What Is Phylogeny? Definition and Examples (2024)

Phylogeny is the study of relationships among different groups of organisms and their evolutionary development. Phylogeny attempts to trace the evolutionary history of all life on the planet. It is based on the phylogenetic hypothesis that all living organisms share a common ancestry. The relationships among organisms are depicted in what is known as a phylogenetic tree. Relationships are determined by shared characteristics, as indicated through the comparison of genetic and anatomical similarities.

In molecular phylogeny, analysis of DNA and protein structure is used to determine genetic relationships among different organisms. For example, the analysis of cytochrome C, a protein in cell mitochondria that functions in the electron transport system and energy production, is used to determine degrees of relationship among organisms based on similarities of amino acid sequences in cytochrome C. Similarities in characteristics of biochemical structures, such as DNA and proteins, are then used to develop a phylogenetic tree based on inherited shared traits.

Phylogenetic Tree

A phylogenetic tree, or cladogram, is a schematic diagram used as a visual illustration of proposed evolutionary relationships among taxa. Phylogenetic trees are diagrammed based on assumptions of cladistics, or phylogenetic systematics. Cladistics is a classification system that categorizes organisms based on shared traits, or synapomorphies, as determined by genetic, anatomical, and molecular analysis. The main assumptions of cladistics are:

1. All organisms descend from a common ancestor.
2. New organisms develop when existing populations split into two groups.
3. Over time, lineages experience changes in characteristics.

Phylogenetic tree structure is determined by shared traits among different organisms. Its tree-like branching represents diverging taxa from a common ancestor. Terms that are important to understand when interpreting a phylogenetic tree diagram include:

• Nodes: These are points on a phylogenetic tree where branching occurs. A node represents the end of the ancestral taxon and the point where a new species splits from its predecessor.
• Branches: These are the lines on a phylogenetic tree that represent ancestral and/or descendant lineages. Branches arising from nodes represent descendant species that split from a common ancestor.
• Monophyletic Group (Clade): This group is a single branch on a phylogenetic tree that represents a group of organisms that are descended from a most recent common ancestor.
• Taxon (pl.Taxa): Taxa are specific groupings or categories of living organisms. The tips of branches in a phylogenetic tree end in a taxon.

Taxa that share a more recent common ancestor are more closely related than taxa with a less recent common ancestor. For example, in the image above, horses are more closely related to donkeys than to pigs. This is because horses and donkeys share a more recent common ancestor. Additionally, it can be determined that horses and donkeys are more closely related because they belong to a monophyletic group that does not include pigs.

How Taxa Relatedness May Be Misinterpreted

Relatedness in a phylogenetic tree is determined by descent from a recent common ancestor. When interpreting a phylogenetic tree, there is a tendency to presume that distance between taxa can be used to determine relatedness. However, branch tip proximity is positioned arbitrarily and can not be used to determine relatedness. For example, in the above image, the branch tips including penguins and turtles are positioned closely together. This may be incorrectly interpreted as close relatedness between the two taxa. By looking at the most recent common ancestors, it can be correctly determined that the two taxa are distantly related.

Another way that phylogenetic trees can be misinterpreted is by counting the number of nodes between taxa to determine relatedness. In the phylogenetic tree above, pigs and rabbits are separated by three nodes, while dogs and rabbits are separated by two nodes. It could be misinterpreted that dogs are more closely related to rabbits because the two taxa are separated by fewer nodes. Taking into consideration the most recent common ancestry, it can be correctly determined that dogs and pigs are equally related to rabbits.

What Are Phylogeny and Taxonomy?

Phylogeny and taxonomy are two systems for classifying organisms. They represent the two main fields of systematic biology. Both of these systems rely on characteristics or traits for classifying organisms into different groups. In phylogenetics, the goal is to trace the evolutionary history of species by attempting to reconstruct the phylogeny of life or the evolutionary tree of life. Taxonomy is a hierarchical system for naming, classifying, and identifying organisms. Phylogenic characteristics are used to help establish taxanomic groupings. The taxonomic organization of life classifies organisms into three domains:

• Archaea: This domain includes prokaryotic organisms (those that lack a nucleus) that differ from bacteria in membrane composition and RNA.
• Bacteria: This domain includes prokaryotic organisms with unique cell wall compositions and RNA types.
• Eukarya: This domain includes eukaryotes, or organisms with a true nucleus. Eukaryotic organisms include plants, animals, protists, and fungi.

Organisms in the domain Eukarya are further categorized into smaller groupings: Kingdom, Phylum, Class, Order, Family, Genus, and Species. These groupings are also divided into intermediate categories such as subphyla, suborders, superfamilies, and superclasses.

Taxonomy is not only useful for categorizing organisms but also establishes a specific naming system for organisms. Known as binomial nomenclature, this system provides a unique name for an organism consisting of a genus name and species name. This universal naming system is recognized worldwide and avoids confusion over the naming of organisms.

Sources

• Dees, Jonathan et al. "Student interpretations of phylogenetic trees in an introductory biology course" CBE life sciences education vol. 13,4 (2014): 666-76.
• "Journey Into Phylogenetic Systematics." UCMP, www.ucmp.berkeley.edu/clad/clad4.html.