Phylogenetic tree
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A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor. A phylogenetic tree is a form of a cladogram. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and edge lengths correspond 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.
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. Figure 1 depicts a rooted phylogenetic tree, which has been colored according to the three-domain system [Woese 1998].
An unrooted phylogenetic tree is, loosely speaking, a tree derived from a rooted phylogenetic tree by omitting the root. More precisely, it is a forest of rooted phylogenetic trees depicted so that the roots are all linked. Figure 2 depicts an unrooted phylogenetic tree¹ for myosin, a superfamily of proteins. Links to other pictures are given in the Pictures on the Web subsection below.
Caveats
- By their very nature, phylogenetic trees hide any hybridization and lateral gene transfer [Woese 2002] that may have taken place. For these reasons, the proposed PhyloCode (see External Link below) does not assume a tree structure.
- The phylogenetic tree of a single gene or protein taken from a group of species often differs from similar trees for the same group of species, and therefore great care is needed in inferring phylogenetic relationships amongst species.
- Trees that do not include extinct species must also be interpreted with care.
See also
Footnote
- T. Hodge, M.J.T.V. Cope (2000) A Myosin Family Tree. Journal of Cell Science 113, 3353-3354. See also the Myosin external link below.
References
- C.R. Woese, "The Universal Ancestor", Proceedings of the National Academy of Sciences, 95:6854-6859 (1998).
- C.R. Woese, "On the evolution of cells", Proceedings of the National Academy of Sciences, 99:8742-7 (June 25, 2002).
External links
Pictures on the web
- Phylogenetic Trees Based on 16s rDNA (http://tolweb.org/tree/eukaryotes/accessory/treeoverview.html)
- A 3D View (http://www.ii.uib.no/~tim/treeOfLifeImagePage.html)
- Human Y-Chromosome 2002 Phylogenetic Tree (http://ycc.biosci.arizona.edu/nomenclature_system/fig1.html)
General
- PhyloCode (http://www.ohiou.edu/phylocode/index.html)
- A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree (http://www.mrc-lmb.cam.ac.uk/myosin/trees/trees.html)
- Tree of Life Web Project (http://tolweb.org/tree)
- B.A. Maher, Uprooting the Tree of Life, 16:18 (Sep. 16, 2002) (http://www.the-scientist.com/yr2002/sep/research1_020916.html)
de:phylogenetischer Baum