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.

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.

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.

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

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.