Building Phylogenetic Trees with Analysis of DNA Sequence Alignments


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The image depicts a branching diagram (a tree-like structure) where the branches spread horizontally from a main ancestor on the left. On the right, organism names are labeled. The cascading branching starts with a single stem at the upper left corner labeled ‘Ancestral green algae’. This has a branching point giving rise to three horizontal branches. The top two branches extend all the way to the right and are labeled ‘Coelochaetes (green algae)’ and ‘Charophytes (green algae) from top to bottom. The third branch is a short branch labeled ‘Embryophytes’ on the left. It branches into two new branches. The top branch extends all the way to the right and is labeled ‘Marchantiopsida (liverworts)’. The bottom branch divides into two additional branches, the top labeled ‘Anthocerotopsida (hornworts)’. The bottom branch splits into two branches, the top labeled at the right ‘Bryopsida (mosses)’. The liverworts, hornworts, and mosses are collectively labeled Bryophytes. The bottom branch splits into additional two branches, the top labeled at the right ‘Aglaophyton (extinct)’. The bottom splits into two branches, labeled ‘Rhynopsida (extinct)’, and one branch which splits again. The top branch splits into several branches which all end in several organisms collectively labeled ‘Lycophytes’. The order of organisms in this group from top to bottom is ‘Drepanophycales (exctinct); Lycopodiaceae (club moses)’; Protolepidodendrales (exctinct); Selaginellales (spike mosses); Isoetales (quillworts); Zosterophyllopsida (extinct). The bottom branch splits in two additional branches, the first labeled ‘Psilophyton (extinct)’, and the bottom splits again. The top branch gives rise to two branches that are labeled ‘Sphenopsids (horsetails)’; and ‘Pteriodophyta (ferns)'. The Psilophyton, horsetails, and ferns are collectively labeled 'Pterophytes'. Finally the bottom branch splits into two branches, the top labeled ‘Gymnosperms’ and the bottom 'Angiosperms’. These are collectively labeled ‘Spermatophytes’.
Plant phylogeny. This phylogenetic tree shows the evolutionary relationships of plants. Source: OpenStax Biology 2e

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: