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Distorted metrics on trees and phylogenetic forests [article]

Elchanan Mossel
2004 arXiv   pre-print
We study distorted metrics on binary trees in the context of phylogenetic reconstruction.  ...  Our metric results are used in order to show how to reconstruct phylogenetic forests with small number of trees from sequences of length logarithmic in the size of the tree.  ...  Similar tightness results hold for the number of trees in the forest in the phylogenetic reconstruction.  ... 
arXiv:math/0403508v1 fatcat:3jhhgnt6izgnfmupwpawtlax3a

Distorted Metrics on Trees and Phylogenetic Forests

Elchanan Mossel
2007 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We study distorted metrics on binary trees in the context of phylogenetic reconstruction.  ...  Both the metric result and its applications to phylogeny are almost tight. Abstract We study distorted metrics on binary trees in the context of phylogenetic reconstruction.  ...  Similar tightness results hold for the number of trees in the forest in the phylogenetic reconstruction.  ... 
doi:10.1109/tcbb.2007.1010 pmid:17277418 fatcat:ryifd3h52rduziet2z6zoa47dq

Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep

Constantinos Daskalakis, Elchanan Mossel, Sebastien Roch
2011 SIAM Journal on Discrete Mathematics  
How much of the true tree is recovered depends on the sequence length provided. The algorithm is distance-based and runs in polynomial time.  ...  We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree.  ...  , distorted metrics.  ... 
doi:10.1137/09075576x fatcat:d4jcqh2mpvcbtof4svtblniy6a

The productivity-biodiversity relationship varies across diversity dimensions

Philipp Brun, Niklaus E. Zimmermann, Catherine H. Graham, Sébastien Lavergne, Loïc Pellissier, Tamara Münkemüller, Wilfried Thuiller
2019 Nature Communications  
In forests, trait and phylogenetic diversity typically increase with productivity, while in grasslands, relationships shift from unimodal to declining with greater land-use intensity.  ...  High productivity may increase trait/phylogenetic diversity in ecosystems with few external constraints (forests) by promoting complementary strategies, but under external constraints (managed grasslands  ...  Moreover, the authors thank Isabelle Boulangeat for providing the stickTips function to calculate random binary trees; Dirk Karger, Julien Renaud, and Maya Gueguen for preparing the climate data; and Achilleas  ... 
doi:10.1038/s41467-019-13678-1 pmid:31831803 pmcid:PMC6908676 fatcat:np2z32ljvvaqtdfr4ipc2nkbxi

Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep [article]

Constantinos Daskalakis, Elchanan Mossel, Sebastien Roch
2009 arXiv   pre-print
How much of the true tree is recovered depends on the sequence length provided. The algorithm is distance-based and runs in polynomial time.  ...  We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree.  ...  In phylogenetic reconstruction, a distorted metric is naturally derived from samples of a Markov model on a tree-a common model of DNA sequence evolution used in Biology.  ... 
arXiv:0801.4190v2 fatcat:zleqtftckzaq3ajq6rksgcny7q

Effects of land‐use change on avian taxonomic, functional and phylogenetic diversity in a tropical montane rainforest

Marie Laure Rurangwa, Jesús Aguirre‐Gutiérrez, Thomas J. Matthews, Protais Niyigaba, Joseph P. Wayman, Joseph A. Tobias, Robert J. Whittaker, Ana Benítez López
2021 Diversity and Distributions: A journal of biological invasions and biodiversity  
This study aimed to quantify the effects of habitat transformation on taxonomic, functional and phylogenetic diversity in Afrotropical bird communities.  ...  Our results suggest that monitoring and conservation in these landscapes can be refined using taxonomic, functional and phylogenetic diversity metrics to provide complementary information about the current  ...  et al., 2008) Faith's (1992) phylogenetic diversity metric (PD), which is the sum of branch lengths of a phylogenetic tree encompassing a given sample; and (c) the standardized effect size of mean  ... 
doi:10.1111/ddi.13364 fatcat:bnbrd6rgwzbb3fcimvz7tad5tq

Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia

Yasmine Antonini, Carolina de Barros Machado, Pedro Manoel Galetti, Marcio Oliveira, Rodolfo Dirzo, Geraldo Wilson Fernandes, Fabio S. Nascimento
2017 PLoS ONE  
Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales.  ...  We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them.  ...  Acknowledgments Renzo Lanza, Emmanuel Almada and Matheus Freitas for help in field work. Terravision in a person of Allan Brandt, for the files with the shapes of the plateaus.  ... 
doi:10.1371/journal.pone.0175884 pmid:28410432 pmcid:PMC5391963 fatcat:ggnnq5o37bhspnikifrox7uoui

Network Delay Inference from Additive Metrics [article]

Shankar Bhamidi, Ram Rajagopal, Sebastien Roch
2009 arXiv   pre-print
Our inference algorithm is based on additive metric techniques widely used in phylogenetics. It runs in polynomial time and requires a sample of size only ( n).  ...  on network paths.  ...  Acknowledgments We thank Gang Liang, Elchanan Mossel, and Bin Yu for discussions and encouragements.  ... 
arXiv:math/0604367v2 fatcat:26hxh3li6rhjhdfhjyxw5mgqr4

