Phylogenetics

Introduction

Phylogenetics is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end," or the present, in an evolutionary lineage. Phylogenetics has become central to understanding biodiversity, evolution, ecology, and genomes.

History of Phylogenetics

The science of phylogenetics has its roots in the works of the ancient Greek philosopher Aristotle, who classified living organisms and arranged them in a hierarchical order. However, the modern discipline of phylogenetics is a product of the synthesis of several scientific fields, and it has many links with bioinformatics.

Principles of Phylogenetics

Phylogenetics is based on the principle that species are related by descent from a common ancestor. This is inferred from the similarity of their physical or genetic characteristics. The degree of similarity is considered the result of shared genetic features passed down from a common ancestor. The discipline therefore relies heavily on the disciplines of genetics, evolutionary biology, and computational biology.

Phylogenetic Trees

A phylogenetic tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit.

Phylogenetic Inference Methods

Phylogenetic inference methods are used to evaluate observable heritable traits, such as DNA sequences, protein sequences, or morphology, under a model of evolution of these traits. There are several types of methods used in phylogeny, including phenetic methods, cladistic methods, and Bayesian inference methods.

Applications of Phylogenetics

Phylogenetics is used in the field of molecular epidemiology to trace the spread of infectious diseases by identifying the pathogen's strain. It is also used to understand the evolutionary history of certain groups of organisms and to classify organisms. The field of phylogenetics is also applied in the study of genomes, as it aids in the understanding of the genomic evolution of a species or group of species.