AP Bio Evolution (Unit 7) Mega-Review (25–26): From Natural Selection to Speciation to Phylogeny

Main ideas, concepts, and lessons (Unit 7: Evolution)

1) Big-picture goals of AP Bio Unit 7

• Evolution explains biological change across extremely long time scales.
• The unit’s flow:
  • Types of natural selection (natural, artificial, sexual)
  • Population genetics + Hardy–Weinberg equilibrium
  • Evidence for evolution
  • Speciation (how one species splits into multiple descendant species)
  • Phylogeny (tree/branching history of life)
  • Origin of life

---

2) Selection types (with examples and key mechanisms)

A. Artificial selection (selective breeding)

• Core idea: humans breed organisms toward desired traits over many generations.
• Process:
  • Breeders choose organisms with a target trait.
  • Over many generations, they repeatedly select those organisms.
  • This produces a population with a “guarded” gene pool biased toward the desired trait.
• Examples:
  • Brassica oleracea varieties (cauliflower, broccoli, Brussels sprouts, kale): all are varieties of the same species shaped by selection for different traits.
  • Dog breeds: bred from the same species lineage (Canis lupus) for human purposes (protection, hunting, aesthetics).

B. Natural selection

• Core idea: evolution occurs because inherited variation affects survival and reproduction.
• Key inputs:
  • Populations contain variation.
  • The important variation is inherited (genetic), produced by:
    • Mutation
    • Recombination
• Mechanism (sequence described):
  1. Variation exists in a population.
  2. In reproduction, more are born than survive.
  3. Survivors tend to have a beneficial inherited trait.
  4. Mutation keeps generating new variants each generation.
  5. Repeated cycles produce adaptation.
• Adaptation examples:
  • Bat wing structure
  • Bat sonar behavior + ear structure
  • Camouflage (satanic leaf gecko)
  • Molecular fit (enzymes matching substrates)

C. Sexual selection

• Core idea: selection for traits that directly increase reproductive success.
• Result: sexual dimorphism (males and females show different phenotypes).
• Two subtypes:
  • Intersexual selection (mate choice)
    • Typically females choose among males.
    • Example: female turkey chooses among males displaying tail extension, wattles, and behavior.
    • Example: peacocks—colorful males + choosy females.
  • Intrasexual selection (competition among same sex)
    • Males compete for harems or territories.
    • Leads to aggressive, larger, stronger males.
    • Example: elephant seals (large males vs females).

---

3) How selection changes phenotype distributions

Phenotypes often start as bell-curve continuous variation

• Example analogy: height distribution in a school.

Three standard selection patterns

• Directional selection
  • Selects against one extreme phenotype and shifts the population toward the other extreme.
• Stabilizing selection
  • Selects against both extremes; favors average phenotype.
  • Example: birth weight—too small or too big reduces survival; average survives most.
• Disruptive selection
  • If the average phenotype is maladaptive, selection favors both extremes, potentially splitting the population into two groups.

---

4) Adaptive melanism (directional selection example)

• Definition: darkening of organisms due to changing environmental conditions, driven over evolutionary time by changes in allele frequencies.
• Selective agent: typically predation.
• Mechanism described:
  • Genes for light coloration are selected against.
  • Genes for darker coloration are selected for.
  • A mutation increases melanin production; it spreads and produces darker subpopulations.

Peppered moth case study (directional selection + adaptive melanism)

• Two forms: light (“peppered”) and dark.
• Before the Industrial Revolution:
  • Trees/trunks were lighter and covered by whitish lichens.
  • Light moths had camouflage advantage → mostly light moths.
• During the Industrial Revolution:
  • Soot darkened trees and killed lichens.
  • Dark moths gained camouflage advantage.
  • Population mean phenotype shifted from light to dark.
• After ~1960:
  • Pollution declined (e.g., Clean Air Act).
  • Lichens returned; trunks lightened.
  • Population shifted back from dark to light.
• Scientific validation mentioned:
  • Work by Michael Majerus (early 2000s) replicating/confirming earlier work by B. D. Kettlewell.

