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Encyclopedia > Phylogenetic tree
Fig. 1: A speculatively rooted tree for rRNA genes
Fig. 1: A speculatively rooted tree for rRNA genes

A phylogenetic tree, also called an evolutionary tree, is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, with edge lengths sometimes corresponding to time estimates. Each node in a phylogenetic tree is called a taxonomic unit. Internal nodes are generally referred to as Hypothetical Taxonomic Units (HTUs) as they cannot be directly observed. Image File history File links Phylogenetic_tree. ... Image File history File links Phylogenetic_tree. ... A labeled tree with 6 vertices and 5 edges In graph theory, a tree is a graph in which any two vertices are connected by exactly one path. ... This article is about evolution in biology. ... The hierarchy of scientific classification. ... A group of organisms is said to have common descent if they have a common ancestor. ... The most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in the group are directly descended. ... A pocket watch, a device used to tell time Look up time in Wiktionary, the free dictionary. ...


Alhough the idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to higher forms of life (such as in the Great Chain of Being), Charles Darwin (1859) first illustrated and popularized the notion of an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary biologists still use tree diagrams to depict evolution because the floral analogy effectively conveys the concept that speciation occurs through the adaptive and random splitting of lineages. The Tree-of-Life is a fictional plant (the ancestor of yams, with similar appearance and taste) in Larry Nivens Known Space universe, for which all Hominids have an in-built genetic craving. ... For other uses, see Life (disambiguation). ... 1579 drawing of the great chain of being from Didacus Valades, Rhetorica Christiana The great chain of being or scala naturæ is a classical and western medieval conception of the order of the universe, whose chief characteristic is a strict hierarchical system. ... For other people of the same surname, and places and things named after Charles Darwin, see Darwin. ... Darwins illustrations of beak variation in the finches of the Galápagos Islands, which hold 13 closely related species that differ most markedly in the shape of their beaks. ... Charles Darwins Origin of Species (publ. ... This article or section does not cite any references or sources. ... A tree structure is a way of representing the hierarchical nature of a structure in a graphical form. ... This article is about evolution in biology. ... Simplified schematic of an islands flora - all its plant species, highlighted in boxes. ... Analogy is both the cognitive process of transferring information from a particular subject (the analogue or source) to another particular subject (the target), and a linguistic expression corresponding to such a process. ... Charles Darwins first sketch of an evolutionary tree from his First Notebook on Transmutation of Species (1837) Speciation is the evolutionary process by which new biological species arise. ... A biological adaptation is an anatomical structure, physiological process or behavioral trait of an organism that has evolved over a period of time by the process of natural selection such that it increases the expected long-term reproductive success of the organism. ... Random redirects here. ...

Contents

Types of phylogenetic trees

Fig. 1: Unrooted tree of the myosin supergene family[1]
Fig. 2: A highly resolved, automatically generated Tree Of Life, based on completely sequenced genomes .
Fig. 2: A highly resolved, automatically generated Tree Of Life, based on completely sequenced genomes [2][3].
A phylogenetic tree, showing how Eukaryota and Archaea are more closely related to each other than to Bacteria, based on Cavalier-Smith's theory of bacterial evolution.
A phylogenetic tree, showing how Eukaryota and Archaea are more closely related to each other than to Bacteria, based on Cavalier-Smith's theory of bacterial evolution.

A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup - close enough to allow inference from sequence or trait data, but far enough to be a clear outgroup. Download high resolution version (2374x1673, 345 KB)Myosin Unrooted Phylogenetic Tree, July 2000 Permission to use this image on Wikipedia (with rights to redistribute) was granted in email from the designated agent. ... Download high resolution version (2374x1673, 345 KB)Myosin Unrooted Phylogenetic Tree, July 2000 Permission to use this image on Wikipedia (with rights to redistribute) was granted in email from the designated agent. ... Image File history File links Download high-resolution version (1355x1356, 284 KB) A highly resolved Tree Of Life, based on completely sequenced genomes [1]. The image was generated using iTOL: Interactive Tree Of Life[2], an online phylogenetic tree viewer and Tree Of Life resource. ... Image File history File links Download high-resolution version (1355x1356, 284 KB) A highly resolved Tree Of Life, based on completely sequenced genomes [1]. The image was generated using iTOL: Interactive Tree Of Life[2], an online phylogenetic tree viewer and Tree Of Life resource. ... Darwins work was originally entitled Phylogeny via Oogeny. ... Image File history File links This is a lossless scalable vector image. ... Image File history File links This is a lossless scalable vector image. ... Phyla Actinobacteria Aquificae Chlamydiae Bacteroidetes/Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia Bacteria (singular: bacterium) are unicellular microorganisms. ... Professor Thomas (Tom) Cavalier-Smith (born October 21, 1942), FRS, FRSC, NERC Professorial Fellow, is a Professor of Evolutionary Biology in the Department of Zoology, at the University of Oxford. ... This article just presents the basic definitions. ... There is also an imputation disambiguation page. ... 9, 14, 19, 67 and 76 are leaf nodes. ...


Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about common ancestry. While unrooted trees can always be generated from rooted ones by simply omitting the root, a root cannot be inferred from an unrooted tree without some means of identifying ancestry; this is normally done by including an outgroup in the input data or introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis. Figure 1 depicts an unrooted phylogenetic tree for myosin, a superfamily of proteins.[4] The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ... Myosin is a motor protein filament found in muscle tissue. ... A gene family is a set of genes defined by presumed homology, i. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ...


Both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. A bifurcating tree has a maximum of two descendants arising from each interior node, while a multifurcating tree may have more than two. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, only defines a topology. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For labeled bifurcating trees, there are It has been suggested that Parent node, Internal node, Root node and Subtree be merged into this article or section. ...

 frac{(2n-3)!}{2^{n-2}(n-2)!}

total rooted trees and

 frac{(2n-5)!}{2^{n-3}(n-3)!}

total unrooted trees, where n represents the number of leaf nodes. The number of unrooted trees for n input sequences or species is equal to the number of rooted trees for n-1 sequences.[5]


A dendrogram is a broad term for the diagrammatic representation of a phylogenetic tree.


A cladogram is a tree formed using cladistic methods. This type of tree only represents a branching pattern, i.e., its branch lengths do not represent time. It has been suggested that Clade be merged into this article or section. ...


A phylogram is a phylogenetic tree that explicitly represents number of character changes through its branch lengths.


An ultrametric tree or chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch lengths.


Phylogenetic tree construction

Phylogenetic trees among a nontrivial number of input sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic distance from multiple sequence alignments, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as ClustalW produce both sequence alignments and phylogenetic trees. Methods including maximum parsimony, maximum likelihood and Bayesian inference apply an explicit model of evolution to phylogenetics.[5] Identifying the optimal tree using many of these techniques is NP-hard[5], so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data. Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... In bioinformatics, neighbor-joining is a bottom-up clustering method used for the creation of phylogenetic trees. ... UPGMA (Unweighted Pair Group Method with Arithmetic mean) is a simple bottom-up data clustering method used in bioinformatics for the creation of phylogenetic trees. ... Genetic distance is a measure of the disimilarity of genetic material between different species or individuals of the same species. ... First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. ... Clustal is a widely used multiple sequence alignment computer program. ... // Maximum parsimony, often simply referred to as parsimony, is a commonly used, non-parametric statistical method for estimating phylogenies. ... Maximum likelihood estimation (MLE) is a popular statistical method used to make inferences about parameters of the underlying probability distribution from a given data set. ... Bayesian inference is statistical inference in which evidence or observations are used to update or to newly infer the probability that a hypothesis may be true. ... In computational complexity theory, NP-hard (Non-deterministic Polynomial-time hard) refers to the class of decision problems that contains all problems H such that for all decision problems L in NP there is a polynomial-time many-one reduction to H. Informally this class can be described as containing... Look up Heuristic in Wiktionary, the free dictionary. ... In mathematics, the term optimization, or mathematical programming, refers to the study of problems in which one seeks to minimize or maximize a real function by systematically choosing the values of real or integer variables from within an allowed set. ...


Tree-building methods can be assessed on the basis of several criteria:[6]

  • efficiency (how long does it take to compute the answer, how much memory does it need?)
  • power (does it make good use of the data, or is information being wasted?)
  • consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)
  • robustness (does it cope well with violations of the assumptions of the underlying model?)
  • falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)

Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using T-theory. [7] T-theory is a branch of discrete mathematics dealing with analysis of trees and discrete metric spaces. ...


Limitations of phylogenetic trees

Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, they do have important limitations. Phylogenetic trees do not necessarily (and likely do not) represent actual evolutionary history. The data on which they are based is noisy; horizontal gene transfer[8], hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences can all confound the analysis. One method of analysis implemented in the program PhyloCode does not assume a tree structure to avoid these limitations. For a non-technical introduction to the topic, see Introduction to Genetics. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... In science, and especially in physics and telecommunication, noise is fluctuations in and the addition of external factors to the stream of target information (signal) being received at a detector. ... Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. ... // This article is about a biological term. ... In evolutionary biology, convergent evolution is the process whereby organisms not closely related, independently evolve similar traits as a result of having to adapt to similar environments or ecological niches. ... Conservation is a high degree of similarity in the primary or higher structure of homologous proteins amongst various phyla. ... Types of Clade (Note: Stem-based is now branch-based, to avoid confusion with the term stem group which means total clade minus crown clade.) The PhyloCode is a developing draft for a formal set of rules governing phylogenetic nomenclature. ...


Furthermore, basing the analysis on a single gene or protein taken from a group of species can be problematic because such trees constructed from another unrelated gene or protein sequence often differ from the first, and therefore great care is needed in inferring phylogenetic relationships amongst species. This is most true of genetic material that is subject to lateral gene transfer and recombination, where different haplotype blocks can have different histories. For a non-technical introduction to the topic, see Introduction to Genetics. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Recombination usually refers to the biological process of genetic recombination and meiosis, a genetic event that occurs during the formation of sperm and egg cells. ... A haplotype is the genetic constitution of an individual chromosome. ...


When extinct species are included in a tree, they should always be terminal nodes, as it is unlikely that they are direct ancestors of any extant species. Scepticism must apply when extinct species are included in trees that are wholly or partly based on DNA sequence data, due to evidence that "ancient DNA" is not preserved intact for longer than 100,000 years.[citation needed] 9, 14, 19, 67 and 76 are leaf nodes. ... Ancient DNA can be loosely described as any DNA recovered from biological samples that have not been preserved specifically for later DNA analyses. ...


See also

Like the other multicellular kingdoms most scientists now believe that it is the Colonial theory by which the animals (metazoans) evolved. ... Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... A dendrogram is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm (see cluster analysis). ... An endosymbiont (also known as intracellular symbiont) is any organism that lives within cells of another organism, i. ... This article is about evolution in biology. ... The first organisms that existed were undoubtedly unicellular. ... // When applied to comparative data, conventional statistical methods assume, in effect, that all species are completely unrelated, as if they descended from a big bang of special creation. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ... Look up taxonomy in Wiktionary, the free dictionary. ... The Ancestors Tale cover The Ancestors Tale (subtitled A Pilgrimage to the Dawn of Life) is a 2004 popular science book by Richard Dawkins, with contributions from Dawkins research assistant Yan Wong. ... Clinton Richard Dawkins (born March 26, 1941) is a British ethologist, evolutionary biologist, and popular science writer who holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University. ... A tree structure is a way of representing the hierarchical nature of a structure in a graphical form. ... Wikispecies is a sister project supported by the Wikimedia Foundation that anybody can edit with a great potential use to students and researchers. ...

References

  1. ^ Hodge T, Cope M (2000). "A myosin family tree". J Cell Sci 113 Pt 19: 3353-4. PMID 10984423. 
  2. ^ Letunic, I (2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation." (Pubmed). Bioinformatics 23(1): 127-8. 
  3. ^ Ciccarelli, FD (2006). "Toward automatic reconstruction of a highly resolved tree of life." (Pubmed). Science 311(5765): 1283-7. 
  4. ^ Maher BA (2002). "Uprooting the Tree of Life". The Scientist 16: 18. 
  5. ^ a b c Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
  6. ^ Penny, D., Hendy, M. D. & M. A. Steel. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7: 73-79.
  7. ^ A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. Documenta Mathematica LSU 2001: 121-139
  8. ^ Woese C (2002). "On the evolution of cells". Proc Natl Acad Sci U S A 99 (13): 8742-7. PMID 12077305. 

Medline is a comprehensive literature database of life sciences and biomedical information. ... Medline is a comprehensive literature database of life sciences and biomedical information. ...

External links

Images

  • Phylogenetic Trees Based on 16s rDNA
  • A 3D View
  • Human Y-Chromosome 2002 Phylogenetic Tree
  • In 2003, the Science journal dedicated a special issue to the tree of life, including an online version of a tree of life.
  • iTOL: Interactive Tree Of Life
  • Phylogenetic Tree of Artificial Organisms Evolved on Computers

Science is the journal of the American Association for the Advancement of Science (AAAS). ...

General

  • Discover Life An interactive tree based on the U.S. National Science Foundation's Assembling the Tree of Life Project
  • PhyloCode
  • A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree
  • Tree of Life Web Project
  • http://www.aisee.com/graph_of_the_month/jura.htm — The most detailed and comprehensive family tree of dinosaurs yet available
  • http://www.omne-vivum.com tree of life with lots of pictures
  • Phylogenetic inferring on the T-REX server

  Results from FactBites:
 
29+ Evidences for Macroevolution: Phylogenetics (5163 words)
Phylogenetics is the scientific discipline concerned with describing and reconstructing the patterns of genetic relationships among species and among higher taxa.
cladogram: A hierarchical classification of taxa represented as a tree.
Edwards, A. and Cavalli-Sforza, L. (1964) "Reconstruction of phylogenetic trees." in Phenetic and Phylogenetic Classification.
The PhyloCode: Glossary (2379 words)
A clade originating from a particular branch (internode) on a phylogenetic tree; a clade encompassing a particular branch on a phylogenetic tree and all nodes and branches descended from that branch; a clade whose name is defined using a branch-based definition.
A point or vertex on a tree (graph theory); on a phylogenetic tree, a node is commonly used to represent the split of one lineage to form two or more lineages (internal node) or the lineage at the present time (terminal node).
A clade originating from a particular node on a phylogenetic tree; a clade encompassing a particular node on a phylogenetic tree and all branches (internodes) and nodes descended from that node; a clade whose name is defined using a node-based definition.
  More results at FactBites »

 
 

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