Phylogenetic tree

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 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.

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

• dendrogram
• endosymbiosis
• phylogeny
• evolutionary tree
• taxonomy
• tree structure

Footnote

1. 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
• A 3D View

General

• PhyloCode
• A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree
• Tree of Life Web Project
• B.A. Maher, Uprooting the Tree of Life, 16:18 (Sep. 16, 2002)