Phylogenetic Trees and Geologic Time

Learning Objectives

  • Define and use formal terminology to describe and interpret a phylogenetic tree
  • Interpret relatedness of extant and extinct species based on phylogenetic trees, including identifying monophyletic groups, identifying most recent common ancestors (MRCA), and using the MRCA to evaluate how closely species are related
  • Name the different types of data used to create phylogenetic trees, and recognize that hypotheses represented by phylogenetic trees are revised as we gather more evidence
  • Define geologic time, list the four major eons in chronological order, and identify the major events of life (or absence thereof) that define each eon

Biological Diversity is Represented in Phylogenetic Trees

Biological diversity is the topic of this module. All organisms that ever existed on this planet are related to other organisms in a branching evolutionary pattern called the tree of life. To decipher this relatedness between the diversity of organisms, both living and extinct, “tree thinking” is invaluable. Tree thinking, or phylogenetic thinking, helps us unravel the branching evolutionary relationships between extant species, while thinking about the passage of time and the ancestors of each of those living species.

A phylogenetic tree is a visual representation of the relationship between different organisms, showing the path through evolutionary time from a common ancestor to different descendants. Trees can represent relationships ranging from the entire history of life on earth, down to individuals in a population. Trees that show species help us understand how new species form from common ancestral species. The process of new species formation, called speciation, is the starting point for a discussion of biological diversity. The natural endpoint will be extinction.

The diagram below shows a tree of 3 taxa (singular taxon, also known as a taxonomic unit). A biological taxon is one or more populations of organisms that form an evolutionary meaningful unit. A taxon might be a domain (e.g., Eukaryota), a kingdom (e.g., Animalia), a Phylum (e.g., Chordata), a class (e.g., Mammalia), an order (e.g., Primates), a family (e.g., Hominidae), a genus (e.g., Homo), a species (e.g., Homo sapiens), one or more populations within a species, or even an individual gene.

3 taxon tree
Modified from

Terminology of Phylogenetic Trees

Notice that the tree above branches from a single trunk into two branches, the vertical lines, and then the left side branches again. In this tree, the vertical branches represent a lineage, which is a taxon, shown at the tip, and all its ancestors. The nodes are where lineages diverge, representing a speciation event from a common ancestor. The trunk at the base of the tree is actually called the root, and the root node represents the most recent common ancestor of all of the taxa represented on the tree. Time in this particular style of tree is represented vertically, proceeding from the oldest pictured here at the bottom to the most recent at the top.

What this particular tree tells us is that taxon A and taxon B are more closely related to each other than either taxon is to taxon C. The reason is that taxon A and taxon B share a more recent common ancestor than A and B do with taxon C. The least related taxon in a tree is called the outgroup of that phylogeny, and it often included because it has contrasting characteristics relative to the other included taxa. A group of taxa that includes a common ancestor and all of its descendants is called a monophyletic group, or a clade. Groups that exclude one or more descendants or that exclude the common ancestor are not monophyletic groups (clades); these groups are called paraphyletic and polyphyletic, respectively.  

Mono-, poly-, and paraphyletic tree comparison
This figure shows several monophyletic (top row) vs a polyphyletic (bottom left) or paraphyletic (bottom right) trees. from

The video below focuses on terminology and explores some misconceptions about reading trees:

Misconceptions and How to Correctly Read a Phylogenetic Tree

Trees can be confusing to read. Below we list some common misconceptions and how to correct your thinking:

  • Misconception: you can identify relationships by reading across the tips. One very common mistake is to read “across the tips” of the trees and think the order of the tips has meaning. In the image below, the closest relative to the star is not the square. In the tree show below (also at the top of this page), the closest relative to taxon C is not taxon B. Both A and B are equally distant from, or related to, taxon C. In fact, switching the labels of taxa A and B would result in a topologically equivalent tree. It is the order of branching along the time axis that matters.
3 taxon tree
Modified from

The illustration below shows that one can rotate branches and not affect the structure of the tree, much like a hanging mobile; in other words, all three trees below show identical relationships because the topology (branching patterns) are the same, even though the order across the tips is different:

Tips for Reading a Tree
From > Tips for Reading a Tree
Hanging bird mobile by Charlie Harper
Hanging bird mobile by Charlie Harper
  • Misconception: everything represented in the tree is also visible in the tree: Another common mistake is to assume that the tips on tree you see include all taxa in the clade. In reality, taxa along the branches may be not shown because they are extinct or omitted for space. Also, the phyletic evolution that occurs along a branch is not usually included in the branching tree. Phyletic evolution is the evolutionary change along a branch that doesn’t result in speciation. Finally, the root connects the part of the tree that you see out to the rest of the “tree of life.” Any tree represents a minuscule subset of the tree of life. The image below shows the phylogenetic relationships among vertebrates, but shows only one representative species for each group; for example, bony fish are not the only type of fish, but they are the only example shown on this tree to represent all fish. In addition, extinct species and phyletic evolution are represented within the branch patterns but are not shows visually on the tree.
Vertebrate phylogeny. Image credit: Donna Fernstrom,
  • Misconception: The longest branch shows the most “primitive” species. Another common error in interpreting trees is to assume that the taxon with the longest branch back to a node of common ancestry must be the most primitive taxon in the tree. In reality, none of the currently living taxa are any more “primitive” or any more “advanced” than any of the others; all the living taxa have all evolved for the same length of time from their most recent common ancestor. In the tree above, the Fish taxon has the longest branch. While it is tempting to think that fish are most “primitive,” or most like the common ancestor represented by the root node, there were undoubtedly many branches off that lineage during the course of evolution, most leading to extinct taxa (99% of all species are thought to have gone extinct), and many to living taxa that are just not shown in the tree. The tree is drawn with time on the vertical axis; the horizontal axis has no meaning, and serves only to visually separate the taxa and their lineages. 
  • Misconception: Time always runs top to bottom, or along the angle of the branches. A final misconception we will discuss here is assumptions about how time is represented in trees. In some cases, it is incorrectly assumed that time is always oriented from “recent” at the top to “old” at the bottom. In other cases, it is incorrectly assumed that time runs at an angle if branches are shows running at an angle rather than horizontal or vertical. In reality, phylogenetic trees can have different forms; they may be oriented sideways, inverted (most recent at bottom), or the branches may be curved, or the tree may be radial (oldest at the center). Regardless of how the tree is drawn, the tips are more recent in time, and the root is older in time; branching patterns all convey the same information: evolutionary ancestry and patterns of divergence.

