De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species

Scutellaria L. (family Lamiaceae) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. Scutellaria L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since Scutellaria L. has not been studied genetically, to expand the knowledge of species in the genus Scutellaria L., de novo whole-genome assembly was performed in Scutellaria indica var. tsusimensis (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify S. indica var. tsusimensis (H. Hara) Ohwi, S. indica L. and three other Scutellaria L. species. The assembly results for S. indica var. tsusimensis (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered Scutellaria nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of Scutellaria L. was developed.     

Structural Diversity and State of Knowledge of Flavonoids of the <Emphasis Type="Italic">Scutellaria</Emphasis> L. Genus

The review presents the results of scientometric analysis of data on the level of study and chemical diversity of flavonoids of the Scutellaria L. genus species of the world’s flora. Flavonoid composition in 63 species of skullcap is reported, together with the data on distribution in plants, structure, and sources of 301 flavonoids belonging to the groups of flavones, flavanones, flavanonols, flavonols, chalcones, isoflavones, flavolignans, and bioflavonoids. The greatest number of flavonoids was shown to be isolated from plants of S. indica, S. baicalensis, S. barbata, S. amoena, S. prostrata, S. galericulata, S. discolor, S. ramosissima, and S. supina. Scientometric studies indicate the constantly growing interest in the study of species of the Scutellaria L. genus by scientists of various branches of science, including phytochemists, biologists, and pharmacologists. Information provided in the review can be used to address issues of chemosystematics of plants of the Scutellaria L. genus.     

Speciation ofBotryobasidium subcoronatum (Basidiomycota) collected in Taiwan: Morphology, mating tests, and molecular data

Taiwan is a phytogeographically isolated area, with a rate of ca. 40% endemism in higher plants. In this study, the strong tendency towards genetic isolation and speciation ofBotryobasidium subcoronatum (Basidiomycota) from Taiwan is evaluated in comparison with European specimens. Mating tests amongB. subcoronatum specimens collected in Taiwan and Europe were performed. Mon-mon and di-mon matings confirm different intersterility groups or biological species. The biological species concept was compared with results from morphological comparison and molecular data from mtSSU rDNA and the nuclear ITS2 region. Three intersterility groups have been detected comprising European and Taiwanese strains from temperate and subtropical areas. MtSSU rDNA and the ITS2 rDNA sequences confirm consepecifity ofB. subcoronatum.     

Climate change may alter genetic diversity of Duchesnea indica,a clonal plant species

Climate change may alter the genetic diversity of plants. However, the relationship between genetic diversity in clonal plant species and climate change is unclear. To address this, we examined a representative clonal plant species, Duchesnea indica. We used microsatellite markers to analyze the genetic diversity of the species and used a correlation analysis to infer the relationship between climatic suitability and genetic diversity by using Maxent modeling. Then, we used a geographical information system approach to evaluate the change in genetic diversity of D. indica under climate change scenarios. There was a significantly negative relationship between climatic suitability and the genetic diversity of the clonal plant species. Using a proxy of genetic diversity, we found that climate change may alter the genetic diversity and even lead to a reduction in regional genetic diversity in D. indica. Annual precipitation, in particular, contributes to these changes in genetic diversity. Hence, climatic factors can be used as indicators of genetic diversity for clonal plant species, and studies should examine the impact of climate change on the maintenance of genetic diversity in plant species.     

Comparative phylogeography of two codistributed endemic cyprinids in southeastern Taiwan

Two cyprinid fishes, Spinibarbus hollandi and Onychostoma alticorpus, are endemic to southeastern Taiwan. This study examined the phylogeography of these two codistributed primary freshwater fishes using mitochondrial DNA cytochrome b sequences (1140 bp) to search for general patterns in the effect of historical changes in southeastern Taiwan. In total, 135 specimens belonging to these two species were collected from five populations. These two codistributed species revealed similar genetic variation patterns. The genetic variation in both species was very low, and the geographical distribution of the genetic variation corresponded neither to the drainage structure nor to the geographical distances between the samples. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of these two species were distributed in southern Taiwan before their dispersal. Our study suggests that the initial colonization occurred in the Kaoping River followed by eastern and northward dispersal. Our results also indicate that the Central Range in Taiwan did not act as a barrier to the dispersal of S. hollandi or O. alticorpus.     

