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Phylogenetic Community and Nearest Neighbor Structure of Disturbed Tropical Rain Forests Encroached by Streblus macrophyllus

Nguyen Hong Hai, Yousef Erfanifard, Tran Quang Bao, Any Mary Petritan, Trinh Hien Mai, Ion Catalin Petritan
2020 Forests  
Results showed that phylogenetic distance, phylogenetic diversity, and mean phylogenetic distance increased when species diversity increased and the abundance of S. macrophyllus decreased in forest communities  ...  According to the forest disturbance effects, phylogenetic community properties showed the loss of phylogenetic relatedness when S. macrophyllus increased in abundance.  ...  When increasing species diversity, phylogenetic distance (PD), and phylogenetic diversity (Pd) also increased from P1 to P3.  ... 
doi:10.3390/f11070722 fatcat:vexatcragrdmxcqp4bdoqxkcde

Impact of pine invasion on the taxonomic and phylogenetic diversity of a relict Mediterranean forest ecosystem

Federico Selvi, Elisa Carrari, Andrea Coppi
2016 Forest Ecology and Management  
phylogenetic diversity of the native seed plant community.  ...  Both the NRI and NTI indices showed a significant reduction of phylogenetic evenness in the pine forest.  ...  for providing information on the distribution and current management of the maritime pine and cork oak forest areas.  ... 
doi:10.1016/j.foreco.2016.02.013 fatcat:kurjbqr6pbcxrpnzphajsfivwu

Phylogenetics and Conservation Biology: Drawing a Path into the Diversity of Life [chapter]

Roseli Pellens, Philippe Grandcolas
2016 Biodiversity Conservation and Phylogenetic Systematics  
It has turned the focus to the need of protecting the Tree of Life, i.e. the diversity of features resulting from the evolution of Life on Earth.  ...  Phylogenetic diversity is one of the variables taken in account.  ...  The consideration of phylogenetic systematics in biodiversity conservation opened a completely new line of investigation as it has turned the focus to the need of protecting the Tree of Life , i.e. the  ... 
doi:10.1007/978-3-319-22461-9_1 fatcat:o3rhdhlzqnf5zedyjqapmmfnme

Do drivers of forestry vehicles also drive herb layer changes (1970-2015) in a temperate forest with contrasting habitat and management conditions?

Déborah Closset-Kopp, Tarek Hattab, Guillaume Decocq, David Edwards
2019 Journal of Ecology  
The resurvey of plant communities sampled some decades ago is increasingly used for this purpose. 2.We used a life history trait-based approach to test a number of hypothesized drivers behind decadal changes  ...  tested using paired comparisons (old vs new records) of community weighted means and conditional inference classification trees for a number of traits across soil and management types.  ...  Acknowledgements We thank Paul Tombal who provided data of the initial survey and kindly gave further information on the methodology he used; and Jérôme Buridant who provided historical information on  ... 
doi:10.1111/1365-2745.13118 fatcat:3u5xm7oxn5g6zky6lv2x6nh4wa

Phylogenetic clustering increases with succession for lianas in a Chinese tropical montane rain forest

Mareike Roeder, Michael McLeish, Philip Beckschäfer, Marleen de Blécourt, Ekananda Paudel, Rhett D. Harrison, Ferry Slik
2014 Ecography  
Th e research was fi nanced by the Chinese Academy of Science and the National Natural Science Foundation China (Research Fund for International Young Scientists, grant number 31150110468).  ...  Fougere and Y. Surget-Groba for advice on the molecular lab work and to Lu Yun for fi eld assistance.  ...  As lianas have diff erent life histories compared to trees, the phylogenetic structure of the liana community may reveal diff erent patterns from those of trees, and thus provide a more complete picture  ... 
doi:10.1111/ecog.01051 fatcat:oeher6xianfe7cwmbjsrvmh5m4

The Phylogenetic Diversity of Metagenomes

Steven W. Kembel, Jonathan A. Eisen, Katherine S. Pollard, Jessica L. Green, David Liberles
2011 PLoS ONE  
Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context.  ...  The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets.  ...  Acknowledgments Thanks to Srijak Bhatnagar, Jessica Bryant, Alexandros Stamatakis, Dongying Wu, and Martin Wu for assistance and advice on bioinformatics and phylogenetic analyses.  ... 
doi:10.1371/journal.pone.0023214 pmid:21912589 pmcid:PMC3166145 fatcat:pxfslginbnfqphoa3ii7hx5dpa

Mutualistic interactions reshuffle the effects of climate change on plants across the tree of life

Jordi Bascompte, María B. García, Raúl Ortega, Enrico L. Rezende, Samuel Pironon
2019 Science Advances  
Using seven pollination networks across Europe that include the phylogeny and life history traits of plants, we show a substantial variability across networks in climatically predicted plant extinction—and  ...  These coextinctions not only increase the total number of plant species being driven to extinction but also add a bias in the way the major taxonomic and functional groups are pruned.  ...  and phylogenetic diversity.  ... 
doi:10.1126/sciadv.aav2539 pmid:31106269 pmcid:PMC6520021 fatcat:3yxf5xk3j5fwviho23y4zqe464

Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers

Angelina Ceballos-Escalera, John Richards, Maria Belen Arias, Daegan J. G. Inward, Alfried P. Vogler
2022 MycoKeys  
However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that  ...  Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short  ...  We thank Nicolas Magain and Brendan Furneaux for their most helpful comments on an earlier version of the manuscript.  ... 
doi:10.3897/mycokeys.88.77106 pmid:35585929 pmcid:PMC8924126 fatcat:jtdodr7nxvebtkldzibdgiqm2i

