Phylogenetics

Abstract

Phylogenetics concerns the development of methods for reconstructing evolutionary relationships among organisms and the application of such methods to reconstruct phylogenetic trees using morphological or molecular data.

Keywords: phylogenetic trees; distance methods; parsimony methods; likelihood methods; man's closest relatives

Figure 1.

Two alternative representations of a phylogenetic tree for five OTUs. (a) Unscaled branches: extant OTUs are lined up, and nodes are positioned proportionally to times of divergence. (b) Scaled branches: lengths of branches are proportional to the numbers of molecular changes. 1 unit: a nucleotide substitution or amino acid substitution. (Reproduced with permission from Li and Graur, .)

Figure 2.

Rooted (a) and unrooted (b) phylogenetic trees. Arrows indicate the unique path leading from the root (R) to OTU D. (Reproduced with permission from Li and Graur, .)

Figure 3.

Diagram illustrating the stepwise construction of a phylogenetic tree for four OTUs, according to the UPGMA method. (Reproduced with permission from Li and Graur, .)

Figure 4.

Unrooted trees with (a) four OTUs and (b) five OTUs. (Reproduced with permission from Li and Graur, .)

Figure 5.

(a) A starlike tree with no hierachical structure. (b) A tree in which OTUs 1 and 2 are clustered. (c) Any pair of OTUs can take the positions of 1 and 2 in the tree, and there are n(n−1)/2 ways of choosing them (see text) by permission of Oxford University Press. Reproduced with permission from Saitou and Nei, .

Figure 6.

Three possible unrooted trees for four DNA sequences that have been used to choose the most parsimonious tree. The terminal nodes indicate the nucleotide type at homologous positions in the extant species. Each dot on a branch means a substitution is inferred on that branch. Note that the nucleotides at the two internal nodes of each tree represent one possible reconstruction from among several alternatives. For example, the nucleotide at both the internal nodes of tree III (c) (bottom right) can be G instead of A. In this case, the two substitutions will be positioned on the branches leading to species 3 and 4. However, the minimum number of required substitutions remains the same. (Reproduced with permission from Li and Graur, .)

Figure 7.

Model tree for the derivation of the likelihood function under a constant rate of evolution.

Figure 8.

Four alternative phylogenies and classifications of modern apes and humans (Hominoidea). (a,b) Traditional classifications setting humans apart. (c) Clustering of humans with the orangutan. (d) Cumulative molecular as well as morphological evidence before the DNA era favored this classification. H: human; C: chimpanzee; G: gorilla; O: orangutan; B: gibbon. (Reproduced with permission from Li and Graur, .)

Figure 9.

Phylogenetic tree for humans, chimpanzees, gorillas, orangutans and rhesus monkeys inferred from the (a) UPGMA method and (b) the neighbor‐joining method. (Reproduced with permission from Li and Graur, .)

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Further Reading

Kosiol C, Bofkin L and Whelan S (2006) Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. Journal of Biomedical Informatics 39: 51–61.

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How to Cite close
Li, Wen‐Hsiung(Apr 2008) Phylogenetics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005135.pub2]