7.9Natural Selection

Phylogeny — AP BIOLOGY Revision Notes & Topical Questions

5 min read 8 parts Lesson 10 of 13 2 quizzes

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Lesson summary

7.9 Phylogeny — Notes — AP Biology notes: Describe the evidence used to infer evolutionary relationships and how phylogenetic trees and cladograms show them.Purpose — phylogenetic trees and cladograms show hypothesised evolutionary relationships among groups, based on shared char…

Synapomorphy
Molecular clock
Root — the common ancestor of all members of the tree
Clade (monophyletic group) — an ancestor and all its descendants; reptiles excluding birds are not a true clade
Rotation — rotating branches around a node does not change relationships, and a tree is not a ladder of progress
Unresolved branches — three clades from one ancestor show too little data to say which are more closely related

Section 1 of 8Trees and cladograms

Purpose — phylogenetic trees and cladograms show hypothesised evolutionary relationships among groups, based on shared characteristics; they are testable hypotheses that are revised as evidence arises, not facts.

Phylogenetic tree — shows relationships plus evolutionary time or genetic divergence; it may be scaled to time or amount of change, calibrated using the fossil record or molecular clocks.

Cladogram — shows branching patterns of shared derived characters (synapomorphies) with no time scale,

so it shows neither time nor number of changes between nodes.

Root — the common ancestor of all members of the tree.

Section 2 of 8Reading a tree

Node (branch point) — the most recent common ancestor of the lineages that branch from it; a more recent common ancestor means closer relatedness.

Clade (monophyletic group) — an ancestor and all its descendants; reptiles excluding birds are not a true clade.

Shared derived characters — traits that evolved in the common ancestor of a clade and are present in its members; shared ancestral characters occur in a wider group and do not define the clade.

Outgroup — the lineage that diverged earliest (least closely related), lacking the derived characters,

and used as a reference; it is not the oldest organism.

Sister taxa — two groups sharing an immediate common ancestor, such as humans and chimpanzees; neither evolved from the other.

Rotation — rotating branches around a node does not change relationships, and a tree is not a ladder of progress.

Tracing — count nodes back to a common ancestor; only one node links crocodilians and birds, so they are closer to each other than to any other clade.

Unresolved branches — three clades from one ancestor show too little data to say which are more closely related.

Section 3 of 8Evidence for relationships

Molecular data — DNA and amino acid sequences give many quantifiable characters and are more accurate than morphology.

Convergent evolution — morphological traits may arise independently (wings in bats, birds and insects), misleading anatomical trees.

Molecular clock — differences accumulate at a fairly constant mutation rate, so more differences mean an earlier divergence.

Parsimony — the best tree needs the fewest evolutionary changes.

Section 4 of 8Reading phylogenetic trees

Feature	Meaning	Note
Root	Common ancestor of all	Base of tree
Node	Divergence point	Where branches split
Branch length	Time or change	Meaningful only if scaled
Sister taxa	Share most recent ancestor	Adjacent branches
Shared derived trait	Defines a clade	Hair in mammals

Section 5 of 8Classification: ranks, clades and historical systems

Use classification together with phylogeny. Taxonomy names and groups organisms; phylogeny describes hypotheses about their evolutionary relationships. A branching tree is not a ladder of progress, and living groups should not be ranked as more or less evolved.

Ranks and relatedness

The main ranks, from broad to specific, are domain, kingdom, phylum (or division), class, order, family, genus and species.

Family is more specific than order, class and phylum, but less specific than genus and species.
In a multiple-choice question, distinguish the most specific rank among the listed options from the most specific rank in the full hierarchy.
See OpenStax: organising life.

A shared recent ancestor indicates close relatedness. Jellyfish and corals are both cnidarians. Chordates and echinoderms are grouped within the deuterostome clade of bilaterian animals. This does not mean that deuterostomes are simply the latest or most advanced animals to evolve. See OpenStax: animal phylogeny.

Land plants and fungi

Charophyte green algae share the closest common ancestry with land plants among the broad algal groups used here. Living charophytes are relatives, not the literal ancestors of living land plants. Protective reproductive structures helped early plants reproduce on land; bryophytes retain a dominant gametophyte generation and do not produce seeds or flowers. See green-algal relationships and early land-plant adaptations.

Flower structures include the anther and the carpel, whose parts include the stigma and style. A hypha is a fungal filament, not a flower part. Moulds are fungi, and a network of hyphae is a mycelium. Moulds are not all members of one group called Deuteromycota. See OpenStax: fungal structure.

Read the classification framework in the question

In the traditional five-kingdom scheme, Monera grouped prokaryotes, while Protista grouped many eukaryotes often described as plant-like, animal-like or fungus-like. These are historical categories and should not be confused with modern evolutionary clades. In the three-domain framework, Bacteria and Archaea are separate from Eukarya; the thermoacidophile Sulfolobus is an archaeon. Arthropods belong to Animalia.

Modern evidence has split the former Protista grouping into multiple evolutionary lineages. When an older question uses five-kingdom names, answer within its explicitly stated historical framework. See Bacteria and Archaea and changes to protist classification.

Section 6 of 8More from the specification

1Environmental change

A change in abiotic or biotic conditions, often caused by humans.

2Sympatric speciation

Speciation in the same area without a geographical barrier.

3Habitat

The place where an organism lives.

4Protein

A long chain of amino acids containing carbon, hydrogen, oxygen and nitrogen.

5Genetic diversity

The range of alleles within a population.

6Selection pressure

A factor, such as an antibiotic, that favours survival of some individuals.

7Allopatric speciation

Speciation caused by geographical isolation.

8Natural selection

Survival and reproduction of the best-adapted individuals.

9Genetic drift

Change in allele frequency due to chance, most important in small populations.

10Punctuated equilibrium

Speciation in rapid bursts between long stable periods.

11Species

A group of organisms that can reproduce to produce fertile offspring.

12Speciation

The formation of new species.

13Extinction

Loss of every member of a species.

14Population

A group of organisms of one species in the same area at the same time.

15Isolation

Separation of populations so that they cannot interbreed.

16Barrier

A structure that prevents pathogens from entering.

Section 7 of 8Key terms

Term	Meaning
Phylogenetic tree	diagram of hypothesised evolutionary relationships
Cladogram	diagram of branching based on shared derived characters
Clade	an ancestor and all its descendants
Node	branch point representing a common ancestor
Outgroup	least closely related lineage in the tree
Synapomorphy	shared derived character
Molecular clock	use of mutation rate to time divergence

Section 8 of 8Exam technique

Reading relatedness from the order of tips — relatedness is shown by the most recent common node.

Assuming one sister taxon evolved from the other — they share an ancestor.

Treating a cladogram as having a time scale, or reading branch length as time.

Thinking the outgroup is the oldest organism — it is the least closely related.

Last updated: 20 October 2026