An assessment of the efficiency of protection status through determinations of biodiversity hotspots based on endemic bird species,Taiwan

Evaluations of species richness patterns have been performed at diverse scales, and biodiversity hotspots, especially endemism hotspots, have received much attention in conservation biology. We estimated the distributions of endemic bird species based on a 12-yr avian inventory project in Taiwan, identified biodiversity hotspots of endemism on a regional scale based on predictions from the ensemble forecasting framework and frequency histogram approach, and assessed the efficiency of protected areas. The results indicated that the predicted endemism hotspots were mostly located in mid- and high-elevation areas along the Central Mountain Range of Taiwan. An observed endemism hotspot was defined as one in which at least five of Taiwan's 17 endemic bird species were present. This criterion was used because the 5% of the sampled grid squares that were the richest in endemic bird species all had 5 endemic bird species or more. Seventy to seventy-one percent of the observed biodiversity hotspots matched the predicted biodiversity hotspots. This outcome was obtained whether the richness biodiversity in a grid square was based on summed predicted probability or summed predicted richness. The majority of the protected areas for these Taiwanese endemic bird species were national parks, protecting 24.1% of the predicted hotspot areas, whereas nature reserves and wildlife refuges protected less than 7%. Most of the predicted endemism hotspots were not adequately protected. We conclude that the ensemble forecasting framework and the frequency histogram approach are useful for selecting critical habitats and biodiversity hotspots for endemic species and for appraising the efficiency of the protection status provided by governments.     

The Role of MPK6 as Mediator of Ethylene/Jasmonic Acid Signaling in <Emphasis Type="Italic">Serendipita indica</Emphasis>-Colonized Arabidopsis Roots

Serendipita indica is an axenically cultivable fungus, which colonizes a broad range of plant species including the model plant Arabidopsis thaliana. Root colonization by this endophyte leads to enhanced plant fitness and performance and promotes resistance against different biotic and abiotic stresses. The involvement of MPK6 in this mutualistic interaction had been previously shown with an mpk6 A. thaliana mutant, which failed to respond to S. indica colonization. Here, we demonstrate that mpk6 roots are significantly less colonized by S. indica compared to wild-type roots and the foliar application of plant hormones, ethylene, or jasmonic acid, restores the colonization rate at least to the wild-type level. Further, hormone-treated mpk6 plants show typical S. indica-induced growth promotion effects. Moreover, expression levels of several genes related to plant defense and hormone signaling are significantly changed at different colonization phases. Our results demonstrate that the successful root colonization by S. indica depends on efficient suppression of plant immune responses. In A. thaliana, this process relies on intact hormone signaling in which MPK6 seems to play a pivotal role.     

Phylogeography and genetic structure of the endemic cyprinid fish Microphysogobio brevirostris in northern Taiwan

This study used the mitochondrial DNA cytochrome b and control region sequences to examine the population genetic structure of Microphysogobio brevirostris, an endemic cyprinid species in northern Taiwan. In total, 90 specimens were collected from six populations belonging to four major rivers. All haplotypes were identified as two major clades (Clades N and S), exhibiting a southern and a northern distribution. The results of statistical dispersal-vicariance analysis (S-DIVA) revealed that two vicariance events and one dispersal event shaped the phylogeographic pattern of M. brevirostris. These results suggest that the ancestral populations of M. brevirostris are widely distributed throughout northern Taiwan, north of the Miaoli Plateau. The ancestral populations then diverged into two clades (N and S) by the raising of the Taoyuan Plateau. Finally, two major rivers of the S clade diverged and dispersed into adjacent rivers. Besides, our results revealed that Microphysogobio alticorpus and M. brevirostris colonized Taiwan during the same ice age through different colonization routes.     

海南和台湾蕨类植物多样性及其大陆性特征

海南和台湾是我国南部和东部两个最重要的大陆性岛屿,具有极为丰富的蕨类植物多样性。特有现象揭示着植物区系和植物多样性的历史,间断分布揭示着与邻近或相关植物区系的联系;特别是在岛屿地区,这种现象和意义尤其明显。海南有蕨类植物区系55科、135属、466种,其中特有种有32种,台湾蕨类植物区系57科、142属、599种,其中特有种达66种。在海南与台湾两地,有共有属104属,共有种仅有176种。台湾海峡出现始于晚白垩世,持续至第四纪;琼州海峡出现于早第四纪,因此,两地的特有现象远少于种子植物(台湾有801种,海南有501种),原因与蕨类植物具有更广的散布性相关,而且在被子植物中起重要作用的物种生物学障碍(机制)在蕨类是缺乏的;形态学的、生殖生物学特征导致蕨类植物具有较缓慢的物种演化历史和较低的灭绝率(Smith,1972)。海南和台湾蕨类植物区系的比较还表明,地理位置和海拔高度对植物区系的物种分化和物种多样性产生了极大的影响。     

Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata

Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end of the last glacial maximum, which obstructed gene flow, differentiated the Taiwanese and Chinese populations. Founders that colonized from both outlets of the Taiwan Strait were sourced from the northern South China Sea and the Ryukyus, thereby creating a melting pot in the Taiwan Strait. Inner-strait currents played roles as vectors for propagule dispersal among populations. Upon examination of the allele-frequency distributions of outlier loci, most negative outliers reflected the widespread polymorphisms shared by common ancestors. Furthermore, significant differentiation in the genetic components of positive outliers between this and other populations and the negative correlation with geographic distance suggested the presence of geography- or latitude-independent population divergence. Restored populations were compared with their sources and revealed biased sampling of nursery seedlings, which caused within-population substructures and reduced effective population sizes. This study indicated that multiple factors affect the population structure of the mangroves off southeast China.     

Phylogeography of Pinus armandii and Its Relatives: Heterogeneous Contributions of Geography and Climate Changes to the Genetic Differentiation and Diversification of Chinese White Pines

Geographic barriers and Quaternary climate changes are two major forces driving the evolution, speciation, and genetic structuring of extant organisms. In this study, we used Pinus armandii and eleven other Asian white pines (subsection Strobus, subgenus Pinus) to explore the influences of geographic factors and Pleistocene climatic oscillations on species in South China, a region known to be centers of plant endemism and biodiversity hotspots. Range-wide patterns of genetic variation were investigated using chloroplast and mitochondrial DNA markers, with extensive sampling throughout the entire range of P. armandii. Both cpDNA and mtDNA revealed that P. armandii exhibits high levels of genetic diversity and significant population differentiation. Three geographically distinct subdivisions corresponding to the Qinling-Daba Mountains (QDM), Himalaya-Hengduan Mountains (HHM) and Yungui Plateau (YGP) were revealed in mainland China by cpDNA. Their break zone was located in the southeastern margin of the Qinghai-Tibetan Plateau (QTP). A series of massive mountains, induced by the QTP uplift, imposed significant geographic barriers to genetic exchange. The disjunct distribution patterns of ancestral haplotypes suggest that a large continuous population of the white pines may have existed from southwest to subtropical China. Repeated range shifts in response to the Pleistocene glaciations led to the isolation and diversification of the subtropical species. The two Taiwanese white pines share a common ancestor with the species in mainland China and obtain their chloroplasts via long-distance pollen dispersal from North Asian pines. Distinct genetic patterns were detected in populations from the Qinling-Daba Mountains, Yungui Plateau, Himalaya-Hengduan Mountains, and subtropical China, indicating significant contributions of geographic factors to the genetic differentiation in white pines. Our study depicts a clear picture of the evolutionary history of Chinese white pines and highlights the heterogeneous contributions of geography and Pleistocene climatic fluctuations to the extremely high plant species diversity and endemism in South China.     

