A DNA barcode reference library for the native woody seed plants of Japan.

DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.

Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species (Toxicodendron vernicifluum, Anacardiaceae) in East Asia.

Species' phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the "middle step", which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the "low step", which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).

What is disjunctive xylem parenchyma? A case study of the African tropical hardwood Okoubaka aubrevillei (Santalaceae).

The morphological variation and structure-function relationships of xylem parenchyma still remain open to discussion. We analyzed the three-dimensional structure of a poorly known type of xylem parenchyma with disjunctive walls in the tropical hardwood Okoubaka aubrevillei (Santalaceae). Disjunctive cells occurred among the apotracheal parenchyma cells and at connections between axial and ray parenchyma cells. The disjunctive cells were partly detached one from another, but their tubular structures connected them into a continuous network of axial and ray parenchyma. The connecting tubules had thick secondary walls and simple pits with plasmodesmata at the points where one cell contacted a tubule of another cell. The imperforate tracheary elements of the ground tissue were seven times longer than the axial parenchyma strands, a fact that supports a hypothesis that parenchyma cells develop disjunctive walls because they are pulled apart and partly separated during the intrusive growth of fibers. We discuss unresolved details of the formation of disjunctive cell walls and the possible biomechanical advantage of the wood with disjunctive parenchyma: the proportion of tissue that improves mechanical strength is increased by the intrusive elongation of fibers (thick-walled tracheids), whereas the symplastic continuum of the parenchyma is maintained through formation of disjunctive cells.

Variable wood formation and adaptation to the alpine environment of Ephedra pachyclada (Gnetales: Ephedraceae) in the Mustang district, western Nepal.

BACKGROUND AND AIMS: Plants of Ephedra normally have vessels, but are known to become nearly vessel-less in some alpine localities. Previous studies implied that wood formation in Ephedra differs fundamentally from that in dicotyledons in which vessel-bearing and vessel-less taxa are systematically distinct. Using E. pachyclada in the Mustang district of Nepal, growing in an altitudinal range of over 2000 m, variation in wood formation and adaptation to alpine environment was studied in this normally vessel-bearing species. METHODS: Variation in wood anatomy and wood formation was observed with conventional optical microscopy. The lengths of three kinds of tracheary elements were measured and statistically analysed against habitat altitude and plant size of the individuals studied. KEY RESULTS: In E. pachyclada three kinds of tracheary elements, vessel elements, tracheids and fibre-tracheids, were nearly equal in length within individuals showing no elongation after differentiation from cambial initials. Tracheary element lengths among individuals had a negative correlation with altitude and a positive correlation with plant size. Multivariate analyses showed that altitude has a stronger correlation with tracheary element lengths than plant height or stem diameter. Moreover, several individuals from high elevations completely lacked vessels, and vessel formation fluctuated even in individuals from lower elevations. CONCLUSIONS: Wood anatomical trends in E. pachyclada are considered as an adaptation to extremely dry conditions in high mountains. Fluctuation in vessel formation in individuals from low elevations indicated that vessels differentiate only when their lateral expansion is allowed. These results showed that E. pachyclada has a different system of wood formation from dicotyledons and supported the opinion that the wood structure of Gnetales is fundamentally different from that of angiosperms.

Lack of latitudinal trends in wood anatomy of Dodonaea viscosa (Sapindaceae), a species with a worldwide distribution.

Latitudinal or altitudinal variation in several anatomical characters of wood is common for woody dicotyledonous genera with a wide distribution, but whether such variation exists at the species level is disputed. Latitudinal and altitudinal trends in wood anatomy of Dodonaea viscosa were studied, using 102 samples collected between 41.2° S and 33.3° N latitude and 7-2750 m altitude. We studied variation in four quantitative features: vessel element length, fiber length, vessel frequency, and tangential vessel diameter. Ontogenetic trends were minimal with a slight decrease or increase in the innermost stem and were negligible among the studied specimens. Throughout the distributional range of the species, no latitudinal trends were detected in either the Northern or Southern Hemispheres. Altitudinal trends were also nonexistent, except for two features in specimens from China and Japan. Absence of latitudinal or altitudinal trends in this widely distributed species suggests that in some species the species-level variation in wood anatomy is not controlled by ecological gradients.