---

5) Evolutionary fitness (what “fit” means)

• Not about strength or speed.
• Definition: evolutionary fitness = number of offspring that survive and reproduce (including offspring-of-offspring over time).
• Key point: fitness applies across stages of the life cycle (example montage of penguin stages: feeding, migration/march, breeding, juvenile huddling).

---

6) Population genetics + Hardy–Weinberg equilibrium

Population genetics

• Definition: study of how genes are distributed in populations and how they change over time.
• Key quantity: allele frequency
  • Evolution = change in allele frequencies within a gene pool (all alleles of genes in the population).

Misconception corrected

• Allele frequency (common vs rare) is not determined by dominance/recessiveness.
• Frequency depends on:
  • advantage/harm to phenotype
  • or random historical factors

The Hardy–Weinberg equations

• Equations:
  • P + Q = 1
  • P² + 2PQ + Q² = 1
• Meaning:
  • P = dominant allele frequency
  • Q = recessive allele frequency
  • P² = homozygous dominant genotype frequency
  • 2PQ = heterozygote genotype frequency
  • Q² = homozygous recessive genotype frequency
• Example problem structure described:
  • If recessive trait frequency is 0.49 (= Q²), then:
    • Q = √0.49 = 0.7
    • P = 1 − Q = 0.3
    • 2PQ = 2(0.3)(0.7) = 0.42
    • P² = (0.3)² = 0.09

Hardy–Weinberg principle (conditions required for no evolution)

• Core idea: allele frequencies remain constant unless conditions are violated.
• Five conditions for equilibrium (as listed):
  1. Population is infinitely large
  2. No harmful or beneficial alleles
  3. Random mating
  4. No immigration or emigration
  5. No net mutation between alleles
• If violated, allele frequencies change due to:
  • Genetic drift (especially in small populations)
  • Natural selection
  • Sexual selection (contrasted with random mating)
  • Gene flow
  • Directional mutation

Genetic drift (random allele frequency change)

• Definition: random change in allele frequencies, usually from small population size.
• Population bottleneck:
  • Catastrophic event wipes out most individuals.
  • Survivors may not represent original allele frequencies → some alleles disappear.
  • Example discussed: cheetahs show high genetic uniformity consistent with an extreme bottleneck; survivors were not “selected” (not natural selection), just lucky.
• Founder effect:
  • A small number colonize a new area.
  • Sampling error changes allele frequencies compared to source population.
  • Example described: allele frequencies shift dramatically on islands due to founder sampling.

Gene flow

• Definition: movement of alleles between populations.
  • Can be via migration of individuals or gametes.
  • Example mentioned: pollen movement in plants.
• Effect:
  • Alters allele frequencies in recipient populations
  • Reduces differences between nearby populations

Mutation and Hardy–Weinberg violation

• Role: ultimate source of genetic variation.
• Directional mutation can bias allele frequency changes (e.g., A mutating toward a specific other allele).

Heterozygote advantage (sickle-cell example)

• Sickle cell disease caused by a recessive allele (point mutation in hemoglobin gene):
  • valine substituted for glutamic acid
• Fitness pattern described:
  • SS homozygotes: selected against (disease)
  • SS heterozygotes (AS): selected for due to protection from malaria with less severe sickling
  • AA homozygotes (implied): less protected in malaria regions
• Key correlation: high frequency of the allele aligns with malaria intensity in parts of Africa.
• Other possible cases noted: cystic fibrosis, Tay-Sachs (speculated as potentially similar heterozygote-advantage scenarios).

---

7) Evidence for evolution (homology-centered)

Homologous traits (anatomy)

• Definition: shared underlying structure + shared embryological origin.
• Reason: descent with modification from a common ancestor.
• Example: vertebrate forelimbs (human, dog, bird, whale) share bone types and embryological origin.

Adaptive radiation

• Definition: one ancestral species produces multiple descendant species, each filling different ecological niches with unique adaptations.
• Example: Galápagos finches—same ancestor, different beaks as adaptations (homologous ancestry with divergent form).

Vestigial structures

• Definition: inherited structures with little/no current function, originally functional in ancestors.
• Examples: whale pelvis/hind-limb remnants; human tailbone (coccyx).

Homology vs analogy (convergent vs divergent evolutionary origin)

• Homology: same structure/underlying origin (common ancestry).
• Analogy: similar function but different underlying structure (convergent evolution).
• Examples:
  • Shark vs ichthyosaurs vs dolphins: hydrodynamic form is analogous (convergent).
  • Bird vs bat wings: could be considered analogous by function but homologous by shared forelimb bone inheritance.

Molecular homologies (genetic-level evidence)

• Definition: molecular similarities reflecting shared ancestry (structure/monomer sequence).
• Example: hemoglobin amino acid sequence differences correlate with relatedness.
  • humans vs gorillas = fewer differences than humans vs rhesus monkeys vs mice vs chickens vs frogs.

Pseudogenes

• Definition: nonfunctional gene variants from functional genes in related species.
• Example: human GULO pseudogene (vitamin C synthesis):
  • primates and some other mammals share remnants but with different mutations
  • indicates shared ancestry for gene presence but different disabling mutations later (convergent aspects across lineages)

Evidence reaching back to origin of life

Shared cellular/process features among all life:

• DNA as genetic material, ATP energy coupling
• universal genetic code
• ribosomes for protein synthesis
• shared metabolism (glycolysis, Krebs cycle, electron transport, ATP synthesis via chemiosmosis)

Embryology evidence

• Early embryos of vertebrates look similar; differentiation leads to adult forms.
• Embryos can retain vestigial features (tail, pharyngeal gill slits).
• Developmental gene evidence:
  • shared developmental “master switch” genes
  • Eyeless gene: transferred between species can trigger eye development despite different eye types
  • Homeotic genes: common patterning roles across diverse animals

Biogeography

• Definition: geographic distribution of species and varieties.
• Evidence logic: evolution happens in one area then spreads to adjacent areas; patterns match Earth-space and time-space distribution.
• Example: marsupials mostly confined to Australia due to isolation; only certain placental animals could reach via flight or rafting.
• Parallel evolution: marsupials fill niches similar to placental mammals elsewhere (convergent similarity by niche).

Fossils and dating

• Fossils: petrified remains; demonstrate change over time via transitional forms.
• Relative dating: uses superposition
  • younger layers on top of older layers in sedimentary rock (complications possible from faults/volcanism)
• Absolute dating: uses radioactive decay + half-life
  • Example: carbon-14 decay to nitrogen-14
  • half-life ~ 5,730 years; sample age inferred from remaining proportion
• Mentioned broader use: dating dinosaur extinction and other major evolutionary timelines.

Observed evolution happening today

• DDT resistance in mosquitoes
  • DDT kills many initially, but resistant individuals survive.
  • Their alleles increase quickly because mosquitoes have short generation time.
  • Reported timeline: mortality drops over months and becomes very low after ~16–18 months.
  • Parallel examples: antibiotic resistance (bacteria), herbicide resistance (weeds), chemotherapy resistance (cancer).

---

8) Species concept, reproductive isolation, and speciation

Biological species concept (BSC)

• Definition: species are groups that can naturally interbreed to produce viable, fertile offspring and are reproductively isolated from other such groups.
• Example: dog breeds can interbreed; duck species cannot (or only minimally).

Limitations of BSC

• Closely related species may hybridize yet remain “mostly separated.”
• Extinct or asexual species: hard to test fertility/viability.
• Prokaryotes: reproductive isolation rules are less clear.

Reproductive isolating mechanisms

• Definition: traits/behaviors that keep gene pools separate.
• Prezygotic isolation (prevents zygote formation):
  • Behavioral (different courtship/mating behaviors)
  • Temporal (different times/seasons)
  • Mechanical/structural (barriers preventing sperm/pollen transfer)
  • Habitat (different environments)
  • Gametic (molecular mismatch prevents fertilization)
• Postzygotic isolation (zygote forms but gene pools remain separate):
  • Hybrid inviability: hybrids fail to develop
  • Hybrid sterility: hybrids alive but cannot reproduce (example: mule sterility)
  • Hybrid breakdown: F2 generation inviable or infertile

Modes of speciation

• Allopatric speciation
  • Geographic barrier splits populations.
  • Stages described:
    1. Species widespread; gene flow between subpopulations
    2. Barrier arises; gene flow stops
    3. Different environments create different selection pressures and genetic differentiation
    4. When barrier disappears, populations diverged enough to be reproductively isolated
• Sympatric speciation
  • Occurs without geographic barrier.
  • Plant example: polyploidy can instantly create reproductive isolation in one generation.
  • Animal examples:
    • Lake Victoria cichlids: sexual selection contributes to reproductive isolation (experimentally verified in case study)
    • Microhabitat specialization: lice specialize to different bird body regions (head vs wings); specialization drives speciation over time

Adaptive radiation recap (ties to phylogeny)

• Adaptive radiation is the branching of descendant species into different niches.
• Phylogeny reflects such branching histories on a large scale.

---

9) Why phenotypic variation matters (raw material for selection)

Core lesson

• Phenotypic variation is essential because:
  • natural selection acts on phenotypes, not genotypes directly
  • selection increases survival/reproduction of beneficial phenotypes
  • without variation, there is no natural selection/adaptation and extinction risk increases

Examples of adaptive phenotypic variation

• Phospholipid saturation in snowy browsing mammals
  • More saturated in core, more unsaturated in extremities to maintain appropriate membrane fluidity and diffusion.
• Human hemoglobin variation across life stages
  • Fetal hemoglobin (gamma chains) has higher oxygen affinity to pull oxygen from maternal blood across placenta.
  • Transition from fetal to adult hemoglobin involves increasing beta chains after birth.
• Chlorophyll A vs B variation
  • Chlorophyll B absorbs more blue (shade/indirect light).
  • Chlorophyll A absorbs more red (direct light).
  • Proportions differ across shade-adapted vs direct-light-adapted plants; having both increases photosynthetic efficiency over time/seasons.

---

10) Phylogeny, phylogenetic trees, and how relationships are inferred

Definitions

• Phylogeny: evolutionary history.
• Phylogenetic tree: branching diagram showing evolutionary relationships.
• Clade: common ancestor + all its descendants.
• Shared derived character (synapomorphy):
  • trait that evolved in the common ancestor of a clade
  • defines/characterizes the clade compared to others
• Node: branching point; represents common ancestor of diverging lineages.
• Sister groups (sister clades): lineages that share a node (split from same ancestor).
• Outgroup: more distantly related group used for comparison to root/interpret relationships.
• Ancestral feature: trait shared but not specific enough to define a particular clade (also present in more inclusive groups).

Common mistake to avoid

Horizontal “closeness” on a drawing does not equal evolutionary closeness. Evolutionary closeness depends on recency of common ancestry. Trees can often be rotated around nodes without changing meaning.

Evidence and methods for building trees

• Morphology was used historically.
• Since ~post-1960, molecular evidence is gold standard:
  • DNA/RNA sequences, amino acid sequences in proteins
• Molecular clocks
  • constant-ish mutation rates over time for particular genes/proteins
  • calibrated using fossil record to infer timing of divergences
  • concept: number of mutations suggests time since split (hemoglobin used as a clock example)

---

11) Origin of life (high-level model + key experimental evidence)

Key questions

• How life emerged naturally (first cell problem).
• How complex biology chemistry arose without enzymes.

Major steps in a described origin-of-life scenario

1. Earth becomes habitable and stable enough for life to begin (asteroid/comet bombardment declines).
2. Abiotic chemistry produces monomers used in life:
   • amino acids, nucleotides, fatty acids, etc.
3. Abiotic formation of polymers from monomers plus formation of vesicles (capsules).
4. Formation of protocells (not fully living cells, but cell-like).
5. Emergence of self-replicating systems (leading to a last universal common ancestor).

Miller–Urey experiment (proof of concept)

• Setup:
  • sealed apparatus with chamber simulating early oceans
  • gases simulating early atmosphere (notably no oxygen)
  • electricity sparks simulating lightning