4.1: Phylogenetic Trees

LEARNING OBJECTIVES

• Understand how life can be organized

• Describe how phylogenetic trees show how we organize life

Categorizing Life

We interpret all life on Earth as related based on its shared characteristics. For example, all life uses DNA to store genetic information, that DNA is translated into RNA, and RNA is transcribed into proteins that do the biochemistry of cells. Various lineages of life share similar characteristics within a lineage, but they differ from other lineages. For example, the composition of bacterial cell walls are similar to each other but differ from those of animals in important ways. Similarly, the symmetry in the bodies of different types of animals vary in systematic ways; echinoderms have 5-fold symmetry whereas bilaterians have 2-fold symmetry. Most of these similarities and differences in characteristics reflect historical evolutionary processes, and we use those that do to classify subsets of life and to reconstruct the evolutionary history of life. One of the ways we perform, evaluate, and interpret the classifications is by making phylogenetic trees.

Phylogenetic trees are diagrams that show relationships among organisms. Scientists consider phylogenetic trees as hypotheses of the evolutionary past built from the observable characteristics of the organisms in the tree. In other words, a “tree of life”, as it is sometimes called, can be constructed to illustrate the relationships among different organisms. These organisms can be modern or fossil with the trees based on data from genomes, function, or morphology. The trees illustrate hypotheses about when different organisms diverged from their ancient common ancestors and how they evolved. 

The hypothesized relationships are graphically represented by lines that connect the organisms at the tips of the lines to their ancestors deeper in the tree. The lines branch where one lineage of life evolved (or split) into two lineages. These branch points and their order in the tree record the hypothesized relationships among the organisms. The length of each line represents the relative evolutionary difference of the organism at the tip to the most recent common ancestor with other lineages at the branch point; long lines represent significant amounts of evolutionary difference, whereas short lines represent closer evolutionary relationships among the organisms. Sometimes the lines are calibrated to time, with the location of each branch point corresponding to the hypothesized time the younger lineages diverged.

If a phylogenetic tree has a line at the base (usually drawn at the bottom or left; see phylogenetic tree (a) in the figure below), the tree is "rooted". Rooted trees can be read like a map of evolutionary history, starting from a single lineage at the base of the tree, which represents a common ancestor to all of the life shown in the tree, and up through the branches to the tips, which represent living organisms or the most recent fossil representative of the lineage. The rooted phylogenetic tree (a) shown below includes the three domains of life (Bacteria, Archaea, and Eukarya), with the "last common ancestor" of all life diverging into two Bacteria and Archaea lineages first. At some later point in time, the last common ancestor to Archaea and Eukarya diverged into two lineages, leading to modern Archaea and Eukarya. The Eukarya lineage eventually diverged into many more lineages, including plants and animals (including humans). The short lines between plants and animals show that they are more closely related to each other than any of the bacteria are to animals, for example. Similarly, the location of the branch point between plants and animals near the outside of the tree shows that they shared a common ancestor in much more recent times than the last common ancestor between animals and any of the Archaea, for example. Unrooted trees (see phylogenetic tree (b) in the figure below) do not show a last common ancestor to all the life in the tree. The branch geometry shows evolutionary relationships among the organisms, but the central point does not always indicate a common ancestor. Unrooted trees show hypothesized relationships among organisms, but not necessarily their evolutionary history.

Phylogenetic trees: Both of these phylogenetic trees shows the relationship of the three domains of life (Bacteria, Archaea, and Eukarya), but the (a) rooted tree attempts to identify when various species diverged from a common ancestor, while the (b) unrooted tree does not. 

Drawing Trees and Terminology

In a phylogenetic tree, each branch point represents a single lineage evolving into two distinct ones. A lineage that evolved early from the root of a tree and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the evolutionary relationships.

Rooted phylogenetic trees: The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where lineages diverged from each other. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.

It is important to note that the lines making up the tree represent ancestral organisms, not the organisms that are present at the tips of the lines. Sister taxa and polytomy share an ancestor, but the groups of organisms did not split or evolve from each other.; rather they split and evolved from a common ancestor. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other; both have evolved, as represented by the length of the lines extending from the branch point to the tips.

Phylogenetic trees can be drawn in multiple ways, but the order of branches is always the same for all trees based on the same data. Phylogenetic trees can look very different, but still illustrate the same relationships. For example, sister taxa can be rotated around their branch point, but they are still sister taxa. The location of the Animals and Fungi can be exchanged in the rooted tree above (a rotation around their branch point). When branch points are rotated, the taxon order changes but the information in the tree is the same because the sequence of branch points is the same. If you trace the evolutionary path from a common ancestor to an organism at a branch tip, the path does not change even if the branches are rotated. In other words, the evolution of each taxon from a branch point is independent of the other organisms in the tree. Similarly, branches can be drawn at angles to each other or with horizontal/vertical/circumfential bars connecting them (compare trees (a) and (b) above). These geometrical options in drawing phylogenetic trees allow scientists to visualize complicated data to help with interpretations. Scientists often choose options that emphasize the aspects of the evolutionary relationships that they are most interested in illustrating. 

Interpreting Rooted Trees

Rooted phylogenetic trees can serve as a pathway to understanding evolutionary history. A pathway can be traced from an ancestor, or even the origin of life, to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the “trunk” of the tree, one can discover that species’ ancestors, as well as where various lineages share a common ancestry. In addition, the tree can be used to study the evolutionary relationships within or between entire groups of organisms.

Many disciplines within biology contribute to understanding how past and present life evolved over time; together, these disciplines contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of organisms. Since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.

Key Points

• Rooted trees have a single lineage at the base representing a common ancestor that connects all organisms presented in a phylogenetic diagram.
• Branch points in a phylogenetic tree represent a split where a single lineage evolved into a distinct new one, while basal taxon depict unbranched lineages that diverged early from the root.
• Unrooted trees portray relationships among species, but do not depict their common ancestor.
• Phylogenetic trees are hypotheses and are, therefore, modified as more and better data becomes available.
• Systematics uses data from fossils, the study of bodily structures, molecules used by a species, and DNA analysis to contribute to the building, updating, and maintaining of phylogenetic trees.

Key Terms

• polytomy: a section of a phylogeny in which the evolutionary relationships cannot be fully resolved to dichotomies (splits into only two lineages)
• basal taxon: a lineage, displayed using a phylogenetic tree, that diverged early from the root and from which no other branches have diverged
• systematics: research into the relationships of organisms; the science of systematic classification
• phylogeny: the visual representation of the evolutionary history of organisms; based on rigorous analyses

Questions to ponder

• What aspects of organisms provide useful data for their classification?
• Look up a phylogenetic tree in a scientific publication. Are you comfortable interpreting it? What questions do you have about it?