Evolution of Populations – Key Vocabulary

Natural Selection – Core Principles

• Natural selection = process where individuals with heritable traits that confer a survival / reproductive advantage leave more offspring.- Summarized by the phrase “survival of the fittest,” where fitness is always relative to a particular environment.

• It is one of several evolutionary mechanisms; others include genetic drift, gene flow, and mutation.

• Darwin’s 3 big ideas (1844 essay)- Unity of life – all organisms share ancestry.

  • Diversity of life – descendants diversified over time.

  • Adaptation – organisms are suited to their environments through natural processes.

• Key historical observations from the voyage of the Beagle:- Fossils often resemble extant species in the same regions.

  • Geographic variation in related species hinted at common descent and local adaptation.

Observations ➔ Inferences Underlying Natural Selection

• Observation #1 – Individuals in a population vary in inherited traits.

• Observation #2 – All species can produce more offspring than the environment can support.

• Inference #1 – Individuals with advantageous traits survive/reproduce more.

• Inference #2 – Differential survival causes favorable alleles to accumulate over generations, producing adaptation.

Limits & Clarifications on Natural Selection

• Acts on individuals, but only populations evolve.

• Can act only on heritable variation.

• Does not create new traits, merely edits the variation present.

• Adaptations are environment-specific; change the setting and a trait’s fitness value can flip.

• Today biologists recognize natural selection as the sole mechanism that consistently produces adaptive evolution, yet drift, flow, and mutation also drive change.

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Genetic Variation – The Raw Material

• Evolution requires heritable variation in populations.

• Variation arises from:- Mutation (changes DNA sequence).

  • Recombination during meiosis.

  • Sexual reproduction shuffling alleles.

• Natural selection only uses the component of variation with a genetic basis.

The Population as the Smallest Evolutionary Unit

• Microevolution = change in allele frequencies within a population across generations.

• Example: Medium ground finches on Daphne Major Island shifted beak‐depth distribution after droughts.

• Macroevolution = evolution above the species level (origin of new taxa).

Modes of Selection

1. Directional – favors one extreme; mean phenotype shifts (e.g., DDT resistance in flies).

2. Disruptive – favors both extremes; variance increases, bimodal distribution.

3. Stabilizing – favors intermediates; variance decreases (e.g., human birth weight).

Sexual Selection

• Form of natural selection based on differential mating success.

• Leads to sexual dimorphism (size, color, weapons).-

  • Intrasexual selection – competition within one sex (usually males) for mates.

  • Intersexual selection – mate choice; one sex (usually females) is choosy.

Four Micro-evolutionary Mechanisms

1. Natural selection – generally reduces genetic variation by favoring some alleles.

2. Genetic drift – random, non-adaptive loss/fixation; reduces variation.

3. Gene flow – migration introduces/exits alleles; usually increases variation and homogenizes populations.

4. Mutation – ultimate source of novel alleles; increases variation.

Genetic Drift – Founder & Bottleneck Effects

• Genetic drift = evolution via random sampling error; strongest in small populations.

• Founder effect – few individuals colonize new area; allele frequencies differ from source.

• Bottleneck effect – drastic population reduction (fire, storm, human action). Remnant gene pool often unrepresentative.- Small populations that pass through bottlenecks are prone to inbreeding and further drift.

Inbreeding

• Mating among relatives increases homozygosity, uncovers deleterious recessives.

• Does not change allele frequencies directly but alters genotype frequencies (more AA & aa, fewer Aa), harming reproductive success.

Gene Flow

• Movement of alleles among populations via fertile individuals or gametes (e.g., pollen).

• Can introduce beneficial alleles or swamp local adaptation.

Hardy–Weinberg Gene-Pool Accounting

• Gene pool = all alleles at all loci in population.

• For two-allele locus, allele frequencies satisfy p + q = 1.

• Genotype frequencies (if HW equilibrium) = p^2 + 2pq + q^2 = 1.

• Deviation from HW expectations signals evolution.

• Example wildflower population (incomplete dominance):- 320 red (RR), 160 pink (Rr), 20 white (rr)

  • Total individuals = 500; alleles = 1000

  • R copies = (2\times320) + (1\times160) = 800 ⇒ p = 800/1000 = 0.80

  • r copies = 200 ⇒ q = 0.20 (check p+q=1).

Mutation Rates & Rapid Reproduction

• Average mutation ≈ 1 per 10⁴ gametes in plants/animals.

• Prokaryotes: lower rate per division but short generation times → accumulate mutations quickly.

• Viruses: both high mutation rate and short cycles (reason influenza vaccines updated yearly).

Evidence for Evolution

1. Homology- Shared traits due to common ancestry; anatomical (limb bones), molecular (DNA/rRNA), developmental (embryonic tails).

   • Vestigial structures = remnants once functional in ancestors (whale pelvis).

2. Convergent evolution & Analogy- Similar traits evolve independently in similar environments (shark vs dolphin fins = analogous).

   • Homoplasy (molecular or morphological) complicates phylogenies.

3. Fossil record- Documents extinction, transition forms (tetrapod limbs, whale ancestors), and temporal sequence.

   • Fossils form via rapid burial, mineralization, amber, freezing; deeper strata generally older.

4. Biogeography- Pangaea breakup explains continental patterns.

   • Endemic island species resemble nearest mainland relatives (e.g., Galápagos finches, Madagascar lemurs).

5. Genetic evidence- Universal genetic code; degree of sequence homology correlates with divergence time.

   • Example: two 30-bp sequences with 3 vs 5 differences ⇒ 90 % vs 83 % similarity.

   • Functional interchangeability: transgenic crops expressing Bacillus thuringiensis toxin.

   • Orthologs (speciation), paralogs (duplication), xenologs (horizontal transfer) give rise to homologous DNA segments.

Phylogeny & Systematics

• Phylogeny = evolutionary history of a species/group.

• Systematics = discipline deciphering relationships, combining taxonomy + phylogenetics.

Linnaean Hierarchy & Binomials

• Carolus Linnaeus (18th c.)- Two-part Latin name (Genus species) e.g., Homo sapiens.

  • Categories: Domain ➔ Kingdom ➔ Phylum ➔ Class ➔ Order ➔ Family ➔ Genus ➔ Species.

  • Each category = taxon; type specimens anchor species definitions.

Reading Phylogenetic Trees

• A tree is a hypothesis of relationships.

• Branch point = divergence; sister taxa share an immediate ancestor.

• Branch lengths may represent genetic change or chronological time (if calibrated).

• Trees show patterns of descent, not morphological similarity or “progress.”

Building Trees: Homology vs Analogy

• Systematists analyze morphology, genes, biochemistry.

• Must decide if similarity stems from homology (common ancestry) or analogy (convergence).

• Molecular homoplasy = coincidental similarity; use statistical methods (e.g., maximum parsimony, maximum likelihood) to pick most plausible tree.

Cladistics

• Cladogram groups taxa into clades (monophyletic – ancestor + all descendants).

• Paraphyletic – ancestor + some, not all, descendants.

• Polyphyletic – lacks most recent common ancestor of included taxa.

• Derived characters (synapomorphies) diagnose clades (e.g., vertebral column, jaws, amnion, hair).

Horizontal (Lateral) Gene Transfer

• Genes can move across species boundaries (plasmids, viruses, endosymbiosis).

• HGT blurs the “tree of life,” suggesting early evolutionary history resembles a reticulated network rather than a strict bifurcating tree.

Speciation – The “Mystery of Mysteries”

• Speciation = one lineage splits into two or more.

• Multiple species concepts (biological, morphological, ecological, phylogenetic) discussed in Ch. 24 of textbook.

Summary of Mechanism Effects on Genetic Variation

• Only natural selection adapts populations to environment; the rest are non-adaptive.

Exam 1 Review

Phylogenetic Trees
Definition: graphic hypotheses about evolutionary relationships among taxa.
Implications / weaknesses

• Based on available data; incomplete or biased sampling can mislead.

