Evolution

The forces that change populations, and how we reconstruct their history

About this course

Evolution treated quantitatively — selection, drift, mutation and migration, fitness landscapes, sex and life histories — then speciation, phylogenetic trees, molecular clocks and human evolution.

What you will be able to do

  • Quantify the effects of selection and drift on allele frequencies
  • Explain the two-fold cost of sex and how sexual selection and conflict arise
  • Explain how life-history trade-offs account for ageing
  • Build a phylogenetic tree and date divergences with a molecular clock
  • Evaluate the evidence for evolution, including the evidence for human evolution

What this course covers

  • The Twofold Cost of Sex
  • Recombination, Outcrossing, and Anisogamy as Distinct Layers
  • The Fisher-Muller Effect
  • Muller's Ratchet
  • The Paradox of Sex and Its Two Resolutions
  • The Red Queen Hypothesis
  • Worked Example: Pricing a Clonal Lineage
  • The factor-of-two divergence problem and four dials
  • Pedigree rate vs. fossil-calibrated clock rate
  • Coalescent: two gene copies tracing to a common ancestor
  • Gorilla test: reading ancestral population size from incomplete lineage sorting
  • Darwin's four postulates as measurable claims
  • Weismann's test of acquired inheritance
  • Mutation before selection: Luria-Delbrück and the source of variation
  • Predicted fossil discovery: Tiktaalik
  • Fossil record as a Poisson sample
  • Embryos, vestiges, and construction carrying history
  • Species-area law and biogeographic distribution
  • Shared broken genes and retroviral insertions as descent markers
  • Consilience: congruent trees and multiplied likelihoods
  • Worked example: applying all three quantitative tools
  • Dobzhansky-Muller Incompatibilities and the Snowball
  • The Biological Species Concept and Its Edges
  • Isolation by Distance and Ring Species
  • The Hybrid Zone: Width, Selection, and Movement
  • Lake Victoria as a Test Case: Preference-Driven Speciation
  • Reinforcement: Selection Building a Mating Barrier
  • Worked Example: Integrating Snowball, Fitness, and Zone Width
  • Selective sweep: lactase persistence
  • Hominin tree and out-of-Africa dispersal
  • Effective population size from nucleotide diversity
  • Neanderthal admixture: fraction and date from tract lengths
  • Human genetic variation and population structure
  • Mitochondrial Eve and the coalescent
  • Worked example: integrating all three genomic methods
  • S as a number and the log-odds fitting rule
  • S is context-dependent, not a gene property
  • The peppered moth century: two slopes, one gene
  • Dominance, hidden recessives, and the plateau
  • The finch drought: selection differential and breeder's equation
  • The LTEE flask: fitness as a power law over 50,000 generations
  • Three fits by hand: one formula across all three cases
  • Bateman's Gradient and Sexual Selection Asymmetry
  • Parental Investment and Gradient Causation
  • Fisher's Runaway Sexual Selection
  • Runaway, Handicap, and Honest Origin as Sequential Stages
  • The Handicap Principle and Honest Signaling
  • Fisher's Sex Ratio Argument
  • Local Mate Competition and Sex Ratio Departures
  • Lek Worked Example: Opportunity for Selection and Adjusted Sex Ratio
  • Counting the number of possible trees
  • Characters, homology, and homoplasy
  • Parsimony as tree inference
  • Bootstrap support for tree splits
  • Long-branch attraction and Felsenstein's zone
  • Distance methods and the four-point condition
  • Worked example: counting, Fitch's rule, bootstrap SE
  • Genetic drift as a random lottery
  • Buri's experiment and reading Ne from variance
  • Mutation–drift balance and steady-state heterozygosity
  • Effective population size: three rules that shrink Ne
  • Kimura's fixation probability formula and the 4NS boundary
  • Nearly-neutral theory and Ohta's threshold
  • Island worked example: combining all three Ne rules
  • The Neutral Substitution Rate
  • Clock Speed Differences Between Proteins
  • Clock Dispersion and the Index of Dispersion R
  • Calibrating the Clock Against Fossils
  • DN/DS as a Selector of Neutral vs. Selected Sites
  • Synthesis: The Molecular Clock as an Instrument
  • Worked Example: Dating, Dispersion, and DN/DS
  • Lenski's Long-Term Evolution Experiment
  • Historical Contingency and the Citrate Replay
  • Mutation Supply at an Antibiotic Front
  • Cancer as Clonal Evolution: Drivers and the Incidence Exponent
  • Evolvability and the Mutator Allele
  • The Course Spine: Fourteen Clauses
  • Worked Example: Three Conversions by Reflex
  • Life History as an Energy Budget
  • Lack's Clutch Size Optimum
  • Hamilton's Force of Selection
  • The Grandmother Effect and Hamilton's Extended Force
  • Williams's Antagonistic Pleiotropy
  • R and K Life History Strategies
  • Lifespan Scaling, External Risk, and the Disposable Soma
  • Mutation-selection balance
  • Haldane's first human mutation rate estimate
  • Mutation supply and the mutational load
  • Wright's island model and FST
  • Geographic clines: width from selection and dispersal
  • All four evolutionary forces on one board
  • Worked balances: disease frequency and village migration
  • Fitness landscapes and the uphill-only rule
  • Fisher's microscope and middling fixed mutations
  • Orr's walk and the length of adaptation
  • Rugged landscapes and local peaks
  • Weinreich's enzyme and sign epistasis
  • Valley crossing by stochastic tunneling
  • Worked example: two-step drug resistance in a tumor

Syllabus

  1. Forces of Evolution

    1. L1 · The Factor of Two
    2. L2 · Selection, Measured
    3. L3 · Drift, Measured
    4. L4 · Mutation and Migration
    5. L5 · Fitness Landscapes

  2. Sex, Conflict and Life History

    1. L6 · Sex, Recombination, and the Two-Fold Cost
    2. L7 · Sexual Selection and Conflict
    3. L8 · Life Histories and Ageing

  3. Species and Phylogeny

    1. L9 · Speciation
    2. L10 · Building a Tree
    3. L11 · Molecular Clocks

  4. Evidence and Human Evolution

    1. L12 · The Evidence, Argued
    2. L13 · Human Evolution
    3. L14 · Evolution as an Experiment, and Where This Leads