The Tree of Life over Geologic Time

Learning Objectives

  1. When provided with a phylogenetic tree with specific evolutionary milestones, use evidence to place an unknown organism with specific, given traits on the phylogenetic tree of life and within the geologic time scale.
  2. Define adaptive radiations and their evolutionary importance
  3. Place specific origins of groups (nodes) and adaptive radiations (such as Cambrian Explosion, mammals) on the geologic time scale.
  4. Describe the movement of continents over geologic time and recognize how their past locations explain why organisms are found where they are today
  5. Describe climatic conditions over geologic time (ex: Snowball Earth) and recognize how past conditions shape the traits of organisms over time (oxygenic photosynthesis)

Apply your knowledge to place unknown organisms onto the tree of life

We began the module by learning how to read phylogenies. In the previous readings in this Biodiversity Module, we’ve noted that key innovations or adaptations arose in lineages and came to define the clade. For example, in the tetrapod phylogeny depicted at this link, all living tetrapods share the derived trait of five digits, with wrists and ankles turned forward for walking on land. If you were presented with a vertebrate specimen that also had these characteristics, you would logically label it as a tetrapod, and then use other additional characteristics to further categorize it and consider when it lived and what else flourished at that time. As the module wraps up, you now have the additional biodiversity knowledge to place organisms of unknown origin onto the phylogenetic tree of life and into the geologic time scale.

Adaptive Radiations

As we’ve learned, the Cambrian “explosion” refers to an increase in biodiversity of multicellular organisms at the start of the Cambrian, 542 million years ago. Multicellular life appeared only several tens of millions of years before the start of the Cambrian, as enigmatic fossils (Ediacaran biota) exhibiting body plans unlike present-day animals. These largely disappeared and were replaced by Cambrian fauna, whose variety includes all of the body plans found in present-day animal phyla. The appearance of Cambrian fauna, although relatively quick in evolutionary time, actually spans millions of years; they did not all appear simultaneously, as the term “explosion” inaccurately implies.

Adaptive radiations are periods of increasing biodiversity and rapid speciation in geologic time, and they occur when new ecological niches become available, as occurs after a major climate event like the oxygen revolution or after a mass extinction. Adaptive radiations may also occur in response to a “key innovation,” an adaptive trait that is novel in the environment. Examples include traits like multicellularity, wings, nectar spurs in flowers, or flat molars in mammals. Each of these opens up newly available resources to the individuals with the trait. Consider the evolution of jaws. The ability to bite other organisms opens up an array of available prey items.

In a phylogeny, an adaptive radiation often looks “tufty,” like the tip of a paintbrush, with lots of short bristles (branches) coming off a longer branch.

The Cambrian species radiation also coincided with an increase in free oxygen to near-present day levels (more on that below), which matters because available oxygen allows for highly efficient metabolic energy use.

Origins and radiations can be mapped to the geologic time scale

Reflect back on the diversity of species from this module and consider when adaptive radiations occurred in each group. For instance, mammals arose in the Mesozoic but didn’t radiate into the diverse group they are today until the Cenozoic, after the dinosaurs’ extinction opened up access to resources. If we map those radiations (“flourished” in the table below) to the geologic time scale, we can correlate major earth events with lineage diversification: the change in atmospheric oxygen over time, changes in global climate, the location of continental land masses through continental drift and associated sea-level changes.

Stop and check: Reading the chart below, can you confirm the information in the above paragraph for the origins and flourishing of groups? Be sure you can do this before moving on, as it will greatly increase your understanding of events across geologic time.

Geologic time scale with major life and climate events. Image credit: Chrissy Spencer CC BY-NC-SA 4.0.

This short PBS Eons video ties together a group’s proliferation or radiation with the major geologic periods, and gives some perspective on both how much we can understand about the history of life using fossils, and how much mystery might remain in the fossil record for the 99% of taxa that have gone extinct already.

Continental drift over geologic time helps explain species distributions

Over geologic time, not only have species diversity and composition changed, but also the location of the continents themselves have shifted. Continental drift is the very gradual movement, assembly, and rifting of the crustal plates and their associated continents. This process means that when a taxon arose millions of years ago, it probably lived in a different location with respect to the equator and poles, and in a location that may have been connected physically with what are now separate continents. The short animation below shows the projected movement of continents, based on evidence from the magnetic rock record and other geological clues. As you view it, consider a specific group, such as reptiles, and when they arose and flourished globally.


Climate shapes evolution

The rock record holds more than the fossils themselves. It also gives evidence for climate conditions on early Earth. Here we’ll describe three that are inter-related: “Snowball Earth,” oxygenation of the atmosphere, and temperature changes over time.

