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)

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

Will the negative psychological perceptions of investors reduce platform liquidity? Evidence from China's online loans.

Market liquidity can reflect whether financial market conditions are favorable and is the primary concern for investors when making investment decisions. Therefore, investors' psychological perception and confidence in the quality of products (assets) are particularly important. Using 264 of China's online loan platforms from August 2017 to November 2018, we investigate the impact of the negative psychological perceptions of investors on platform liquidity. The empirical results suggest that the negative psychological perceptions of investors reduce platform liquidity and increase platform liquidity risk. Using the Baidu Search Index to measure investor sentiment, we find that the negative psychological perceptions of investors affect platform liquidity by affecting investor sentiment, which provides a good channel for explaining the main conclusions. Heterogeneity analysis shows that the impact of the negative psychological perceptions of investors on platform liquidity is smaller in high-quality platforms with higher market share and higher registered capital. Meanwhile, we also find that the impact of negative psychological perceptions of investors is greater in private platforms, after the rectification policy, with positive net inflow, and in first- and second-tier cities and coastal cities. Precautionary financial regulatory policies are necessary, not punishment ex post. The research findings of this article can assist investors, platform managers, and regulatory agencies in identifying the liquidity characteristics of platforms, which can contribute to strengthening market liquidity management and financial risk control and provide some reference and support for formulating sustainable development policies in the financial industry

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)

Heterogeneous effects of the negative psychological perceptions of investors on platform liquidity.

Note: Blue diamond’s mark the estimated coefficients, and the dashed black lines show 95% confidence intervals. Each row corresponds to a separate regression using a corresponding subsample. We adopt the mean values to separate the high (H) from the low (L) group for the first two pairs of heterogeneity analyses. For example, if a platform’s market share is higher than its mean market share, the platform falls into a high market share group. For platform type, the sample is divided into private or non-private groups. The dashed orange lines divide our heterogeneity analyses into five categories (from top to bottom): platform quality, platform background, rectification policy, net inflows, and city characteristics. Each regression implements the first model (Eq (1)) and controls for all control variables and fixed effects.</p

Phylogeny and biogeography of Chinese Heracleum (Apiaceae tribe Tordylieae) with comments on their fruit morphology

Abstract The Sino-Himalayan Mountain Region is a major center of diversity of Heracleum (Apiaceae, Tordylieae, Tordyliinae), yet the phylogenetic relationships among its rich diversity of endemic taxa are largely unknown. In this study, we (1) investigate the monophyly of Heracleum and ascertain the phylogenetic placements of those species of Heracleum from China that fall outside of the group; (2) estimate phylogenetic relationships within Heracleum sensu stricto, particularly among those species occurring in the Hengduan Mountain Region of southwestern China; and (3) reconstruct the biogeographic history of Heracleum sensu stricto. To achieve these objectives, Bayesian inference and maximum-parsimony analyses of the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region and five noncoding chloroplast DNA (cpDNA) loci (rps16-trnK, rps16 intron, trnQ-rps16, rpl32-trnL, and psbA-trnH), separately and in combination, were carried out. Fruit morphology of the Chinese Heracleum species was examined. Statistical dispersal-vicariance analysis (S-DIVA) was used to reconstruct the biogeographic history. In total, 114 accessions were considered, which included 88 species representing eight genera of subtribe Tordyliinae, 28 of the 29 species of Heracleum occurring in China, and 4 species of Angelica as outgroups. The genus Heracleum is monophyletic upon the exclusion of nine species of Heracleum from China and the inclusion of the Caucasian monotypic genera Mandenovia and Symphyoloma. These nine excluded species show affinities to Tetrataenium, Semenovia, and Angelica. The species of Heracleum endemic to southwestern China form a moderately to strongly supported clade; however, major discordance between the ITS-and cpDNA-derived phylogenies, lack of resolution in the trees, and polyphyly of several species preclude unequivocal hypotheses of phylogenetic relationship. The distinctly clavate vittae, shorter than the length of the mericarp, is a diagnostic feature for Heracleum sensu stricto. Heracleum originated in the West Palearctic, with three possible migration routes leading to its present-day distribution. Major topological conflicts between the ITS and cpDNA trees may be due to interspecific hybridization and/or incomplete lineage sorting. The taxonomic limits of many Chinese Heracleum species remain unclear, possibly because of recent radiation in the Hengduan Mountains

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

Robustness check: Adjust the cluster, FE, and sample size and consider rectification policies and quantile narrowing.

Robustness check: Adjust the cluster, FE, and sample size and consider rectification policies and quantile narrowing.</p

Robustness check: Adjust the explanatory variable.

Robustness check: Adjust the explanatory variable.</p