• Homoplasies (analogous similarities) can obscure true history.

• Horizontal gene transfer, hybridization, incomplete lineage sorting complicate signal.

• Always a hypothesis, subject to revision with new evidence.

• Cannot reveal absolute ages unless calibrated with fossils or molecular clocks.

Core Terminology

• Phylogeny – evolutionary history of a species/group.

• Binomial nomenclature – two-part Latin name: Genus + specific epithet (e.g., Homo sapiens)

• Homology – similarity due to shared ancestry

• Analogy – similarity due to convergent evolution/adaptation, not ancestry (e.g., wings of birds & insects).

• Homoplasies – any trait similarity not caused by common ancestry; includes analogy & evolutionary reversals.

• Clade (monophyletic group) – ancestor and ALL descendants; basis of modern systematics.

• Paraphyletic group – ancestor + SOME descendants (e.g., traditional “Reptilia” excluding birds).

• Polyphyletic group – taxa with different ancestors grouped together (e.g., warm-blooded animals: birds + mammals).

• Holotype – single physical specimen designated as the name-bearing example for a new species.

Taxonomic Hierarchy (broad → narrow)

• Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

• Mnemonic: “Dear King Philip Came Over For Good Soup.”

Dichotomous Keys
1a. Leaves opposite … go to 2
1b. Leaves alternate … go to 3.

Three Domains of Life

• Bacteria

  • Prokaryotic, peptidoglycan cell walls, circular chromosomes.

  • Examples: Escherichia coli, cyanobacteria.

• Archaea

  • Prokaryotic, no peptidoglycan, unique membrane lipids, some extremophiles (thermophiles, halophiles).

  • Example: Halobacterium, methanogens.

• Eukarya

  • Membrane-bound nucleus & organelles, linear chromosomes.

  • Kingdoms: Protista (various), Plantae, Fungi, Animalia.

  • Example: humans, oak trees, yeast.

Lines of Evidence for Evolution

• Direct Observation – e.g., antibiotic resistance in bacteria, beak depth shifts in Galápagos finches.

• Fossil Record – chronological appearance of forms; transitional fossils (Tiktaalik, archaeopteryx).

• Homology – anatomical (vertebrate limbs), molecular (shared genes such as Hox), developmental (embryonic tails in mammals).

• Biogeography – island endemism (Darwin’s finches), continental drift patterns.

Fossils & Fossil Record

• Fossil: any preserved remains, impression, or trace of an organism older than ~10^4 years.

• Formation pathways

  • Permineralization (bone/wood pores filled with minerals)

  • Casts & molds

  • Amber entrapment

  • Freezing, tar pits

  • Trace fossils (footprints, burrows)

• Fossil record: ordered assemblage of fossils globally; biased toward hard parts, abundant species, aquatic habitats, and recent time.

Darwin: Observations & Inferences

• Observations

  • Populations vary in inherited traits.

  • All species produce more offspring than environment can support → many fail to survive/reproduce.

• Inferences

  • Individuals with traits giving higher probability of survival/reproduction leave more offspring.

  • Favorable traits accumulate in population over generations (descent with modification).

Darwin vs. Lamarck

• Lamarck: species evolve via use & disuse; acquired traits transmitted (e.g., giraffes stretching necks). No modern genetic basis.

• Darwin: natural selection acts on heritable variation already present; environment filters traits.

Evolutionary Processes & Related Terms

• Natural Selection – differential survival/reproduction of phenotypes.

• Artificial Selection – human-directed breeding (dogs, crops).

• Fitness (W) – relative genetic contribution to next generation; measured between 0–1 or as offspring number.

• Speciation – formation of new species; often via reproductive isolation.

• Microevolution – change in allele frequencies within a population.

• Mechanisms:

  • Natural selection (adaptive)

  • Genetic drift (random)

  • Founder effect: small colonizing group → allele frequency shift.

  • Bottleneck effect: sudden population reduction (fire, overhunting) → drift in survivors.

