V.PhyloMaker2:An updated and enlarged R package that can generate very large phylogenies for vascular plants

An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological studies.Here,we update and enlarge this package,which is now called‘V.PhyloMaker2’.With V.PhyloMaker2,one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature systems.V.PhyloMaker2 can generate phylogenies for very large species lists(the largest species list that we tested included 365,198 species).V.PhyloMaker2 generates phylogenies at a fast speed.We provide an example(including a sample species list and an R script to run it)in this paper to show how to use V.PhyloMaker2 to generate phylogenetic trees.

Latitudinal trends in genus richness of vascular plants in the Eocene and Oligocene of North America

The latitudinal richness gradient is a frequent topic of study on the modern landscape,but its history in deep time is much less well known.Here,we preliminarily evaluated the paleolatitudinal richness gradient of vascular plants for the Eocene(56-33.9 million years ago) and Oligocene(33.9-23 million years ago) epochs of North America north of IVlexico using 201 fossil floras.We calculated the direction and shape of the gradient using quadratic regression to detect linear and curvilinear trends.We performed regressions for the Eocene and Oligocene as well as for informal time intervals within the Eocene:early,middle,and middle + late.We found that quadratic models better explain the data than linear models for both epochs as well as for the early Eocene.A roughly linear trend in the middle and middle + late intervals may reflect limited sampling of high latitude floras for those times.The curvilinear relationship was weak for the Eocene and the model showed a peak in richness at 45.5°N.The curvilinear relationship was much stronger for the Oligocene and the peak occurred at 48.5°N.In the Eocene,the mid-latitude peak in richness may be explained by mean annual temperature,which was probably higher at some mid-latitudes than at lower ones.For the Oligocene,the peak in richness at midlatitudes may be explained by evolutionary diversification within the temperate zone or by increased aridity at low latitudes.We also assessed the latitudinal richness gradient of genera within modern floras in North America north of Mexico and we found a weak,curvilinear trend with a peak in richness at 31.5°N.Our results suggest that the latitudinal genus richness gradient of vascular plants in North America continued to develop into its modern structure following the Oligocene.

The role of glacial gravel in community development of vascular plants on the glacier forelands of the Third Pole

On a deglaciated terrain,glacial gravel is the primary component of the natural habitat for vascular plant colonization and succession.Knowledge regarding the role of glacial gravel in vascular plant growth,however,remains limited.In this study,an unmanned aerial vehicle(UAV)was used to investigate plant family composition,species richness,fractional vegetation cover(FVC),and gravel cover(GC)along elevational gradients on the three glacier forelands(Kekesayi,Jiangmanjiaer,and Koxkar Baxi)of the Third Pole(including the eastern Pamir Plateau and western Tianshan Mountains)in China.We then analyzed the spatial characteristics of vascular plants followed by exploring the effect of glacial gravel on vascular plants.Findings indicated that FVC on these glacier forelands generally decreased as the elevation increased or distance from the current glacier terminus decreased.The shady slope(Kekesayi)was more vegetated in comparison to the sunny slope(Jiangmanjiaer)at the glacier basin scale,and the warm and humid deglaciated terrain(Koxkar Baxi)had the highest FVC at the regional scale.Plant family composition and species richness on the glacier forelands decreased with rising elevation,with the exception of those on the Jiangmanjiaer glacier foreland.The relationships between FVC and GC presented negative correlations;particularly,they exhibited variations in power functions on the Kekesayi and Jiangmanjiaer glacier forelands of the eastern Pamir Plateau and a linear function on the Koxkar Baxi glacier foreland of the western Tianshan Mountains.Glacial gravel was found to be conducive to vegetation colonization and development in the early succession stage up until vascular plants adapted to the cold and arid climatic condition,whereas it is unfavorable to the expansion of vascular plants in the later succession stage.These findings suggested that the spatial difference of plant characteristics had close connections with regional climatic and topographic conditions,as well as glacial gravel distribution.In addition,we concluded that aerial photographs can be an asset for studying the functions of micro-environment in vegetation colonization as well as succession on the glacier forelands.

Area-corrected species richness patterns of vascular plants along a tropical elevational gradient

The relationship and elevation is a hot issue between species richness in ecology and has been documented extensively. It is widely accepted that area size can significantly affect this relationship and thus mask the effects of other predictors. Despite the importance of the relationship between species richness and elevation while accounting for the area effect, it is insufficiently studied. Here, we evaluated area-corrected species richness patterns of all vascular plants as well as six vascular plant subgroups （seed plants, ferns, trees, shrubs, herbs and vines） along a tropical elevational gradient （Hainan Island, China）. If assessed in equal-elevation bands, uncorrected species richness showed bell-shaped curves, while area-corrected species richness assessed in equal-area bands appeared to increase monotonically due to the small proportion of highlands on Hainan Island. The mid-domain effect （MDE） was significantly correlated with both uncorrected and area-corrected species richness. On Hainan Island, the use of equal-area elevational bands increased the explanatory power of MDE.These findings provide useful insights to adjust for the area effect and highlight the need to use equal- area bands along the elevational gradient.

Species Richness of Vascular Plants along the Climatic Gradient of Mountain Shennongjia in Central China

A case study on the richness variation of vascular plant species along the climatic gradient from mountain foot (400 m asl) up to the summit (3,100 m) was carried out in Mt. Shennongjia of central China. The results show that climatic features such as mean annual temperature ( Y =16.26-0.506 X, R 2 =0.995), mean annual precipitation ( Y=235.48+82.663X, R 2 =0.951) and frost free day ( Y=283.54-7.148X, R 2 =0.964) are linearly responding to the elevational increase. However the variation of species richness is not uniformly linearly correlated to the climatic gradients. From 400 m up to 1,000 m, the species number increases from 933 to 1718, with a increase rate of 126.18 species/100 m ( R 2=0.951, P <0.001). From 1,000 m up to the highest peak of 3,100 m, species richness gradually declines with a rate of 94.36 species/100 m ( R 2=0.961, P <0.001). This variation can be described by a cubic model, y =-458.22+463.93 x -30.64 x 2+0.53 x 3 ( R 2=0.989, P <0.0001). Analysis calls for further study for better understanding of the relationship between biodiversity and environmental variation in this key area.

Seasonal variations of leaf wax n-alkane distributions and δ^(2) H values in peat-forming vascular plants from the Dajiuhu peatland, central China

Leaf wax n-alkane compositions have been widely applied to reconstruct paleoclimate histories in peat deposits,yet understanding of how the n-alkanes vary during seasonal plant growth remains limited.Here we report variations in the molecular and wax-derived nalkane hydrogen isotope(δ^(2) Halk)in the three dominant vascular plant species(Sanguisorba officinalis,Carex argyi,Euphorbia esula)and surface peat deposits nearby from the Dajiuhu peatland over a growing season.All three species show a relatively high carbon preference index(CPI)in the beginning of the growing season,with the CPI values reaching as high as 50 in two of the three species.Two species(S.officinalis,E.esula)display relatively stable average chain length(ACL)values over the four sampling intervals,with standard derivations of 0.2-0.3.In contrast,C.argyi exhibits a significant fluctuation of ACL values(averaging 28.11.4)over the growing season.Theδ^(2) Halk in all three species decreased during leaf growth.In the final stage of growth,theδ^(2) Halk values of the three species are similar to those in the surface peats collected from the peatland.Combining the results of our measurements of alkane concentration andδ^(2) H values,it is likely that de novo synthesis of leaf wax n-alkanes in the peatforming plant species is mainly at the early stage of leaf development.In the following months,the removal process exceeds renewal,resulting in a general decrease of the concentration of the total n-alkanes and the integratedδ^(2) Halk values.Thus theδ^(2) Halk values probably integrate the environmental variations at the end of the plant growth period rather than the whole period or the early growth period.These results are significant and have the potential to improve the utility ofδ^(2) Halk values in paleoenvironmental reconstructions.

