Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the Tree of Life. The Tree of Life then represents the phylogeny of organisms, such as the history of organismal lineages as they change through time. It shows that different species arise from previous forms via descent, and that all organisms, from the smallest microbe to the largest plants and vertebrates, are connected by the passage of genes along the branches of the phylogenetic tree that links all of Life.
Phylogeny is the study of relationships among different groups of organisms and their evolutionary development. Phylogeny attempts to trace the evolutionary history of all life on the planet. It is based on the phylogenetic hypothesis that all living organisms share a common ancestry.
The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866 and the Darwinian approach to classification became known as the "phyletic" approach.
Phylogeny may be represented by a tree diagram called phylogenetic tree (also called evolutionary tree). The diagram depicts the relationships among organisms or the relatedness between taxa. A phylogenetic tree may be rooted or unrooted. A rooted phylogenetic tree implicates a common ancestor where closely-related taxa descended from. An unrooted phylogenetic tree, in contrast, does not show a common ancestor but it hypothesizes on the degree of evolutionary relatedness between taxa.
Phylogeny is essential in the scientific study of the identification, classification, ecology, and evolutionary histories of organisms. It becomes vital in understanding biodiversity, genetics, evolutions, and ecology among groups of organisms. Apart from phylogenetics, it is also vital in the field of taxonomy. It expands the basis of evolutionary relationships of organisms from the morphological aspect to the genetic constructs of organisms.
Inferences derived from phylogenetic studies are not absolute. The data derived from genomic studies may possibly contain erroneous data. For example, the genomic analyses may be based on faulty data, e.g. those flawed by horizontal gene transfer between species. Phylogeny that is based on several genes or proteins from different genomic sources (e.g. nuclear or mitochondrial) are also likely to be more precise than on a single gene or protein alone. Otherwise, the analysis may be a phylogeny of the gene and not of the species. Another important limitation is the lack or insufficiency of quality DNA sample from extinct species.
Phylogeny is the system for classifying organisms. It represents the two main fields of systematic biology. It relies on characteristics or traits for classifying organisms into different groups.
In phylogenetics, the goal is to trace the evolutionary history of species by attempting to reconstruct the phylogeny of life or the evolutionary tree of life.
In molecular phylogeny, analysis of DNA and protein structure is used to determine genetic relationships among different organisms. For example, the analysis of cytochrome C, a protein in cell mitochondria that functions in the electron transport system and energy production, is used to determine degrees of relationship among organisms based on similarities of amino acid sequences in cytochrome C.
Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed.