PHYLOGENETICS

Phylogenetic systematics is that field of biology that does deal with identifying and understanding the evolutionary relationships among the many different kinds of life on earth, both living (extant) and dead (extinct).

Systematics describes the pattern of relationships among taxa and is intended to help us understand the history of all life. But history is not something we can see—it has happened once and leaves only clues as to the actual events. Scientists use these clues to build hypotheses, or models, of life's history. In phylogenetic studies, the most convenient way of visually presenting evolutionary relationships among a group of organisms is through illustrations called phylogenetic trees.

Molecular phylogenetics

The field of molecular phylogenetics has grown, both in size and in importance, since its inception in the early 1990s, attributable mostly to advances in molecular biology and more rigorous methods for phylogenetic tree building. The importance of phylogenetics has also been greatly enhanced by the successful application of tree reconstruction, as well as other phylogenetic techniques, to more diverse and perplexing issues in biology. Phylogenies are used essentially by drawing inferences from the structure of the tree or from the way the character states map onto the tree. Broadly speaking, the relationships established by phylogenetic trees often describe a species' evolutionary history and, hence, its phylogeny, the historical relationships among lineage's or organisms or their parts, such as their genes.

Molecular phylogenetics attempts to determine the rates and patterns of change occurring in DNA and proteins and to reconstruct the evolutionary history of genes and organisms. Two general approaches may be taken to obtain this information. In the first approach, scientists use DNA to study the evolution of an organism. In the second approach, different organisms are used to study the evolution of DNA. Whatever the approach, the general goal is to infer process from pattern: the processes of organismal evolution deduced from patterns of DNA variation and processes of molecular evolution inferred from the patterns of variations in the DNA itself.

Studies of gene and protein evolution often involve the comparison of homologs, sequences that have common origins but may or may not have common activity. Sequences that share an arbitrary level of similarity determined by alignment of matching bases that are homologous. These sequences are inherited from a common ancestor that possessed similar structure, although the ancestor may be difficult to determine because it has been modified through descent.

A straightforward phylogenetic analysis consists of four steps: Alignment—building the data model and extracting a dataset. Determining the substitution model—consider sequence variation. Tree building. Tree evaluation.