Analysis of wild medicinal vascular plant resources and diversity in Dabie Mountains, Anhui Province

Dabie Mountains are located at the junction of Anhui,Henan and Hubei provinces in the East of China.With its varied altitude,climate,and soil texture,Dabie Mountains are extremely rich in wild plant resources.The 12th Traditional Chinese Medicine(TCM)Resources Scientific Expedition Team of Shenyang Pharmaceutical University conducted a study on wild vascular plants resources,especially medicinal vascular plants,through field investigation,literature review and specimen identification.There were 472 species of vascular plants belonging to 347 genera and 125 families collected during July 2018 in this area,of which 424 species were medicinal vascular plants,accounting for 89.83%of the total.From the perspective of medicinal parts,most of the medicinal plants there have values in their roots and rhizomes,as well as the whole plants.The efficacy and characteristics of these pharmaceutical dimensions were also summarized and analyzed in detail.Besides,among the wild vascular plants collected,the most dominant families with the biggest numbers of species are Compositae,Lamiaceae,Liliaceae,Rosaceae,Leguminosae,Ranunculaceae,Saxifragaceae and Polygonaceae,and the dominant genus are Viola and Sedum.In terms of life form,perennial herbs are dominant,accounting for 55.72%of the total species,followed by some annual(or biennial)herbs,shrubs and lianas.Finally,recommendations are put forward for strengthening the protection and utilization of wild medicinal plant resources in Dabie Mountains.

Twenty years of Chinese vascular plant novelties,2000 through 2019

From 2000 to 2019,11,895 new names or new additions to the Chinese vascular flora were proposed by 4226 individuals(4086 articles and 140 books),as documented in the Chinese Plant Names Index(CPNI).During those 20 years,4407 new taxa of vascular plants were described from China,including 7 new families,132 new genera,3543 new species,68 new subspecies,497 new varieties and 160 new forms.Additionally,3562 new combinations and names at new rank and 306 new replacement names were also proposed.Among these various new names were 150 invalid names and 108 illegitimate names,including some that have not been resolved.Six hundred and forty three vascular plants were reported as new to China,while 2349 names were reduced to synonyms of 1406 taxa.The data show that the Chinese flora increased in size at the rate of about 200 taxa annually during those years.Despite the increased attention given to biodiversity in recent years,the evidence indicates that a large number of species in China have yet to be discovered.Further basic investigation of the Chinese flora is needed.Additionally,in the past two decades only 8.5%of the newly published species have been based on molecular evidence,but in the past five years such data have increased significantly,reaching about 20%.Molecular data will undoubtedly become increasingly significant in the discovery of new species in the coming years.Yunnan,Guangxi,Sichuan,Xizang and Taiwan were important sources of new discoveries,with more than 3300 new taxa and records from these five provinces.By area,Taiwan and Hainan,two islands in southern China,have the highest density of newly discovered species.Regional plant surveys are still needed,especially in areas in the southwest and on the southern islands.

Alterations to biological soil crusts with alpine meadow retrogressive succession affect seeds germination of three plant species

Biological soil crusts(BSCs) are the important components of alpine meadow ecosystems.The extent and morphology of BSCs vary greatly with alpine meadow retrogressive succession due to grazing pressure.There is significant interest in impacts of crust composition on plant seed germination,especial l y in(semi-) arid environments.However,little is known about the influences of BSCs,and their associations with alpine meadow succession,on germination of typical alpine meadow vascular plant species.In a full factorial common-gardenexperiment,we studied effects of:(1) crust type,(2) seed position,and(3) surface texture on seed germination.We chose three typical alpine meadow plant species(i.e.Poa pratensis,Tibetia himalaica and Potentillen nivea),which belonged to different functional groups(graminoids,legumes,and forbs) and play important roles in all alpine meadow succession stages.Crust type and seed position influenced seed germination,and the inhibitory effects of BSCs depended on the crust type and seed species tested.The major factors influencing seed germination were BSC type,seed position,soil texture,and the interactions between BSC type and seed position; species and seed position; species andsurface texture; and species,crust type,and surface texture.Cyanobacteria crust significantly inhibited germination of all seeds.Seed position also had a significant effect on seed germination(p < 0.001).Fewer seedlings germinated on the surface than below the surface,this was especially true for P.nivea.seeds within cyanobacteria and lichen crusts.Only germination rates of T.himalaica on the soil surface were significantly correlated with plant occurrence frequency within the alpine meadow community.The poor correlation for the other two species is possibly that they are perennials.Our results clearly demonstrated that BSCs can be biological filters during seed germination,depending on the BSC succession stage.Through their influences on seed germination,BSCs can strongly influence community assemblages throughout alpine meadow retrogressive succession.

