Phylogenetics Lab - Biology 106: Lab Topic 1 Reconstruction...

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1 Biology 106: Lab Topic 1 Reconstruction of Phylogenetic Relationships Laboratory Objectives After completing this lab topic, you should be able to: 1. Discuss the concepts associated with inferring evolutionary relationships. 2. Discuss the process of defining characters and character states used in phylogenetic reconstruction. 3. Describe the process of performing phylogeny reconstruction and character evolution using the computer programs MacClade and PAUP. Introduction Phylogeny is a term adopted from the Greek root phyle for tribe (referring to a group of organisms) and the English genesis to convey the origin of organisms. Evolutionary biology and systematics (the study of organismal relationships and classification) are greatly concerned with phylogeny. Phylogenetic studies aim to explain not only the origins of organisms but also the evolutionary relationships of these organisms, their patterns of evolutionary diversification, and how these organisms can be classified. A key tool for the study of phylogeny is the cladogram. In this laboratory, we will construct cladograms and explore their use for understanding character evolution and the diversity of organisms. Cladograms Cladograms are used by biologists to represent evolutionary relationships among organisms. They are branching diagrams that have a tree-like form (Figure 1) and have taxa 1 on their terminal tips. Each branch of a cladogram is called a clade . Clades can be thought of as entire lineages of organisms. The point at which two clades diverge is called a node . We can think of the node as representing the point of a common ancestor for the two clades. The common ancestor of two clades is generally not known; thus, no taxon is listed on cladograms at any of the nodes. The two clades that diverge from a node are called sister clades and the taxa at the tips of sister clades are called sister taxa . The sister clade relationship is fundamental to the structure of cladograms and to understanding their interpretation. In Figure 2, we would infer that the closest relative of Eukarya is Archaea because they are sister clades. That is, a taxon’s closest relative is its sister taxon. Using the diagram in Figure 2, we could say that Eukarya is more closely related to Archaea than either of these is to Bacteria. 1 Taxon (plural: taxa) is a term for a group of organisms that could be at any rank (e.g., a taxon could be a species, genus, family, etc.).
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2 The concept of monophyly is among the most important in phylogeny and systematics. Monophyly refers to having a common ancestor. A monophyletic group consists of all of the descendants of a single ancestor. In a cladogram, sister clades are the basis of monophyletic groups. For example, in Figure 3, the Eukarya form a monophyletic group, but the Protists do not form a monophyletic group.
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4 To hypothesize monophyletic groups, we look for attributes shared by taxa that have been derived in the course of evolution. These are so-called
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This note was uploaded on 06/24/2008 for the course BIOL 106 taught by Professor Unknown during the Spring '08 term at Washington State University .

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Phylogenetics Lab - Biology 106: Lab Topic 1 Reconstruction...

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