Microevolutionary patterns and processes of the Native Hawaiian colonizing fern Odontosoria chinensis (Lindsaeaceae)

Abstract.— The vascular‐plant flora of the Hawaiian Islands is characterized by one of the highest rates of species endemism in the world. Among flowering plants, approximately 89% of species are endemic, and among pteridophytes, about 76% are endemic. At the single‐island level, however, rates of species endemism vary dramatically between these two groups with 80% of angiosperms and only 6% of pteridophytes being single‐island endemics. Thus, in many groups of Hawaiian angiosperms, it is possible to link studies of phylogeny, evolution, and biogeographic history at the interspecific and interisland levels. In contrast, the low level of single‐island species endemism among Hawaiian pteridophytes makes similar interspecific and interisland studies nearly impossible. Higher levels of interisland gene flow may account for the different levels of single‐island endemism in Hawaiian pteridophytes relative to angiosperms. The primary question we addressed in the present study was: Can we infer microevolutionary patterns and processes among populations within widespread species of Hawaiian pteridophytes wherein gene flow is probably common? To address this broad question, we conducted a population genetic study of the native Hawaiian colonizing species Odontosoria chinensis. Data from allozyme analyses allowed us to infer: (1) significant genetic differentiation among populations from different islands; (2) historical patterns of dispersal between particular pairs of islands; (3) archipelago‐level patterns of dispersal and colonization; (4) founder effects among populations on the youngest island of Hawaii; and, (5) that this species primarily reproduces via outcrossing, but may possess a mixed‐mating system.     

An old adaptive radiation of forest dung beetles in Madagascar

Adaptive radiations of mammals have contributed to the exceptionally high levels of biodiversity and endemism in Madagascar. Here we examine the evolutionary history of the endemic dung beetle tribe Helictopleurini (Scarabaeidae) and its relationship to the widely distributed Oniticellini and Onthophagini. Helictopleurini species are dependent on mammals for their resources. We date the single origin of the tribe at 37 to 23 MY ago, indicating overseas colonization of Madagascar. The main radiation occurred concurrently with the main radiations of lemurs. The ancestors of Helictopleurini are inferred to have been coprophagous species inhabiting open habitats. Subsequent evolution has involved a shift into forests, changes in resource use to a more generalized diet, and changes in body size. Four species of the extant 65 species have shifted to use the dung of the recently introduced cattle in open habitats, allowing these species to greatly expand their geographical ranges.     

Origin,diversity, and biogeography of Antarctic scale worms (Polychaeta: Polynoidae): a wide‐scale barcoding approach

The Antarctic marine environment hosts diversified and highly endemic benthos owing to its unique geologic and climatic history. Current warming trends have increased the urgency of understanding Antarctic species history to predict how environmental changes will impact ecosystem functioning. Antarctic benthic lineages have traditionally been examined under three hypotheses: (1) high endemism and local radiation, (2) emergence of deep‐sea taxa through thermohaline circulation, and (3) species migrations across the Polar Front. In this study, we investigated which hypotheses best describe benthic invertebrate origins by examining Antarctic scale worms (Polynoidae). We amassed 691 polynoid sequences from the Southern Ocean and neighboring areas: the Kerguelen and Tierra del Fuego (South America) archipelagos, the Indian Ocean, and waters around New Zealand. We performed phylogenetic reconstructions to identify lineages across geographic regions, aided by mitochondrial markers cytochrome c oxidase subunit I (Cox1) and 16S ribosomal RNA (16S). Additionally, we produced haplotype networks at the species scale to examine genetic diversity, biogeographic separations, and past demography. The Cox1 dataset provided the most illuminating insights into the evolution of polynoids, with a total of 36 lineages identified. Eunoe sp. was present at Tierra del Fuego and Kerguelen, in favor of the latter acting as a migration crossroads. Harmothoe fuligineum, widespread around the Antarctic continent, was also present but isolated at Kerguelen, possibly resulting from historical freeze–thaw cycles. The genus Polyeunoa appears to have diversified prior to colonizing the continent, leading to the co‐occurrence of at least three cryptic species around the Southern and Indian Oceans. Analyses identified that nearly all populations are presently expanding following a bottleneck event, possibly caused by habitat reduction from the last glacial episodes. Findings support multiple origins for contemporary Antarctic polynoids, and some species investigated here provide information on ancestral scenarios of (re)colonization. First, it is apparent that species collected from the Antarctic continent are endemic, as the absence of closely related species in the Kerguelen and Tierra del Fuego datasets for most lineages argues in favor of Hypothesis 1 of local origin. Next, Eunoe sp. and H. fuligineum, however, support the possibility of Kerguelen and other sub‐Antarctic islands acting as a crossroads for larvae of some species, in support of Hypothesis 3. Finally, the genus Polyeunoa, conversely, is found at depths greater than 150 m and may have a deep origin, in line with Hypothesis 2. These “non endemic” groups, nevertheless, have a distribution that is either north or south of the Antarctic Polar Front, indicating that there is still a barrier to dispersal, even in the deep sea.     

Anagenetic speciation in Ullung Island, Korea: genetic diversity and structure in the island endemic species, Acer takesimense (Sapindaceae)

Anagenetic speciation is an important mode of speciation in oceanic islands; one-fourth of the endemic plants are estimated to have been derived via this process. Few studies, however, have critically examined the genetic consequences of anagenesis in comparison with cladogenesis (involved with adaptive radiation). We hypothesize that endemic species originating via anagenetic speciation in a relatively uniform environment should accumulate genetic variation with limited populational differentiation. We undertook a population genetic analysis using nine nuclear microsatellite loci of Acer takesimense, an anagenetically derived species endemic to Ullung Island, Korea, and its continental progenitor A. pseudosieboldianum on the Korean Peninsula. Microsatellite data reveal a clear genetic distinction between the two species. A high F value in the cluster of A. takesimense was found by Bayesian clustering analysis, suggesting a strong episode of genetic drift during colonization and speciation. In comparison with A. pseudosieboldianum, A. takesimense has slightly lower genetic diversity and possesses less than half the number of private and rare alleles. Consistent with predictions, weak geographical genetic structure within the island was found in A. takesimense. These results imply that anagenetic speciation leads to a different pattern of specific and genetic diversity than often seen with cladogenesis.     

Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards

Oceanic islands are well known for harboring diverse species assemblages and are frequently the basis of research on adaptive radiation and neoendemism. However, a commonly overlooked role of some islands is their function in preserving ancient lineages that have become extinct everywhere else (paleoendemism). The island archipelago of Bermuda is home to a single species of extant terrestrial vertebrate, the endemic skink Plestiodon (formerly Eumeces) longirostris. The presence of this species is surprising because Bermuda is an isolated, relatively young oceanic island approximately 1000 km from the eastern United States. Here, we apply Bayesian phylogenetic analyses using a relaxed molecular clock to demonstrate that the island of Bermuda, although no older than two million years, is home to the only extant representative of one of the earliest mainland North American Plestiodon lineages, which diverged from its closest living relatives 11.5 to 19.8 million years ago. This implies that, within a short geological time frame, mainland North American ancestors of P. longirostris colonized the recently emergent Bermuda and the entire lineage subsequently vanished from the mainland. Thus, our analyses reveal that Bermuda is an example of a “life raft” preserving millions of years of unique evolutionary history, now at the brink of extinction. Threats such as habitat destruction, littering, and non-native species have severely reduced the population size of this highly endangered lizard.     

Distribution patterns of four Termitomyces species cultivated by a fungus-growing termite,Odontotermes formosanus,in Taiwan

Fungus-growing termites inoculate the obligate symbiotic fungus Termitomyces into the fungus comb in their colonies. In this study, Taiwanese Termitomyces species were determined by diagnostic PCR using the metagenome of the body of Odontotermes formosanus (the only host termite living in Taiwan) as a template. Phylogenetic analyses revealed that four different Termitomyces species are cultivated by O. formosanus in Taiwan. Three have previously been registered in the DNA database, but one was first recorded in Taiwan. Only Termitomyces sp. Type C was distributed in all areas investigated in Taiwan, whereas the other three species were distributed regionally. Field observations indicated that the flush period and the number of fruit bodies in each colony varied between species. The distribution patterns of Termitomyces spp. in Taiwan may be related to the Taiwanese climate and/or the fruiting pattern.     

Balancing defense and growth—Analyses of the beneficial symbiosis between Piriformospora indica and Arabidopsis thaliana

The mutualistic interaction between the endophytic and root-colonizing fungus Piriformospora indica and Arabidopsis thaliana is a nice model system to study beneficial and non-benefical traits in a symbiosis. Colonized Arabidopsis plants are taller, produce more seeds and are more resistant against biotic and abiotic stress. Based on genetic, molecular and cellular analyses, Arabidopsis mutants were identified which are impaired in their beneficial response to the fungus. Several mutants are smaller rather than bigger in the presence of the fungus and are defective in defense responses. This includes mutants with defects in defense-signaling components, defense proteins and enzymes, and defense metabolites. The mutants cannot control root colonization and are often over-colonized by P. indica. As a consequence, the benefits for the plants are lost and they try to restrict root colonization by activating unspecific defense responses against P. indica. These observations raise the question as to how the plants balance defense gene activation or development and what signaling molecules are involved. P. indica promotes the synthesis of phosphatidic acid (PA), which binds to the 3-PHOSPHOINOSITIDE-DEPENDENT-KINASE1 (PDK1). This activates a kinase pathway which might be crucial for balancing defense and growth responses. The review describes plant defense compounds which are necessary for the mutualistic interaction between the two symbionts. Furthermore, it is proposed that the PA/PDK1 pathway may be crucial for balancing defense responses and growth stimulation during the interaction with P. indica.     

Piriformospora indica promotes cucumber tolerance against Root-knot nematode by modulating photosynthesis and innate responsive genes

Root Knot Nematode (RKN, Meloidogyne incognita) is one of the greatest damaging soil pathogens causes severe yield losses in cucumber and many other economic crops. Here, we evaluated the potential antagonistic effect of the root mutualistic fungus Piriformospora indica against RKN and their impact on vegetative growth, yield, photosynthesis, endogenous salicylic acid (SA) and its responsive genes. Our results showed that P. indica dramatically decreased the damage on shoot and root architecture of cucumber plants, which consequently enhanced yield of infested plants. Likewise, P. indica colonization clearly improved the chlorophyll content and delimited the negative impact of RNK on photosynthesis. Moreover, P. indica colonization exhibited a significant reduction of different vital nematological parameters such as soil larva density, amount of eggs/eggmass, eggmasses, females and amount of galls at cucumber roots. Additionally, the results showed that SA level was significantly increased generally in the roots of all treatments especially in plants infested with RKN alone as compared to control. This suggests that P. indica promoting SA levels in host cucumber plant roots to antagonize the RKN and alleviate severity damages occurred in its roots. This higher levels of SA in cucumber roots was consistent with the higher expressional levels of SA pathway genes PR1 and PR3. Furthermore, P. indica colonization reduces PR1, PR3 and increased NPR1 in roots of RKN infested cucumber plants when compared to non-colonized plants. Interestingly, our in vitro results showed that direct application of P. indica suspension against the J2s exhibited a significant increase in mortality ratio. Our results collectively suggest that P. indica promoting morphological, physiological and SA levels that might together play a major important role to alleviate the adverse impact of RKN in cucumber.