Intraspecific divergence in a coastal plant, Euphorbia jolkinii, at a major biogeographic boundary in East Asia.

PREMISE: Quaternary climatic fluctuations and long-distance seed dispersal across the sea are critical factors affecting the distribution of coastal plants, but the spatiotemporal nature of population expansion and distribution change of East Asian coastal plants during this period are rarely examined. To explore this process, we investigated the genome-wide phylogenetic patterns of Euphorbia jolkinii Boiss. (Euphorbiaceae), which grows widely on littoral areas of Japan, Korea, and Taiwan. METHODS: We used plastome sequences and genome-wide single nucleotide polymorphisms in samples across the species range to reveal phylogeographic patterns and spatiotemporal distributional changes. We conducted ecological niche modeling for the present and the last glacial maximum (LGM). RESULTS: Genetic differentiation was observed between the northern and southern populations of E. jolkinii, separated by the major biogeographic boundary, the Tokara Gap. These two groups of populations differentiated during the glacial period and subsequently intermingled in the intermorainic areas of the central Ryukyu Islands after the LGM. Ecological niche models suggested that the potential range of E. jolkinii was restricted to southern Kyushu; however, it was widespread in the southern Ryukyu Islands and Taiwan during the LGM. CONCLUSIONS: This study provides evidence of genetic differentiation among coastal plant populations separated by the prominent biogeographical boundary. Although coastal plants are typically expected to maintain population connectivity through sea-drifted seed dispersal, our findings suggest that genetic differences may arise because of a combination of limited gene flow and changes in climate during the glacial period.

Development of a system for the automated identification of herbarium specimens with high accuracy.

Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on morphology and distribution. Recently, digitised herbarium specimens have begun to be used in comprehensive research to address broader issues. However, some specimens have been misidentified, and if used, there is a risk of drawing incorrect conclusions. In this study, we successfully developed a system for identifying taxon names with high accuracy using an image recognition system. We developed a system with an accuracy of 96.4% using 500,554 specimen images of 2171 plant taxa (2064 species, 9 subspecies, 88 varieties, and 10 forms in 192 families) that grow in Japan. We clarified where the artificial intelligence is looking to make decisions, and which taxa is being misidentified. As the system can be applied to digitalised images worldwide, it is useful for selecting and correcting misidentified herbarium specimens.

Estimation of rooting depth of 137Cs uptake by plants.

Understanding the soil-to-plant transfer process of 137Cs is essential for predicting the contamination levels of plants in contaminated areas. The rooting depth is considered one of the key factors explaining the difference in the activity concentration of 137Cs in different plant species. In this study, the distributions of 137Cs and 133Cs in soils and plants were investigated, and the plants' rooting depth of 137Cs uptake was estimated using the 137Cs/133Cs ratios in exchangeable fractions of soils and biological samples. The results showed that different plant species accumulate different levels of 137Cs and 133Cs. The 137Cs/133Cs ratios were fairly constant in plants of the same species. The average 137Cs/133Cs ratios in bamboo grasses and ferns were 0.015 ± 0.009 (n = 5) and 0.13 ± 0.04 Bq ng-1 (n = 10) in Yamakiya, respectively. The percentage of 137Cs in the exchangeable fraction of the uppermost soil layer was lower than that in the deeper soil layers. The activity concentrations of 137Cs in the soil profiles decreased sharply with depth, whereas the depth distributions of 133Cs were uniform. Therefore, the 137Cs/133Cs ratios were driven mainly by the 137Cs activity concentrations in soil. The plants' rooting depths of 137Cs uptake were estimated on the basis of the relationships between the averaged 137Cs/133Cs ratio in the soil layer and the 137Cs/133Cs ratio in the plant. The results indicate that the deeper-rooted species such as bamboo grasses have a lower accumulation of 137Cs than the superficial-rooting species such as ferns. The soil-to-plant transfer factors would be determined using rooting depth by calculating the averaged activity concentration of 137Cs within the estimated rooting depth.

Non-destructive DNA extraction from herbarium specimens: a method particularly suitable for plants with small and fragile leaves.

