In biology, phylogenetics is the study of various groups of organisms that are related due to evolutionary factors. This is also known as cladistics or phylogenetic systematics. In phylogeny, each species is treated as groups of individuals that re connected. Fields like taxonomy have been greatly enhanced by the use of phylogeny but yet can remain logically distinct.
Evolution in biology is regarded as a sort of branching process where populations become altered over time and they may branch into different branches, come together or become extinct. Phylogeny provides a simple method of being able to understand phylogenetic trees. Some of the most commonly used methods to understand phylogenies include:
- Parsimony
- Maximum Likelihood
- MCMC Interface
- Distance Based Methods
No matter which method is used, they all depend on a computational mathematical model that describes the evolution of species. In the early days of biology and discovery, biologists were finding ways to use phylogeny in classification of species. Ernst Haeckel developed a recapitulation theory that was accepted as biogenetic law. The early version of his hypothesis has been rejected and has been amended to indicate that embryos development now mirrors the development of their ancestors.
Most modern day biologists do recognize that there are numerous connections between the theories of ontogeny and phylogeny and can explain them by using the evolution theory and view them as supporting evidence. Other ways biologists use phylogeny in classification include the theory that larvae and embryos are both represented in other taxa that have been transferred by hybridization, this is known as the larval transfer theory.
Gene transfer is another way that biologists use phylogeny in classification. Organisms usually inherit genes by one of two ways: vertical gene transfer or lateral gene transfer. Lateral gene transfer has made the determinations of phylogeny complicated because of inconsistencies being reported from the chosen gene. This sparked the three-domain theory by Carol Woese. He theorized that based on the discovery of genes that encode ribosomal RNA are ancient and are then distributed over all kinds of life with very little or no lateral gene transfer. Because of this, rRNA is usually recommended for reconstructing phylogenies by acting like molecular clocks.
Because of the advanced sequencing techniques that have been established in molecular biology, it is now possible to gather large amounts of data from DNA and amino acid sequences to be able to estimate phylogeny. It has also been proposed that it is also more important to be able to increase the number of taxa inside of a matrix than to increase the number of characters. Because of this notion, it is an important reason for biologists to incorporate the data from fossils when they can.
There is another important factor that also affects how accurate the reconstruction of the tree is depending on whether the data analyzed does contain phylogenetic signals. This is a term that is used to describe if related organisms do resemble each other because of their genetic material, or because of phenotypic traits.