Getting Started
The immense diversity of life on Earth, from single-celled bacteria to giant sequoias, is the product of billions of years of evolution. To make sense of this diversity, biologists seek to understand the historical relationships among organisms. The core challenge is to reconstruct this "family tree" of life, a process that relies on piecing together clues from the past and present to map out the branching patterns of descent.
What You Should Be able to Do
After completing this section, you will be able to:
Describe the different types of morphological and molecular data used to build evolutionary trees.
Interpret a phylogenetic tree or cladogram to determine the evolutionary relationships between different lineages.
Explain how the gain or loss of traits, particularly shared derived characters, is used to group organisms.
Distinguish between a phylogenetic tree, which can represent time, and a cladogram, which only shows branching patterns.
Justify why these diagrams are considered testable and dynamic scientific hypotheses.
Key Concepts & Mechanisms
The study of phylogeny, the evolutionary history of a species or group of related species, is fundamentally a story of change and continuity over time. We use branching diagrams to visualize these relationships, which are inferred from various lines of evidence.
Baseline Condition: Common Ancestry
The foundational principle of phylogeny is that all life is related through descent from a common ancestor. For any two species, we can trace their lineages back in time to a point where they converge. This point of convergence, called the most recent common ancestor (MRCA), represents the ancestral organism from which both species evolved. The traits that organisms share because they were inherited from a distant ancestor are called shared ancestral characters. For example, a backbone is a shared ancestral character for all mammals, but it doesn't help us distinguish a tiger from a whale, as both inherited it from a much older vertebrate ancestor. This deep, shared history provides the continuity against which we measure evolutionary change.
Key Changes: Speciation and the Evolution of Traits
Evolutionary history is marked by change, primarily through two processes: the divergence of populations and the evolution of new characteristics.
Speciation: This is the evolutionary process by which populations evolve to become distinct species. On a phylogenetic tree, a speciation event is represented by a node, or branch point. The node signifies the MRCA of all the species that descend from that branch point, known as lineages.
Evolution of New Traits: As lineages evolve independently after a speciation event, they accumulate unique changes. A novel trait that appears in a lineage and is passed down to its descendants is called a shared derived character. These characters are the key to building phylogenetic trees because they are unique to a particular group, or clade. For example, hair is a shared derived character for mammals. It evolved in the ancestor of all mammals and is unique to that group, distinguishing them from other vertebrates like reptiles and birds. The loss of a trait, such as the loss of limbs in snakes, can also be a derived character that defines a group.
Key Continuities: Conserved Traits and Molecular Data
While new traits drive the branching of the tree, continuities provide the evidence for deeper relationships. Shared ancestral characters, like the genetic code or the presence of ribosomes in all known life, demonstrate a profound shared history. In modern phylogeny, molecular data—such as similarities in DNA, RNA, or protein sequences—has become a primary source of evidence. Genes and proteins that are essential for basic life functions are often highly conserved, meaning they change very slowly over time. By comparing these sequences between species, scientists can quantify their genetic similarity and infer evolutionary relationships, even between organisms that look vastly different, like a yeast and a human. The more similar the sequences, the more recently the species shared a common ancestor.
Key Models & Diagrams
Phylogenetic trees and cladograms are constructed by analyzing and grouping organisms based on shared derived characters. A character matrix is a common tool for organizing this data. An outgroup—a species or group known to have diverged before the lineage containing the groups we are studying—is used to determine which character states are ancestral and which are derived.
Constructing a Simple Cladogram from a Character Matrix
| Character | Lancelet (Outgroup) | Lamprey | Tuna | Salamander | Turtle | Leopard |
|---|---|---|---|---|---|---|
| Vertebrae | 0 | 1 | 1 | 1 | 1 | 1 |
| Jaws | 0 | 0 | 1 | 1 | 1 | 1 |
| Four Limbs | 0 | 0 | 0 | 1 | 1 | 1 |
| Amniotic Egg | 0 | 0 | 0 | 0 | 1 | 1 |
| Hair | 0 | 0 | 0 | 0 | 0 | 1 |
Step 1: All the study organisms share vertebrae, which the outgroup lacks. This is a shared derived character for the entire group (vertebrates).
Step 2: Jaws evolved next, uniting all but the lamprey.
Step 3: Four limbs unite the salamander, turtle, and leopard.
Step 4: The amniotic egg unites the turtle and leopard.
Step 5: Hair is a shared derived character unique to the leopard.
This matrix leads to a cladogram with a nested hierarchy: the leopard is a turtle-like amniote, which is a four-limbed tetrapod, which is a jawed vertebrate.
Key Components & Evidence
Phylogenetic Tree: A diagram representing the evolutionary history of a group of organisms. Phylogenetic trees can show the amount of change or time along their branches, whereas cladograms are simpler and only show the branching pattern of shared characters.
Node: A branch point on a tree representing a speciation event and the most recent common ancestor of the descendant lineages.
Lineage: A continuous line of descent from an ancestor.
Shared Derived Character: An evolutionary novelty unique to a particular clade (e.g., feathers in birds). It is used to establish a group's distinct identity.
Shared Ancestral Character: A character that originated in an ancestor that is not a member of the group being studied (e.g., vertebrae in mammals, which originated in an earlier vertebrate ancestor).
Morphological Data: Evidence from the physical structures of organisms, including fossils. This was the original basis for phylogenetic analysis.
Molecular Data: Evidence from DNA, RNA, or protein sequences. It is highly quantitative and has revolutionized the field of phylogeny.
Hypothesis: Phylogenetic trees are not facts but testable hypotheses. They are constantly being revised and refined as new evidence emerges, particularly from DNA sequencing.
Skill Snapshots
Causation
Cause: A mutation leads to the evolution of feathers in an ancestral dinosaur lineage. Effect: This shared derived character becomes the defining trait for the clade we now call birds.
Cause: A new fossil is discovered with a unique combination of traits from two different groups. Effect: The existing phylogenetic hypothesis for those groups may need to be revised to accommodate this new evidence.
Cause: Scientists compare the sequence of the cytochrome c gene across dozens of species. Effect: The number of differences in the DNA sequence is used to infer the relative time since the species last shared a common ancestor.
Comparison
Phylogenetic trees vs. Cladograms: Phylogenetic trees can have branch lengths that are proportional to evolutionary time or genetic change, while cladograms only illustrate the pattern of evolutionary relationships.
Morphological vs. Molecular Evidence: Morphological evidence is based on observable physical traits (e.g., bone structure), whereas molecular evidence is based on similarities in genetic code and protein structure.
Derived vs. Ancestral Characters: A derived character (like hair in mammals) defines a specific clade, while an ancestral character (like the vertebral column in mammals) is shared with a larger group of more distantly related organisms.
Change and Continuity Over Time (CCOT)
Baseline: The last universal common ancestor passed on a shared genetic code and basic cellular machinery to all subsequent life.
Change 1: The evolution of the amniotic egg allowed a lineage of vertebrates to reproduce on land, leading to the divergence of reptiles, birds, and mammals.
Change 2: The evolution of flowers in an ancestral plant led to the massive diversification of the angiosperm lineage.
Continuity: The presence of mitochondria is a shared ancestral trait for all eukaryotes, indicating their origin from a common ancestor that engulfed an ancient bacterium.
Common Misconceptions & Clarifications
Misconception: Organisms shown at the tips on the right side of a tree are more "advanced" or "evolved" than those on the left.
Clarification: A phylogenetic tree shows patterns of relatedness, not a ladder of progress. All living (extant) species at the tips of the tree are equally successful in their own environments. The branching order can be rotated around any node without changing the relationships.
Misconception: Two species that are next to each other at the tips of a tree are always each other's closest relatives.
Clarification: To find the closest relative of a species, you must trace back to find its most recent common ancestor (the first node you encounter). An organism's closest relative is the one with which it shares the most recent node.
Misconception: Phylogenetic trees are absolute facts.
Clarification: Trees are scientific hypotheses based on the best available evidence. They are dynamic and subject to change. The discovery of new fossils or, more commonly, the analysis of new molecular data can lead to significant revisions of our understanding of evolutionary history.
One-Paragraph Summary
Phylogeny is the science of reconstructing the evolutionary history and relationships among organisms. This history is visualized using phylogenetic trees and cladograms, which are testable hypotheses, not definitive facts. These diagrams are built using evidence from both morphology (physical traits of living and fossilized organisms) and molecular sequences (DNA and proteins). The key to their construction is identifying shared derived characters—novel traits that define a specific group, or clade—which indicate divergence from a common ancestor. By interpreting these branching diagrams, we can determine how closely related species are based on their most recent common ancestor. As new evidence emerges, these hypotheses are constantly tested and revised, reflecting the dynamic nature of scientific inquiry into the history of life.