation and gene duplication data gathered using RNA-seq. Moreover, we evaluate the genetic diversity and structure of these populations using SNP data acquired using MIG-seq. The results obtained indicate that the V. raddeana populations have declined but remain robust towards environmental changes and can undergo voluntary mating at all sites. Moreover, there is clear genetic differentiation between two populations in close geographic proximity. If the majority of the remaining individuals of V. raddeana in each genetically related population were transplanted and cultivated, it would be possible to maintain their genetic diversity through ex-situ conservation.

Plantago hakusanensis (2n = 4x = 24) is an endangered endemic species that occurs in subalpine zones in Japan. To clarify the unresolved taxonomic status of P. hakusanensis within the subgenus Plantago, we conducted a phylogenetic analysis based on the nuclear-encoded single-copy gene sucrose–proton symporter 1 (SUC1) using 60 previously reported alleles from 24 taxa in the subgenus Plantago. We found that P. hakusanensis was closely related to P. asiatica var. densiuscula. The phylogenetic relationships between P. hakusanensis and P. asiatica var. densiuscula were examined by analyses of the SUC1 nuclear regions and the internal transcribed spacer (ITS) of rDNA, genome-wide single-nucleotide polymorphism genotyping (via multiplexed inter-simple sequence repeat genotyping by sequencing), as well as additional analyses of three chloroplast (cp) regions (trnL-F, ndhF-rpl32, and rpl32-trnL) in 25 individuals of P. hakusanensis and 53 individuals of P. asiatica var. densiuscula. Monophyly of P. hakusanensis was suggested by the nuclear marker analyses, whereas the cp haplotypes of P. hakusanensis were shared with P. asiatica var. densiuscula and P. asiatica in China. The disparity between the nuclear and cp data may be explained by introgression of the cp genome (cp capture) during Quaternary climate changes. Our results provide (i) a molecular phylogenetic basis for the taxonomy and (ii) insight into the intraspecific diversification history of P. hakusanensis.

Aim The genus Camellia is widely distributed, primarily in East Asia. Camellia japonica is located at the northern limit of this genus distribution, and elucidating its distribution changes is crucial for understanding the evolution of plants in this region, as well as their relationship with geological history and climate change. Also, the classification of sect. Camellia in Japan has not been clarified. Therefore, the aim of this study is to understand the evolutionary history of Japanese sect. Camellia. Location Japan, Korea, Taiwan, and the coastal area of China Taxon Camella (Theaceae). Methods The genetic population structure was analyzed by SNP data using MIG-seq. The relationship between Japanese sect. Camellia including the related species in China was further inferred from the phylogeny generated by RA x ML, SplitsTree and PCA. Population genetic structure was inferred using a Bayesian clustering method (ADMIXTURE). We then employed approximate Bayesian computation to explore the changes in population, asking which events best explain the phylogeographical signature. Ecological niche modeling was combined with genetic analyses to compare current and past distributions. Results The analyses consistently showed that C. japonica and C. rusticana are distinct, having diverged from each other between approximately 5.4 and 12 million years ago. Furthermore, C. japonica differentiated into four major populations (North, South, Ryukyu-Taiwan, and Continent). Main Conclusion Japanese sect. Camellia underwent speciation during archipelago formation, reflecting its ancient evolutionary history compared with other native Japanese plants. The conventional hypothesis that C. rusticana diverged from C. japonica in snow-rich environments under Quaternary period was rejected. Our results suggest that both species have been independent since ancient times, and that ancestral populations of C. japonica have persisted in northern regions. Furthermore, it is estimated that C. japonica population on the continent experienced a back-dispersal event from southern Japan during the late Pleistocene glaciation.

Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Here, we provide the first high-throughput sequencing (HTS) 5S intergenic spacer (5S-IGS) data for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S-IGS variants reflect a long history of repeated incomplete lineage sorting and lineage mixing since the early Cenozoic of two or more paralogous-homoeologous 5S rDNA lineages. Extant species of Fagus are genetic mosaics and, at least to some part, of hybrid origin.

Anthropogenic activities are leading to changes in the environment at global scales, and understanding these changes requires rapid, high-throughput methods of assessment. Pollen DNA metabarcoding and related methods provide advantages in throughput and efficiency over traditional methods, such as microscopic identification of pollen and visual observation of plant-pollinator interactions. Pollen DNA metabarcoding is currently being applied to assessments of plant-pollinator interactions and their responses to land-use change such as increased agricultural intensity and urbanisation, surveillance of ecosystem change, and monitoring of spatiotemporal distribution of allergenic pollen. In combination with historical specimens, pollen DNA metabarcoding can compare contemporary and past ecosystems. Current technical challenges with pollen DNA metabarcoding include the need to understand the relationship between sequence read and species abundance, develop methods for determining confidence limits for detection and taxonomic classification, increase method standardisation, and improve of gaps in reference databases. Future research expanding the method to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens could open further avenues for research. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for assessing these changes and providing timely management recommendations to preserve biodiversity and the evolutionary and ecological processes that support it.