Elevational diversity of arrow bamboo (Fargesia spathacea) communities on Mount Shennongjia in Central China

Altitudinal changes in species richness, species diversity, species evenness, life-form spectrum, and community structure of arrow bamboo (Fargesia spathacea) were studied within 11 plots from 1 500 m to 2 600 m asl on Mount Shennongjia in Central China. From the lowest plot (1 680 m) to the highest one (2 570 m), vascular plants declined from 30 to 7 species, following a linear model ofY=55.99-1.83X (d.f.=9,F-value=48.64,r 2=0.84,P<0.001); species diversity, reduced from 3.13 to 1.78, following a linear model ofY=4.67–0.10X (d.f.=9,F-value=22.82,r 2=0.72,P=0.001); species evenness varied from 0.83 to 0.99, but presented little relationship to the altitude (r=0.112,P=0.742). In the life-form spectra, with the increase of altitude, the percentage of annual plants (r=0.60), underground bulb perennials (r=0.40), and big trees (r=0.35) tended to increase; shrubs (r=?0.52) and middle-sized trees (r=?0.45) tended to decline; perennial grasses (r=0.04) and semi-shrubs (r=0.03) were not strongly related to the altitudinal gradient. Arrow bamboo communities could be classified into five groups: bamboo under evergreen broad-leaved forest, under deciduous broad-leaved forest, under temperate coniferous forest, under cold-temperate coniferous and mixed forest, and pure bamboo community.

An updated megaphylogeny of plants,a tool for generating plant phylogenies and an analysis of phylogenetic community structure

Aims The aim of this article is 3-fold.First,we present an updated version of a published megaphylogeny of vascular plants that can be used in studies of plant ecology and biogeography.second,we develop a tool that can be used by botanists and plant ecologists to generate phylogenetic hypotheses in three scenarios.Third,we use a set of regional assemblages of angiosperm trees in North america as a model system to evaluate the effect of differences in phylogenies generated using the three scenarios on the quantification of phylogenetic properties and the relationship between measures of phylogenetic properties and environment.Methods The taxonomy and nomenclature of plant species in the megaphy-logeny were standardized according to The Plant list(version 1.1).a tool for generating phylogenies was created using the r language.The robustness of derived phylogenies was evaluated using correlation and regression analyses.Important Findingsan updated megaphylogeny of vascular plants(PhytoPhylo)and a tool for reconstructing phylogenies of seed plants(s.Phylomaker)were generated.our study shows that phylogenies generated by s.Phylomaker using the PhytoPhylo megaphylogeny as a backbone are nearly as good as phylogeny resolved at the species level when using derived phylogenies to quantify phylogenetic properties(e.g.phylogenetic diversity and phylogenetic relatedness)of biological assemblages,and that s.Phylomaker-generated phylogenies are robust for studies of community ecology and biogeography,par-ticularly those seeking for patterns of phylogenetic properties along environmental gradients.

The plant vascular systemⅠ:From resource allocation,inter-organ communication and defense,to evolution of the monocot cambium

In recent years, considerable attention has been paid to exploring the complex gene regulatory networks involved in the development of the plant vascular system. Such information is crucial to our understanding of the molecular and cellular events which give rise to the integrated tissues of the xylem and phloem, leading to the formation of structurally continuous conduits that interconnect various organs of the plant. Vascular development begins in the embryo to form progenitor cells, and upon germination, these progenitor cells and their decedents in the shoot and root meristems will form phloem and xylem, and the cambium.

The plant vascular system Ⅱ:From resource allocation,inter-organ communication and defense,to evolution of the monocot cambium

In this Special Issue, a focus is placed on the role of the xylem as an essential conduit for the long-distance delivery of water and mineral nutrients from the soil to the vegetative （above-ground） regions of the plant. Xylem cells destined to form tracheids or vessel members, which will make up the conduit for this water and mineral transport from the roots to the shoots, undergo apoptosis, a process of programmed cell death.

Plant Vascular Biology and Agriculture

The evolution of animal and plant vascular systems played a pivotal role in the advancement from simple to complex organisms, through the provision of a delivery system for the distribution of components essential for both metabolism and growth. Interestingly, although these two vascular systems conform to the same general rules of fluid dynamics （Murray 1926; McCulloh et al. 2003）, the developmental mechanisms adopted by plants and animals, to generate these long-distance transport systems,

Paleo-polyploidization in Lycophytes

Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.