Protocols for DNA extraction from plants generally involve physical and chemical destruction of tissues. Use of these conventional methods precludes preservation of morphological information from herbarium specimens, especially for small plants with few leaves, and reduces the voucher value of specimens. Here, we developed a new, non-destructive DNA extraction protocol (Protocol 1) that only needs a small piece of leaf (< 25 mm2) to obtain DNA suitable for DNA sequencing from fragile herbarium specimens. The protocol was very simple and rapid; an extraction buffer was placed on the leaf surface of an intact specimen for 30 min at room temperature (20 °C). The quality of extracted DNA was checked by PCR amplification of two standard plant DNA barcode regions, the maturase K gene (matK, ca. 850 bp) and the ribulose-1,5-bisphosphatecarboxylase/oxygenase gene (rbcL, ca. 550 bp), for 14 vascular plant species encompassing various taxonomic groups. The protocol retrieved sequences from 80.0% of specimens for matK and 46.2% of specimens for rbcL. Placing of the extraction buffer onto specimens did not cause any tears or deformation, but caused discoloration in some plants. To improve DNA yield for specimens incompatible with Protocol 1, we developed an alternative protocol for DNA extraction with minimally invasive destruction of specimens (Protocol 2). In this protocol, a cut leaf was immersed in the extraction buffer for 30 min and stored subsequently in a fragment pocket on the specimen sheet. This alternative method retrieved matK sequences from 80.0% of specimens and rbcL sequences from 92.8% of specimens. The combination of Protocols 1 and 2 enabled us to obtain matK sequences from 90.0% of specimens and rbcL sequences form 92.8% of specimens. The new protocols facilitate the use of museum specimens for use of DNA of museum specimens while still preserving morphological information.

Comparative morphological analysis of two parallel mycoheterotrophic transitions reveals divergent and convergent traits in the genus Pyrola (Pyroleae, Ericaceae).

The genus Pyrola includes species with different degree of mycoheterotrophy; some species possess individuals that rely on all carbon through their associations with fungi (full mycoheterotrophy, FM), whereas some species obtain carbon through both fungi and photosynthesis by itself (partial mycoheterotrophy, PM). To investigate how plant functional traits of photosynthesis and reproduction are related to the degree of mycoheterotrophy in the initial stage of the transition from PM to FM, we determined morphological traits in FM (or nearly FM) and PM species in two independent lineages, P. picta and P. japonica complexes. We used herbarium specimens and examined leaf number, leaf area, flower number, and scape length in FM or nearly FM species (P. aphylla and P. subaphylla) and PM species (P. picta s.l. and P. japonica). We found a leaf area reduction in FM (or nearly FM) species in both lineages, suggesting that this is a convergent trait. The number of flowers was not significantly different between FM (or nearly FM) and PM species in both lineages. On the other hand, differences in the variation between FM (or nearly FM) and PM species were found in some traits between the two lineages. The FM (or nearly FM) species in one lineage only possessed rudimentary leaves, whereas that in the other linage possessed a few small, ordinary leaves in addition to those with only rudimentary leaves. The scape length of the FM (or nearly FM) species was significantly longer than that of PM species in one lineage, whereas it was shorter in the other lineage. The different and common variations are divergent and convergent traits, respectively, that could be associated with the transition to FM in Pylora. In addition, shoots of both PM species occasionally lacked ordinary leaves, possibly indicating possession of these shoots is preadaptation for the transition to FM in Pyrola.

Genetic analysis of Japanese and American specimens of Scirpus hattorianus suggests its introduction from North America.

Scirpus hattorianus is a possible alien species in Japan, and a clarification of its unclear taxonomy is required to reveal its origin. It is not known whether the plants initially described from Japan represent the same species distributed in North America. To clarify the origin of the species, we attempted to sequence old specimens collected about 80 years ago using newly designed primer pairs specific for short sequences, including the variable sites. Chloroplast sequences of ndhF were compared among Japanese and North American S. hattorianus, and the closely related species, S. atrovirens, S. flaccidifolius, and S. georgianus. We succeeded in sequencing all samples, and two haplotypes were detected in S. hattorianus: one was unique to the species and the other, detected from specimens potentially collected from the same population as the types, was shared by both North American S. hattorianus and two closely related species, S. atrovirens and S. flaccidifolius. Our results suggest that Japanese S. hattorianus is an alien species that was introduced from North America at least twice.

Development of microsatellite markers for partially and putative fully mycoheterotrophic varieties of Pyrola japonica sensu lato (Ericaceae).