The image below shows a radial tree; time moves from the root to the arc, where the root is “old” and all taxa represented by the tips along the arc are “recent” in the same time:

Phylogeny of South African native ungulates within placental mammals. Image credit: Avilla L. S.; Mothé D. (2021). “Out of Africa: A New Afrotheria Lineage Rises From Extinct South American Mammals“. Frontiers in Ecology and Evolution9doi:10.3389/fevo.2021.654302. ISSN 2296-701X

The image below shows two identical phylogenetic trees. In both trees, time runs vertically, with “older” at the bottom where the root is, and “more recent” at the top, where the tips are; time does NOT run at an angle in the tree on the left.

Two seemingly different, though identical, cladograms, illustrating the idea that neither shape, nor a particular arrangement of the terminal branches really matters. The only information included in the cladogram is the information on the nested pattern of the sister-group relationships. Image credit: Alexei Kouprianov;

The vertebrate evolution phylogeny linked here shows time running from left to right, with the present day at the right. Because this phylogeny overlays a timescale, it has a special term called an evogram. Notice also that in the phylogeny, some taxa are alive today (extant), but others are not (extinct); extinct taxa don’t extend to the present day, such as Tiktaalik in the center of the image. Key character states are indicated with small ticks along the branches. The immediate descendant have these shared, derived character states, and most of their descendants will have them as well, unless the traits are lost in a future branch of the lineage.

Constructing Phylogenetic Trees

A phylogenetic tree represents a hypothesis about how taxa are related to each other. That hypothesis is derived from existing evidence: data collected through observation of morphological or genetic traits, also called character states. Morphological data include structural features, types of organs, and specific skeletal arrangements. Genetic data include mitochondrial DNA sequences, ribosomal RNA gene sequences, and any genomic genes of interest.

These types of data are used to identify homology, which means similarity due to common ancestry. In that same way that individuals inherit traits from their parents, homology indicates a shared, derived ancestry for a trait. For example,

  • all humans have large brains and opposable thumbs because they inherited it from their ancestors.
  • all mammals produce milk from mammary glands because they inherited it from their ancestors.

Trees are evolutionary hypotheses constructed on the principle of parsimony, which is the idea that the most likely branching pattern is the pattern that requires the fewest changes. For example, it is much more likely, or parsimonious, that all mammals produce milk because they all inherited mammary glands from a common ancestor that produced milk from mammary glands, versus the alternate hypothesis that mammary glands evolved independently in multiple lineages.

As with any hypothesis, a tree can be revised if biologists gain additional data that contradicts the current thinking. Therefore, we will likely see substantial uncertainty in some of the trees we work with in this module. Instead of feeling frustrated by this, consider that you are observing the scientific process in real time. We don’t always have answers, but we can always make a new hypothesis of how lineages arose and diversified.

Geologic Time and the Evolution of Life on Earth

The story of the history of life is one of diversification, which is the proliferation of new taxa, and extinction, or the loss of taxa. As you read above, 99% of all species that ever lived are now extinct. Evidence for life in the past is embedded in the rock record as fossils and trace fossils, like oil or coal beds in the place where and when many organisms died. The earth is 4.6 billion years (BY) old, so geologists work on immensely long time scales broken into four eons, defined by how many billion years ago (BYA) or million years ago (MYA) they occurred:

  • Hadean (4.6-4.0 BYA) occurred before life arose (or at least, before there is compelling evidence of life).
  • Archaean (4.0-2.5 BYA) featured the evolution of early life.
  • Proterozoic (2.5 BYA-542 MYA) featured oxygen accumulation and the flourishing of early microbial and multicellular life.
  • Phanerozoic (542 MYA to present) is defined by a proliferation of animal and plant life.
geologic time scale, ccs

The eons we will focus on are subdivided into a series of eras and periods. Famous eras you may already have heard of include the Paleozoic, which literally translates as old life. The well known periods may also familiar: the Cambrian is when animal life  diversified greatly, the Carboniferous featured land plants, the Jurassic and the Cretaceous are remembered for domination and demise of the dinosaurs. We will take time to place organism groups into their eons, eras, and periods, so it’s worth orienting yourself to the geologic time scale before we begin to meet the diversity of life that lived in the past and were the ancestors to modern taxa.

The video below from the PBS series Eons summarizes key geologic time scale events and emphasizes the evolution of life milestones that will get us started as we move forward in this module on Biodiversity.

Additional Resources

Here is an excellent resource on phylogenetic trees for more information: Understanding Evolution: the Tree Room

If you notice that you would benefit from more practice reading trees and reviewing tree thinking, the following video is a great review to tree thinking: