Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes (which may be referred to as taxa). The major elements of phylogenetics are summarised in Figure 1 below.
Figure 1 Elements of phylogenetics.
Typically phylogeneticists study one of the following types of question:
• What are the evolutionary relationships or histories among my species/individuals/genes of interest?
• How do sequences evolve?
• Can I better describe processes of sequence evolution with a mathematical model?
We can reconstruct a phylogenetic tree by looking at the nucleotide or protein sequences and combining this with our understanding of sequence evolution, which is described using an evolutionary model. This enables us to infer evolutionary events that happened in the past, and also provides more information about the evolutionary processes operating on sequences. Thus we may refine our understanding of how evolution works and develop better mathematical models of evolution.