Phylogeny

AP Biology Notes — Evidence for Evolution, Fossils, Phylogeny & Cladistics

Fossils

  • Fossil: Preserved remains or traces of organisms in rock.

  • From Latin fossus = “dug up.”

  • Form only under special conditions (rapid burial, low oxygen).

What fossils tell us

  • What organisms lived in the past.

  • Transitional forms linking ancestors and descendants.

  • Timing of speciation, migration, and extinction.

  • Information about ancient environments (climate, geography).

Fossil Formation (Simplified)

  1. Organism dies and is buried by sediment.

  2. Sediment layers accumulate.

  3. Pressure compacts sediment into rock.

  4. Remains become preserved as fossils.

Fossil Record

  • Shows gradual change and lineage splitting over time.

  • Contains gaps due to:

    • Rare fossilization

    • Geological processes

  • Used to identify:

    • Speciation

    • Extinction

    • Migration

Classic fossil examples

  • Horse evolution: changes in size, teeth, feet.

  • Whale evolution: Pakicetus → Ambulocetus → Rodhocetus → modern whales.

  • Burgess Shale: Cambrian explosion, early complex life.

Evidence for Evolution (AP Core)

1. Fossil Record

  • Direct evidence of evolutionary change.

  • Shows order of appearance of species.

2. Comparative Anatomy

  • Homologous structures

    • Same structure, different function.

    • Indicate common ancestry.

    • Example: pentadactyl limb.

  • Analogous structures

    • Same function, different structure.

    • Result of convergent evolution.

    • Example: bird wings vs butterfly wings.

  • Vestigial structures

    • Reduced, nonfunctional remnants.

    • Evidence of ancestry.

    • Example: human tailbone, snake pelvic bones.

3. Embryology

  • Early embryos of different species look similar.

  • Indicates shared ancestry.

  • Early development reflects basic body plan genes.

  • Examples:

    • Pharyngeal pouches in vertebrates.

    • Human embryonic tail.

4. Molecular Biology (Strongest Evidence)

  • DNA and protein comparisons show relatedness.

Amino acid sequences

  • Same species → identical proteins.

  • More differences = longer divergence time.

  • Can act as a molecular clock.

  • Limitation: only ~2% of DNA codes for proteins.

DNA comparisons

  • DNA hybridization measures similarity.

  • Higher hybridization = closer relationship.

  • Same species ≈ 100% match.

  • Useful when fossil evidence is missing.

Mass Extinction

  • Rapid loss of many species in short time.

  • Identified in geological record.

  • Often followed by adaptive radiation.

Major extinctions (know examples)

  • Permian (250 mya): largest; trilobites extinct.

  • Cretaceous (65 mya): dinosaurs, ammonites extinct.

Phylogeny

  • Study of evolutionary relationships.

  • Represented by phylogenetic trees.

  • Trunk = common ancestor.

  • Branches = diverging lineages.

  • Closely related species = closer branches.

Cladistics

What cladistics is

  • Method of classification based on evolutionary relationships.

  • Groups organisms by shared derived traits.

  • Focuses on branching, not “advancement.”

Key terms

  • Derived trait: new trait not in ancestor.

  • Primitive trait: old ancestral trait.

  • Synapomorphy: shared derived trait.

  • Outgroup: helps identify ancestral traits.

  • Sister groups: two lineages from same node.

How to build a cladogram (AP-style)

  1. Choose taxa.

  2. Choose traits (characters).

  3. Determine ancestral vs derived traits.

  4. Group by shared derived traits.

  5. Apply parsimony (fewest changes).

  6. Draw branching diagram.

Cladogram Rules

  • Organisms go at the tips, not nodes.

  • Each node = common ancestor.

  • Each trait should appear once, unless convergent.

  • No organism is “more evolved.”

Key AP Exam Triggers

  • Homologous → common ancestry.

  • Analogous → convergent evolution.

  • Vestigial → evolutionary history.

  • DNA similarity → closest relationship.

  • Mass extinction → adaptive radiation.

  • Cladistics → shared derived traits only.