phylogenetics | noun | phy·lo·genetics

The study of evolutionary relatedness among various groups of organisms
through molecular sequencing data and morphological data matrices.

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A Brief History of Phylogenetics

The idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to higher forms of life (such as in the Great Chain of Being). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).

Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages. Over time, species classification has become less static and more dynamic.

Evolutionary trees depict clades. A clade is a group of organisms that includes an ancestor and all descendants of that ancestor. You can think of a clade as a branch on the tree of life.

Reading Phylogenetic Trees

A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two descendents that split from the same node are called sister groups. In the tree below, species A & B are sister groups — they are each other's closest relatives.

Many phylogenies also include an outgroup — a taxon outside the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees.

Types: Rooted tree vs Unrooted tree

Rooted tree
A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.

Unrooted tree
Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis.

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Tree reconstruction methods

Some methods have been proposed for the construction of phylogenetic trees. They can be classified into two groups, the cladistic methods and the phenetic method.

Maximum parsimony

Maximum parsimony trees imply that simple hypotheses are more preferable than complicated ones. This means that the construction of the tree using this method requires the smallest number of evolutionary changes in order to explain the phylogeny of the species under study. In the procedure, this method compares different parsimonious trees and chooses the tree that has the least number of evolutionary steps (substitutions of nucleotides in the context of DNA sequence).

Maximum likelihood

In statistics, maximum likelihood estimation (MLE) is a method of estimating the parameters of a statistical model given observations, by finding the parameter values that maximize the likelihood of making the observations given the parameters. MLE can be seen as a special case of the maximum a posteriori estimation (MAP) that assumes a uniform prior distribution of the parameters, or as a variant of the MAP that ignores the prior and which therefore is unregularized.

Distance matrix

Distance matrix is a phenetic approach preferred by molecular biologists for genomic analysis. This method estimates the mean number of changes in two taxa that have descended from a common ancestor. There is much information in the gene sequences that must be simplified in order to compare only two species at a time. The relevant measure is the number of differences in two sequences, which can be interpreted as the distance between the species in terms of relatedness.

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