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Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events [article]

Marc Hellmuth, Maribel Hernandez-Rosales, Yangjing Long, Peter F. Stadler
2017 arXiv   pre-print
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial  ...  We showthat the graph-representation of this relation must be a tree. Moreover, we characterize completely the relationshipbetween the tree of such relations and the underlying phylogenetic tree.  ...  YJL acknowledges support of National Natural Science Foundation of China (No. 11671258) and Postdoctoral Science Foundation of China (No. 2016M601576)  ... 
arXiv:1612.09093v2 fatcat:gf622rvj6bhwhfeabxaatyhqfy

Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes

Yves Van de Peer, Tancred Frickey, John S. Taylor, Axel Meyer
2002 Gene  
Evolutionary distances between sequences can be computed from the fraction of unsaturated sites only and evolutionary trees inferred by pairwise distance methods.  ...  The program graphically displays the number of observed frequent and rare amino acid replacements between pairs of sequences against their overall evolutionary distance.  ...  reading of an earlier version of the paper.  ... 
doi:10.1016/s0378-1119(02)00689-3 pmid:12354655 fatcat:nrw65wvxcrgptg57ccwr2wbhm4

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Tiratha Raj Singh
2008 Bioinformation  
Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms.  ...  Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships.  ...  Gene rearrangements are considered to be rare evolutionary events, and as such the existence of a shared derived gene order between taxa is often indicative of common ancestry [2] .  ... 
doi:10.6026/97320630003095 pmid:19238195 pmcid:PMC2639673 fatcat:xend3ccxszcrrkdjmskemjsjua

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

Paul D Thomas
2010 BMC Bioinformatics  
tree of life, and knowledge of the complete complement of genes in a species' genome.  ...  An important innovation in GIGA is that, at every step in the agglomeration process, the tree is interpreted/reinterpreted in terms of the evolutionary events that created it.  ...  Acknowledgements The author is indebted to Stan Dong for implementing the comparisons between the different tree methods. This work was supported in part by NIGMS grant R01GM081084.  ... 
doi:10.1186/1471-2105-11-312 pmid:20534164 pmcid:PMC2905364 fatcat:ctzjj4py3rdttii3lrpgrtzbve

Inferring explicit weighted consensus networks to represent alternative evolutionary histories

Mehdi Layeghifard, Pedro R Peres-Neto, Vladimir Makarenkov
2013 BMC Evolutionary Biology  
can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny.  ...  The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods.  ...  Acknowledgments This study was supported by the FQRNT (Fonds de Recherche sur la Nature et les Technologies du Québec) team research grant to V. Makarenkov  ... 
doi:10.1186/1471-2148-13-274 pmid:24359207 pmcid:PMC3898054 fatcat:pcakrdp3xngizlngbn3xlktvwe

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin
2017 BMC Bioinformatics  
Results: On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence  ...  We inferred their phylogenetic trees in 69 sequenced chordate genomes.  ...  Authors' contributions LK, WY and ZY conceived of this project and improved the manuscript. SJ designed the experiment, performed the analysis and wrote the manuscript.  ... 
doi:10.1186/s12859-017-1850-2 pmid:28974198 pmcid:PMC5627428 fatcat:qqbihnlxdndpdpylc3hyh437ly

Automation of gene function prediction through modeling human curators' decisions in GO phylogenetic annotation project [article]

Haiming Tang, Paul D Thomas, Huaiyu Mi
2018 arXiv   pre-print
Here we present an automated pipeline for phylogenetic annotation and inference, which simulates the standard annotation procedures of curators and models the curators' decisions during the manual curation  ...  PAINT uses a phylogenetic model to infer gene function by homology, a process that requires manual curation of experienced biocurators.  ...  evolutionary inferences of internal nodes of the gene tree.  ... 
arXiv:1802.07204v1 fatcat:q62otjeidbc5zoxlghkqlmlvi4

Evolutionary Puzzles: An Introduction to Genome Rearrangement [chapter]

Mathieu Blanchette
2001 Lecture Notes in Computer Science  
We then consider the problem of inferring phylogenetic (evolutionary) trees from genetic data. We briefly present the two major approaches to solve this problem.  ...  The second approach to inferring phylogenetic trees consists of finding a minimal Steiner tree in the space of the data considered, whose leaves are the species of interest.  ...  Inferring Phylogenetic Trees Inferring the phylogenetic (evolutionary) relationships among a set of species is a problem of both pure scientific and practical interest.  ... 
doi:10.1007/3-540-45718-6_106 fatcat:4gmsmubsmfbitfryfdmrhmw42y

