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Inferring evolutionary trees with strong combinatorial evidence [chapter]

Vincent Berry, Olivier Gascuel
1997 Lecture Notes in Computer Science  
We propose a quartet reconstruction method which speciÿcally produces trees whose edges have strong combinatorial evidence.  ...  We consider the problem of inferring the evolutionary tree of a set of n species.  ...  We investigate here a phylogenetic reconstruction method which speciÿcally produces trees whose edges have a strong combinatorial support.  ... 
doi:10.1007/bfb0045078 fatcat:wdyexuu7lvh47cskdffltpd4zq

Inferring evolutionary trees with strong combinatorial evidence

Vincent Berry, Olivier Gascuel
2000 Theoretical Computer Science  
We propose a quartet reconstruction method which speciÿcally produces trees whose edges have strong combinatorial evidence.  ...  We consider the problem of inferring the evolutionary tree of a set of n species.  ...  We investigate here a phylogenetic reconstruction method which speciÿcally produces trees whose edges have a strong combinatorial support.  ... 
doi:10.1016/s0304-3975(99)00235-2 fatcat:3ct56ylc7rc4tbjfyictkv5g3u

Page 4383 of Mathematical Reviews Vol. , Issue 99f [page]

1999 Mathematical Reviews  
John Haigh (4-SUSX; Brighton) 99f:92011 92D15 68Q25 Berry, Vincent (F-MONT2-FI; Montpellier) ; Gascuel, Olivier (3-MTRLC-G; Montreal, PQ) Inferring evolutionary trees with strong combinatorial evidence  ...  We propose a quartet reconstruction method which specifically produces trees whose edges have strong combinatorial evidence. For this purpose we use the Q* relation {H.-J. Bandelt and A. W. M.  ... 

Page 3617 of Mathematical Reviews Vol. , Issue 2000e [page]

2000 Mathematical Reviews  
Press, Los Alamitos, CA, 1993; MR 95k:68059] have provided strong evidence that the VC-dimension decision problem is not in P.  ...  Provided the r points are chosen indepen- dently from the same (unknown, arbitrary) distribution, the target rectangle may be inferred with small error in polynomial time.  ... 

The evolution of tumour phylogenetics: principles and practice

Russell Schwartz, Alejandro A. Schäffer
2017 Nature reviews genetics  
bursts of rapid evolution under strong selection, although this model cannot explain the evidence for a lack of selection in some tumours 48 .  ...  FIGURE 2 provides a simplified overview of the pitfalls in this process, as we seek to infer a true tree (FIG. 2a) but struggle with erroneous inferences induced by a mis match between the evolutionary  ... 
doi:10.1038/nrg.2016.170 pmid:28190876 pmcid:PMC5886015 fatcat:h2rpqbaxdjfkxdbaj7nlirw6xy

PastView: a user-friendly interface to explore evolutionary scenarios [article]

Francois Chevenet, Guillaume Castel, Emmanuelle Jousselin, Olivier Gascuel
2019 bioRxiv   pre-print
The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios  ...  Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology  ...  "Gene Ontology », any data related to patients), are used and without evidence of a strong structuring of data between tree and annotations.  ... 
doi:10.1101/651661 fatcat:y7ijpgqxzra5hmkbtl4ewp7k3a

Page 6830 of Mathematical Reviews Vol. , Issue 2001I [page]

2001 Mathematical Reviews  
evolutionary trees with strong combinatorial evidence.  ...  The authors consider the problem of inferring the evolutionary tree (phylogeny) for a set S of n species using quartets.  ... 

