RASP 4: ancestral state reconstruction tool for multiple genes and characters

With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code)

Response of fermentation quality and microbial community of oat silage to homofermentative lactic acid bacteria inoculation

Oat (Avena sativa L.) is one of the important forage crops in the world. However, oat grown in Southwest China has higher moisture content and their preservation face significant challenges. In addition, existing commercial lactic acid bacteria (LAB) have poor fermentation effects in hot and humid regions. Consequently, the current study investigated the response of oat fermentation quality and microbial community to self-selected LAB inoculation. The treatments were: CK, sterilized water; LP694, Lactobacillus plantarum 694; LR753, Lactobacillus rhamnosus 753; and LPLR, LP694 combined with LR753, followed by 1, 3, 7, 14, and 60 days (d) of fermentation. The results showed that LAB inoculation significantly raised the lactic acid content, and decreased the level of pH value, acetic acid, and ammonia-N in oat silage. The LR753 group had a significantly higher (p < 0.05) lactic acid content (60.95 g kg–1 DM), and lower pH value (3.95) and ammonia-N content (10.1 g kg–1 DM) followed by the LPLR group. The LR753 showed lower NDF (54.60% DM) and ADF (39.73% DM) contents than other groups. The Lactobacillus was a prevalent genus in LAB-treated groups, and its relative abundance reached maximum in LP694 (69%) on day 3, while in the LR753 group (72%) on 60 days. The Lactobacillus rhamnosus, Lactobacillus plantarum, and Lactobacillus fermentum became the dominant species in LAB-treated groups with fermentation time. The Lactobacillus genus was positively correlated with WSC (R = 0.6, p < 0.05), while negatively correlated with pH (R = −0.5, p < 0.05), and BA (R = −0.5, p < 0.01). Overall, the LR753 group had better fermentation quality and preservation of nutritional components providing theoretical support and guidance for future oat silage production in Southwest China

Historical invasion and expansion process of Alternanthera philoxeroides

Alternanthera philoxeroides is a perennial herbaceous amphibious aquatic weed of the family Amaranthaceae, native to South America. It was first found in Shanghai, China in 1892. After a stagnant phase of 50 years (1890s–1940s), A. philoxeroides spread rapidly throughout areas of central and southern China, and the range is still expanding. It is one of the most harmful and widely distributed alien species in mainland China. We applied Genetic Algorithm for Rule-Set Production (GARP) ecological niche modeling to predict the species’ potential range in China on the basis of occurrence points within colonized areas where A. philoxeroides had reached equilibrium. Environmental factors such as slope, flow accumulation, mean annual temperature, annual precipitation greatly influenced the size of A. philoxeroides’s potential range, while parameters such as solar radiation and elevation had little impact. Areas that we predict to have potential for invasion were still larger than those areas that had been invaded. Therefore, A. philoxeroides is predicted to continue to expand in China. Most Chinese provinces excluding Tibet, Qinghai, western Sichuan, southern Xinjiang, western Gansu, north-eastern Inner Mongolia, Jilin, Heilongjiang and Hainan are likely to be invaded. Because they are adjacent to areas that had been invaded, Shaanxi, Shanxi and south-eastern Gansu were most liable to be invaded; hence urgent measures should be taken there to prevent this species from further spreading

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

Hansenia trifoliolata, a new species (Apiaceae) from Shaanxi, China

Hansenia trifoliolata Q.P.Jiang & X.J.He (Apiaceae), is described as new from Shaanxi Province, northwest China. The mericarp features of H. trifoliolata resemble H. himalayensis and H. phaea and molecular phylogenetic analyses (combining ITS and plastid genomes data) suggest that H. trifoliolata is closely related to the group formed by H. oviformis and H. forbesii. The new species H. trifoliolata has unique 3-foliolate leaves and differ from other Hansenia species in its leaves, umbel numbers and size. A comprehensive description of H. trifoliolata is provided, including habitat environment and detailed morphological traits

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 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