Snowball Earth

Evidence from geology, the oxygenation of the atmosphere, and models of plate tectonics indicate predict a likely scenario: the earth was covered with glacial ice sometime preceding 600 MYA. The hypothesis for this “snowball earth” ties together evidence the following ideas, not all of which are necessary for a global and long ice age to have occurred:

  • Continental land would need to be massed near the equator to maximize the albedo effect (cooling due to reflected sunlight). While oceans absorb heat from the sun rather than reflect it, land at the equator actually reflects light and heat, preventing surface temperature from increasing.
  • Cyanobacteria in the oceans produced oxygen in excess of the amount that could be sequestered by reactions in the ocean with iron. These reactions formed rock layers with alternating bands of iron-rich sediment. These so-called banded iron formations indicate that oxygen was present in the oceans or seas and reacting with dissolved iron to form iron oxides, which were heavy and sank to the ocean floor.
  • Once iron and other reactants, like organic carbon, in the ocean became depleted, the excess oxygen eventually accumulated in the atmosphere, where it may have reacted with the “greenhouse gas” methane to form carbon dioxide. The subsequent reduction in methane would have reduced the ability of the planet to retain the reflected light and heat, allowing the surface to cool.
  • Burial of large quantities of organic material in anaerobic sediments (eventually turning into coal and petroleum) allowed oxygen to accumulate in the atmosphere to present-day levels. The increase in oxygen enabled the evolution of larger bodies and organs and tissues, such as brains, with high metabolic rates.

Evolution of oxygenic photosynthesis changed the planet’s atmosphere over billions of years, and in turn caused radical shifts in the biosphere. Life continues to alter the planet: the latest in a succession of evolutionary innovations, humans are now impacting the composition of atmospheric gases, with yet undetermined consequences for life on Earth.

Oxygenation of the atmosphere

No other planet in our solar system has oxygen gas in the atmosphere. Oxygen is highly reactive, and quickly consumed by oxidation reactions. On Earth, oxygenic photosynthesis continually replenishes the oxygen consumed by respiration and other oxidative processes (e.g., rusting of iron, weathering of rocks). The history of oxygen gas in the Earth’s atmosphere sums up the history of life, as follows:

  • Stage 1 (3.85–2.45 Ga): The early Earth had practically no oxygen gas (O2) in the atmosphere.
  • Stage 2 (2.45–1.85 Ga): Bacteria split water and generate O2 as a byproduct via oxygenic photosynthesis in the oceans. The O2 is absorbed in oceans and seabed rock by reacting with soluble iron and precipitated iron oxide (rust) from the oceans, generating banded iron formations. Oxygen dissolved in the water column led to aerobic metabolism, which is energetically more efficient, and eventually enabled the evolution of eukaryotes (around 2 BYA)
  • Stage 3 (1.85–0.85 Ga): O2 starts to gas out of the oceans into the atmosphere and is absorbed by land surfaces and formation of ozone layer. These function as “sinks” for the O2.
  • Stages 4 and 5 (0.85 Ga–present): O2 sinks become saturated, and the gas accumulates in the atmosphere. In the oceans, the first multicellular organisms arose (around 800 MYA).
Image credit: Oxygenation-atm.svg: Heinrich D. Hollandderivative work: Loudubewe [CC-BY-SA-3.0 ( or GFDL (], via Wikimedia Commons
Oxygen gas (O2) accumulation in the Earth’s atmosphere, represented from a range of different estimates (red and green lines) over time in billions of years (BYA or Ga).
Image credit: Oxygenation-atm.svg: Heinrich D. Hollandderivative work: Loudubewe [CC-BY-SA-3.0 ( or GFDL (], via Wikimedia Commons

Temperature and sea level

The Earth has experienced large swings in global temperature, from the probable “Snowball Earth” in the Proterozoic to a fluctuation between hothouse and intermittent glaciation, shown below, in the Phanerozoic.

Global temperatures in the Phanerozoic, relative to the 1960-1990 average temperature. Note the change in the timescale on the X axis. Image credit: Glen Fergus [CC BY-SA 3.0 (], from Wikimedia Commons.

Multiple factors caused these large swings in global temperature, including changes in solar output, extreme volcanic activity, meteor strikes, and atmospheric greenhouse gases, such as carbon dioxide. In fact, carbon dioxide levels are currently above 400 ppm, the highest in the past 10 million years.

The Khan Academy video below on the Proterozoic Eon below reviews many of these ideas:


and here’s a PBS Eons video with an overview of oxygen, diversification, and extinction, which makes a nice bridge to the reading for next time on extinction: