Phylogenetic tree
From Palaeos
A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor.
Contents |
[edit] Introduction
A phylogenetic tree is similar in form to 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 (ref Woese, C. R}}. 1998. The Universal Ancestor. Proceedings of the National Academy of Sciences 95: 6854-6859.). 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.
While unrooted phylogenetic trees can be generated from rooted ones by omitting the root from a rooted tree, a root cannot be inferred on an unrooted tree without either an outgroup or additional assumptions (for instance, about relative rates of divergence). Links some pictures are given in the pictures on the web subsection below.
There are three main methods of constructing phylogenetic trees: distance-based methods such as neighbor-joining, parsimony-based methods such as maximum parsimony, and character-based methods such as maximum likelihood or Bayesian inference.
Tree-building methods can be assessed on the basis of several criteria (ref Penny, D., Hendy, M. D. & M. A. Steel}}. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7: 73-79. ):
- 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?)
[edit] Caveats
- By their very nature, phylogenetic trees cannot represent actual evolutionary patterns and are in fact distorted by any lateral gene transfer (ref Woese, C. R. 2002. On the evolution of cells. Proceedings of the National Academy of Sciences 99: 8742-8747.) or hybridisation between species that are not nearest neighbors on the tree before hybridisation takes place. For these reasons, the proposed PhyloCode (see external links 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. This is most true of genetic material that is subject to lateral gene transfer and recombination, where different haplotype blocks can have different histories.
- 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 DNA is not preserved intact for longer than 100,000 years (see Ancient DNA.)
[edit] Always Treelike?
An interesting conundrum is posed by organisms that have originated by symbiosis, since their phylogeny cannot be easily fit into a treelike topology. Lichens are the symbiosis of a fungus and an alga, which gives lichens that problem. But the fungus is more choosy about which alga than the alga about which fungus, meaning that lichen taxonomy follows that of their component fungi.
Related to this conundrum is organisms that have performed much lateral gene transfer, and sometimes even lateral genome transfer (endosymbiosis), as many one-celled organisms have done. In particular, the taxonomy of prokaryotes has traditionally been descriptive, because it has been difficult to work out their phylogeny without using molecular sequences. And if their molecules are all scrambled, as has been suggested, then one may be stuck with descriptive taxonomy. But the "average" molecular phylogeny approximates that of information-system macromolecules like often-used ribosomal RNA. So as with lichens, a treelike phylogeny-based taxonomy remains reasonable when one uses some reasonable subset of the organism.
[edit] External links
[edit] Pictures on the web
[edit] General
- PhyloCode
- A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree
- Tree of Life Web Project
[edit] Credits
Credits: This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Phylogenetic tree"; copied to Palaeos org MAK061004. The section "Always Treelike"? is from This page incorporates material from EvoWiki and so is licensed under the Attribution-NonCommercial-ShareAlike Creative Commons License). EvoWiki url: http://wiki.cotch.net/index.php/Taxonomy_and_Phylogeny
