Evolution, Plant Biology, and Ecology – Vocabulary Review

Evolution & Population Genetics

• Population

  • Group of individuals of the same species living in the same area.
  • Share a gene pool → the sum of all alleles in that population.

• Evolution (Modern-Synthesis Definition)

  • Change in allele frequencies in a population across generations.
  • Measured by comparing successive gene pools.

• Five Mechanisms of Evolution (ordered as in transcript)

  • Mutation
  • Random changes in DNA; ultimate source of new alleles.
  • Introduces genetic variation on which other mechanisms act.
  • Gene Flow (Migration)
  • Movement of individuals or gametes between populations.
  • Adds/removes alleles, usually ↑ variation, can homogenize populations.
  • Genetic Drift
  • Random fluctuations in allele frequency, strongest in small populations.
  • Sub-types:
    • Bottleneck Effect – drastic size reduction (e.g.
      volcanic eruption) → loss of rare alleles, ↓ variation.
    • Founder Effect – new population started by a few colonists;
      allele frequencies differ from source (e.g. island iguanas).
  • Non-random Mating (Sexual Selection / Inbreeding)
  • Alters genotype frequencies, may expose deleterious recessives.
  • Natural Selection
  • Only mechanism that consistently produces adaptation (fit between organism & environment).
  • Three Modes
    • Directional – favors one extreme (e.g. giraffe neck length).
    • Stabilizing – favors intermediates (e.g. human birth weight).
    • Disruptive – favors both extremes, can lead to speciation (e.g. seed-cracker finches).

• Key Genetic Concepts

  • Pleiotropy – one gene → multiple phenotypic effects (e.g. cystic fibrosis gene affects lungs, pancreas, sweat glands).
  • Polygeny (Polygenic Inheritance) – many genes → one trait (e.g. human height); opposite relationship to pleiotropy.
  • Allele vs Gene – gene = DNA region coding for trait; allele = alternative version of that gene.

• Hardy–Weinberg Equilibrium (HWE)

  • Describes a non-evolving population.
  • Conditions: large size, random mating, no mutation, no migration, no selection.
  • Algebraic form: $p+q=1$ and $p^2+2pq+q^2=1$ where
  • $p$ = frequency of dominant allele, $q$ = recessive.
  • Deviation → evolution occurring; used as null model in population genetics.

• Fixation Probability Under Drift

  • Probability that a neutral allele with frequency $p$ becomes fixed = $p$.
  • Smaller populations reach fixation/loss faster.

• Why Beneficial Mutations Can Disappear

  • Stochastic loss via drift when rare.
  • Opposing selection pressures, pleiotropic costs, or gene flow.

Phylogenetics & Taxonomy

• Taxonomy – naming/classifying organisms.
• Systematics – infers evolutionary relationships (phylogeny).
• Cladogram – branching diagram showing relationships (no branch length meaning).
• Phylogenetic Tree – may include branch lengths = time/changes.
• Homology vs Analogy
  • Homologies (shared ancestry) are informative; analogies (convergence) are misleading if unrecognized.
• Monophyletic (clade) – ancestor + all descendants.
• Paraphyletic – ancestor + some descendants.
• Polyphyletic – unrelated taxa grouped by homoplasy.
• Reading trees: locate common ancestors, trait origins, sister taxa.

Fungi (Chapter 32)

• General Traits

  • Eukaryotic heterotrophs by absorption.
  • Cell walls of chitin.
  • Unicellular (yeasts) or multicellular (molds, mushrooms).

• Structures

  • Hyphae – microscopic filaments; can be septate or coenocytic.
  • Mycelium – interwoven hyphae network; high SA : V for absorption.
  • Mushroom (Basidiocarp/Ascoma) – reproductive, elevates spores.

• Life Cycle Highlights

  • Phases: haploid (N), dikaryotic (N+N), diploid (2N).
  • Karyogamy (nuclear fusion) often delayed → long dikaryotic stage.

• Major Groups (emphasis on two most diverse)

  • Ascomycota – sac fungi, produce ascospores in asci (e.g.
    morels, Penicillium).
  • Basidiomycota – club fungi, basidiospores on basidia (e.g.
    mushrooms, rusts). Key difference = spore-bearing structure.
  • Others: Chytridiomycota (only flagellated spores, alternation of generations present), Zygomycota (bread molds), Glomeromycota (arbuscular mycorrhizae), Deuteromycota ("imperfect", asexual stages only).

• Symbioses

  • Lichen – fungus + photosynthetic partner (alga/cyanobacterium).
  • Mycorrhizae – fungus + plant roots; types:
  • Ectomycorrhizae – sheath around roots.
  • Arbuscular (Endo-) Mycorrhizae – penetrate root cells.

Algae & Opisthokonts / Archaeplastida Context

• Algae Monophyly? – Algae overall are polyphyletic; green algae ⊂ Archaeplastida.

• Green Algae Closest to Land Plants – Charophytes.

• Green Algae Monophyletic? – No; Chlorophytes + Charophytes not exclusive of plants.

• Volvox – colonial green alga; asexual & sexual reproduction.

• Spirogyra – filamentous; sexual conjugation.

• Brown Algae – multicellular, fucoxanthin pigment, alternation of generations (e.g.
  kelp).

• Red Algae – phycoerythrin pigment, can live deeper, no flagella.

• Opisthokonts – clade containing fungi, animals, choanoflagellates.

• Archaeplastida – red algae, green algae, land plants; unified by primary plastid origin.

• Endosymbiotic Theory – mitochondria & chloroplasts derived from engulfed bacteria; supported by double membranes, circular DNA, ribosomes, independent division.

Plant Evolution & Reproduction (Weeks 5 & 28-27)

Alternation of Generations

• Sporophyte (2N) – produces spores via meiosis.
• Gametophyte (N) – produces gametes via mitosis.
• Dominance trend: gametophyte dominant in bryophytes; sporophyte dominant in ferns, gymnosperms, angiosperms.
• Antithetic Theory – sporophyte originated as independent generation added onto ancestral gametophyte.
• Heterospory – microspores (♂) & megaspores (♀); precursor to seeds; advantages: resources focused on female, pollen dispersal of male.

Bryophytes

• Dominant green plant = gametophyte.
• Antheridia = sperm; Archegonia = eggs.
• No true roots; require water for sperm.
• Sporophyte stalks derive nutrients from gametophyte.

Seedless Vascular Plants

• Sporophyte dominant (ferns, lycophytes, horsetails).
• Sori on fern fronds house sporangia (meiosis → spores).
• Swimming sperm; no seeds.

Gymnosperms

• Sporophyte dominant (trees).
• Pollen replaces swimming sperm.
• Male vs female cones; seed = embryo + food reserves + seed coat (parent sporophyte tissue).

Angiosperms

• Flowers, fruits, double fertilization.

  • Pollen tube delivers two sperm → egg $+$ sperm → zygote (2N); central cell (N+N) $+$ sperm → endosperm (3N) = nutrition.

• ABC Model of Flower Development

  • Gene sets specify organ identity.
  • A alone → sepals; A+B → petals; B+C → stamens; C alone → carpels.

• Flower Parts

  • Sepals (outer, protective), petals (attraction), stamens (anther+filament, male), carpels/pistil (stigma+style+ovary, female).
  • Hypogynous – ovary superior; Epigynous – ovary inferior.
  • Symmetry: radial vs bilateral.

• Fruit – mature ovary; protects seeds & aids dispersal.

  • Develops from ovary wall (pericarp) → layers: exocarp, mesocarp, endocarp.

• Seed Morphology

  • Embryo (2N) + endosperm (3N) + seed coat (2N maternal).
  • Monocot vs Dicot Embryogenesis – monocots form one cotyledon/coleoptile; dicots two cotyledons.

• Hormones in Seeds

  • Auxin – apical dominance, embryonic patterning.
  • Cytokinins – cell division, shoot initiation.
  • ABA (Abscisic Acid) – induces dormancy (physiological, physical, combinational types).

• Pollen Importance – allows fertilization without water, key to terrestrial success.

Cell Biology: Mitosis & Meiosis (Ch. 11, 14)

• Chromosome – DNA molecule with proteins; haploid (N) vs diploid (2N).
• Mitosis
  • Growth/repair; $2$ identical diploid daughters.
• Meiosis
  • Gametogenesis; $4$ unique haploid cells; promotes variation via crossing-over & independent assortment.
• Gametes – haploid sex cells.

