Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

Background and Aims Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling and insufficient information on DNA markers. Its morphological characters, such as capitulum, life form and leaf, show marked variations and are widely used in its infrageneric taxonomy. However, their evolution within Artemisia is poorly understood. Here, we aimed to reconstruct a well-resolved phylogeny for global Artemisia via a phylogenomic approach, to infer the evolutionary patterns of its key morphological characters and to update its circumscription and infrageneric taxonomy. Methods We sampled 228 species (258 samples) of Artemisia and its allies from both fresh and herbarium collections, covering all the subgenera and its main geographical areas, and conducted a phylogenomic analysis based on nuclear single nucleotide polymorphisms (SNPs) obtained from genome skimming data. Based on the phylogenetic framework, we inferred the possible evolutionary patterns of six key morphological characters widely used in its previous taxonomy. Key Results The genus Kaschgaria was revealed to be nested in Artemisia with strong support. A well-resolved phylogeny of Artemisia consisting of eight highly supported clades was recovered, two of which were identified for the first time. Most of the previously recognized subgenera were not supported as monophyletic. Evolutionary inferences based on the six morphological characters showed that different states of these characters originated independently more than once. Conclusions The circumscription of Artemisia is enlarged to include the genus Kaschgaria. The morphological characters traditionally used for the infrageneric taxonomy of Artemisia do not match the new phylogenetic tree. They experienced a more complex evolutionary history than previously thought. We propose a revised infrageneric taxonomy of the newly circumscribed Artemisia, with eight recognized subgenera to accommodate the new results.This work was supported by the National Natural Science Foundation of China (grant nos. 31870179, 31570204, 31270237 and J1310002), the International Partnership Program (grant no. 151853KYSB20190027), Sino-Africa Joint Research Center (grant no. SAJC201614), Key technology projects of Jiangxi Province's major scientific and technological research and development project (grant no. 20223AAF01007), Survey of Wildlife Resources in Key Areas of Tibet (grant no. ZL202203601) and National Plant Specimen Resource Center (grant no. E0117G1001) of the Chinese Academy of Sciences, Key Project at Central Government Level: The Ability Establishment of Sustainable Use of Valuable Chinese Medicine Resources (grant no. 2060302) and Project of the Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (grant no. AAAA-A21-121011290024-5).Abstract INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION Conclusions SUPPLEMENTARY DATA FUNDING ACKNOWLEDGEMENTS CONFLICT OF INTEREST LITERATURE CITED Supplementary dat

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees

Data accessibility statement: Full census data are available upon reasonable request from the ForestGEO data portal, http://ctfs.si.edu/datarequest/ We thank Margie Mayfield, three anonymous reviewers and Jacob Weiner for constructive comments on the manuscript. This study was financially supported by the National Key R&D Program of China (2017YFC0506100), the National Natural Science Foundation of China (31622014 and 31570426), and the Fundamental Research Funds for the Central Universities (17lgzd24) to CC. XW was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB3103). DS was supported by the Czech Science Foundation (grant no. 16-26369S). Yves Rosseel provided us valuable suggestions on using the lavaan package conducting SEM analyses. Funding and citation information for each forest plot is available in the Supplementary Information Text 1.Peer reviewedPostprin

DNA-Immobilized Special Conformation Recognition of L-Penicillamine Using a Chiral Molecular Imprinting Technique

A new chiral molecularly imprinted polymer (MIP) sensor with dual recognition ability was developed for the highly selective separation of enantiomers with toxic side effects in drugs. The sensor contains double-stranded deoxyribonucleic acid (dsDNA) as the element that immobilizes the chiral molecular conformation: the dsDNA enables the imprinted cavities to match the three-dimensional structure and functional groups from the chiral molecule. By embedding the spatial orientation of dsDNA in MIPs, one can accurately capture and immobilize the molecular conformation, eliminating the influence of interfering analogues. Herein, L-penicillamine (L-Pen) was selected as the chiral template molecule and embedded into dsDNA to form dsDNA-L-Pen complex, which was then embedded into the MIPs by electropolymerization. After elution, the stereo-selective imprinted cavities were obtained. The ATATATATATAT-TATATATATATA base sequence showed a high affinity for the embedded L-Pen, which endowed the imprinted cavities with a larger number of sites and improved the selectivity toward Pen enantiomers. Under the optimal working conditions, the current response of the MIP/dsDNA sensor exhibited a positive linear relationship with the logarithm of the L-Pen concentration in the range of 3.0 × 10−16 to 3.0 × 10−13 mol/L, and the detection limit was 2.48 × 10−16 mol/L. After the introduction of dsDNA into the MIP, the selectivity of the sensor toward D-Pen increased by 6.4 times, and the sensor was successfully applied in the analysis of L-Pen in penicillamine tablets

Plant phylogenomics based on genome-partitioning strategies: Progress and prospects

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research. Keywords: Plant phylogenomics, Next-generation sequencing, Whole-genome sequencing, Genome skimming, RAD-Seq, Targeted captur

Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China

Liu, Zhenwen, Liu, Ende, He, Deming, Ma, Yongpeng, Gao, Lianming (2023): Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China. Phytotaxa 619 (1): 97-104, DOI: 10.11646/phytotaxa.619.1.5, URL: http://dx.doi.org/10.11646/phytotaxa.619.1.

FIGURE 2 in Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China

FIGURE 2. Maximum Likelihood tree based on the concatenate sequences of the three DNA barcodes (rbcL, matK and ITS) under the General Time Reversible model. Bootstrap values (>50%) are shown along the clades.Published as part of Liu, Zhenwen, Liu, Ende, He, Deming, Ma, Yongpeng & Gao, Lianming, 2023, Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China, pp. 97-104 in Phytotaxa 619 (1) on page 99, DOI: 10.11646/phytotaxa.619.1.5, http://zenodo.org/record/842579

FIGURE 1. Rhododendron mingii A. Flowing branch. B in Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China

FIGURE 1. Rhododendron mingii A. Flowing branch. B. Close-up view of leaf blade abaxial surface. C. Gynoecium. D. Stamens. E. Opened corolla. F. Habit. (A–E drawn by Y. Luo from the holotype).Published as part of Liu, Zhenwen, Liu, Ende, He, Deming, Ma, Yongpeng & Gao, Lianming, 2023, Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China, pp. 97-104 in Phytotaxa 619 (1) on page 99, DOI: 10.11646/phytotaxa.619.1.5, http://zenodo.org/record/842579

Multi-Objective Load Dispatch Control of Biomass Heat and Power Cogeneration Based on Economic Model Predictive Control

This paper proposes a multi-objective load dispatch algorithm based on economic predictive control to solve the real-time multi-objective load dispatch problem of biomass heat and power cogeneration. According to the energy conservation law and production process, a real-time multi-objective load dispatch optimization model for heat and power units is established. Then, the concept of multi-objective utopia points is introduced, and the multi-objective load comprehensive objective function is defined to coordinate the conflict between the economic performance and pollutant emission performance of the units. Furthermore, using the online receding optimization characteristics of economic predictive control, the comprehensive objective function of multi-objective load dispatching is optimized online. Then, the fuel rate satisfying the economic performance and pollutant emission performance of the units is calculated to realize the economic performance and environmental protection operation of biomass heat and power cogeneration. Finally, the proposed multi-objective load dispatch control method is compared to traditional dispatch strategies by using industrial data. The results show that the method presented here can well balance the production cost and pollutant emission objective under the fluctuation of the thermoelectric load demand, and provides a feasible scheme for real-time dispatching of the multi-objective load dispatch problem of biomass heat and power cogeneration

Editorial : Rise to the challenges in plastome phylogenomics

Non peer reviewe

Trait variation and functional diversity maintenance of understory herbaceous species coexisting along an elevational gradient in Yulong Mountain, Southwest China

Characterizing trait variation across different ecological scales in plant communities has been viewed as a way to gain insights into the mechanisms driving species coexistence. However, little is known about how changes in intraspecific and interspecific traits across sites influence species richness and community assembly, especially in understory herbaceous communities. Here we partitioned the variance of four functional traits (maximum height, leaf thickness, leaf area and specific leaf area) across four nested biological scales: individual, species, plot, and elevation to quantify the scale-dependent distributions of understory herbaceous trait variance. We also integrated the comparison of the trait variance ratios to null models to investigate the effects of different ecological processes on community assembly and functional diversity along a 1200-m elevational gradient in Yulong Mountain. We found interspecific trait variation was the main trait variation component for leaf traits, although intraspecific trait variation ranged from 10% to 28% of total variation. In particular, maximum height exhibited high plasticity, and intraspecific variation accounted for 44% of the total variation. Despite the fact that species composition varied across elevation and species richness decreased dramatically along the elevational gradient, there was little variance at our largest (elevation) scale in leaf traits and functional diversity remained constant along the elevational gradient, indicating that traits responded to smaller scale influences. External filtering was only observed at high elevations. However, strong internal filtering was detected along the entire elevational gradient in understory herbaceous communities, possibly due to competition. Our results provide evidence that species coexistence in understory herbaceous communities might be structured by differential niche-assembled processes. This approach –– integrating different biological scales of trait variation –– may provide a better understanding of the mechanisms involved in the structure of communities