Long-term droughts may drive drier tropical forests towards increased functional, taxonomic and phylogenetic homogeneity

Jesús Aguirre-Gutiérrez, Yadvinder Malhi, Simon L. Lewis, Sophie Fauset, Stephen Adu-Bredu, Kofi Affum-Baffoe, Timothy R. Baker, Agne Gvozdevaite, Wannes Hubau, Sam Moore, Theresa Peprah, Kasia Ziemińska (+2 others)
2020 Nature Communications  
Notably, we find that all three facets of diversity tended to be higher in wetter forests. Drier forests showed functional, taxonomic and phylogenetic homogenization.  ...  Taxonomic and functional diversity increased in wetter forests but tended to decrease in forests with drier climate. Phylogenetic diversity showed a large decrease along a wet-dry climatic gradient.  ...  Acknowledgements This work is a product of the Global Ecosystems Monitoring (GEM) network (gem. tropicalforests.ox.ac.uk), the African Tropical Rainforest Observation Network (Afri-TRON; www.afritron.org) and  ... 
doi:10.1038/s41467-020-16973-4 pmid:32620761 fatcat:5ufy3i5v5fbbfctsnlviev7mci

Genomic data analysis in tree spaces [article]

Sakellarios Zairis, Hossein Khiabanian, Andrew J. Blumberg, Raul Rabadan
2016 arXiv   pre-print
In many problem settings one encounters heavily populated phylogenetic trees, where the large number of leaves encumbers visualization and analysis in the relevant evolutionary moduli spaces.  ...  Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces  ...  Acknowledgments The authors gratefully acknowledge the constructive feedback of Gillian Grindstaff, Melissa McGuirl, and Daniel Rosenbloom.  ... 
arXiv:1607.07503v1 fatcat:3pbgdgnk6nhgte5uuhx3tifbju

Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot

W. John Kress, David L. Erickson, Nathan G. Swenson, Jill Thompson, Maria Uriarte, Jess K. Zimmerman, Jerome Chave
2010 PLoS ONE  
data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and  ...  Methodology/Principal Findings: Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical  ...  Forest Service, and the University of Puerto Rico for assistance in this work. Author Contributions  ... 
doi:10.1371/journal.pone.0015409 pmid:21085700 pmcid:PMC2976767 fatcat:fwzcvm7vefb2pcm4l2wnm43dua

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life [chapter]

Pere Puigbò, Yuri I. Wolf, Eugene V. Koonin
2012 Msphere  
Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes  ...  The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support.  ...  Acknowledgments The authors' research is supported by the Department of Health and Human Services intramural program (NIH, National Library of Medicine).  ... 
doi:10.1007/978-1-61779-585-5_3 pmid:22399455 pmcid:PMC3842619 fatcat:xx55mye7nraxrfwgg3pgtzh7em

Evolutionary Trees and the Ising Model on the Bethe Lattice: a Proof of Steel's Conjecture [article]

Constantinos Daskalakis, Elchanan Mossel, Sebastien Roch
2009 arXiv   pre-print
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree.  ...  Our proof and results demonstrate that extremality of the free Gibbs measure on the infinite binary tree, which has been studied before in probability, statistical physics and computer science, determines  ...  Steel for his enthusiastic encouragement for studying the connections between the reconstruction problem and phylogenetics. We thank Allan Sly for helpful discussions.  ... 
arXiv:math/0509575v3 fatcat:fyxcqts7crbqrdopwlxyso3nbe

Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China

Wen-wen Li, Wen-xia Zhao, Wen-xia Huai
2017 International Journal of Systematic and Evolutionary Microbiology  
Based on sequences of the internal transcribed spacer and the combined b-tubulin and elongation factor 1a gene sequence data, isolates of the new species cluster together into a single branch and are close  ...  survey of forest Phytophthora from 2011 to 2013.  ...  We are appreciative of Ms Jia-qing Jiang and Dr Ruozhu Lin for help with field work and laboratory routines. Conflicts of interest The authors declare that there are no conflicts of interest.  ... 
doi:10.1099/ijsem.0.002254 pmid:28857022 fatcat:au6hxflqffg7dizcxnp3nwm2au

Phylogenetic Endemism Hotspots of North American Birds Are Associated With Warm Temperatures and Long- and Short-Term Climate Stability

Sebastian Acevedo, Brody Sandel
2021 Frontiers in Ecology and Evolution  
These components are combined in an assemblage-level measure called phylogenetic endemism (PE), which measures the degree to which the species in an assemblage are small-ranged and phylogenetically distinct  ...  Broad-scale patterns and correlates of PE are becoming better known for a variety of groups, and have been shown to depend on current climate, geographic isolation and long-term climate stability.  ...  ACKNOWLEDGMENTS We are grateful to the thousands of volunteers who collect the BBS data, and the coordinators who manage it and make it available.  ... 
doi:10.3389/fevo.2021.645396 fatcat:spueww3ornchxgwgmdrte2dwyi
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