Comparative phylogeography of two closely related Viola species occurring in contrasting habitats in the Japanese archipelago

Effect of environmental factors on seed germination and seedling emergence of Viola prionantha, a cleistogamous plant

Environmental conditions during seed development and maturation can affect seed traits and germination behavior, yet systematic research on the effects of seed maturation time on seed traits, germination behavior and seedling emergence of cleistogamy plants is lacking. Here, we determined the difference in phenotypic characteristics of CH and CL (namely CL1, CL2 and CL3 based on maturation time, respectively) fruits/seeds that were collected from Viola prionantha Bunge, a cleistogamous perennial plant, and evaluated the effects of various environmental factors on seed germination and seedling emergence. The fruit mass, width, seed number per fruit and mean seed mass of CL1 and CL3 were greater than that of CH and CL2, while seed setting of CH was lower than that of CL1, CL2 and CL3. Germination of CH, CL1, CL2, and CL3 seeds was < 10% in the dark at 15/5 and 20/10 ℃, whereas germination (0%-99.2%) of CH, CL1, CL2, and CL3 seeds changed significantly under light conditions. In contrast, more than 71% (from 71.7 to 94.2%) germination of both CH, CL1, CL2 and CL3 seeds occurred under both light/dark conditions and continuous darkness at 30/20 ℃. Germination of CH, CL1, CL2 and CL3 seeds was sensitive to osmotic potential, but CL1 seeds were more resistant to osmotic stress, compared with CH, CL2 and CL3. Seedling emergence of CH seeds was more than 67% (from 67.8 to 73.3%) at a burial depth of 0 cm-2 cm, while all types of CL seeds were below 15% at a burial depth of 2 cm. Information gathered from this study indicates that CH and CL seeds of V. prionantha were different in fruit size, seed mass, thermoperiod and photoperiod sensitivity, osmotic potential tolerance and seedling emergence, especially, maturation time significantly affect phenotypic characteristics and germination behavior of CL seeds matured at different periods. These results indicate that V. prionantha adapts to unpredictable environmental conditions by developing a variety of adaptation strategies, and ensures the survival and reproduction of the populations.

Virtual issue: phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants

Phylogeographic studies have investigated genetic variation and structure within species or closely related lineages and are fundamental for understanding factors and processes of genetic divergence as well as speciation. This virtual issue collects 35 papers on phylogeographic studies published in the Journal of Plant Research and focuses on three major topics in biodiversity: (1) biogeography, (2) systematics, and (3) evolution.

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

BACKGROUND

Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding". Viola have been recognized as a taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. philippica adulterants were sampled. A total of 24 complete chloroplast (cp) genomes were analyzed, among these 5 cp genome sequences were downloaded from GenBank and 19 cp genomes, including 2 "Zi Hua Di Ding" purchased from a local TCM pharmacy, were newly sequenced.

RESULTS

The Viola cp genomes ranged from 156,483 bp to 158,940 bp in length. A total of 110 unique genes were annotated, including 76 protein-coding genes, 30 tRNAs, and four rRNAs. Sequence divergence analysis screening identified 16 highly diverged sequences; these could be used as markers for the identification of Viola species. The morphological, maximum likelihood and Bayesian inference trees of whole cp genome sequences and highly diverged sequences were divided into five monophyletic clades. The species in each of the five clades were identical in their positions within the morphological and cp genome tree. The shared morphological characters belonging to each clade was summarized. Interestingly, unique variable sites were found in ndhF, rpl22, and ycf1 of V. philippica, and these sites can be selected to distinguish V. philippica from samples all other Viola species, including its most closely related species. In addition, important morphological characteristics were proposed to assist the identification of V. philippica. We applied these methods to examine 2 "Zi Hua Di Ding" randomly purchased from the local TCM pharmacy, and this analysis revealed that the morphological and molecular characteristics were valid for the identification of V. philippica.

CONCLUSIONS

This study provides invaluable data for the improvement of species identification and germplasm of V. philippica that may facilitate the application of a super-barcode in TCM identification and enable future studies on phylogenetic evolution and safe medical applications.

Independent allopatric polyploidizations shaped the geographical structure and initial stage of reproductive isolation in an allotetraploid fern, Lepisorus nigripes (Polypodiaceae)

Although polyploidy is pervasive and its evolutionary significance has been recognized, it remains unclear how newly formed polyploid species become established. In particular, the impact of multiple origins on genetic differentiation among populations of a polyploid species and whether lineages of independent origins have different evolutionary potentials remain open questions. We used population genetic and phylogenetic approaches to identify genetic differentiation between lineages with independent origins within an allotetraploid fern, Lepisorus nigripes. A total of 352 individuals from 51 populations were collected throughout the distribution range. To examine the genetic structure, multilocus genotyping, Bayesian population structure analysis, and neighbor-net analysis were carried out using single-copy nuclear genes. Phylogenetic trees were constructed to detect recurrent polyploid origins. Proportions of abortive spores were analysed as the measure of postzygotic reproductive isolation. Two genetically distinct lineages, the East-type and the West-type, were distributed mainly in the eastern and western parts, respectively, of the Japanese archipelago. Phylogenetic analyses indicated independent origins of these types and detected additional independent origins within each type. We also revealed limited genetic recombination between both types, even in their sympatric regions. F₁ hybrids between the East- and West-types showed a reduction in fertility. It is likely that the East- and West-types formed independently in the eastern and western parts of Japan, respectively. The limited genetic recombination and reduced fertility of hybrids suggest that the two types are at an incipient stage of speciation. Two polyploid lineages with independent geographic origins could develop reproductive isolation barrier(s).

