The historical paths taken by evolving groups of animals and plants over geological time. Often used interchangeably with biological evolution, the two terms need to be distinguished from each other. The distinction is between providing a descriptive evolutionary history of a species (phylogeny) and attempting to explain the processes (phyletic gradualism or punctuated equilibrium) and mechanisms behind this history such as gene recombination, genetic drift, mutation and natural selection (biological evolution). Historically, the process of evolution was explained by cladogenesis (multiplication of species by isolation and their subsequent divergence) and its mechanisms by anangenesis (transformation of structures and functions by mutation etc.). The introduction of the term phylogenesis complicated matters as it was used as synonym for cladogenesis when it should have included anangenesis as well. Eventually, the term biological evolution was mostly used as a synonym of cladogenesis plus anangenesis. All very confusing. The solution is to consider biological evolution as the transformation of organism properties (anangenesis) through the effects of the mechanisms of mutation etc. The best way to understand phylogenesis is to treat it as a general process of evolutionary change (anangenesis), together with the process of speciation (cladogenesis), while referring to the history of organisms as a historical fact. As only organisms have a phylogeny and not properties, which do have an evolution, certain statements can be incorrect. For example, saying the ‘phylogeny of the hominid hand’ and the ‘evolution of the great apes’ are both wrong. What should have been said was the ‘evolution of the hominid hand’ and the ‘phylogeny of the great apes’.
See Biological evolution, Cladistics, Cladogram, Development, General theory of biological classification, Lineage, Ontogeny, Ossification, Phylogenetic mapping, Phyletic, Phyletic gradualism and punctuated equilibrium, Recapitulation theory (or biogenetic law), Speciation, Species