shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

The molecular clock model is fundamental for inferring species divergence times from molecular sequences.However,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling times.Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences.Furthermore,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary rates.Supporting a relaxed molecular clock model better aligns with the complexities of evolution.The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals.Despite its utility,there remains a lack of corresponding software implementations for broader applications.To address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal.This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models.By extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

Functional traits of tree species with phylogenetic signal co-vary with environmental niches in two large forest dynamics plots

Aims While using phylogenetic and functional approaches to test the mechanisms of community assembly,functional traits often act as the proxy of niches.However,there is little detailed knowledge regarding the correlation between functional traits of tree species and their niches in local communities.We suggest that the co-varying correlation between functional traits and niches should be the premise for using phylogenetic and functional approaches to test mechanisms of community assembly.Using functional traits,phylogenetic and environmental data,this study aims to answer the questions:(i)within local communities,do functional traits of co-occurring species covary with their environmental niches at the species level?and(ii)what is the key ecological process underlying community assembly in Xishuangbanna and Ailaoshan forest dynamic plots(FDPs)?Methods We measured seven functional traits of 229 and 36 common species in Xishuangbanna and Ailaoshan FDPs in tropical and subtropical China,respectively.We also quantified the environmental niches for these species based on conditional probability.We then analyzed the correlations between functional traits and environmental niches using phylogenetic independent contrasts.After examining phylogenetic signals of functional traits using Pagel’sλ,we quantified the phylogenetic and functional dispersion along environmental gradients within local tree communities.Important Findings For target species,functional traits do co-vary with environmental niches at the species level in both of the FDPs,supporting that functional traits can be used as a proxy for local-scale environmental niches.Functional traits show significant phylogenetic signals in both of the FDPs.We found that the phylogenetic and functional dispersion were significantly clustered along topographical gradients in the Ailaoshan FDP but overdispersion in the Xishuangbanna FDP.These patterns of phylogenetic and functional dispersion suggest that environmental filtering plays a key role in structuring local tree assemblages in Ailaoshan FDP,while competition exclusion plays a key role in Xishuangbanna FDP.

Evolutionary fingerprint, phylogenetic and forest structure of tropical montane Atlantic cloud forests along an elevation gradient

Environmental conditions can change markedly over geographical distances along elevation gradients,making them natural laboratories to study the processes that structure communities.This work aimed to assess the influences of elevation on Tropical Montane Cloud Forest plant communities in the Brazilian Atlantic Forest,a historically neglected ecoregion.We evaluated the phylogenetic structure,forest structure(tree basal area and tree density)and species richness along an elevation gradient,as well as the evolutionary fingerprints of elevation-success on phylogenetic lineages from the tree communities.To do so,we assessed nine communities along an elevation gradient from 1210 to 2310 m a.s.l.without large elevation gaps.The relationships between elevation and phylogenetic structure,forest structure and species richness were investigated through Linear Models.The occurrence of evolutionary fingerprint on phylogenetic lineages was investigated by quantifying the extent of phylogenetic signal of elevation-success using a genus-level molecular phylogeny.Our results showed decreased species richness at higher elevations and independence between forest structure,phylogenetic structure and elevation.We also verified that there is a phylogenetic signal associated with elevation-success by lineages.We concluded that the elevation is associated with species richness and the occurrence of phylogenetic lineages in the tree communities evaluated in Mantiqueira Range.On the other hand,elevation is not associated with forest structure or phylogenetic structure.Furthermore,closely related taxa tend to have their higher ecological success in similar elevations.Finally,we highlight the fragility of the tropical montane cloud forests in the Mantiqueira Range in face of environmental changes(i.e.global warming)due to the occurrence of exclusive phylogenetic lineages evolutionarily adapted to environmental conditions(i.e.minimum temperature)associated with each elevation range.

Behaviour of cranes(family Gruidae)mirrors their phylogenetic relationships

Background:The behavioural repertoire of every species evolved over time and its evolution can be traced through the phylogenetic relationships in distinct groups.Cranes(family Gruidae)represent a small,old,monophyletic group with well-corroborated phylogenetic relationships on the species level,and at the same time they exhibit a complex and well-described behavioural repertoire.Methods:We therefore investigated the evolution of behavioural traits of cranes in a phylogenetic context using several phylogenetic approaches and two types of trait scoring.The cranes exhibit more than a hundred behavioural displays,almost one third of which may be phylogenetically informative.Results:More than half of the analysed traits carry a significant phylogenetic signal.The ancestor of cranes already exhibited a quite complex behavioural repertoire,which remained unchanged in Balearicinae but altered greatly in Gruinae,specifically by the shedding of traits rather than their creation.Trait scoring has an influence on results within the Gruinae,primarily in genera Bugeranus and Anthropoides.Conclusions:Albeit the behavioural traits alone cannot be used for resolving species-level relationships within the Gruidae,when optimized on molecular tree,they can help us to detect interesting evolutionary transformations of behaviour repertoire within Gruiformes.The Limpkin(Aramus guarauna)seems to be the most enigmatic species and should be studied in detail for its behavioural repertoire,which may include some precursors of crane behavioural traits.

Emerging directions in the study of the ecology and evolution of plant-animal mutualistic networks: a review

The study of mutualistic plant and animal networks is an emerging field of ecological research. We reviewed progress in this field over the past 30 years. While earlier studies mostly focused on network structure, stability, and biodiversity maintenance, recent studies have investigated the conservation implications of mutualistic networks, specifically the influence of invasive species and how networks respond to habitat loss. Current research has also focused on evolutionary questions including phylogenetic signal in networks, impact of networks on the coevolution of interacting partners, and network influences on the evolution of interacting species. We outline some directions for future research, particularly the evolution of specialization in mutualistic networks, and provide concrete recommendations for environmental managers.

Using a mega-phylogeny of seed plants to test for non-random patterns of areal-types across the Chinese tree of life

The species composition of plant assemblages can in large part be explained by a long history of biogeographic and evolutionary events.Over the past decade,botanists and plant ecologists have increasingly sought to quantify phylogenetic signal in ecological traits to help inform their inferences regarding the mechanisms driving plant assemblages.However,most studies with a test of phylogenetic signal in the ecological traits have focused on a local scale,while comparatively few studies have been carried out on a regional scale.In this study,I presented a family-level phylogeny and a genus-level phylogeny that included all families and genera of extant seed plants in China,and use both phylogenies to examine whether areal-types or distribution patterns of families and genera of seed plants are non-randomly distributed across the Chinese tree of life.My study shows that the areal-types of families and genera of seed plants exhibit significant phylogenetic signal across the family-or genus-level phylogeny of seed plants in China.

Intraspecific trait variation of woody species reduced in a savanna community,southwest China

Plants deploy various ecological strategies in response to environmental heterogeneity.In many forest ecosystems,plants have been reported to have notable inter-and intra-specific trait variation,as well as clear phylogenetic signals,indicating that these species possess a degree of phenotypic plasticity to cope with habitat variation in the community.Savanna communities,however,grow in an open canopy structure and exhibit little species diversification,likely as a result of strong environmental stress.In this study,we hypothesized that the phylogenetic signals of savanna species would be weak,the intraspecific trait variation(ITV)would be low,and the contribution of intraspecific variation to total trait variance would be reduced,owing to low species richness,multiple stresses and relatively homogenous community structure.To test these hypotheses,we sampled dominant woody species in a dry-hot savanna in southwestern China,focusing on leaf traits related to adaptability of plants to harsh conditions(yearround intense radiation,low soil fertility and seasonal droughts).We found weak phylogenetic signals in leaf traits and low ITV(at both individual and canopy-layer levels).Intraspecific variation(including leaf-,layer-and individual-scales)contributed little to the total trait variance,whereas interspecific variation and variation in leaf phenology explained substantial variance.Our study suggests that intraspecific trait variation is reduced in savanna community.Furthermore,our findings indicate that classifying species by leaf phenology may help better understand how species coexist under similar habitats with strong stresses.

Phylogenetic and spatial patterns of herbal medicine compounds:Which medicinal plants are phytochemically characterized?

