Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae (Rosaceae) based on genomic evidence from conserved orthologs.

Background And Aims: The section Synstylae in genus Rosa (Rosaceae) comprises 25-36 species and includes several major progenitors of modern rose cultivars. East Asian Synstylae species have recently diverged and are closely related, and their phylogenetic relationships remain unclear. In the present study, we employed a conserved ortholog set (COS) markers and genome-wide nuclear orthologs to elucidate their phylogenetic relationships and unravel their complex evolutionary history.

Potential contribution of floral thermogenesis to cold adaptation, distribution pattern, and population structure of thermogenic and non/slightly thermogenic species.

The genus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic and non/slightly thermogenic .

Plastome-based backbone phylogeny of East Asian (Subgenus : Crassulaceae), with special emphasis on Korean endemics.

Although the monophyly of has been strongly demonstrated, the species relationships among approximately 20 species of have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of species from East Asia and generated a plastome-based backbone phylogeny of the subgenus . As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently.

The complete chloroplast genome sequence of var. (Ranunculaceae).

(Ranunculaceae) is widely distributed in the Eurasian Continent and Japan and comprises some intraspecific taxa. We report here the complete chloroplast genome of var. .

The complete chloroplast genome sequence of var. (Asteraceae) and phylogenetic relationships within Gnaphalieae.

var. is a perennial herb adapted to the severe environment of pebbled river banks, where it is frequently found. In this study, we determined the complete chloroplast genome of var.

Construction of three-dimensional weather radar data from volcanic eruption clouds.

Analysis tools of three-dimensional weather radar data (ANT3D) was originally developed at the National Research Institute for Earth Science and Disaster prevention (NIED) to retrieve three-dimensional (3D) precipitation and wind fields for convective storms. In 2013, Kagoshima University significantly revised ANT3D for analyses of volcanic eruption clouds, mainly to improve the temporal and spatial interpolation of radar data and estimation of the advection vector, which is required for temporal interpolation. Detailed information pertaining to these algorithms is listed as additional information in this paper.

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of in Ulleung Island: The Genetic Consequences of Anagenetic Speciation.

Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor.

Species cohesion of an extremophyte (Carex angustisquama, Cyperaceae) in solfatara fields maintained under interspecific natural hybridization.

Background And Aims: Hybridization is the main driver of plant diversification, and gene flow via hybridization has multifaceted effects on plant evolution. Carex angustisquama is an extremophyte that grows on soils heavily acidified by volcanism. Despite its habitat distinct from that of other species, this species is known to form interspecific hybrids, implying interspecific gene flow.

Visualizing weather radar data from volcanic eruption clouds.

This paper is submitted to accompany the article "Analyses of three-dimensional weather radar data from volcanic eruption clouds" [1]; it describes three-dimensional (3D) visualizations of the Sakurajima volcanic eruption clouds and the weather radar data used for analyses, as well as their availability and downloading procedures. The radar data were acquired by an operational X-band weather radar located approximately 11 km south of the Showa vent of Sakurajima in Kagoshima, Japan. The original raw radar data are available from the "XRAIN Precipitation Original Data search and Download System", which is hosted on the website "Data Integration and Analysis System (DIAS)".

Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino.

Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes.

Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation.

Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S.

Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies.

Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically.

Comparison of Whole Plastome Sequences between Thermogenic Skunk Cabbage and Nonthermogenic (Orontioideae; Araceae) in East Asia.

, a skunk cabbage genus, includes two sister groups, which are drastically different in life history traits and thermogenesis, as follows: The nonthermogenic summer flowering and thermogenic early spring flowering . Although the molecular basis of thermogenesis and complete chloroplast genome (plastome) of thermogenic have been well characterized, very little is known for that of . We sequenced the complete plastomes of sampled from Japan and Korea and compared them with that of sampled from Korea.

Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation.

To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius.

Phylogeographic Analysis and Genetic Structure of an Endemic Sino-Japanese Disjunctive Genus (Caprifoliaceae).

