Fitch notation

Fitch Notation is a method used in genetics and bioinformatics for representing the evolutionary relationships between different species or genes. This notation, named after the American biologist and computer scientist Walter M. Fitch, is a way of illustrating these relationships in a tree-like diagram known as a phylogenetic tree. The Fitch algorithm, which underlies this notation, is designed to infer the ancestral states that could have existed in the tree's history, given the states observed in the present-day species or genes.

Overview

The Fitch Notation is primarily concerned with parsimony analysis in phylogenetics. The principle of parsimony, often summarized by the phrase "the simplest explanation is most likely the correct one," is applied to infer the evolutionary pathways and ancestral states with the least number of evolutionary changes. The Fitch algorithm operates by first constructing a tree based on the input data, usually sequences of DNA, RNA, or protein from various organisms. It then assigns states (for example, the presence or absence of a genetic trait) to the internal nodes of the tree in a way that minimizes the total number of state changes throughout the tree.

Methodology

The process involves two main steps: a downward pass and an upward pass through the tree. In the downward pass, the algorithm starts from the root and goes towards the leaves, determining the set of possible states for each internal node that would require the minimum number of changes. In the upward pass, the algorithm moves from the leaves back to the root, choosing a specific state for each node from the set of possible states determined in the downward pass. This two-step process ensures that the final state assignments are consistent with the observed data and require the fewest evolutionary changes.

Applications

Fitch Notation and the underlying algorithm have wide applications in the fields of molecular biology, genomics, and evolutionary biology. They are used to:

• Reconstruct ancestral DNA sequences or protein sequences.
• Infer the evolutionary history of a set of species or genes.
• Identify conserved genetic sequences that may have important functional roles.
• Study the mechanisms of evolutionary change.

Limitations

While the Fitch algorithm is powerful, it has limitations. It assumes that all changes are equally probable and does not account for the possibility that some changes might be more likely than others due to biological constraints. Additionally, the algorithm does not handle well the cases where the evolutionary history involves recombination or horizontal gene transfer.

See Also

• Phylogenetics
• Cladistics
• Molecular clock
• Evolutionary biology