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phylogenetic signal in gut microbial community rather than in rodent metabolic traits

National Science Review 2023年第10期10卷 20-31页

作者： Xue-Ying Zhang Saeid Khakisahneh Wei Liu Xinyi Zhang Weiwei Zhai Jilong Cheng John R.Speakman De-Hua Wang State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of Sciences Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences CAS Center for Excellence in Animal Evolution and Genetics University of Chinese Academy of Sciences Shenzhen Key Laboratory of Metabolic Health Center for Energy Metabolism and Reproduction Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Institute of Biological and Environmental Sciences University of Aberdeen State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Life Sciences Shandong University CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences

Host phylogeny and environment have all been implicated in shaping the gut microbiota and host metabolic traits of ***,few studies have evaluated phylogeny-associated microbial assembly and host metabolic plasticity concurrently,and their relationships on both short-term and evolutionary *** report that the branching order of a gut microbial dendrogram was nearly congruent with phylogenetic relationships of seven rodent species,and this pattern of phylosymbiosis was intact after diverse laboratory *** rearing,diet or air temperature(Ta) acclimation induced alterations in gut microbial communities,but could not override host phylogeny in shaping microbial community assembly.A simulative heatwave reduced core microbiota diversity by 26% in these species,and led to an unmatched relationship between the microbiota and host metabolic phenotypes in desert ***,the similarity of metabolic traits across species at different Tas was not correlated with phylogenetic *** data demonstrated that the gut microbial assembly showed strong concordance with host phylogeny and may be shaped by environmental variables,whereas host metabolic traits did not seem to be linked with phylogeny.

关键词： gut microbiota metabolic plasticity phylogenetic signal host–bacteria interactions air temperature ( T a )

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

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Journal of Plant Ecology 2014年第2期7卷 115-125页

作者： Jie Yang Xiuqin Ci Mengmeng Lu Guocheng Zhang Min Cao Jie Li Luxiang Lin Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesNo.88 Xuefu RoadKunmingYunnan 650223China University of Chinese Academy of Sciences No.19A Yuquan RoadBeijing 100049China

Aims While using phylogenetic and functional approaches to test the mechanisms of community assembly,functional traits often act as the proxy of ***,there is little detailed knowledge regarding the correlation between functional traits of tree species and their niches in local *** 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 *** 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,*** also quantified the environmental niches for these species based on conditional *** then analyzed the correlations between functional traits and environmental niches using phylogenetic independent *** examining phylogenetic signals of functional traits using Pagel’sλ,we quantified the phylogenetic and functional dispersion along environmental gradients within local tree *** 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 *** traits show significant phylogenetic signals in both of the *** found that the phylogenetic and functional dispersion were significantly clustered along topographical gradients in the Ailaoshan FDP but overdispersion in the Xishuangbanna *** patterns of phylogenetic and functional dispersion suggest that environmental filterin

关键词： forest dynamics plot local scale phylogenetic independent contrast phylogenetic signal phylogenetic dispersion functional dispersion

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

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Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,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 *** a relaxed molecular clock model better aligns with the complexities of *** 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 *** its utility,there remains a lack of corresponding software implementations for broader *** 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://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** 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.

关键词： Molecular clock Root-to-tip regression Temporal signal phylogenetic signal

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

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Journal of Mountain Science 2024年第4期21卷 1259-1271页

作者： Ravi Fernandes MARIANO Vanessa Leite REZENDE Cléber Rodrigo de SOUZA Patrícia Vieira POMPEU Rubens Manoel dos SANTOS Carolina Njaime MENDES Aloysio Souza de MOURA Felipe Santana MACHADO Warley Augusto Caldas CARVALHO Marco Aurélio Leite FONTES Department of Forest Sciences Federal University of LavrasLavras 37200-900Brazil 2Environmental Defence Association of Minas Gerais Belo Horizonte 30360-110Brazil Department of Ecology and Conservation Federal University of LavrasLavras 37200-900Brazil Department of Forest Sciences State University of Mato Grosso do SulAquidauana 79200-000Brazil Agência Zetta Federal University of LavrasLavras 37200-900Brazil. Department of Natural Sciences Federal University of São João del-ReiSão João del-Rei 36307-352Brazil.

Environmental conditions can change markedly over geographical distances along elevation gradients,making them natural laboratories to study the processes that structure *** work aimed to assess the influences of elevation on Tropical Montane Cloud Forest plant communities in the Brazilian Atlantic Forest,a historically neglected *** 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 *** do so,we assessed nine communities along an elevation gradient from 1210 to 2310 m *** large elevation *** relationships between elevation and phylogenetic structure,forest structure and species richness were investigated through Linear *** occurrence of evolutionary fingerprint on phylogenetic lineages was investigated by quantifying the extent of phylogenetic signal of elevation-success using a genus-level molecular *** results showed decreased species richness at higher elevations and independence between forest structure,phylogenetic structure and *** also verified that there is a phylogenetic signal associated with elevation-success by *** concluded that the elevation is associated with species richness and the occurrence of phylogenetic lineages in the tree communities evaluated in Mantiqueira *** the other hand,elevation is not associated with forest structure or phylogenetic ***,closely related taxa tend to have their higher ecological success in similar ***,we highlight the fragility of the tropical montane cloud forests in the Mantiqueira Range in face of environmental changes(*** warming)due to the occurrence of exclusive phylogenetic lineages evolutionarily adapted to environmental conditions(*** temperature)associated with each elevation range.

关键词： Atlantic Forest Cloud forest Conservation Community ecology Montane forests phylogenetic diversity phylogenetic signal

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

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Plant Diversity 2022年第2期44卷 163-169页

作者： Lubing Liu Jie Yang Min Cao Qinghai Song CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesYunnan 666303China University of Chinese Academy of Sciences Beijing 100049China

Plants deploy various ecological strategies in response to environmental *** 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 *** communities,however,grow in an open canopy structure and exhibit little species diversification,likely as a result of strong environmental *** 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 *** 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 *** study suggests that intraspecific trait variation is reduced in savanna ***,our findings indicate that classifying species by leaf phenology may help better understand how species coexist under similar habitats with strong stresses.

关键词： phylogenetic signal Savanna Intraspecific trait variation(ITV) Leaf phenology Coexistence

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

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mLife 2023年第1期2卷 89-100页

作者： Wenjie Wan Geoffrey MGadd Ji‐Dong Gu Wenzhi Liu Peng Chen Quanfa Zhang Yuyi Yang Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden Chinese Academy of SciencesWuhanChina Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station Chinese Academy of Sciences&Hubei ProvinceWuhanChina Geomicrobiology Group School of Life SciencesUniversity of DundeeDundeeScotlandUK State Key Laboratory of Heavy Oil Processing State Key Laboratory of Petroleum Pollution ControlChina University of PetroleumBeijingChina Environmental Science and Engineering Group Guangdong Technion‐Israel Institute of TechnologyGuangdongChina

Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they ***,ecological processes shaping distribution patterns of microorganisms across large spatial‐scale watersheds remain largely *** 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 *** microbial distribution patterns were found between soils and sediments,and microbial community similarity significantly decreased with increasing geographical *** properties showed a larger effect on microbial community composition than geospatial and climatic *** and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments,but opposite for ***,bacteria,and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments,suggesting stronger environmental *** dominated community assemblies of archaea and fungi in soils and sediments,whereas determinism dominated bacterial community *** 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 *** 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.

关键词： environmental breadth environmental constraint phylogenetic signal species replacement stochasticity versus determinism

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phylogenetic patterns suggest frequent multiple origins of secondary metabolites across the seed-plant ‘tree of life’

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National Science Review 2021年第4期8卷 66-77页

作者： Yongzeng Zhang Tao Deng Lu Sun Jacob B.Landis Michael J.Moore Hengchang Wang Yuehua Wang Xiaojiang Hao Jijun Chen Shenghong Li Maonian Xu Pema-Tenzin Puno Peter H.Raven Hang Sun CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences University of the Chinese Academy of Sciences Department of Botany and Plant Sciences University of California Riverside School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell University Department of Biology Oberlin College CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Chinese Academy of Sciences School of Life Science Yunnan University State Key Laboratory of Phytochemistry and Plant Resources in West China Kunming Institute of BotanyChinese Academy of Sciences Pharmaceutical Sciences University of Iceland Missouri Botanical Garden

To evaluate the phylogenetic patterns of the distribution and evolution of plant secondary metabolites(PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. A significant phylogenetic signal was detected in 17 of the 18 tested seed-plant clades for at least 1 of the 8 PSM classes using the D statistic. The phylogenetic signal, nevertheless, indicated weak clustering of PSMs compared to a random distribution across all seed plants. The observed signal suggests strong diversifying selection during seed-plant evolution and/or relatively weak evolutionary constraints on the evolution of PSMs. In the survey of the current phylogenetic distributions of PSMs, we found that multiple origins of PSM biosynthesis due to external selective forces for diverse genetic pathways may have played important roles. In contrast, a single origin of PSMs seems rather uncommon. The distribution patterns for PSMs observed in this study may also be useful in the search for natural compounds for medicinal purposes.

关键词： secondary metabolites phylogenetic tree phylogenetic signal co-diversification evolution bioprospecting seed plants

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Behaviour of cranes(family Gruidae)mirrors their phylogenetic relationships

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Avian Research 2021年第3期12卷 285-295页

作者： Nela Nováková Jan Robovský Faculty of Science University of South BohemiaBranišovská176037005ČeskéBudějoviceCzechia

Background:The behavioural repertoire of every species evolved over time and its evolution can be traced through the phylogenetic relationships in distinct ***(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 ***:We therefore investigated the evolution of behavioural traits of cranes in a phylogenetic context using several phylogenetic approaches and two types of trait *** cranes exhibit more than a hundred behavioural displays,almost one third of which may be phylogenetically ***:More than half of the analysed traits carry a significant phylogenetic *** 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 *** scoring has an influence on results within the Gruinae,primarily in genera Bugeranus and ***: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 *** 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.

关键词： Ancestral behavioural repertoire Evolution phylogenetic signal

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

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Journal of Plant Ecology 2014年第4期7卷 321-329页

作者： Werner Ulrich Marcin Piwczyński Markus K.Zaplata Susanne Winter Wolfgang Schaaf Anton Fischer Nicolaus Copernicus University in Torun Lwowska 1PL 87-100 ToruńPoland Center Landscape Development and Mining Landscapes(FZLB) Brandenburg University of Technology Cottbus-SenftenbergKonrad-Wachsmann-Allee 6D-03046 CottbusGermany Center of Life and Food Sciences Technische Universität MünchenEmil-Ramann-Straße 6D-85354 FreisingGermany Technische Universität Dresden Pienner Straße 8D-01737 TharandtGermany Brandenburg University of Technology Cottbus Konrad-Wachsmann-Allee 6D-03046 Cottbus-SenftenbergGermanyl Center of Life and Food Sciences Technische Universität MünchenHans-Carl-von-Carlowitz-Platz 2D-85354 FreisingGermany

Aims the total space of traits covered by the members of plant com-munities is an important parameter of ecosystem functioning and *** trace the variability of trait space during early plant succession and ask how trait space co-varies with phylogenetic community structure and soil ***,we are inter-ested in the small-scale variability in trait space and the influence of biotic and abiotic *** 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 *** functional attribute diversity serves as a proxy to total trait *** Findingstotal trait space steadily increased during *** 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 *** space increased with soil carbonate content,while pH and the fraction of sandy material behaved *** 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.

关键词： primary succession trait space phylogenetic signal habitat filtering species co-occurrence null model

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

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Integrative Zoology 2021年第5期16卷 769-784页

作者： Francesc MUÑOZ-MUÑOZ Nonito PAGÈS Ana.F.DURAO Marion ENGLAND Doreen WERNER Sandra TALAVERA Departament de Biologia Animal de Biologia Vegetal i d’EcologiaFacultat de BiociènciesUniversitat Autònoma de BarcelonaBarcelonaSpain Centre de Recerca en Sanitat Animal(CReSA) UAB-IRTACampus de la Universitat Autònoma de BarcelonaBarcelonaSpain CIRAD UMR ASTREGuadeloupeFrance ASTRE CIRADINRAeUniversitéde MontpellierMontpellierFrance The Pirbright Institute SurreyUK Leibniz-Centre for Agricultural Landscape Research MünchebergGermany

While wing form is known to differ between males and females of the genus Culicoides,detailed studies of sexual dimorphism are *** this study,we analyze sex-specific differences in the wing form of 5 species of the subgenus Avaritia,using geometric morphometrics and comparative phylogenetic *** 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 *** shape dimorphism was found to be poorly associated to size and the evolutionary history of 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 ***,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.

关键词： aspect ratio geometric morphometrics phylogenetic signal shape size

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