Population Genetics and Evolution: Study Notes

Population Genetics and Microevolution

• Diversity in terms of allele differences: how populations differ genetically and how those genes/alleles change in frequency over time.
• Evolution (as a concept): the genetic changes within a population over time.
• Microevolution: the smallest scale of evolution; variations in allele frequencies within a population over time.
• Gene pool: all the alleles present within a population at all loci; the total genetic material in that population.
• For each trait, we look at genotype frequencies; frequency means a ratio or proportion of how common a genotype is within the population.
• Allele frequency terminology:
  • p usually denotes the frequency of the dominant allele (uppercase), across the population.
  • q usually denotes the frequency of the recessive allele (lowercase).
  • In all cases, p + q = 1.
  • Note: this convention (p for dominant, q for recessive) is a standard not a universal rule; some contexts use different letters, but we stick to p and q here.
• When talking about a single trait, we typically analyze one gene at a time (one locus) — many genes can be considered, but the class tends to focus on one at a time.
• Peppered moth example (two alleles for coloration): dark allele (dominant) vs light allele (recessive). Dominant does not mean “more prominent”; presence depends on allele frequency, not dominance alone.
• Microevolution occurs at the population level, not at the level of an individual — individuals mutate, but evolution acts on populations.
• Any change in allele composition over time is evolution (even if you don’t see a visible phenotype change).
• Allele frequencies are a proportion; they must add up to 1 across all alleles at a locus.
• Hardy–Weinberg equilibrium (HWE): a baseline model describing a non-evolving population. It provides expectations for genotype frequencies given allele frequencies.
• Key role of HWE: serves as a baseline/control group to detect evolution in real populations.
• Conditions for Hardy–Weinberg (not often fully met in real populations):
  • No mutations
  • No migration (gene flow)
  • Very large population size (no genetic drift)
  • Random mating (no nonrandom mating)
  • No natural selection
• Genotype vs allele frequencies in HWE:
  • If allele frequencies are p and q with p + q = 1, the expected genotype frequencies are $p^2, \; 2pq, \; q^2$ for ll, heterozygotes, and ll recessives, respectively.
  • The overall sum is $p^2 + 2pq + q^2 = 1$.
• Relationship between allele and genotype frequencies:
  • Allele frequencies can be inferred from genotype frequencies and vice versa (under HWE). If you know p and q, you can predict genotype frequencies; if you know genotype frequencies, you can back-calculate p and q (under HW assumptions).
• Practical use of p and q: tracking how allele frequencies change over time to determine whether a population is evolving.
• When allele frequencies change over time, that’s microevolution; when they stay constant, one can say the population is not evolving (under the HW assumptions).
• Gene flow: movement of alleles between populations (e.g., pollen, seeds, or organisms moving between populations).
  • Gene flow tends to increase genetic diversity within a population and reduces differences between populations; it helps maintain a single species by mixing gene pools.
  • Disruption of gene flow can lead to divergence and speciation.
• Genetic drift: random changes in allele frequencies independent of selection.
  • More pronounced in small populations; can lead to fixation (loss of all but one allele) or loss of diversity.
  • Bottleneck effect: drastic reduction in population size due to a random event (natural disaster, etc.) leading to a non-representative surviving subset.
  • Founder effect: new population formed by a small number of individuals; allele frequencies in the new population may not reflect the original population.
  • Inbreeding can increase homozygosity and expose recessive deleterious alleles, with potential negative fitness effects.
  • Both bottlenecks and founder effects reduce genetic variation and can accelerate genetic drift.
• Nonrandom mating and sexual selection:
  • Assortative mating: individuals select mates with similar phenotypes/genotypes.
  • Sexual selection: a form of nonrandom mating where one sex selects mates based on certain traits; often results in increased frequency of certain homozygotes at those loci.
  • Good genes hypothesis: females choose mates with traits that improve offspring survival; traits signal fitness.
