OpenStax Biology 2e
All living organisms display patterns of relationships derived from their evolutionary history. Phylogeny is the science that describes the relative connections between organisms, in terms of ancestral and descendant species. Phylogenetic trees, such as the plant evolutionary history shown in the image below, are tree-like branching diagrams that depict these relationships. Species are found at the tips of the branches. Each branching point, called a node, is the point at which a single taxonomic group (taxon), such as a species, separates into two or more species.
Phylogenetic trees have been built to describe the relationships between species since the first sketch of a tree that appeared in Darwin’s Origin of Species. Traditional methods involve comparison of homologous anatomical structures and embryonic development, assuming that closely related organisms share anatomical features that emerge during embryo development. Some traits that disappear in the adult are present in the embryo; for example, an early human embryo has a postanal tail, as do all members of the Phylum Chordata. The study of fossil records shows the intermediate stages that link an ancestral form to its descendants. However, many of the approaches to classification based on the fossil record alone are imprecise and lend themselves to multiple interpretations. As the tools of molecular biology and computational analysis have been developed and perfected in recent years, a new generation of tree-building methods has taken shape. The key assumption is that genes for essential proteins or RNA structures, such as the ribosomal RNAs, are inherently conserved because mutations (changes in the DNA sequence) could possibly compromise the survival of the organism. DNA from minute samples of living organisms or fossils can be amplified by polymerase chain reaction (PCR) and sequenced, targeting the regions of the genome that are most likely to be conserved between species. The genes encoding the 18S ribosomal RNA from the small subunit and plastid genes are frequently chosen for DNA alignment analysis.
Once the sequences of interest are obtained, they are compared with existing sequences in databases such as GenBank, which is maintained by The National Center for Biotechnology Information. A number of computational tools are available to align and analyze sequences. Sophisticated computer analysis programs determine the percentage of sequence identity or homology. Sequence homology can be used to estimate the evolutionary distance between two DNA sequences and reflect the time elapsed since the genes separated from a common ancestor. Molecular analysis has revolutionized phylogenetic trees. In some cases, prior results from morphological studies have been confirmed: for example, confirming Amborella trichopoda as the most primitive angiosperm known. However, some groups and relationships have been rearranged as a result of DNA analysis.
Clark, M., Douglas, M., Choi, J. Biology 2e. Houston, Texas: OpenStax. Access for free at: https://openstax.org/details/books/biology-2e