Applications of Shallow Water SPH Model in Mountainous Rivers

In this paper, the Shallow Water Equations (SWEs) are solved by the Smoothed Particle Hydrodynamics (SPH) approach. The proposed SWE-SPH model employs a novel prediction/correction two-step solution algorithm to satisfy the equation of continuity. The concept of buffer layer is used to generate the fluid particles at the inflow boundary. The model is first applied to several benchmark water flow applications involving relatively large bed slope that is typical of the mountainous regions. The numerical SWE-SPH computations realistically disclosed the fundamental flow patterns. Coupled with a sediment morph-dynamic model, the SWE-SPH is then further applied to the movement of sediment bed load in an L-shape channel and a river confluence, which demonstrated its robust capacity to simulate the natural rivers

Morphological and molecular evidence gives insight into the taxonomic position of Peucedanum pubescens (Apiaceae, Selineae)

In this study, morphological and molecular evidences were combined to determine the taxonomic position of Peucedanum pubescens Hand.-Mazz. Morphologically, Peucedanum pubescens is similar to the species of the genus Ligusticopsis in having fibrous remnant sheaths at the stem base, pinnate and linear coexisted bracts, strongly compressed dorsally mericarps, filiform median and lateral ribs, winged marginal ribs, numerous vittae in each furrow and commissure, but can also be easily distinguished from members of Ligusticopsis by its hispid fruit and linear-lanceolate bracteoles. Molecular phylogenetic analyses based on the single-copy protein-coding sequences (CDS) of plastomes and internal transcribed space (ITS) region showed that Peucedanum pubescens nested in the genus Ligusticopsis. As both morphological and molecular data supported the inclusion of Peucedanum pubescens within Ligusticopsis, the species is here transferred and the new combination, Ligusticopsis pubescens (Hand.-Mazz.) J.J.Deng, C.K.Liu & X.J.He, made

Plastid Phylogenomics Provide Evidence to Accept Two New Members of <i>Ligusticopsis</i> (Apiaceae, Angiosperms)

Peucedanum nanum and P. violaceum are recognized as members of the genus Peucedanum because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar to other Peucedanum taxa but resemble Ligusticopsis in overall morphology. To check the taxonomic positions of P. nanum and P. violaceum, we sequenced their complete plastid genome (plastome) sequences and, together with eleven previously published Ligusticopsis plastomes, performed comprehensively comparative analyses. The thirteen plastomes were highly conserved and similar in structure, size, GC content, gene content and order, IR borders, and the patterns of codon bias, RNA editing, and simple sequence repeats (SSRs). Nevertheless, twelve mutation hotspots (matK, ndhC, rps15, rps8, ycf2, ccsA-ndhD, petN-psbM, psbA-trnK, rps2-rpoC2, rps4-trnT, trnH-psbA, and ycf2-trnL) were selected. Moreover, both the phylogenetic analyses based on plastomes and on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences robustly supported that P. nanum and P. violaceum nested in Ligusticopsis, and this was further confirmed by the morphological evidence. Hence, transferring P. nanum and P. violaceum into Ligusticopsis genus is reasonable and convincing, and two new combinations are presented

The complete chloroplast genome of Chamaesium paradoxum

Chamaesium paradoxum H. Wolff is an endemic species naturally distributed in China. The complete chloroplast genome sequence of C. paradoxum was generated by de novo assembly using whole genome next generation sequencing data. The complete chloroplast genome of C. paradoxum is 153,512 bp in length, consisting of a pair of inverted repeats (IRs, 25,987 bp) separated by a large single-copy region (LSC, 84,162 bp) and a small single-copy region (SSC, 17,376 bp). There are 129 genes annotated, including 84 coding genes, 37 transfer RNA genes (tRNA), and eight ribosomal RNA genes (rRNA)

New insights into the phylogeny and taxonomy of Chinese Physospermopsis (Apiaceae)

Physospermopsis (Apiaceae) comprises about 10 species, but its taxonomy and phylogeny are disputed. The genus is mostly distributed in the Himalayas and Hengduan Mountains at high elevation. Earlier molecular studies involving six species of Physospermopsis indicated that this genus is not monophyletic and is nested in the East Asia Clade. Therefore, the aims of this study were to re-assess the phylogenetic position of, and interspecific relationships within, Physospermopsis based on two chloroplast loci (rpl16, rps16) and one nuclear region, the internal transcribed spacers of ribosomal DNA (ITS). Eight species involving 13 populations of Physospermopsis were collected. These were sequenced and analyzed with the sequences of 31 other Apiaceae species obtained from the NCBI to determine phylogenetic relationships using Bayesian inference (BI) and Maximum likelihood (ML). Our study found that Physospermopsis is monophyletic, nested in Pleurospermeae of Apiaceae, sister to Pleurospermum. And we propose that the Physospermopsis clade should be replaced by the East Asia Clade. However, the interspecific relationships within Physospermopsis were not well resolved and the positioning of species was unclear. Diagnostic characteristics to distinguish Physospermopsis species in the field and laboratory are provided for future Physospermopsis phylogenetic studies

Semenovia gyirongensis (Apiaceae), a new species from Xizang, China

Based on morphology and molecular data, a new species Semenovia gyirongensis Q.Y.Xiao & X.J.He, from Gyirong County, Xizang, China, is described and illustrated. It is morphologically most similar to S. malcolmii (Hemsley & Pearson) Pimenov, but differs in its cylindric much-branched root, intensively branching long underground caudex with distinct nodes, narrowly ovate to ovate terminal leaf lobes, oblong bracts with obtuse-rounded or cuneate apex

The complete chloroplast genome of Lilium Lankongense Franchet (Liliaceae)

The complete chloroplast genome sequence of Lilium lankongense Franchet is presented here. It is 152,611 bp in length and divides into four distinct regions: small single copy region of 17,506 bp, large single copy region of 81,995 bp, and a pair of inverted repeat regions (26,555 bp). The L. lankongense chloroplast genome annotation predicted a total of 131 genes, which contains 83 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. In the maximum likelihood tree, all kinds of Lilium were clustered into two monophyletic groups

Plastid Phylogenomic Analyses Reveal a Cryptic Species of <i>Ligusticopsis</i> (Apiaceae, Angiosperms)

Ligusticopsis litangensis is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of Ligusticopsis capillacea and Ligusticopsis dielsiana, the morphological boundaries between them are explicit and have obviously distinguishable characters. The main distinguishing features of the cryptic species are as follows: long conical multi-branched roots, very short pedicels in compound umbels, unequal rays, oblong-globose fruits, 1–2 vittae per furrow and 3–4 vittae on the commissure. The above-mentioned features differ somewhat from other species within the genus Ligusticopsis, but generally coincide with the morphological boundaries defined for the genus Ligusticopsis. To determine the taxonomic position of L. litangensis, we sequenced and assembled the plastomes of L. litangensis and compared them with the plastomes of 11 other species of the genus Ligusticopsis. Notably, both phylogenetic analyses based on ITS sequences and the complete chloroplast genome robustly supported that three accessions of L. litangensis are monophyletic clade and then nested in Ligusticopsis genus. Moreover, the plastid genomes of 12 Ligusticopsis species, including the new species, were highly conserved in terms of gene order, gene content, codon bias, IR boundaries and SSR content. Overall, the integration of morphological, comparative genomic and phylogenetic evidence indicates that Ligusticopsis litangensis actually represents a new species

Plastid Phylogenomic Analyses Reveal the Taxonomic Position of <i>Peucedanum franchetii</i>

Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis. However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii, we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis. Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions (infA, rps8, matK, ndhF, rps15, psbA-trnH, rps2-rpoC2, psbA-trnK, ycf2-trnL, and ccsA-ndhD) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L. likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L. likiangensis, but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented