Phylogeny
Tree of Life

Discover how biologists reconstruct evolutionary relationships using phylogenetic trees, shared derived characters, and molecular evidence.

AP Biology

What is Phylogeny?

Phylogeny is the study of the evolutionary history and relationships among organisms or groups of organisms. It answers the fundamental question: How are living things related to one another?

Phylogenetics connects to every major topic in biology: it explains why organisms share traits, predicts characteristics of undiscovered species, and helps us understand the mechanisms of evolution.

Essential Vocabulary

Clade

A group consisting of an ancestor and all of its descendants: a single "branch" on the tree of life.

Node

A branching point representing the most recent common ancestor (MRCA) of the taxa that diverge from it.

Taxon

Any named group of organisms (species, genus, family, etc.) that appears as a tip or internal branch on a tree.

Outgroup

A distantly related taxon used to root the tree, establishing the direction of evolutionary change.

Synapomorphy

A shared derived character: a trait that evolved in the ancestor of a clade and is shared by all its members.

Anatomy of a Phylogenetic Tree

How Are Trees Constructed?

Biologists build phylogenetic trees using two main categories of evidence. The goal is to identify homologous traits: features shared due to common ancestry, not convergent evolution.

Morphological Data

Compare physical structures like bone anatomy, flower structure, or embryonic development. Homologous structures (e.g., forelimbs of mammals) indicate shared ancestry.

Molecular Data

Compare DNA, RNA, or protein sequences. More similar sequences indicate closer relatedness. This is the most powerful modern method.

Building Trees: Parsimony vs. Maximum Likelihood

With multiple possible tree topologies, biologists need a principle to choose the best one. Two major approaches dominate:

Maximum Parsimony

Select the tree that requires the fewest evolutionary changes. Based on Occam's Razor: the simplest explanation is preferred.

Maximum Likelihood

Select the tree that has the highest probability of producing the observed data, given a model of sequence evolution.

Homology vs. Analogy

A critical distinction in phylogenetics: not all similar traits indicate common ancestry. You must distinguish homologous from analogous structures.

	Homology	Analogy
Definition	Similarity due to shared ancestry	Similarity due to convergent evolution
Example	Human arm and bat wing	Bird wing and insect wing
Underlying structure	Same bone arrangement	Different structure
Useful for phylogeny?	Yes	No: misleading
Also called	Homologous structures	Analogous / Convergent

Human, bat and cat forelimb illustrations are compared. A separate schematic marks corresponding humerus, radius, ulna, wrist and five digits, with elongated bat digits and short thumb. An unresolved shared-ancestry companion has three living tips. — These independently enlarged forelimb topology schematics identify corresponding humerus, radius, ulna, wrist and five digits. They compare homology rather than exact bone shapes or proportions, and do not make living species ancestors of one another.

Homologous forelimbs versus analogous wings

Human arm, bat wing, whale flipper and cat foreleg specimens accompany an authored proximal-to-distal skeletal correspondence diagram.

Corresponding forelimb bones reflect shared ancestry despite different functions. Bird and bat forelimb bones are homologous, while bird and insect flight surfaces are analogous.

Same skeletal plan, different uses

Corresponding forelimb bones reflect shared ancestry despite different functions. Bird and bat forelimb bones are homologous, while bird and insect flight surfaces are analogous.

Types of Groupings

Monophyletic

An ancestor and all of its descendants. This is a true clade and the only valid grouping in cladistics.

Paraphyletic

An ancestor and some but not all of its descendants. Example: "Reptilia" excluding birds.

Polyphyletic

A group that does not include the most recent common ancestor. Grouped by convergent traits, not ancestry.

Shared Derived Characters

Phylogenetic trees are built on the principle of shared derived characters (synapomorphies). Understanding the difference between ancestral and derived characters is essential.

Ancestral Character

A trait that was present in the common ancestor of the group being studied. Example: vertebrae in all vertebrates.

Derived Character

A trait that evolved after divergence from the ancestor. Example: hair in mammals (not found in other vertebrates).

How to Read a Phylogenetic Tree

1

Identify the root. The root is the common ancestor of all taxa on the tree. It establishes the direction of evolution (bottom to top, or left to right).

2

Find the nodes. Each internal node represents a speciation event where one lineage split into two. The node is the most recent common ancestor (MRCA) of the taxa above it.

3

Trace shared ancestry. Two taxa are more closely related if they share a more recent common ancestor. Follow branches back to find their MRCA.

4

Ignore tip order. Branches can rotate around any node without changing relationships. What matters is the branching pattern, not the left-right position of taxa.

5

Identify the outgroup. The taxon that branches off first (closest to the root) is the outgroup and is the most distantly related to the other taxa.

Example: Reading a Vertebrate Tree

Example: Molecular Phylogeny

Scientists compare DNA sequences to determine relatedness. Fewer differences in sequence = more recent divergence.

Species Pair	DNA Differences (per 1000 bp)	Inferred Relatedness
Human vs. Chimpanzee	12	Very close
Human vs. Gorilla	18	Close
Human vs. Orangutan	35	Moderate
Human vs. Lemur	82	Distant

Example: Character Matrix to Tree

A character matrix lists which taxa possess which derived characters. Use it to build a cladogram step by step.

Taxon	Hair	Amniotic Egg	Four Limbs	Jaws
Lamprey (outgroup)	-	-	-	-
Salamander	-	-	+	+
Lizard	-	+	+	+
Cat	+	+	+	+

Common Mistakes

✕ Reading Tip Proximity

Students assume taxa next to each other on the tips are most closely related. Only the branching pattern matters, not the left-right order of tips.

✕ Counting Branch Steps

Relatedness is NOT determined by counting branches between tips. Trace back to the most recent common ancestor instead.

✕ Confusing Analogy with Homology

Using convergently evolved traits (like wings in bats and birds) to infer close relatedness. Always check if the underlying structure is the same.

✕ "More Evolved" Fallacy

Thinking some organisms are "more evolved" than others. All living species have been evolving for the same amount of time since their common ancestor.

✕ Ignoring the Outgroup

Failing to identify the outgroup, which roots the tree and establishes the direction of character evolution (ancestral vs. derived).

Summary of Key Concepts

Concept	Definition	AP Exam Significance
Clade	Ancestor + all descendants	Must identify on trees
Synapomorphy	Shared derived character	Basis of cladistic grouping
Outgroup	Distantly related taxon	Roots the tree
Parsimony	Fewest evolutionary changes	Know the principle
Molecular clock	Mutation rate estimates time	Divergence time estimation
Monophyletic	Valid clade (all descendants)	Only valid grouping
Homology	Similarity from ancestry	Useful for phylogeny
Analogy	Similarity from convergence	Misleading: avoid

Question 1 of 5

On a phylogenetic tree, what does a node represent?

A node (internal branching point) represents a speciation event: the most recent common ancestor of the lineages that diverge from that point. Tips represent extant taxa, not nodes.

Question 2 of 5

A group that includes an ancestor and all of its descendants is called:

A monophyletic group (clade) includes an ancestor and all of its descendants. Paraphyletic groups exclude some descendants; polyphyletic groups don't include the common ancestor at all.

Question 3 of 5

Wings in birds and wings in insects are an example of:

Bird wings and insect wings have different underlying structures (bone vs. chitin membrane) but serve a similar function (flight). This is convergent evolution, producing analogous, not homologous, structures. They should NOT be used to infer close relatedness.

Question 4 of 5

When comparing DNA sequences between species, a scientist finds 15 differences between Species X and Species Y, but 45 differences between Species X and Species Z. What can be inferred?

Fewer DNA sequence differences indicate more recent divergence. With only 15 differences, X and Y diverged more recently than X and Z (45 differences). This does NOT mean Y evolved from X: they share a common ancestor. We also cannot determine the outgroup without additional information.

Question 5 of 5

The principle of maximum parsimony in phylogenetics states that:

Maximum parsimony applies Occam's Razor to phylogenetics: among all possible trees, the one that requires the fewest evolutionary changes (mutations, character state changes) is considered the most likely. It doesn't address the number of branches or the type of data used.