The Sino-Japanese Floristic Region (SJFR) is a key area for plant phylogeographical research, due to its very high species diversity and disjunct distributions of a large number of species and genera. At present, the root cause and temporal origin of the discontinuous distribution of many plants in the Sino-Japanese flora are still unclear. (Caprifoliaceae; Linnaeoideae) is a genus endemic to Asia, mostly in Japan, but two recent discoveries in China raised questions over the role of the East China Sea (ECS) in these species' disjunctions.

Data that effectively demonstrate the benefits of a 3D CAPPI algorithm.

The data presented in this article are related to the research article entitled "Three-dimensional analysis of the initial stage of convective precipitation using an operational X-band polarimetric radar network" [1]. The data presented were obtained using a three-dimensional constant-altitude plan-position-indicator (3D CAPPI), which was generated by a new method proposed by [1]. The data used to create the 3D CAPPI were derived from two X-band polarimetric radar installations in the Kanto region of Japan, Ebina (139.

Development of microsatellite markers for the wind cave-associated shrub subsp. (Caprifoliaceae).

Premise Of The Study: Microsatellite markers were developed for the wind cave-associated shrub subsp. to conduct phylogeographic studies on the species.

Methods And Results: Based on the sequence data obtained by 454 sequencing, a total of 81 primer pairs were designed and 18 successfully amplified the microsatellite regions.

The giant mycoheterotrophic orchid Erythrorchis altissima is associated mainly with a divergent set of wood-decaying fungi.

The climbing orchid Erythrorchis altissima is the largest mycoheterotroph in the world. Although previous in vitro work suggests that E. altissima has a unique symbiosis with wood-decaying fungi, little is known about how this giant orchid meets its carbon and nutrient demands exclusively via mycorrhizal fungi.

Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes.

Background And Aims: The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology. Eurasian goldenrod species of the Solidago virgaurea complex show remarkable morphological and ecological diversity in the Japanese Archipelago, with ecotypic taxa well adapted to specific environments (climate, edaphic conditions and disturbance regimes). The species complex is a suitable model to investigate the evolutionary processes of actively speciating plant groups, due to its ability to evolve in relation to environmental adaptation and its historical population dynamics.

The tiny-leaved orchid Cephalanthera subaphylla obtains most of its carbon via mycoheterotrophy.

The evolution of mycoheterotrophy has been accompanied by extreme reductions in plant leaf size and photosynthetic capacity. Partially mycoheterotrophic plants, which obtain carbon from both photosynthesis and their mycorrhizal fungi, include species with leaves of normal size and others that are tiny-leaved. Thus, plant species may lose their leaves in a gradual process of size reduction rather than through a single step mutation.

Genetic Diversity and Divergence in Populations of the Threatened Grassland Perennial Vincetoxicum atratum (Apocynaceae-Asclepiadoideae) in Japan.

We examined the genetic diversity and structure in populations of the endangered grassland herb Vincetoxicum atratum using 11 polymorphic microsatellite loci. Although the populations were small and disconnected, our molecular data indicated that the species maintains relatively high levels of genetic diversity and connectivity among populations. Population clustering analyses detected 2 to 3 clusters and most of the populations of V.

Long-term persisting hybrid swarm and geographic difference in hybridization pattern: genetic consequences of secondary contact between two Vincetoxicum species (Apocynaceae-Asclepiadoideae).

Background: During glacial periods, glacial advances caused temperate plant extirpation or retreat into localized warmer areas, and subsequent postglacial glacial retreats resulted in range expansions, which facilitated secondary contact of previously allopatric isolated lineages. The evolutionary outcomes of secondary contact, including hybrid zones, dynamic hybrid swarm, and resultant hybrid speciation, depends on the strengths of reproductive barriers that have arisen through epistatic and pleiotropic effects during allopatric isolation. The aim of this study was to demonstrate refugia isolation and subsequent secondary contact between two perennial Asclepioid species and to assess the genetic consequences of the secondary contact.

Development and characterization of microsatellite markers for Veratrum maackii (Melanthiaceae).

Premise Of The Study: Microsatellite markers were developed in Veratrum maackii (Melanthiaceae) to assess the pattern of population genetic structures across the species' distribution.

Methods And Results: Ten polymorphic loci were isolated from V. maackii using 454 shotgun pyrosequencing and the biotin capture method.