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Phylogenetic tree

About: Phylogenetic tree is a research topic. Over the lifetime, 26643 publications have been published within this topic receiving 1340967 citations. The topic is also known as: evolutionary tree & evolutionary diagram.


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Journal ArticleDOI
24 Oct 1997-Science
TL;DR: Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs), which comprise a framework for functional and evolutionary genome analysis.
Abstract: In order to extract the maximum amount of information from the rapidly accumulating genome sequences, all conserved genes need to be classified according to their homologous relationships. Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs). Each COG consists of individual orthologous proteins or orthologous sets of paralogs from at least three lineages. Orthologs typically have the same function, allowing transfer of functional information from one member to an entire COG. This relation automatically yields a number of functional predictions for poorly characterized genomes. The COGs comprise a framework for functional and evolutionary genome analysis.

3,513 citations

Dissertation
01 Jan 2006
TL;DR: A fast and accurate algorithm that allows ML phylogenetic searches to be performed on datasets consisting of thousands of sequences and the P-GARLI algorithm extends the approach of GARLI to allow simultaneous use of many computer processors.
Abstract: Phylogenetic trees have a multitude of applications in biology, epidemiology, conservation and even forensics. However, the inference of phylogenetic trees can be extremely computationally intensive. The computational burden of such analyses becomes even greater when model-based methods are used. Model-based methods have been repeatedly shown to be the most accurate choice for the reconstruction of phylogenetic trees, and thus are an attractive choice despite their high computational demands. Using the Maximum Likelihood (ML) criterion to choose among phylogenetic trees is one commonly used model-based technique. Until recently, software for performing ML analyses of biological sequence data was largely intractable for more vi than about one hundred sequences. Because advances in sequencing technology now make the assembly of datasets consisting of thousands of sequences common, ML search algorithms that are able to quickly and accurately analyze such data must be developed if ML techniques are to remain a viable option in the future. I have developed a fast and accurate algorithm that allows ML phylogenetic searches to be performed on datasets consisting of thousands of sequences. My software uses a genetic algorithm approach, and is named GARLI (Genetic Algorithm for Rapid Likelihood Inference). The speed of this new algorithm results primarily from its novel technique for partial optimization of branch-length parameters following topological rearrangements. Experiments performed with GARLI show that it is able to analyze large datasets in a small fraction of the time required by the previous generation of search algorithms. The program also performs well relative to two other recently introduced fast ML search programs. Large parallel computer clusters have become common at academic institutions in recent years, presenting a new resource to be used for phylogenetic analyses. The P-GARLI algorithm extends the approach of GARLI to allow simultaneous use of many computer processors. The processors may be instructed to work together on a phylogenetic search in either a highly coordinated or largely independent fashion.

3,391 citations

Journal ArticleDOI
TL;DR: Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965), and a number of other parsimony methods have since appeared in the systematic literature and found widespread use in studies of molecular evolution.
Abstract: Felsenstein, J. (Department of Genetics, University of Washington, Seattle, WA 98195) 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.-For some simple threeand four-species cases involving a character with two states, it is determined under what conditions several methods of phylogenetic inference will fail to converge to the true phylogeny as mo,re and more data are accumulated. The methods are the Camin-Sokal parsimony method, the compatibility method, and Farris's unrooted Wagner tree parsimony method. In all cases the conditions for this failure (which is the failure to be statistically consistent) are essentially that parallel changes exceed informative, nonparallel changes. It is possible for these methods to be inconsistent even when change is improbable a priori, provided that evolutionary rates in different lineages are sufficiently unequal. It is by extension of this approach that we may provide a sound methodology for evaluating methods of phylogenetic inference. [Numerical cladistics; phylogenetic inference; maximum likelihood estimation; parsimony; compatibility.] Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965). This class of methods for inferring an evolutionary tree from discrete-character data involves making a reconstruction of the changes in a given set of characters on a given tree, counting the smallest number of times that a given kind of event need have happened, and using this as the measure of the adequacy of the evolutionary tree. (Alternatively, one can compute the weighted sum of the numbers of times several different kinds of events have occurred.) One attempts to find that evolutionary tree which requires the fewest of these evolutionary events to explain the observed data. Camin and Sokal treated the case of irreversible changes along a character state tree, minimizing the number of changes I This report was prepared as an account of work sponsored by the United States Government. Neither the United States nor the United States Department of Energy, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use would not infringe privatelyowned rights. of character states required. A number of other parsimony methods have since appeared in the systematic literature (Kluge and Farris, 1969; Farris, 1969, 1970, 1972, 1977; Farris, Kluge, and Eckhardt, 1970) and parsimony methods have also found widespread use in studies of molecular evolution (Fitch and Margoliash, 1967, 1970; Dayhoff and Eck, 1968; see also Fitch, 1973). Cavalli-Sforza and Edwards (1967; Edwards and Cavalli-Sforza, 1964) earlier formulated a minimum evolution method for continuous-character data. An alternative methodology for phylogenetic inference is the compatibility method, introduced by Le Quesne (1969, 1972). He suggested that phylogenetic inference be based on finding the largest possible set of characters -which could simultaneously have all states be uniquely derived -on the same ftree. The estimate of the phylogeny is then takento be that tree.-While Le Quesne's specific suggestions as to how this might be done have been criticized by Farris (1969), his general approach, which is based on Camin and Sokal's (1965) concept of the compatibility of two characters, has been made rigorous and extended in a series of papers by G. F. Estabrook, C. S. Johnson, Jr., and F. R. McMorris (Estabrook,

3,220 citations

Journal ArticleDOI
TL;DR: It is concluded that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.
Abstract: GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbourjoining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.

3,212 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20233,929
20228,688
20211,425
20201,405
20191,330
20181,299