Phylogenetic Trees and Geologic Time

Learning Objectives

Define and use the terminology required to describe and interpret a phylogenetic tree.
Interpret relatedness and monophyly of extant and extinct species based on phylogenetic trees, identify most recent common ancestors, and use the most recent common ancestor (MRCA) to recognize how closely related species are
Name the different types of data used to create phylogenetic hypotheses (trees) and know that hypotheses are revised as we gather more evidence
Define geologic time, list the four major eons in chronological order, and know the major events of life (or absence thereof) that define each eon
Relate the milestones of the evolution of major life forms (the topics of the upcoming readings: eukaryotes, Plants, Fungi, Animals) to the tree of life

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. The image below represents a basic phylogenetic tree, with the living species represented by letters across the top of the diagram.

What is a phylogenetic tree?

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, a taxonomic unit).

Modified from https://evolution.berkeley.edu/evolibrary/article/phylogenetics_02

Terminology of phylogenetic trees

Notice that the tree above tree 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 https://evolution.berkeley.edu/evolibrary/article/side_0_0/evo_06

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 enumerate some common misconceptions and how to correct your thinking.

A common mistake is to read the tips of the trees and think their order has meaning. In the tree at the top of the 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. The illustration below shows that one can rotate branches and not affect the structure of the tree, much like a hanging mobile:

From https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_primer_01 > Tips for Reading a Tree

Hanging bird mobile by Charlie Harper

2. Misconception: The tree you see includes all taxa in the clade. Reality: Taxa along the branches may be extinct or omitted. 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. Also, the root connects the tree you see out to the rest of the “tree of life.” Any tree represents a minuscule subset of the tree of life.

An ultra-metric tree of 5 taxa (A, Q, D, X, S) with evolutionary time shown in millions of years ago (Mya). The purple dotted line represents an evolutionary lineage with currently living taxa not represented in the 5-taxon tree. The fine dotted lines indicate a few evolutionary lineages that have gone extinct. Diagram is original work of Jung Choi

3. Misconception: The taxon with the longest branch back to a node of common ancestry must be the most primitive taxon in the tree. Reality: None of the currently living taxa are any more “primitive” or any more “advanced” than any of the others; they have all evolved for the same length of time from their most recent common ancestor. All tips, or taxa, in the tree have evolved for the same amount of time from their common ancestor. In the 5-taxon tree above, taxon S has the longest branch. While it is tempting to think that S is the 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 (like the purple dotted line) that are just not shown in the tree. Taxon S evolved for 5 million years, the same length of time as any of the other 4 taxa in that tree. As the tree is drawn, with the time axis vertical, the horizontal axis has no meaning, and serves only to separate the taxa and their lineages.

4. Misconception: Time is always oriented from recent at the top to old at the bottom. 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 branching patterns all convey the same information: evolutionary ancestry and patterns of divergence.

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 at the bottom 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

Phylogenetic trees are 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 our ancestors did.
all mammals produce milk from mammary glands because their ancestors did.

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

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.
Archaean (4.0-2.5 BYA) featured the formation of early life.
Proterozoic (2.5 BYA-542 MYA) featured oxygen accumulation and the flourishing of early life.
Phanerozoic (542 MYA to present) is defined by a proliferation of animal and plant life.

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 are more likely to be 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.

Milestones on the tree of life

Now that we know how to read a tree and consider geologic time scales, let’s relate topics of the upcoming readings: eukaryotes, green plants, fungi, animals, which are a few of the milestones of the evolution of major life forms, to the tree of life.

Notice that the tree is divided into three clades: bacteria, archaea, and eukarya (the eukaryotes). Eukaryotes are a clade that contains green plants, fungi and animals, three taxon groups that are more closely related to each other than to all other taxa depicted on the this tree. As we move forward through the biodiversity module, use this image of the breadth of taxa on the tree to put the small fraction of life we will learn about in perspective.

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 to consider biodiversity.

Additional resources

For more information, here is an excellent resource on phylogenetic trees:

https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_intro

If you want more practice reading trees and reviewing tree thinking, the following video is a supplemental review to tree thinking: