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Molecular phylogenetics is just one portion of a broader field of research known as phylogenetic systematics. Phylogenetic systematics deals with understanding the evolutionary relationships among all of the many different species of organisms on earth; as such, it involves the study of both living and extinct species. Ideally, the relationships determined by phylogenetic systematics should describe a particular species' evolutionary history; that is, its phylogeny. The result of a phylogenetic analysis is expressed in what is termed a phylogenetic tree. A phylogenetic tree shows the probable or hypothesized evolutionary history of a group of organisms
Molecular phylogenetics relies on the use of molecules to infer phylogenetic relationships. That is, molecular data (typically DNA sequence data) are used to build a phylogenetic tree. While the morphology of organisms can (and still does) provide useful characters to be employed in a phylogenetic analysis, in the past several decades the field of phylogenetic systematics has relied heavily on molecules as a source of data. Every living organism contains DNA, RNA, and proteins and these have all been used in molecular phylogenetics. However, DNA sequence data have been particularly useful and DNA is now standardly employed as the tool of choice in molecular phylogenetics. The popularity of molecular characters is the result of several factors, including the following: they provide millions of characters, they are present in all organisms, and they are easily isolated, characterized, and compared. In these comparisons, DNA sequences (of the same genes or regions) of closely related organisms generally have a higher degree of similarity than those of more distantly related organisms. Researchers in the area of molecular phylogenetics initially compared the sequences of individual genes, but sequencing technology has advanced rapidly and now molecular phylogenetics relies on the comparisons of numerous genes, including the sequences of entire plastid genomes, and ultimately large scale comparisons of the nuclear genome (comparative genomics).
Doug Soltis, The University of Florida