Table of Contents
Evolution is a historical process. Just like the history of a human family can be reconstructed from photos, documents, and memories, the history of life can be reconstructed from biological “traces.” These traces are the evidence for evolution.
This chapter gives an overview of the main kinds of evidence that organisms have a common origin and have changed over time. Each of the following subchapters in the course will later expand particular lines of evidence in more detail.
What Counts as Evidence in Evolutionary Biology?
In evolutionary biology, “evidence” means observable facts about living and fossil organisms that are best explained if species share common ancestors and have changed gradually (and sometimes rapidly) over long periods.
Important general features of evolutionary evidence:
- It comes from many independent sources (palaeontology, comparative anatomy, genetics, embryology, biogeography, etc.).
- Different kinds of evidence often converge on the same conclusions (for example, fossils and DNA both support the same branching patterns of relationships).
- Evidence is used to test and refine hypotheses (for example, predictions about “transitional forms” or about similarities in DNA sequences).
In this chapter, we focus on the types of evidence. The detailed cases (fossils, transitional forms, homology, etc.) are treated in their own sections later.
Direct and Indirect Evidence
In the sciences, it is useful to distinguish between direct and indirect evidence:
- Direct evidence: traces of past life or past states of organisms themselves.
- Fossils (preserved remains or traces of ancient organisms)
- Ice cores or sediments with preserved pollen, DNA, or shells
- Indirect evidence: patterns in living organisms that are best explained by descent with modification, even though we do not directly see the past states.
- Similarities in anatomy and molecular sequences
- Developmental patterns during embryogenesis
- Geographic distribution of species
- Presence of vestigial (rudimentary) structures and atavisms
In evolutionary biology, these two forms are combined. For example, fossil skulls (direct evidence) and comparative anatomy of modern skulls (indirect evidence) together support a particular sequence of change.
Evidence That All Organisms Share Common Ancestry
Several observations point specifically to the idea that all living things are related by descent from a common ancestor.
Universal Biochemical and Genetic Features
All known organisms share:
- The same basic genetic material: DNA as the main long-term information carrier, and RNA in information transfer and protein synthesis.
- A nearly universal genetic code (the same codons specify the same amino acids in almost all life forms; deviations are minor and themselves evolutionarily interpretable).
- The same 20 standard amino acids in proteins (with a few rare exceptions).
- Very similar core metabolic pathways:
- Glycolysis
- Citric acid (Krebs) cycle (in aerobic organisms)
- ATP as the universal energy currency
These deep similarities are difficult to explain by chance or by independent creation of each species, but follow naturally if all living things inherited these features from a shared ancestor.
Hierarchical Similarity Patterns
When we compare organisms in detail (morphology, DNA, proteins), similarities form a nested hierarchy:
- For example, cats and dogs share many features with each other and with other mammals; mammals share more distant features with birds and reptiles; all these share features with other vertebrates, and so on.
- The same hierarchical pattern appears in:
- Anatomical structures (bones, organs)
- Protein and DNA sequences
- Developmental genes and pathways
This nested pattern matches what we would expect from a branching tree of life, where lineages split and accumulate differences over time. It is not the pattern we would expect if organisms were assembled independently without historical connections.
Predictive Power of Common Ancestry
Common ancestry allows testable predictions, for example:
- If whales evolved from land mammals, then:
- Whale genomes should be most similar to certain land mammals.
- Whale embryos should temporarily show limb buds and other mammalian features.
- Fossils should exist showing intermediate forms with both terrestrial and aquatic traits.
Many of these predictions have been confirmed, illustrating how common ancestry serves as an explanatory and predictive framework rather than just an after-the-fact description.
Evidence That Species Change Over Time
Besides common ancestry, evolution also involves change within lineages. Several kinds of evidence show that species are not fixed.
The Fossil Record as a Historical Archive
Fossils provide a time-ordered archive of life’s history. Taken together, they show:
- Organisms in older rocks are generally simpler or different from those in younger rocks.
- Entire groups (for example, dinosaurs, trilobites) appear, diversify, and then disappear.
- Many modern groups have earlier, more primitive representatives in older strata.
The fossil record does not preserve every organism or every step, but it contains enough information to trace broad sequences of change in many lineages.
Observed Evolution in Real Time
In some cases, evolutionary change has been observed directly:
- Microorganisms: Bacteria and viruses evolve resistance to antibiotics and antiviral drugs within years or even months.
- Insects and plants: Pesticide resistance and herbicide resistance arise and spread in populations.
- Wild animals: Measurable shifts in beak size, body size, or coloration have been documented over decades in response to environmental changes.
These observations demonstrate that variation and natural selection can produce heritable changes within observable time scales. Over geological time, similar processes can lead to larger-scale differences between species and higher groups.
Geographical Patterns (Biogeography)
The distribution of species on Earth also provides evidence for evolution:
- Many species are restricted to particular continents or islands, even when other areas seem ecologically suitable.
- On islands, species often resemble those on the nearest mainland, but with distinctive modifications (for example, unique island birds and reptiles).
- Similar environments in different parts of the world often host different species that are related to local lineages, not to each other (for example, marsupials in Australia vs. placental mammals in similar niches elsewhere).
These patterns are easier to explain if species originated in certain regions and then diversified and spread, rather than being placed independently in their current locations.
Developmental and Anatomical Clues
The bodies and development of organisms also carry traces of their history:
- Embryos of different vertebrates (fish, amphibians, reptiles, birds, mammals) show stages with remarkable similarities, suggesting shared developmental programs inherited from a common ancestor.
- Adult organisms often carry rudimentary or vestigial structures that no longer serve their original function (for example, reduced hind limb bones in whales and some snakes). These make sense as leftovers from ancestral stages.
Such clues are not easily explained as optimal designs for current function, but they fit well with the idea of descent with modification.
Multiple Independent Lines of Evidence
A key strength of evolutionary theory is that:
- Different disciplines (palaeontology, comparative anatomy, genetics, embryology, biogeography, ecology) produce independent evidence that supports the same broad picture.
- These lines of evidence often make convergent predictions:
- Relationships between species inferred from anatomy match those inferred from DNA sequences.
- Timing of divergence estimated from molecular data agrees (within error limits) with the ages of fossils.
- Transitional forms predicted from comparative anatomy are later found as fossils in rocks of the expected age and location.
This consilience—different sources of evidence pointing toward the same conclusions—greatly increases confidence that evolution has occurred and that evolutionary theory is a reliable explanation.
Overview of the Specific Evidence Types in Later Sections
The rest of this part of the course will examine some major categories of evidence more closely:
- Common Origin of All Living Things: Focus on universal cellular and molecular features and “tree of life” patterns.
- Fossils as Evidence for Evolution: How fossils form, how they are dated, and what broad patterns they show.
- Transitional Forms: Fossil and living examples that bridge major groups.
- Evidence from Ontogeny: What embryonic development reveals about evolutionary history.
- Homology and Analogy: How shared structures distinguish common ancestry from mere functional similarity.
- Rudimentary Organs and Atavisms: How leftover and reappearing traits document past stages of evolution.
Together, these provide a robust, multifaceted foundation for understanding evolution not just as an idea, but as a well-supported scientific explanation for the diversity of life.