Objective: The study of phytometabolites of medicinal plants and their phylogenetic distribution is an important content of pharmacophylogeny. The objectives of this study were to provide an updated estimate of the extent to which the medicinal plants were investigated phytochemically and relate this to the species-level phylogeny and their geographical pattern.Methods: Here, we further characterized 1 648 phytometabolites, including terpenoids, steroids, flavonoids, phenylpropanoids, phenolics, alkaloids, etc., reported in journals Chinese Traditional and Herbal Drugs(Zhong Cao Yao) and Chinese Herbal Medicines(CHM) from the phylogenetic and spatial perspectives. According to the structural characteristics, terpenoids, flavonoids, alkaloids and phenylpropanoids were subdivided into subclasses, and the research effort of phytometabolites was for the first time delineated at both subclass and phylogenetic levels.Results: The phytometabolites of 90 families were reported on two journals in three years. It is noted that terpenoids with diverse bioactivities still constitute the primary object of phytochemical research, followed by flavonoids, phenolics, phenylpropanoids and alkaloids. Among the reported species, the family Asteraceae had the most, followed by Lamiaceae, Fabaceae, and Ranunculaceae. In the phylogenetic distribution of the reported phytometabolites, the net relatedness index(NRI) results revealed a clustered structure for triterpene, iridoid, flavone, flavonol, coumarin, indole alkaloid and terpenoid alkaloid, while the nearest taxon index(NTI) metric identified the clustered structure for triterpene, sesquiterpene,indole alkaloid and terpenoid alkaloid. Especially in Ranunculaceae, there were more reports on triterpene and terpenoid alkaloid subclasses. The overdispersion pattern of diterpene and phenolic was suggested by NRI and NTI respectively, albeit more reported diterpenes and phenolics were in Lamiaceae.The geographical distribution hotspots of reported species and compounds thereof highlighted the enormous progress of herbal medicine research and industry, which play a positive role in the future drug discovery and development.Conclusion: These results provide new dimensions and perspectives in the context of pharmacophylogeny for perceiving and evaluating research trends and flashpoints in medicinal phytochemistry.

Soil conditions and phylogenetic relatedness influence total community trait space during early plant succession

Aims the total space of traits covered by the members of plant com-munities is an important parameter of ecosystem functioning and complexity.We trace the variability of trait space during early plant succession and ask how trait space co-varies with phylogenetic community structure and soil conditions.Particularly,we are inter-ested in the small-scale variability in trait space and the influence of biotic and abiotic filters.Methods We use data on species richness and soil conditions from the first 7 years of initial succession of an artificial catchment in north-east-ern germany.total functional attribute diversity serves as a proxy to total trait space.Important Findingstotal trait space steadily increased during succession.We observed high small-scale variability in total trait space that was positively correlated with species richness and phylogenetic segregation and negatively correlated with total plant cover.trait space increased with soil carbonate content,while pH and the fraction of sandy material behaved indifferently.our results indicate that during early succession,habitat filtering processes gain importance leading to a lesser increase in trait space than expected from the increase in species richness alone.

Patterns and ecological determinants of woody plant height in eastern Eurasia and its relation to primary productivity

Aims Plant height is a key functional trait related to aboveground bio-mass,leaf photosynthesis and plant fitness.However,large-scale geographical patterns in community-average plant height(cAPH)of woody species and drivers of these patterns across different life forms remain hotly debated.Moreover,whether cAPH could be used as a predictor of ecosystem primary productivity is unknown.Methods We compiled mature height and distributions of 11422 woody spe-cies in eastern Eurasia,and estimated geographic patterns in cAPH for different taxonomic groups and life forms.then we evaluated the effects of environmental(including current climate and historical climate change since the Last Glacial Maximum(LGM))and evolutionary factors on cAPH.Lastly,we compared the predictive power of cAPH on primary productivity with that of LiDAR-derived canopy-height data from a global survey.Important Findings Geographic patterns of cAPH and their drivers differed among taxonomic groups and life forms.the strongest predictor for cAPH of all woody species combined,angiosperms,all dicots and deciduous dicots was actual evapotranspiration,while temperature was the strongest pre-dictor for cAPH of monocots and tree,shrub and evergreen dicots,and water availability for gymnosperms.Historical climate change since the LGM had only weak effects on cAPH.No phylogenetic signal was detected in family-wise average height,which was also unrelated to the tested environmental factors.Finally,we found a strong correlation between cAPH and ecosystem primary productivity.Primary productivity showed a weaker relationship with cAPH of the tallest species within a grid cell and no relationship with LiDAR-derived canopy height reported in the global survey.Our findings suggest that current climate rather than historical climate change and evolutionary history determine the geographical patterns in cAPH.However,the relative effects of climatic factors representing environmental energy and water availability on spatial variations of cAPH vary among plant life forms.Moreover,our results also suggest that cAPH can be used as a good predictor of ecosystem primary productivity.

Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling

Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.

Buttress trees in a 20-hectare tropical dipterocarp rainforest in Xishuangbanna, SW China

Aims buttresses are prevalent and are important to many ecological processes in tropical rainforests but are overlooked in many rainforest studies.based on a buttress survey in a 20-hectare plot,this study aims to answer the following questions:(i)is buttress forming a fixed species characteristic?(ii)is there any phylogenetic signal for buttress forming across a broad taxonomic scale?(iii)is buttress form-ing an inherent feature or simply induced by environmental factors,and how is this relevant to the size of the tree?Methods We surveyed buttresses for all 95940 trees with diameter at breast height(DbH)≥10 mm in a 20-ha tropical dipterocarp rainforest in Xishuangbanna,sW China.The occurrence of buttresses was compared across different taxa and across different tree-size classes.a phylogenetic analysis was conducted among buttressed and non-buttressed species in order to understand the evolutionary background of buttress formation.Important Findings This preliminary study showed that buttress trees are very abundant(making up 32%of trees with≥100 mm DbH)in this 20-ha tropical rainforest situated at the northern edge of the tropics.Fifty-one percent of the 468 tree species in the plot had stems that produced buttresses.large trees were more likely to develop buttresses than smaller ones.We found that although buttress formation is not a fixed species characteristic,there is a strong phylogenetic signal for buttress formation in larger species.

Narrow versus broad:sexual dimorphism in the wing form of western European species of the subgenus Avaritia(Culicoides,Ceratopogonidae)

While wing form is known to differ between males and females of the genus Culicoides,detailed studies of sexual dimorphism are lacking.In this study,we analyze sex-specific differences in the wing form of 5 species of the subgenus Avaritia,using geometric morphometrics and comparative phylogenetic methods.Our results confirm the existence of marked sexual dimorphism in the wing form of the studied species and reveal for the first time that while there is a shared general pattern of sexual shape dimorphism within the subgenus,sexual size dimorphism,and particular features of sexual shape dimorphism differ among species.Sexual shape dimorphism was found to be poorly associated to size and the evolutionary history of the species.The tight association of sexual shape dimorphism with aspect ratio suggests that the shape of the wing is optimized for the type of flight of each sex,that is,dispersal flight in females versus aerobatic flight in males.Moreover,the fact that interspecific shape differences are greater and more strongly associated to aspect ratio in males than in females might be indicating that in males the selective pressures affecting flight performance characteristics are more heterogeneous and/or stronger than in females among the studied species.

Beyond biogeographic patterns:Processes shaping the microbial landscape in soils and sediments along the Yangtze River

Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives.However,ecological processes shaping distribution patterns of microorganisms across large spatial‐scale watersheds remain largely unknown.Using Illumina sequencing and multiple statistical methods,we characterized distribution patterns and maintenance diversity of microorganisms(i.e.,archaea,bacteria,and fungi)in soils and sediments along the Yangtze River.Distinct microbial distribution patterns were found between soils and sediments,and microbial community similarity significantly decreased with increasing geographical distance.Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors.Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments,but opposite for bacteria.Archaea,bacteria,and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments,suggesting stronger environmental adaptation.Stochasticity dominated community assemblies of archaea and fungi in soils and sediments,whereas determinism dominated bacterial community assembly.Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments,and emphasized important roles of species replacement,environmental adaptability,and ecological assembly processes on microbial landscape.Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin,and might assist the establishment of environmental policies for protecting fragile watersheds.