Phylogenesis is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics.

Phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

Phylogenetic trees can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram makes no assumption about the ancestral line, and does not show the origin or “root” of the taxa in question or the direction of inferred evolutionary transformations.

Phylogenetics is a component of systematics that uses similarities and differences of the characteristics of species to interpret their evolutionary relationships and origins. Phylogenetics focuses on whether the characteristics of a species reinforce a phylogenetic inference that it diverged from the most recent common ancestor of a taxonomic group.

Phylogenetics has many applications in biology, such as understanding biodiversity, evolution, ecology, and genomes. Phylogenetics can also aid in cancer research, drug design and discovery, and conservation biology.

One of the main methods of phylogenetic inference is cladistics. Cladistics is an approach to biological classification in which organisms are categorized based on shared, derived characteristics that can be traced to a group’s most recent common ancestor and are not present in more distant ancestors. Therefore, members of a group are assumed to share a common history and are considered to be closely related.

The cladistic method interprets each character state transformation implied by the distribution of shared character states among taxa as a potential piece of evidence for grouping. The outcome of a cladistic analysis is a cladogram—a tree-shaped diagram that is interpreted to represent the best hypothesis of phylogenetic relationships.

Cladistics can be contrasted with other approaches to biological classification, such as phenetics and evolutionary taxonomy. Phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead. Evolutionary taxonomy tries to incorporate both phylogeny and overall similarity, but may result in paraphyletic or polyphyletic groups that do not reflect true evolutionary relationships.

Some examples of cladistic groups are monophyletic groups, also known as clades. A clade is a group of organisms that includes a common ancestor and all of its descendants. Clades are nested within larger clades, forming a hierarchy of relationships. For example, mammals are a clade within the clade of vertebrates, which is itself a clade within the clade of animals.

To choose the characters for cladistic analysis, one must select features that are heritable, variable, and independent. Heritable features are those that are passed down from parent to offspring, such as DNA sequences or morphological traits. Variable features are those that show differences among the taxa being studied, such as presence or absence of a structure or a particular nucleotide or amino acid. Independent features are those that are not influenced by other features, such as convergent or parallel evolution.

The advantages of cladistics are that it provides a clear and testable hypothesis of phylogenetic relationships, based on observable and objective criteria. It also allows for the reconstruction of ancestral states and the identification of synapomorphies—shared derived characters that define a clade. The disadvantages of cladistics are that it may be difficult to find enough suitable characters for some groups, especially those with few morphological differences or high rates of molecular evolution. It may also be affected by homoplasy—the occurrence of similar characters in unrelated taxa due to convergent or parallel evolution or reversal.