Bioinformatics Phylogenetics

Basic Terminologies Used in Phylogenetic Tree Construction

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A phylogeny is a tree which estimates the “historical” connections between species or genes that they carry. Parts of phylogenetic tree are;

The tips of the tree branches show the taxa in the study.

Taxa may be at any taxonomic level or orders, species, populations, etc. These taxa may be called OTUs, or Operational Taxonomic Units.

The lines within the tree are called the tree’s branches. The points at which branches connect, or the tips of branches, are both called nodes. Internal nodes connect branches; external nodes are the tips that represent taxa.

Some trees will have a basal node, known as the root. A grouping of an ancestor and all of its descendants is known as a clade. A clade is also said to be monophyletic.

The pattern in which the branches connect shows our understanding of how the species in the tree evolved from a series of common ancestors. Each branch point (also called an internal node) shows a divergence event, or splitting apart of a single group into two descendant groups.

At each branch point usually the most recent common ancestor of all the groups descended from that branch point is present. 

Each horizontal line in the tree represents a series of ancestors, leading up to the species at its end. Similarly, the root represents a series of ancestors leading up to the most recent common ancestor of all the species in the tree.

The tree may be bifurcating. The vertical lines, called branches, show a lineage, which is often synonymous with a tree branch leading to a defined monophyletic group, and nodes are where they diverge, representing a speciation event from a common ancestor. The trunk at the base of the tree is actually called the root. The root node represents the most recent common ancestor of all of the taxa represented on the tree. Time is also represented, proceeding from the oldest at the bottom to the most recent at the top. 

In a monophyletic group, if two taxa share a unique common ancestor not shared by any other taxa then they are referred to as sister taxa to each other. 

The branching pattern in a tree is called tree topology. When all branches bifurcate on a phylogenetic tree, it is referred to as dichotomy. The phylogeny with multifurcating branches is called polytomy. A polytomy can be a result of either an ancestral taxon giving rise to more than two immediate descendants simultaneously during evolution, a process known as radiation, or an unresolved phylogeny in which the exact order of bifurcations cannot be determined precisely. A phylogenetic tree can be either rooted or unrooted. An unrooted phylogenetic tree does not assume knowledge of a common ancestor, but only positions the taxa to show their relative relationships. Because there is no indication of which node represents an ancestor, there is no direction of an evolutionary path in an unrooted tree.

A group that excludes one or more descendants is paraphyletic; a group that excludes the common ancestor is said to be polyphyletic.

One is to use an outgroup, which is a sequence that is homologous to the sequences under consideration, but separated from those sequences at an early evolutionary time. Outgroups are generally determined from independent sources of information.

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