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***: An R package that can generate large phylogenetic trees for plants and animals

Plant Diversity 2023年第3期45卷 347-352页

作者： Yi Jin Hong Qian Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang 550025China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA

The previously released packages of the PhyloMaker series(***,***,and ***2) have been broadly used to generate phylogenetic trees for ecological and biogeographical *** these packages can be used to generate phylogenetic trees for any groups of plants and animals for which megatrees are available,they focus on generating phylogenetic trees for plants based on the megatrees provided by the *** to use these packages to generate phylogenetic trees based on other megatrees is not ***,we present a new tool,which is called ‘***’,and a simple R script that can be used to easily generate large phylogenetic trees for both plants and animals at a relatively fast speed.

关键词： Animals community phylogenetics Megatree Phylogeny Plants Species list

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

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Plant Diversity 2021年第4期43卷 255-263页

作者： Hong Qian Yi Jin Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL62703USA Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang550025China

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 *** 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 ***,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 ***,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 *** 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 *** 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

关键词： Genus-level phylogeny Species-level phylogeny Phylogenetic diversity Phylogenetic relatedness community phylogenetics Environmental gradient

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***2:An updated and enlarged R package that can generate very large phylogenies for vascular plants

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Plant Diversity 2022年第4期44卷 335-339页

作者： Yi Jin Hong Qian Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China Guizhou Normal UniversityGuiyang550025China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL62703USA

An earlier version of *** has been broadly used to generate phylogenetic trees of vascular plants for botanical,biogeographical and ecological ***,we update and enlarge this package,which is now called‘***2’.With ***2,one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature ***2 can generate phylogenies for very large species lists(the largest species list that we tested included 365,198 species).***2 generates phylogenies at a fast *** provide an example(including a sample species list and an R script to run it)in this paper to show how to use ***2 to generate phylogenetic trees.

关键词： community phylogenetics Global plants Phylogeny Species list Vascular plants V.PhyloMaker

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Does disturbance regime change community assembly of angiosperm plant communities in the boreal forest?

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Journal of Plant Ecology 2014年第2期7卷 188-201页

作者： Jian Zhang Stephen J.Mayor Fangliang He Department of Renewable Resources University of AlbertaEdmontonAlberta T6G 2H1Canada Department of Biological Science University of AlbertaEdmontonAlberta T6G 2E9Canada

Aims To examine if and how species and phylogenetic diversity change in relation to disturbance,we conducted a review of ecological literature by testing the consistency of the relationship between phylogenetic diversity and disturbance and compared taxonomic groups,type of disturbance and ecosystem/habitat *** provide a case study of the phylogenetic diversity–disturbance relationship in angiosperm plant communities of a boreal forest region,compared with types of natural and anthropogenic disturbances and plant growth *** Using a large-scale sampling plot network along a complete(0–100%)anthropogenic disturbance gradient in the boreal biome,we compared the changes of angiosperm plant community structure and composition across *** estimated natural disturbance with historical records of major *** then calculated phylogenetic diversity indexes and determined species richness in order to compare linear and polynomial trends along disturbance *** also compared the changes of community structure for different types of anthropogenic disturbances and examined how the relationships between species and phylogenetic diversity and disturbance regimes vary among three different life forms(***,graminoids and woody plants).Important Findings Phylogenetic diversity was inconsistently related to disturbance in previous studies,regardless of taxon,disturbance type or ecosystem *** the understudied boreal ecosystem,angiosperm plant communities varied greatly in species richness and phylogenetic diversity along anthropogenic disturbance gradients and among different disturbance *** general,a quadratic curve described the relationship between species richness and anthropogenic disturbance,with the highest richness at intermediate anthropogenic disturbance ***,phylogenetic diversity was not related to disturbance in any consistent manner and species richness was not correlated with phylogenetic *** rel

关键词： community assembly community phylogenetics community structure biodiversity human disturbance phylogeny taiga

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Scale dependence in the phylogenetic relatedness of alien and native taxa

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Journal of Plant Ecology 2020年第5期13卷 601-610页

作者： Chris M.McGrannachan Gillis J.Horner Melodie A.McGeoch School of Biological Sciences Faculty of ScienceMonash UniversityMelbourne 3800Australia Manaaki Whenua-Landcare Research 231 Morrin RdSt.JohnsAuckland 1072New Zealand Greening Australia Ltd PO Box 470Flinders LaneMelbourne 8009Australia

Aims Darwin’s naturalization hypothesis proposes that successfully established alien species are less closely related to native species due to differences in their ecological *** have provided support both for and against this *** reason for this is the tendency for phylogenetic clustering between aliens and natives at broad spatial scales with overdispersion at fine ***,little is known about how the phylogenetic relatedness of alien species alters the phylogenetic structure of the communities they invade,and at which spatial scales effects may ***,we examine if invaded understorey plant communities,*** both native and alien taxa,are phylogenetically clustered or overdispersed,how relatedness changes with spatial scale and how aliens affect phylogenetic patterns in understorey *** Field surveys were conducted in dry forest understorey communities in south-east Australia at five spatial scales(1,20,500,1500 and 4500 m2).Standardized effect sizes of two metrics were used to quantify phylogenetic relatedness between communities and their alien and native subcommunities,and to examine how phylogenetic patterns change with spatial scale:(i)mean pairwise distance and(ii)mean nearest taxon distance(MNTD).Important Findings Aliens were closely related to each other,and this relatedness tended to increase with *** species and the full community exhibited either no clear pattern of relatedness with increasing spatial scale or were no different from *** intermediate spatial scales(20-500 m2),the whole community tended towards random whereas the natives were strongly overdispersed and the alien subcommunity strongly *** suggests that invasion by closely related aliens shifts community phylogenetic structure from overdispersed towards *** and natives were distantly related across spatial scales,supporting Darwin’s naturalization hypothesis,but only when phylogenetic distance

关键词： alien species community phylogenetics Darwin’s naturalization hypothesis spatial scale phylogenetic beta diversity

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A taxonomic and phylogenetic perspective on plant community assembly along an elevational gradient in subtropical forests

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Journal of Plant Ecology 2021年第4期14卷 702-716页

作者： Ran Zhang Zhaochen Zhang Kankan Shang Mingshui Zhao Jiaxin Kong Xin Wang Yuzhuo Wang Houjuan Song Oukai Zhang Xuan Lv Jian Zhang Zhejiang Tiantong Forest Ecosystem National Observation Research Station School of Ecological and Environmental SciencesEast China Normal UniversityShanghai 200241China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China Shanghai Chenshan Plant Science Research Center Chinese Academy of ScienceShanghai Chenshan Botanical GardenShanghai 201602China Tianmushan National Nature Reserve Management Bureau Hangzhou 311311China

Aims Biodiversity patterns along elevational gradients have been well ***,the variations of biodiversity patterns along elevations and their underlying mechanisms are still *** multiple facets of biodiversity provides novel insights into the mechanisms for driving community *** this study,species abundance information was incorporated into taxonomic and phylogenetic diversity to reveal the ecological and evolutionary forces of plant community assembly along an elevational gradient in subtropical *** We selected 17 woody plant plots along an elevational gradient from 270 to 1470 m in eastern China’s subtropical *** presence-based and abundance-based measures of angiosperm species were used to quantify taxonomic alpha diversity,phylogenetic alpha diversity,phylogenetic relatedness,as well as taxonomic and phylogenetic dissimilarity among these *** the relations between these measures and climatic and topographic variables were *** Findings For both abundance-weighted and unweighted measures,we observed an overall increasing pattern for taxonomic alpha diversity along elevation,and distance-decay trends of taxonomic and phylogenetic similarity with increased elevational ***,there were disparity patterns of phylogenetic alpha diversity between abundance-weighted and unweighted *** phylogenetic structure,there was no significant trend along *** topographical and microclimatic variables were main drivers of diversity patterns and phylogenetic *** with unweighted measures,abundance-weighted measures were strongly related with the slope and stand basal ***,our results prove that deterministic processes mediated by local species abundance imprint on plant community composition along the elevational gradient.

关键词： community phylogenetics phylogenetic structure phylogenetic diversity beta diversity environmental gradient microclimate phylogenetic niche conservatism

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