Divergent evolution: common ancestor, different environments, different adaptations = homologous organs. Example: forelimbs of vertebrates (human arm, bat wing, whale flipper, horse leg - all from same ancestral limb bone pattern but different functions). Convergent evolution: different ancestors, similar environments, similar adaptations = analogous organs. Example: wings of birds (bone-based) vs wings of insects (integument-based). Both solve same problem (flight) but independently evolved. Parallel evolution: closely related species evolve similar features independently. Example: Old World and New World vultures (both evolved large size, soaring, scavenging lifestyle from different hawk/stork ancestors). Coevolution: two or more species evolve in response to each other. Flowers and pollinators, predators and prey, hosts and parasites.

Homologous organs: same structural origin (same embryonic derivation from common ancestor), different function. Examples: forelimb of humans (arm/hand - grasping), bat (wing - flight), whale (flipper - swimming), dog (foreleg - running) - all derived from same ancestral limb bones (humerus, radius, ulna, carpals, metacarpals, phalanges). Evidence for divergent evolution from common ancestor. Analogous organs: different structural origin, same function. Examples: wings of birds (modified forelimb bones + feathers) vs wings of insects (chitinous outgrowths of thorax). Streamlined body of dolphins (mammals) vs sharks (fish) - both have fusiform body for swimming but one is warm-blooded mammal, other is cold-blooded fish. Both evolved by convergent evolution independently. Key test: examine internal anatomy. Homologous = same bone pattern. Analogous = completely different internal structure.

Rapid diversification of one species into many species occupying different ecological niches. Classic examples: Darwin's finches: ~14 species descended from one finch ancestor that reached Galapagos Islands ~2-3 million years ago. Different beak shapes for different food: thick bill (seed cracker), long thin bill (nectar feeder), woodpecker-like (insect extraction), warbler-like. Hawaiian honeycreepers: ~50 species from one finch ancestor. Even more diverse than Galapagos finches. Marsupials of Australia: thylacine (wolf-like), koala (bear-like), Tasmanian devil (badger-like), quoll (cat-like), numbat (anteater-like), kangaroo (grazer), wombat (burrower). All marsupials. Each evolved convergently with placental equivalent in rest of world. Cichlid fish of African Rift Valley lakes: hundreds of species from few ancestors. Incredibly rapid speciation (10,000 years for some lake fauna).

Fossil record: preserved remains of past life. Transitional fossils: Archaeopteryx (reptile + bird features), Tiktaalik (fish + tetrapod - shows limb evolution from fins), Pakicetus (land mammal + whale features), horse series (Hyracotherium to Equus showing size increase, toe reduction). Comparative anatomy: homologous structures = common ancestry. Vestigial organs: remnant non-functional structures (human appendix, ear muscles, coccyx, wisdom teeth, male nipples, whale pelvic bones). Molecular evidence: DNA, protein sequences. More similar sequences = more recent common ancestor. Cytochrome c sequence: human and chimp 99% identical; human and yeast ~65% identical. Biogeography: species distribution patterns explained by continental drift and evolution. Marsupials in Australia (isolated after Gondwana breakup). Embryology: vertebrate embryos similar in early stages (gill slits, tails) = shared ancestry.

Directional selection: phenotype mean shifts toward one extreme. Example: industrial melanism in peppered moths. Drug resistance: bacteria with resistance mutations survive antibiotic treatment, reproduce. Selection for dark moths, for resistant bacteria. Stabilising selection: favours intermediate phenotype, reduces variation. Human birth weight: extremes (too small or too large) have higher mortality. Most common = intermediate. Reduces variance over time. Disruptive (diversifying) selection: favours both extremes, eliminates intermediates. Can lead to sympatric speciation. Example: Coho salmon (large fighting males + small sneaky males both succeed reproductively, intermediate size neither). Sexual selection: traits that increase mating success. Intrasexual: male-male competition (antlers, horns). Intersexual: female choice (peacock tail, bird of paradise). Frequency-dependent selection: fitness of phenotype depends on how common it is. Negative frequency-dependence: rare phenotypes have advantage (mimicry systems).

Biological species concept (Mayr): species = groups that can interbreed and produce fertile offspring, reproductively isolated from other groups. Limitations: does not apply to asexual organisms, allopatric populations (not in contact), fossils. Allopatric speciation: geographic separation (mountains, sea, desert) divides population. Different selective pressures + genetic drift accumulate differences. Eventually reproductive isolation even if reunited. Example: Grand Canyon squirrels (Abert vs Kaibab squirrel on north vs south rim). Sympatric speciation: new species in same geographic area. Polyploidy in plants: allopolyploidy (hybridisation + genome doubling). Triticum aestivum (bread wheat): hexaploid from 3 ancestral diploid species. Ecological specialisation + assortative mating. Prezygotic isolation: prevents mating (habitat, temporal, behavioral, mechanical, gametic isolation). Postzygotic isolation: allows mating but reduces hybrid fitness (hybrid inviability, sterility - mule = horse x donkey, sterile).

Molecular clock: macromolecular sequences change at relatively constant rate over time. More sequence differences = longer evolutionary separation. Calibrated against fossils. Neutral theory of molecular evolution (Kimura, 1968): most DNA changes at molecular level are neutral (no fitness effect), not driven by natural selection. Rate of neutral evolution = mutation rate. Molecular phylogenetics: use DNA/protein sequences to reconstruct evolutionary relationships. Maximum parsimony, maximum likelihood, Bayesian inference methods. 16S rRNA: used to classify bacteria and archaea (Carl Woese - discovered Archaea as separate domain). Mitochondrial DNA: maternally inherited, high mutation rate, used for human population genetics and migration patterns. Human migration out of Africa: mitochondrial Eve (common maternal ancestor ~200,000 years ago in Africa), Y-chromosomal Adam.

Primate evolution: ~55 MYA first primates. ~35 MYA Old World monkeys. ~25 MYA gibbons separate. ~15 MYA orangutans. ~10 MYA gorillas. ~7 MYA chimpanzee-human split. Hominid evolution (after split from chimps): Sahelanthropus tchadensis (~7 MYA, Africa, earliest possible hominin). Ardipithecus (~4.4 MYA). Australopithecus afarensis (~3.2 MYA, Lucy, Ethiopia, bipedal, brain 400-500 cc). Australopithecus africanus (~3-2 MYA, South Africa). Homo habilis (~2.3-1.5 MYA, first tool use, brain 600-700 cc). Homo erectus (~1.8-0.1 MYA, first out of Africa, fire, brain 900-1100 cc). Homo heidelbergensis (~700-200 KYA, Europe + Africa, gave rise to Neanderthals in Europe and modern humans in Africa). Homo neanderthalensis (~400-40 KYA, Europe/Asia, brain ~1500 cc, ritual burial, interbreed with H. sapiens - 1-4% Neanderthal DNA in non-African humans). Homo sapiens (~300 KYA anatomically modern, ~50 KYA behaviourally modern, replaced all other Homo species).