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation

Hyeonsoo Jeong, Bushra Arif, Gustavo Caetano-Anollés, Kyung Mo Kim, Arshan Nasir
2019 Scientific Reports  
Finally, we identified several core and widespread genes least influenced by HGT that could become useful markers for building robust 'trees of life' and address several outstanding technical challenges  ...  Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory  ...  AN would like to thank members of the Computational Biology and Bioinformatics Group at COMSATS and Evolutionary Bioinformatics Laboratory at Illinois for their support and insightful discussions.  ... 
doi:10.1038/s41598-019-42227-5 pmid:30976019 pmcid:PMC6459891 fatcat:c3psvswkzrgshkfingyjyb2euq

Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae)

Laure Barrabé, Sébastien Lavergne, Giliane Karnadi-Abdelkader, Bryan T Drew, Philippe Birnbaum, Gildas Gâteblé, Vincent Savolainen
2018 Systematic Biology  
This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms.  ...  The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of  ...  We thank Daniel and Irène Létocart, Neil Sleddon, Druce Horton, and Kartuz Greenhouses for providing us with pictures of Oxera and habitats.  ... 
doi:10.1093/sysbio/syy070 pmid:30365031 fatcat:c53empml55b7tan2pne66wofn4

Abstracts of the 22nd Annual Meeting of the Willi Hennig Society

Dennis Wm. Stevenson
2004 Cladistics  
The strength and future of the Willi Hennig Society resides in the students and recent meetings indicate a healthy society for the future. The Student Awards Committee consisted of Jonathan A.  ...  Lindgren, the Rosen Prize ($250) for "A New Phylogeny of the Cephalopoda Using Total Evidence".  ...  The potential for using combined molecular and organismal data has opened up new avenues for taxonomy, phylogenetics and biogeography.  ... 
doi:10.1111/j.1096-0031.2003.00006.x pmid:34892975 pmcid:PMC7159319 fatcat:wlq3m4zznjcvdofwi4dyfariyu

A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

Daliang Ning, Mengting Yuan, Linwei Wu, Ya Zhang, Xue Guo, Xishu Zhou, Yunfeng Yang, Adam P Arkin, Mary K Firestone, Jizhong Zhou
2020 Nature Communications  
, and should also be useful for plant and animal ecology.  ...  Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and 'drift' (59%).  ...  The R package and an example with detailed notes are also available in the Supplementary Code file. All custom scripts are available from GitHub (https://github.com/DaliangNing/iCAMP1).  ... 
doi:10.1038/s41467-020-18560-z pmid:32948774 pmcid:PMC7501310 fatcat:4vzacgvxergb5l4ziafnoi2nvu

Global diversity and geography of soil fungi

L. Tedersoo, M. Bahram, S. Polme, U. Koljalg, N. S. Yorou, R. Wijesundera, L. V. Ruiz, A. M. Vasco-Palacios, P. Q. Thu, A. Suija, M. E. Smith, C. Sharp (+46 others)
2014 Science  
Multiple regression models were used to disentangle the roles of climatic, spatial, edaphic, and floristic parameters on fungal diversity and community composition.  ...  rule) and diversity increases toward the equator.  ...  The use of homogenous sampling and analytical methods, as done in this study, are necessary to confidently compare macroecological patterns among distinct life forms and to reliably test degrees of consistency  ... 
doi:10.1126/science.1256688 pmid:25430773 fatcat:2uicmpgqrzh2ncq22ge4g6c3hy

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Alexandre Antonelli, Hannes Hettling, Fabien L. Condamine, Karin Vos, R. Henrik Nilsson, Michael J. Sanderson, Hervé Sauquet, Ruud Scharn, Daniele Silvestro, Mats Töpel, Christine D. Bacon, Bengt Oxelman (+1 others)
2016 Systematic Biology  
SUPERSMART will also accelerate the inference of a "Dated Tree of Life" where all node ages are directly comparable.  ...  This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data  ...  The code was developed, tested, and benchmarked on the bioinformatics computer cluster Albiorix at the Department of Biological and Environmental Sciences, University of Gothenburg; at the Swedish National  ... 
doi:10.1093/sysbio/syw066 pmid:27616324 pmcid:PMC5410925 fatcat:i6wplqodwnf7tnrcbnhtsen7om

Effect of Simulated Climate Warming on the Ectomycorrhizal Fungal Community of Boreal and Temperate Host Species Growing Near Their Shared Ecotonal Range Limits

Joanna Mucha, Kabir G. Peay, Dylan P. Smith, Peter B. Reich, Artur Stefański, Sarah E. Hobbie
2017 Microbial Ecology  
While anthropogenic activity has, and will continue to, cause global temperature increases, few studies have investigated how increases in temperature will affect the community composition of ectomycorrhizal  ...  Manipulations that increased air and soil temperature by 1.7 and 3.4°C above ambient temperatures, respectively, did not change ECM richness but did alter the composition of the ECM community in a manner  ...  Open Access This article is distributed under the terms of the Creative Comm ons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ... 
doi:10.1007/s00248-017-1044-5 pmid:28741266 pmcid:PMC5742605 fatcat:kv6bzn7iine5pk7amxmvj2q2j4
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