Phylogenetics

Phylogenetics is the study of the evolutionary history of biology via phylogenies (sg. phylogeny), taxonomic trees which prioritize placing taxa into complete clades. Examples of full phylogenies include the “Tree of Life,” where all modern organisms (Bacteria, Archaea, Animalia, etc.) are linked to a common ancestor (“LUCA”), or a Chordata phylogeny for all vertebrate organisms.

Phylogenetics emphasizes completeness, accuracy, and simplified reasoning to examine the evolutionary history of all studied organisms. Phylogenetics prioritizes the study of monophyletic groups and the Principle of Parsimony and of Maximum Likelihood. A complete, accurate phylogeny can depict sister groups and identify or assume genetic similarities between taxa.

One should note here that while a phylogeny can do many things, it still has several specific limits.

A phylogeny is only able to show lineage and ancestry; it does not show the phenotypic similarity or the chance of similarity between taxa. Refer to pages on morphology, homology, and analogy.
By default, a phylogeny is only able to show that ancestry and branching was present; it does not show when these events occurred, how long ago they occurred, or how much time transpired between these events unless it is attached to dates and times.
- Additionally, a phylogeny does not show the time transpired between nodes to scale unless it comes with a relative scale for branch lengths.
no assumption of evolution of a species from its sister taxon/taxa

Thinking of phylogenies as hypotheses also allows us to use them in a powerful way: We can make and test predictions based on the assumption that a particular phylogeny—our hypothesis—is correct.”

A basic phylogeny is depicted similarly to a flow chart. The tree begins with a root which extends towards nodes later on the diagram. These points are connected via branches which show the inheritance of evolutionary traits between distinct taxa, with hatch marks that denote specific evolutionary characters.