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. We modeled the range shift of two ecologically distinct Vincetoxicum species using the species distribution model (SDM) and assessed the genetic consequences of secondary contact by combining morphological and genetic approaches. We performed morphometric analysis (592 individuals) and examined 10 nuclear microsatellites (671 individuals) in V. atratum, V. japonicum, and putative hybrid populations.

RESULTS

Multivariate analysis, model-based Bayesian analysis, and non-model-based discriminant analysis of principal components confirmed the hybridization between V. atratum and V. japonicum. High pollen fertility and a lack of linkage disequilibrium suggested that the hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Moreover, our findings show that the pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. Geographically-isolated hybrid populations exist as genetically distinct hybrid swarms that consist of V. atratum-like genotypes, V. japonicum-like genotypes, or admixed genotypes. In addition, Bayesian-based clustering analysis and coalescent-based estimates of long-term gene flow showed patterns of introgressive hybridization in three morphologically 'pure' V. japonicum populations.

CONCLUSION

In this study, we demonstrated that climatic oscillations during the Quaternary period likely led to species range shift and subsequently secondary contact. Hybrid populations may be self-sustaining and have persisted since V. atratum and V. japonicum came into contact during the post-glacial period. Pattern of hybridization between V. atratum and V. japonicum is unidirectional and differs among populations. We concluded that these differences in the genetic consequences of secondary contact are caused by historical colonization processes and/or natural selection.

Comparative phylogeographic study of Hosta sieboldiana and Hosta albomarginata (Asparagaceae) in Japan

We analyzed variations in chloroplast DNA (cpDNA) in the widespread herbaceous species Hosta sieboldiana and Hosta albomarginata across large portions of their geographic ranges in the Japanese archipelago. Our objective was to compare the phylogeographic histories and phylogeographic structures of the two congeneric species in the Japanese archipelago. The location of the study is Japanese archipelago. We sequenced 1380 bp of noncoding cpDNA from 45 populations of H. sieboldiana (n = 362) and 55 populations of H. albomarginata (n = 436) to assess genetic variations within and among populations across almost the entire distributions of the species in Japan. Extant patterns of geographic structure were analyzed using statistical parsimony networks and spatial analysis of molecular variance (SAMOVA). We also used Monmonier's algorithm to detect genetic barriers between regions. Relationships between the populations were examined using a neighbor-joining (NJ) method. Four haplotypes were found for H. sieboldiana, whereas eight haplotypes were identified for H. albomarginata. Total genetic haplotype diversity (hT) and within-population haplotype diversity (hS) for H. sieboldiana were 0.352 and 0.040, respectively, while the values for H. albomarginata were 0.529 and 0.085, respectively. The population differentiations (GST) for H. sieboldiana and H. albomarginata were 0.839 and 0.886, respectively. The SAMOVA analysis revealed two clusters in H. sieboldiana and four clusters in H. albomarginata. Differentiations between and among the clusters were supported by the BARRIER analysis and the NJ tree. We detected differences in the population genetic structure between the two species. We found that H. sieboldiana had lower haplotype diversity than H. albomarginata. These results may be partially explained by the difference in ecological habitats and geographic distributions between the species. Hosta albomarginata is more widely distributed than H. sieboldiana in East Asia including Russia, and this large distribution range would enable more chances to intraspecific gene flow.

Phylogeography of Phytophagous Weevils and Plant Species in Broadleaved Evergreen Forests: A Congruent Genetic Gap between Western and Eastern Parts of Japan

The Quaternary climate cycles played an important role in shaping the distribution of biodiversity among current populations, even in warm-temperate zones, where land was not covered by ice sheets. We focused on the Castanopsis-type broadleaved evergreen forest community in Japan, which characterizes the biodiversity and endemism of the warm-temperate zone. A comparison of the phylogeographic patterns of three types of phytophagous weevils associated with Castanopsis (a host-specific seed predator, a generalist seed predator, and a host-specific leaf miner) and several other plant species inhabiting the forests revealed largely congruent patterns of genetic differentiation between western and eastern parts of the main islands of Japan. A genetic gap was detected in the Kii Peninsula to Chugoku-Shikoku region, around the Seto Inland Sea. The patterns of western-eastern differentiation suggest past fragmentation of broadleaved evergreen forests into at least two separate refugia consisting of the southern parts of Kyushu to Shikoku and of Kii to Boso Peninsula. Moreover, the congruent phylogeographic patterns observed in Castanopsis and the phytophagous insect species imply that the plant-herbivore relationship has been largely maintained since the last glacial periods. These results reinforce the robustness of the deduced glacial and postglacial histories of Castanopsis-associated organisms.

Estimation of genetic diversity and evaluation of relatedness through molecular markers among medicinally important trees: Terminalia arjuna, T. chebula and T. bellerica

Terminalia trees are being over-exploited because of their medicinal and economical importance leading to loss of valuable genetic resources. For sustainable utilization and conservation, assessment of genetic diversity therefore becomes imperative. We report a comprehensive first study on estimation and analysis of genetic variation through Amplified fragment length polymorphism (AFLP), inter simple sequence repeat polymorphism (ISSR) and random amplification of polymorphic DNA (RAPD) across three species of Terminalia. The study included (i) characterization of genetic diversity at interspecific level, and (ii) comparison of efficiency of the marker systems. That the three species are genetically distinct was revealed by all the three marker systems as unique DNA fingerprints were obtained. This led to identification of several species-specific amplification products. Further analysis helped in species-wise clustering. The species specific bands obtained from the present investigation can be used as diagnostic markers to identify the raw materials for herbal drug preparations for authentication purposes.