  • Gene flow: movement of alleles between populations via migration.

• Inbreeding – mating between relatives; increases homozygosity, exposes deleterious recessives.

• Sexual Selection

  • Intrasexual (within same sex): male-male combat.

  • Intersexual (mate choice): peacock tails; selects for ornaments/signals.

Key Notes about Natural Selection

• Acts on phenotypes, but only heritable (genetic) variation affects evolution.

• Not goal-oriented; cannot create perfection, just fits current local environment.

• Environments change → what is adaptive today may not be tomorrow.

• Selection can only edit existing variation; new alleles arise by mutation.

Adaptive Evolution

• Process by which traits that enhance fitness become more common over time.

• Requires:

  • Genetic variation

  • Heritability

  • Differential reproductive success

• Natural selection is only mechanism that consistently causes adaptive evolution.

Modes of Selection

• Directional – favors one extreme phenotype → population mean shifts.

• Disruptive (diversifying) – favors both extremes over intermediates → increases variance.

• Stabilizing – favors intermediate phenotypes → reduces variance, maintains status quo.

Hardy–Weinberg Equilibrium (HWE)

• For a locus with two alleles p and q (where p+q=1): p^2 + 2pq + q^2 = 1

• p^2 = homozygous dominant frequency

• 2pq = heterozygous frequency

• q^2 = homozygous recessive frequency

• Conditions (no evolution):

  • No mutations

  • Random mating

  • Infinite (large) population size

  • No gene flow

  • No natural selection

• Example problem: If q^2 = 0.04, q = 0.2, so p = 0.8; heterozygotes 2pq = 0.32 (32 %).

Source of New Alleles

• Mutation (point mutations, insertions, deletions, gene duplications) is the ultimate origin of genetic variation; sexual reproduction shuffles existing alleles.

Non-Adaptive Evolutionary Processes

• Genetic drift (founder, bottleneck)

• Gene flow (if introducing neutral or maladaptive alleles)

• Mutation (usually neutral or deleterious)

• Inbreeding (alters genotype frequencies but not allele frequencies directly)

Species Concepts (Ch. 24)

• Biological Species Concept (BSC) – groups of actually/potentially interbreeding natural populations that are reproductively isolated from others.

• Morphological Species Concept – differentiates species by structural features; useful for fossils.

• Ecological Species Concept – defines species by niche (role/environment).

• Phylogenetic Species Concept – smallest diagnosable monophyletic group on phylogenetic tree.

• Increasingly used with molecular data.

Reproductive Isolation Barriers

• Pre-zygotic (block fertilization)

  • Habitat isolation – different locales (water vs. land).

  • Temporal isolation – breed at different times/seasons.

  • Behavioral isolation – courtship rituals differ (bird songs).

  • Mechanical isolation – incompatible genitalia/flower structure.

  • Gametic isolation – sperm cannot fertilize egg (sea urchins).

• Post-zygotic (after zygote forms)

  • Reduced hybrid viability – embryos fail or weak hybrids.

  • Reduced hybrid fertility – sterile hybrids (mule).

  • Hybrid breakdown – F2/backcross hybrids weak or sterile (cultivated rice lines).

Ethical & Practical Connections

• Conservation genetics employs phylogenies & HWE to manage endangered species (e.g., avoid inbreeding depression).

• Tracking antimicrobial resistance uses phylogenies for epidemiology.

• Artificial selection in crops must watch for reduced genetic diversity (bottlenecks).

Mathematical/Statistical References

• Hardy–Weinberg: p^2 + 2pq + q^2 = 1

• Effective population size (not covered deeply but related): Ne = \frac{4NmNf}{Nm+N_f} (sex ratio impact on drift).

Real-World Relevance & Integration

• Fossil transitional forms support macroevolution linking lecture on vertebrate anatomy.

• Gene flow concept ties into migration studies in ecology.

• Sexual selection concepts align with animal behavior observations discussed last week.

• Understanding modes of selection informs plant breeding and disease management.