How Phylogeny is Represented in Phylogenetic Trees

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What is Phylogenetics?

Phylogenetics is the study of various groups of organisms that are related due to evolutionary processes. Phylogenetics assumes that each species is a group of a lineage connected set of individuals. In this branch of study, evolution is regarded as a branching kind of process where populations of organisms are changed over time and then may separate into other branches, come together or become extinct. One of the problems posed by phylogenetics is that the genetic data is relatively new and consists only data from present studies and research. The older data before modern archival methods were established can be relatively unreliable.

Phylogeny by Genetics vs. Morphology

Due to the advancement in sequencing techniques in fields like molecular biology, it has now become possible for researchers and scientists to be able to gather up large amounts of data from DNA and amino acid sequences, and use it to be able to estimate different phylogenies. It is not at all rare to have studies that use character matrices that are based on mitochondrial genomes. But is has also been proposed that the importance lies more in increasing the number of taxa in the matrix itself than to simply increase the number of characters. This is partly because the more taxa in a matrix, the more robust and strong the resulting phylogeny can be.

It is also been argued that this can be an important reason to incorporate data from older fossils into phylogenies. It can also affect the accuracy of reconstruction of phylogeny trees and whether or not the data being analyzed actually contains some useful phlyogenetic signals.

Types of Phylogenetic Trees

A phylogenetic tree is also referred to as an evolutionary tree. This tree shows the varying relationships between biological species over time that are believed to come from a common ancestor. In the phylogenetic tree, each node that has descendants is used to represent the most recently known common ancestor of the descendants. Each node is called a taxonomic unit.

There are different types of phylogenetic trees. One type is called a directed tree with is rooted and contains unique nodes that correspond to the most recently known common ancestor and shown as leaves on the tree. The most commonly used method for rooting phylogeny trees is the use of an out group. There is also another type of phylogeny tree known as an un-rooted tree. This kind of tree is used to illustrate how nodes on different leaves are related, without making certain assumptions of what the common ancestry could be rooted to. These trees can be generated from rooted phylogeny trees by leaving out the root.

Both un-rooted and rooted phylogeny trees can be labeled or unlabeled. The labeled trees have a maximum of only two descendants that come from an interior node, while unlabeled phylogeny trees can have more than two descendants coming from an interior node. Phylogenetic trees also have other types such as ulatrametric and chronogram that represent time through the lengths of branches.