Organisms given two species are thought to have a common ancestor. By repeating differentiation into two or more species from one ancestral species (speciation), evolution of organisms have occurred. Therefore, the evolutionary pathway of organisms can be traced back by comparing the extant (or extinct) species. Phylogenetic trees show such processes. The phylogenetic tree has been made from Darwin's age based on certain biological knowledges. For example, the phylogenetic trees have been constructed based on the morphological studies, developmental studies, and paleontological studies.
Recently, various methods that can construct phylogenetic trees based on gene sequences have developed. These phylogenetic trees are referred to as "molecular" phylogenetic trees. There are three methods widely used for the phylogenetic tree construction: maximum parsimony method, maximum likelihood method, and distance matrix method. Among various distance matrix methods, Neighbor-Joining method is most frequently used.
Since the molecular phylogenetic tree is essentially a gene tree, all molecular phylogenetic trees are not identical to the species tree. We have to keep this point in mind especially when we want to discuss about the origin and early evolution of life. In this context, molecular phylogenetic trees of genes for translation machineries, particularly ribosomal RNA gene, are thought to reflect the organism tree. On the other hand, to study recent evolution of animals and plants, fast-evolving genes (sequences) such as mitochondrial genes and intergenic regions are widely used.