We developed microsatellite markers to compare the genetic variation and reproductive biology between the partially mycoheterotrophic Pyrola japonica var. japonica and the putative fully mycoheterotrophic P. japonica var. subaphylla. Fifteen primer pairs were developed for P. japonica sensu lato and they were tested on 77 ramets from three populations of the two varieties. Thirteen loci were polymorphic in at least one of the two var. japonica populations, whereas only four loci were polymorphic in the var. subaphylla population. The considerably lower genetic variation of the var. subaphylla population may be attributed to frequent selfing and/or inbreeding. The markers developed in this study will be useful for comparing the genetic diversity of P. japonica s. l. populations and measuring gene flow within and between populations and varieties.

Variation in vegetative morphology tracks the complex genetic diversification of the mycoheterotrophic species Pyrola japonica sensu lato.

PREMISE OF THE STUDY: Although the evolution of full mycoheterotrophy has attracted many plant researchers, molecular phylogenetic studies that focus on the transition from partial to full mycoheterotrophy are limited to a few taxa. Pyrola japonica sensu lato is an ideal model for examining the evolution of mycoheterotrophy, owing to its variable leaf size, which suggests that the species comprises several transitional stages. METHODS: To elucidate the molecular and morphological changes that occur during the evolutionary transition between partial and full mycoheterotrophy in P. japonica s.l. from 18 populations in Japan, we estimated a parsimony network of plastid haplotypes based on three noncoding regions, measured the leaf size and scape color of the shoots, and compared morphology among haplotypes. KEY RESULTS: The seven haplotypes exhibited star-like relationships, and at least three divergent haplotypes were associated with differences in morphology. The first was mainly observed in large-leaved and green-scaped populations, whereas the second was observed in extremely small-leaved and reddish-scaped populations, which indicated a high degree of mycoheterotrophy, and the last was detected among mixed populations with both green- and reddish-scaped shoots with intermediate leaf sizes. In addition, the inconsistent association between the haplotypes and morphology suggests a complex relationship. CONCLUSIONS: Pyrola japonica s.l. has at least three separate genetic lineages that have different leaf morphologies. The genetic lineages and their coexistence could have led to the variable leaf size and suggest the possibility that gene flow from partial to full mycoheterotrophs could reverse the evolutionary transition to full mycoheterotrophy.

Isolation and characterization of novel microsatellite loci for the endangered orchid Cypripedium japonicum (Orchidaceae).

PREMISE OF THE STUDY: Twenty-six microsatellite markers were developed for the endangered orchid Cypripedium japonicum (Orchidaceae) to estimate the clonal diversity and genetic structure of the remaining populations in Japan. METHODS AND RESULTS: Microsatellite loci of C. japonicum were isolated using Ion Personal Genome Machine (PGM) sequencing. The primer sets were tested on 55 ramets sampled from two populations in Japan. Sixteen loci showed polymorphism in at least one population, with two to five alleles per locus. Observed and expected heterozygosities for the two populations ranged from 0.00 to 0.92 and 0.00 to 0.71, respectively. CONCLUSIONS: The microsatellite markers developed here provide a useful tool to analyze clonal structure and sexual regeneration status and will help to manage the remaining genetic variation within C. japonicum.

Why does Viola hondoensis (Violaceae) shed its winter leaves in spring?

PREMISE OF THE STUDY: Viola hondoensis is a perennial herb that inhabits the understory of temperate, deciduous forests. It is an evergreen plant with a leaf life span that is shorter than a year. Its summer leaves are produced in spring and shed in autumn; winter leaves are produced in autumn and shed in spring. Here we asked why the plant sheds its winter leaves in spring, though climate conditions improve from spring to summer. We proposed four hypotheses for the cause of shedding: (1) changes in seasonal environment such as day length or air temperature, (2) shading by canopy deciduous trees, (3) self-shading by taller summer leaves, and (4) competition for nutrients between summer and winter leaves. • METHODS: To test these hypotheses, we manipulated the environment of winter leaves: (1) plants were transplanted to the open site where there was no shading by canopy trees. (2) Petioles of summer leaves were anchored to the soil surface to avoid shading of winter leaves. (3) Sink organs were removed to eliminate nutrient competition. • KEY RESULTS: Longevity of winter leaves was extended when shading by summer leaves was eliminated and when sink organs were removed, but not when plants were transplanted to the open site. • CONCLUSION: We conclude that the relative difference in light availability between summer and winter leaves is a critical factor for regulation of leaf shedding, consistent with the theory of maximization of the whole-plant photosynthesis.