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.

Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages?

Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages.Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants,researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera.However,whether the result of a study using species-level phylogenies generated in these ways is robust,compared to that based on phylogenies fully resolved at the species level,has not been assessed.Here,we use 1093 angiosperm tree assemblages(each in a 110110 km quadrat)in North America as a model system to address this question,by examining six commonly used metrics of phylogenetic structure(phylogenetic diversity and phylogenetic relatedness)and six climate variables commonly used in ecology.Our results showed that(1)the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level(the mean of correlation coefficients is 0.973),and(2)the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny.Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density,but this has largely not been tested.Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide,we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species.We assessed phylogenetic signal in different taxonomic(e.g.,angiosperms and gymnosperms)and ecological(e.g.,tropical,temperate,and boreal)groups of tree species,explored the biogeographical and phylogenetic patterns of wood density,and quantified the relative importance of current environmental factors(e.g.,climatic and soil variables)and evolutionary history(i.e.,phylogenetic relatedness among species and lineages)in driving global wood density variation.We found that wood density displayed a significant phylogenetic signal.Wood density differed among different biomes and climatic zones,with higher mean values of wood density in relatively drier regions(highest in subtropical desert).Our study revealed that at a global scale,for angiosperms and gymnosperms combined,phylogeny and species(representing the variance explained by taxonomy and not direct explained by long-term evolution process)explained 84.3%and 7.7%of total wood density variation,respectively,whereas current environment explained 2.7%of total wood density variation when phylogeny and species were taken into account.When angiosperms and gymnosperms were considered separately,the three proportions of explained variation are,respectively,84.2%,7.5%and 6.7%for angiosperms,and 45.7%,21.3%and 18.6%for gymnosperms.Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

Identification, pathogenicity, and fungicide sensitivity of Eutiarosporella dactylidis associated with leaf blight on maize in China

Maize(Zea mays L.) is an economically vital grain crop that is cultivated worldwide. In 2011, a maize foliar disease was detected in Lingtai and Lintao counties in Gansu Province, China. The characteristic signs and symptoms of this disease include irregular chlorotic lesions on the tips and edges of infected leaves and black punctate fruiting bodies in dead leaf tissues. Given favourable environmental conditions, this disease spread to areas surrounding Gansu. In this study, infected leaves were collected from Gansu and Ningxia Hui Autonomous Region between 2018and 2020 to identify the disease-causing pathogen. Based on morphological features, pathogenicity tests, and multilocus phylogenetic analysis involving internal transcribed spacer(ITS), 18S small subunit rDNA(SSU), 28S large subunit rDNA(LSU), translation elongation factor 1-alpha(TEF), and β-tubulin(TUB) sequences, Eutiarosporella dactylidis was identified as the causative pathogen of this newly discovered leaf blight. Furthermore, an in vitro bioassay was conducted on representative strains using six fungicides, and both fludioxonil and carbendazim were found to significantly inhibit the mycelial growth of E. dactylidis. The results of this study provide a reference for the detection and management of Eutiarosporella leaf blight.

Boehmeria nivea var. strigosa (Urticaceae), a new variety from Southwest China

Boehmeria nivea var.strigosa Zeng Y.Wu&Y.Zhao,a new variety of B.nivea(Urticaceae)from Southwest China,is here described based on evidence from morphology and molecular phylogeny.This new variety is mainly characterized by its green abaxial leaf blade,partly connate stipules,and densely patent strigose hairs on stems and potioles.The phylogenetic analysis based on rbc L,nrDNA and rbc L+nrDNA datasets,revealed that all individuals of B.nivea var.strigosa formed a monophyletic group.The conservation status of B.nivea var.strigosa is assessed as“Near Threatened”(NT)according to IUCN evaluation criteria.The discovery of this new variety is not only crucial for the taxonomy of ramie,but also provides reference for the exploration and utilization of ramie.

Lineaperpetua gen.nov.:a new diatom genus in the Thalassiosirales supported by morphology and molecular data

Based on a combination of morphology and molecular data of ribosomal DNA genes,a new diatom genus Lineaperpetua gen.nov.Yu,You,Kociolek&Wang is described.The features that help define Lineaperpetua at the level of genus include:a tangentially undulated valve face;continuous cribra areolae on the valve interior consisting of pores arranged as strips;single rimoportula located inside the ring of marginal fultoportulae.Additionally,phylogenetic analysis based on nuclear small subunit(SSU)rDNA sequences and nuclear large subunit(LSU)rDNA gene placed the three strains of L.lacustris in a single,monophyletic clade at a considerable sequence distance from the other genera(Thalassiosira,Conticribra,Planktoniella,Shinodiscus,and other genera)belonging to Thalassiosirales.Despite the similarities with some species of Thalassiosira,Conticribra,and Spicaticribra,the suite of features found in Lineaperpetua differentiate it from these other genera.These molecular data and morphological characters suggest an affinity of the new genus to the Thalassiosiraceae.

Taxonomy of Two New Peritrich Ciliates(Protozoa:Ciliophora)from Inland Saltwaters of China

The inland saltwater lakes harbor exceptional biodiversity.Here,two new species of solitary sessile peritrich ciliates were isolated from Qinghai Lake,the largest inland saltwater lake in China.Their morphology,ciliature,silverline system,and molecular phylogeny were investigated based on live observation,silver staining,and analysis of the small subunit ribosomal DNA(SSU rDNA).Vorticella paraglobosa sp.n.is characterized mainly by its obconical or elongate bell-shaped zooid,C-shaped macronucleus,single ventrally located contractile vacuole,two-rowed infundibular polykinety 3,and 28-38 silverlines between peristome and aboral tro-chal band and 10-15 between aboral trochal band and scopula.Vorticella cotyliformis sp.n.differs from its congeners mainly by its double-layered peristomial lip,cup-shaped zooid,J-shaped macronucleus,single ventrally positioned contractile vacuole,three-rowed infundibular polykinety 3,and 70-85 silverlines between peristome and aboral trochal band and 21-25 between aboral trochal band and scopula.The SSU rDNA sequences of the two new species were obtained,and the subsequent molecular phylogenetic analysis supported their taxonomic classification.

Mitochondrial genomes of Tapes dorsatus and Cardita variegata:insights into Heteroconchia phylogeny

Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.

Chrysosplenium fallax Koldaeva(Chrysosplenium),a newly recorded species from China

Chrysosplenium fallax Koldaeva,recently discovered and collected in Yanji,Jilin Province,repre-sents a newly recorded species of Saxifragaceae in China.This species,native to the Russian Far East,was first described as a new species in 2021.Based on precise field investigations and specimen examination,we provide a comprehensive description of C.fallax and its seed micromorphology.Phylogenetic analysis based on chloroplast genomes of 45 Chrysosplenium species confirmed the systematic position of C.fallax in Chrysosplenium.Voucher specimens were deposited in the Herbarium of South-Central Minzu University(HSN).

A new infrageneric classification of Gastrochilus(Orchidaceae:Epidendroideae)based on molecular and morphological data

Gastrochilus is an orchid genus containing 73 species of mainly epiphytic on trees or rocks in mountain forests of tropical and subtropical Asia.Previous phylogenetic analyses and morphological assessments have failed to produce a well-resolved phylogeny at the infrageneric level.In the present study,a new infrageneric classification of Gastrochilus is proposed based on thoroughly morphological and phylogenetic analyses based on 52 species.Our phylogenetic analysis divided the genus into six sections including three new sections,G.sect.Pseudodistichi,G.sect.Brachycaules and G.sect.Acinacifolii.We also reinstate G.suavis to the specific rank.Furthermore,two new species,G.armeniacus Jun Y.Zhang,B.Xu&Yue H.Cheng and G.minjiangensis Jun Y.Zhang,B.Xu&Yue H.Cheng,are described and illustrated.A key to six sections of the genus is presented.

Morphological,phylogenetic and metabolite profile of Prorocentrum clipeus,a newly recorded epiphytic dinoflagellate in the northern Yellow Sea

More than 30 species of benthic Prorocentrum have been identified,some of which produce okadaic acid(OA)and its derivatives,dinophysistoxins(DTXs),which cause diarrhetic shellfish poisoning(DSP).Increasing numbers of benthic Prorocentrum species have been reported in tropical and subtropical waters of China.In contrast,only a few benthic Prorocentrum species have been reported in temperate waters.In this study,morphological descriptions obtained using light microscopy,scanning electron microscopy and molecular characterization of one Prorocentrum clipeus strain isolated from the Yellow Sea are presented.Prorocentrum clipeus cells were nearly circular in shape,with a collar,ridge,and one protrusion.The periflagellar area was wide U-shaped,with two curved projections on platelet 1a.Nine periflagellar platelets of different sizes were observed.The morphology closely fits that of the species isolated from other locations.Phylogenetic analysis based on the molecular sequences of the small subunit(SSU)rDNA,internal transcribed spacer(ITS),and large subunit(LSU)rDNA was performed.A comprehensive metabolomic analysis incorporating target,suspect and non-target screenings was first applied to investigate the intracellular and extracellular metabolite profiles of the current isolate of P.clipeus.According to the results of the target and suspect screenings,179 metabolites or toxins produced by DSP-related algal species,including OA,dinophysistoxin-1(DTX1),dinophysistoxin-2(DTX2)and pectenotoxin-2(PTX2),were not detected.Non-target screening involving feature-based molecular networking(FBMN)provided a global view of major metabolites produced by the P.clipeus DF128 strain and revealed 23 clusters belonging to at least 13 compound classes,with organometallic compounds,lipids and lipid-like molecules,phenylpropanoids and polyketides,and benzenoids as major types.To date,this is the first record of the characterization of P.clipeus in samples from Chinese waters.Our results support the wide distribution of epibenthic Prorocentrum species.

Evolution history dominantly regulates fine root lifespan in tree species across the world

Understanding the drivers of variations in fine root lifespan is key to informing nutrient cycling and productivity in terrestrial ecosystems.However,the general patterns and determinants of forest fine root lifespan at the global scale are still limited.We compiled a dataset of 421 fine root lifespan observations from 76 tree species globally to assess phylogenetic signals among species,explored relationships between fine root lifespan and biotic and abiotic factors,and quantified the relative importance of phylogeny,root system structure and functions,climatic and edaphic factors in driving global fine root lifespan variations.Overall,fine root lifespan showed a clear phylogenetic signal,with gymnosperms having a longer fine root lifespan than angiosperms.Fine root lifespan was longer for evergreens than deciduous trees.Ectomycorrhizal(ECM)plants had an extended fine root lifespan than arbuscular mycorrhizal(AM)plants.Among different climatic zones,fine root lifespan was the longest in the boreal zone,while it did not vary between the temperate and tropical zone.Fine root lifespan increased with soil depth and root order.Furthermore,the analysis of relative importance indicated that phylogeny was the strongest driver influencing the variation in forest fine root lifespan,followed by soil clay content,root order,mean annual temperature,and soil depth,while other environmental factors and root traits exerted weaker effects.Our results suggest that the global pattern of fine root lifespan in forests is shaped by the interplay of phylogeny,root traits and environmental factors.These findings necessitate accurate representations of tree evolutionary history in earth system models to predict fine root longevity and its responses to global changes.

Teffichthys wui sp. nov., a new perleidid fish from the Early Triassic of Jiangsu and Anhui, China

Perleididae is a group of stem neopterygian fishes known only from the Triassic.Here,we report the discovery of a new perleidid,Teffichthys wui sp.nov.,based on six well-preserved specimens from the late Smithian(Olenekian,Early Triassic)marine deposits of Jurong,Jiangsu and Chaohu,Anhui,China.This new discovery documents the third and youngest species of Teffichthys,which is slightly younger than the Dienerian(Induan)T.elegans from Guizhou and the early Smithian T.madagascariensis from Madagascar.The new species shows diagnostic features of Teffichthys(presence of a spiracular,38-41 lateral line scales,and no more than three epaxial rays in the caudal fin)but differs from T.madagascariensis and T.elegans in some autapomorphies(e.g.,a horizontal opercle/subopercle contact and smooth scales with a nearly straight posterior margin).The diagnostic features for the genus Teffichthys and the family Perleididae are emended based on detailed comparisons of the new taxon with other perleidids.The phylogenetic relationships of perleidids with other stem neopterygians are discussed using a cladistic approach,and the results provide new insights into the phylogeny and classification of main stem neopterygian clades.

Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

A new gnetalean macrofossil from the Lower Cretaceous of the Laiyang Basin, eastern China

Gnetophytes are a key group of plant for understanding seed plant phylogeny,partly because of their unique and elusive morphology,such as xylem with vessels,phloem with chaperones,reticular veins,and double fertilization(Endress,1996).In particular,the ovule bears a membranous integument,the upper part of which extends beyond the seed envelope to form a micropylar tube.Therefore,gnetophytes occupy a unique evolutionary position in the phylogeny of seed plants and apparently represent a transition between angiosperms and other gymnosperms(Ran et al.,2018).Modern gnetophytes consist of only three families:Ephedraceae,Gnetaceae,and Welwitschiaceae,and each family contains only one genus.Ephedraceae(Ephedra L.)are the earliest diverging group of Gnetales,with a total of 70 extant species,and usually occur in cold and arid places in Asia,Europe,northern Africa,western North America and South America(Price,1996;Yang et al.,2017b).

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.

A new genus of galeaspids(jawless stem-Gnathostomata)from the early Silurian Chongqing Lagerstätte,China

The early Silurian Chongqing Lagerstätte(middle Telychian)yields exceptionally preserved articulated jawless and jawed fishes.Here,we describe a new eugaleaspiform(Galeaspida,jawless stem-Gnathostomata),Miaojiaaspis dichotomus gen.et sp.nov.,from the Chongqing Lagerstätte in Xiushan,Chongqing,China.The new form resembles Tujiaaspis vividus in the short medial dorsal canal,and the presence of the branching ends of the lateral transverse canal.They differ in that T.vividus has highly developed subordinate branches of the sensory canals that form a reticulate sensory canal system,and the median dorsal opening is more elongated.Our phylogenetic analysis recovers M.dichotomus and T.vividus as a monophyletic clade(Tujiaaspidae fam.nov.),which is supported by two synapomorphies:the short medial dorsal canal,and the branching ends of the lateral transverse canal.Tujiaaspidae forms a trichotomy with Shuyuidae and a clade comprising Anjiaspis,Sinogaleaspidae,Yongdongaspidae,and the‘eugaleaspid cluster’.The sensory canal patterns in galeaspids are compared to show the transformation sequence of the sensory canal system in Eugaleaspiformes.

Morphological and Molecular Data Revealed One New Species of the Short-legged Toads Brachytarsophrys Tian and Hu,1983(Anura,Megophryidae)from Yunnan,China

A new species of the genus Brachytarsophrys,named Brachytarsophrys wenshanensis sp.nov.,has been identified in southeastern Yunnan,China.This new species can be readily distinguished from other known congeners by both morphological criterion and molecular analysis of three mitochondrial gene segments:16S,COI,and Cytb.This classification is based on the following morphological characters:(1)medium body size(SVL 83.8–85.1 mm in two adult males);(2)enormous head,with head width nearly 1.2 times the length;(3)tongue pyriform,feebly notched;(4)non-meeting heels;(5)male lacking nuptial pad;(6)tibiotarsal articulation reaching angle of mouth when hindlimbs are extended forward alongside the body;(7)absence of outer metatarsal tubercle,inner metatarsal tubercle elliptic and approximately equal to first toe;(8)rudimentary toe webbing,webbing formula:Ⅰ(2–)–(2^(++))Ⅱ(2^(–))–(3^(++))Ⅲ(2^(½))–(4)Ⅳ(4^(+))–(2^(⅔))V;(9)lateral fringes narrow;(10)dermal ridge or glandular fold on dorsum absent;(11)pectoral glands distinct and irregular,femoral gland small.Our work increases the number of species within the genus Brachytarsophrys to 9.

A New Species of the Genus Scincella Mittleman,1950(Squamata:Scincidae)from Sichuan Province,Southwest China

The genus Scincella Mittleman,1950,within the family Scincidae,is a diverse group comprising 39 described species.The taxonomy of the genus is complex due to morphological similarities among species,which often obscures the true extent of biodiversity,resulting in several undescribed species requiring further exploration.In China,particularly within the unique ecosystems of the Hengduan Mountains,the diversity of Scincella is notably underestimated,with only 12 species currently recognized.In the present study,we describe a new species of the genus Scincella,Scincella liangshanensis sp.nov.,from Sichuan Province,Southwest China.Morphological characteristics and phylogenetic analyses revealed that the putative new species is distinct from all other known congeners.This discovery not only expands the known diversity of Scincella but also emphasizes the inadequacies in our current understanding of herpetological diversity in China.The addition of this species to the scientific record highlights the necessity for ongoing biodiversity assessments to uncover hidden species and enhance our understanding of the intricate web of life in one of the world’s biodiversity hotspots.

A review of Vietanna(Hemiptera:Cicadidae)with descriptions of two new species from China

The cicada genus Vietanna is reviewed based on the descriptions of two new species,V.perparva sp.nov.and V.longiloba sp.nov.,from China.The relationship of this genus to related taxa is discussed based on the phylogeny of Vietanna and representative species from subtribes Puranina,Leptopsaltriina,Euterpnosiina and Leptosemiina based on the mitochondrial gene COI and nuclear genes EF-1αand ARD1.