Mathematical approaches to comparative linguistics

T. Warnow
1997 Proceedings of the National Academy of Sciences of the United States of America  
The inference of the evolutionary history of a set of languages is a complex problem.  ...  Evolutionary History Inference of Related Languages.  ...  the evolutionary tree for the languages.  ... 
doi:10.1073/pnas.94.13.6585 pmid:11607730 pmcid:PMC34482 fatcat:u5636dbypfa2hduxbccaoizdlm

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

Minglei Wang, Gustavo Caetano-Anollés
2009 Structure  
These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages,  ...  Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements.  ...  Phylogenetic congruence over such broad timescales provides strong evidence for a historical association between the architecture of functional proteins and the structure of embedded domains.  ... 
doi:10.1016/j.str.2008.11.008 pmid:19141283 fatcat:yz3f3mopmvb7zistfbz4j5wbl4

Analysis of Gene Order Evolution Beyond Single-Copy Genes [chapter]

Nadia El-Mabrouk, David Sankoff
2012 Msphere  
What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes?  ...  We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely  ...  In the presence of a strong phylogenetic signal, inferred trees are usually binary, as a speciation event usually results in the creation of two new species.  ... 
doi:10.1007/978-1-61779-582-4_15 pmid:22407718 fatcat:kerbedfsgrgi5npicdlbd6u4aa

Matrilocal residence is ancestral in Austronesian societies

F. M. Jordan, R. D. Gray, S. J. Greenhill, R. Mace
2009 Proceedings of the Royal Society of London. Biological Sciences  
We thank Robert Blust, John Lynch, Jeff Marck, Cordelia Nickelsen, Malcolm Ross, Laurent Sagart and all contributors to the ABVD for their assistance with lexical data and cognate judgements, and BeSTGRID.org  ...  PMP-p K64.99 8.38 strong evidence for matrilocality POC-m K62.79 POC-p K61.50 K2.58 positive evidence for patrilocality equal rates K63.12 default K59.61 K7.03 strong evidence for unequal  ...  Our results (table 1) show that there is strong evidence in favour of PMP matrilocality, positive evidence for PAn matrilocality and positive evidence for POc patrilocality.  ... 
doi:10.1098/rspb.2009.0088 pmid:19324748 pmcid:PMC2677244 fatcat:7yv2mrpvrzevvmtgxlkiiv4u34

Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core

Sumedha Sadekar, Jason Raymond, Robert E. Blankenship
2006 Molecular biology and evolution  
A relationship of sequence with structure was derived from the reaction center structures; with characteristic decay length of 1.6 Å .  ...  All available evidences suggest that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development.  ...  In addition, we derive sequence alignments and thereby phylogenetic trees based on structure, compare these results with more traditional sequence-based trees, and use the results to make inferences about  ... 
doi:10.1093/molbev/msl079 pmid:16887904 fatcat:k7djmfqnhfg6xgiq4vlntbqugu

Page 7266 of Mathematical Reviews Vol. , Issue 98K [page]

1998 Mathematical Reviews  
Vincent Berry and Olivier Gascuel, Inferring evolutionary trees with strong combinatorial evidence (111-123); Kenneth Rice and Tandy Warnow, Parsimony is hard to beat!  ...  Goli¢ and Luke O’Connor, A combinatorial pattern matching problem with applications to cryptography (473-478); C. Barry Jay, A fresh look at parametric polymorphism: covariant types (525-533).  ... 

Recapitulating phylogenies using k-mers: from trees to networks

Guillaume Bernard, Mark A. Ragan, Cheong Xin Chan
2016 F1000Research  
A typical phylogenetic inference aims to capture and represent, in the form of a tree, the evolutionary history of a family of molecular sequences.  ...  Our findings suggest that the network captures not only key aspects k of microbial genome evolution as inferred from a tree, but also features that are not treelike.  ...  used for tree inference 22 .  ... 
doi:10.12688/f1000research.10225.1 pmid:28105314 pmcid:PMC5224691 fatcat:ptmte5yoebeu5cbfqh7rifrfh4

Index

2000 Theoretical Computer Science  
Gascuel, Inferring evolutionary trees with strong combinatorial evidence (2) 271}298 Bonsangue, M.M., F. Arbab, J.W. de Bakker, J.J.M.M. Rutten, A. Scutella`and G. ( 1 ) 1 49} 90 Hedman, E.J., J.N.  ...  Nishizeki, Algorithms for generalized vertex-rankings of partial k-trees (2) 407}427 MeH tayer, D.  ... 
doi:10.1016/s0304-3975(00)00178-x fatcat:fl3kcc6xtrbjtlzhouuacu7ciu
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