Population Ecology (Week 6, Ch. 28)

• Dispersion Patterns – clumped (resources/social), uniform (territoriality), random (wind-dispersed seeds).
• Life Histories – semelparous (one-shot) vs iteroparous (repeated).
• Growth Models
  • Exponential: $\frac{dN}{dt}=rN$ → J-curve.
  • Logistic: $\frac{dN}{dt}=rN\left(1-\frac{N}{K}\right)$ → S-curve; slows at carrying capacity (K), which can shift with environment.
• Density-Dependent Factors – competition, predation, disease.
• Keystone Species – disproportionate influence (e.g.
  sea otters → kelp forests).
• Trophic Cascade – predator changes reverberate down chain.
• Resource Partitioning – niche subdivision; reduces competitive exclusion.
• Ecological Niche – multidimensional role/requirements of species.
• Shannon Index of diversity: $H'=-\sum<em>{i=1}^{S} p</em>i\ln p<em>i$ where $p</em>i$ = proportion of species $i$.

Ecosystems & Biogeochemical Cycles (Week 7, Ch. 46-47)

• Biogeochemical Cycle – movement of elements between reservoirs via fluxes.
• Major Cycles:
  • Carbon – photosynthesis, respiration; human impact: fossil fuel burning.
  • Nitrogen – N-fixation (bacteria), nitrification, denitrification; agriculture adds $\text{NH}<em>3/\text{NO}</em>3^-$ → eutrophication.
  • Phosphorus – weathering rocks; no atmospheric phase; mining & runoff alter cycle.
• Roles of Bacteria – critical in nitrogen cycle (rhizobia, cyanobacteria).
• Trophic Pyramid – energy/biomass declines (~10 % rule) with each level; chains must end due to energy loss.
• Primary Producer vs Consumers vs Decomposers – base vs herbivores vs carnivores vs recyclers.

Climate & Global Patterns

• Climate vs Weather – long-term patterns vs daily conditions.
• Determinants of Biomes – temp & precipitation (terrestrial); light & nutrients (marine).
• Hadley Cells – equatorial rising air → rain belts; descending dry air at ~30° lat → deserts.
• Rainshadow Effect – windward moist, leeward dry.
• Milankovitch Cycles
  • Eccentricity – orbital shape (~100 k yr).
  • Obliquity – axial tilt (~41 k yr).
  • Precession – wobble (~26 k yr).
  • Modulate insolation, driving glacial cycles; N hemisphere landmass amplifies effects.

Community Interactions & Landscape Ecology

• Species interactions: competition, predation, mutualism, commensalism, parasitism.
• Competitive Exclusion Principle – two species cannot occupy identical niche; leads to resource partitioning.
• Landscape Ecology – spatial patterns (patches, corridors) influence processes.
• Ecotone – boundary where communities meet; high diversity.
• Temperature decline poleward due to lower solar angle; seasons arise from axial tilt.

Lab & Skill Highlights

• Phylogenetics Lab – construct/read cladograms; use homologies.
• Seeds & Fruits Lab
  • Use dichotomous key; identify pericarp layers: exocarp (outer), mesocarp, endocarp (inner, near seed).
  • Embryo = 2N; Endosperm = 3N.
• Life-History Matrices – project population growth, elasticity analysis for conservation.
• Allele vs Genotype Frequency Calculations – apply HWE; genotype freq = $p^2, 2pq, q^2$.

Numerical & Formula Summary

• HWE: $p+q=1$, $p^2+2pq+q^2=1$.
• Exponential growth: $\frac{dN}{dt}=rN$.
• Logistic growth: $\frac{dN}{dt}=rN\left(1-\frac{N}{K}\right)$.
• Shannon Diversity: $H'=-\sum p<em>i\ln p</em>i$.
• Fixation probability: $P_{fix}=p$.

Ethical, Philosophical, Practical Notes

• Conservation uses elasticity analyses to prioritize life stages for protection.
• Recognizing keystone species guides ecosystem management.
• Understanding nutrient cycles critical to mitigate human-induced eutrophication & climate change.
• Endosymbiotic theory reshapes views on the tree of life, highlighting cooperation in evolution.