Lateral gene transfer in eukaryotes

J. O. Andersson
2005 Cellular and Molecular Life Sciences (CMLS)  
Recently accumulating data indicate that the process also occurs in the evolution of eukaryotic genomes.  ...  These findings have implications for eukaryotic genomic research in general, and studies of the origin and phylogeny of eukaryotes in particular.  ...  The author is supported by a Swedish Research Council (VR) Grant.  ... 
doi:10.1007/s00018-005-4539-z pmid:15761667 fatcat:xlx4frj22jevtl5lkm4ru3zuna

Evolution of genes and taxa: a primer [chapter]

Jeff J. Doyle, Brandon S. Gaut
2000 Plant Molecular Evolution  
Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled.  ...  Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction  ...  Inferring the relationships of organisms from molecular data: incongruence among phylogenies Gene trees vs. species trees For many molecular phylogenetic studies the goal is to infer species relationships  ... 
doi:10.1007/978-94-011-4221-2_1 fatcat:3rexmb5kfre6dolggwrkscz75u

Savanna tree evolutionary ages inform the reconstruction of the paleoenvironment of our hominin ancestors

T. Jonathan Davies, Barnabas H. Daru, Bezeng S. Bezeng, Tristan Charles-Dominique, Gareth P. Hempson, Ronny M. Kabongo, Olivier Maurin, A. Muthama Muasya, Michelle van der Bank, William J. Bond
2020 Scientific Reports  
The sparsity of the fossil record, however, imposes a limit to the strength of inference that can be drawn from such data.  ...  Here, using the evolutionary ages of African savanna trees, we suggest an initial tropical or subtropical expansion of savanna between 10 and 15 Ma, which then extended to higher latitudes, reaching southern  ...  Acknowledgements We thank the Government of Canada through Genome Canada and the Ontario Genomics Institute (2008-OGI-ICI-03), and the University of Johannesburg (Analytical Facility) for financial support  ... 
doi:10.1038/s41598-020-69378-0 pmid:32709951 pmcid:PMC7381606 fatcat:6ve46mkuznfzlmuinyiqekgjnu

Bayesian inference of character evolution

2004 Trends in Ecology & Evolution  
Much recent progress in evolutionary biology is based on the inference of ancestral states and past transformations in important traits on phylogenetic trees.  ...  Given a phylogenetic tree, we can also reconstruct the evolutionary history of individual traits of interest.  ...  Much recent progress in evolutionary biology is based on the inference of ancestral states and past transformations in important traits on phylogenetic trees.  ... 
doi:10.1016/j.tree.2004.07.002 pmid:16701310 fatcat:72ioqkl3dzaivmxuulu3l35ybe

Phylogeny of Viruses ☆ [chapter]

Alexander E. Gorbalenya, C. Lauber
2017 Reference Module in Biomedical Sciences  
Alternatively, the root position may be assigned to a tree from knowledge about the analyzed species that was gained independently from phylogenetic analysis.  ...  It can utilize prior knowledge about the evolutionary process, like known substitution rates or clustering of species subsets or dates of species isolation, in combination with repeated sampling from subsequently  ... 
doi:10.1016/b978-0-12-801238-3.95723-4 fatcat:6pme4tifina7demuqali45avj4

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

P. Gaudet, M. S. Livstone, S. E. Lewis, P. D. Thomas
2011 Briefings in Bioinformatics  
To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental  ...  Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are  ...  METHODS AND RESULTS Phylogenetic trees The first element necessary for PAINT curation is the generation of phylogenetic trees to be annotated with functional evolution events.  ... 
doi:10.1093/bib/bbr042 pmid:21873635 pmcid:PMC3178059 fatcat:xiylkiwb6bdktchiy7sasi5nuy

Early and multiple origins of metastatic lineages within primary tumors

Zi-Ming Zhao, Bixiao Zhao, Yalai Bai, Atila Iamarino, Stephen G. Gaffney, Joseph Schlessinger, Richard P. Lifton, David L. Rimm, Jeffrey P. Townsend
2016 Proceedings of the National Academy of Sciences of the United States of America  
Approaches developed for evolutionary biology can reveal the relationship among clonal lineages, the ancestral states of gene sequences, and the timing of evolutionary events.  ...  Last, the temporal order of occurrence of driver mutations can be inferred from phylogenetic analysis of cancer chronograms, guiding development of targeted therapeutics effective against primary tumors  ...  We also thank the Yale High Performance Computing Center for providing computational resources and Robert Bjornson for assistance regarding disposition of clusters and servers to the project.  ... 
doi:10.1073/pnas.1525677113 pmid:26858460 pmcid:PMC4776530 fatcat:guqcot7bqbggfkoul5tf476xaa
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