  • Runaway hypothesis: female preference and male trait co-evolve, accelerating exaggerated traits.
  • Balancing of traits via heterozygote advantage (a form of balancing selection).
• Natural selection: differential survival and reproduction based on heritable variation.
  • Requirements for natural selection:
  • Genetic variation exists in the population.
  • Variation is heritable (inherited).
  • Differential survival/reproduction based on those traits.
  • Natural selection acts on phenotypes but changes allele frequencies over generations.
  • Three main types of natural selection:
  • Directional selection: one extreme trait is favored (e.g., longer giraffe necks become more common).
  • Stabilizing selection: intermediate phenotypes favored; extremes are selected against (e.g., optimal birth weight).
  • Disruptive selection: extreme phenotypes favored over the intermediate (e.g., light and dark morphs, with intermediates being rare).
  • Examples:
  • Peppered moths: light vs dark morphs shift with industrial soot turning trees dark, favoring dark morphs in polluted environments.
  • Giraffes: directional selection for longer necks due to access to higher leaves.
  • Clams/snails: disruptive or stabilizing patterns depending on background habitat and predation.
  • Bacteria and antibiotics: directional selection leading to antibiotic resistance.
  • Galápagos finches: beak size shifts with available food sources; environment drives selection on beak morphology.
  • Polymorphism and subspecies:
  • Polymorphism: multiple distinct morphs within a population due to varying environments or selection pressures.
  • Subspecies: geographically distinct populations within a species that may have distinct morphologies but can still interbreed.
• Diploidy and balancing selection:
  • Being diploid increases genetic variation because there are two alleles per locus, leading to heterozygotes with potentially different phenotypes.
  • Balancing selection maintains two or more alleles in a population at stable frequencies.
  • Heterozygote advantage example: sickle cell trait in malaria-endemic regions — heterozygotes (AS) have malaria resistance while not suffering severe sickle cell disease; homozygotes (AA or SS) either suffer malaria or have sickle-cell disease, respectively.
  • Carriers (heterozygotes) maintain both alleles in the population.
• Practical and ethical implications:
  • Maintaining genetic diversity is important for resilience to environmental changes and disease outbreaks.
  • Antibiotic resistance emerges when antibiotics are overused or not completed; this is a real-world consequence of directional selection in microbial populations.
  • Inbreeding and small population sizes increase the risk of fixed deleterious alleles, reducing population fitness and adaptability.
  • Conservation biology uses these concepts to maintain variation, manage populations, and prevent extinction.
  • Medical genetics (e.g., sickle cell and malaria) illustrates how evolutionary trade-offs shape allele frequencies in human populations.
• Quick practice takeaways:
  • If allele frequencies do not change over time, population is not evolving (under HW assumptions).
  • If a population shows change in allele frequencies, explore possible causes: mutation, migration (gene flow), nonrandom mating, genetic drift, natural selection.
  • Use HW to predict genotype frequencies from allele frequencies and vice versa; use p + q = 1 and p^2, 2pq, q^2 to interpret data.
  • Understand how bottlenecks and founder effects can rapidly alter variation and potentially lead to speciation in the long term.

Key Equations and Concepts (LaTeX)

• Allele frequency sum: $p+q=1$
• Genotype frequencies under Hardy–Weinberg: $p^2,\; 2pq,\; q^2$
• Total genotype frequency: $p^2+2pq+q^2=1$

Worked Example: Hardy–Weinberg and a Frog Population

• Given: 500 frogs; 375 dark green (dominant phenotype); number of light green frogs unknown.
• Step 1: Identify observed phenotype frequency for dark green: $\frac{375}{500}=0.75$
• Step 2: Interpret dark green as the dominant phenotype. Without knowing whether dark green frogs are homozygous dominant (AA) or heterozygous (Aa), you cannot uniquely determine p and q from the phenotype alone.
• Step 3: A common simplifying approach (as illustrated in the transcript) is to check a plausible HW distribution. If one assumes p = q = 0.5 (a common pedagogical assumption for teaching HW basics), then:
  • $p^2 = (0.5)^2 = 0.25$
  • $2pq = 2(0.5)(0.5) = 0.50$
  • $q^2 = (0.5)^2 = 0.25$
  • Proportion dark green (dominant phenotype) = $p^2+2pq = 0.25+0.50 = 0.75$
• Step 4: Under this assumption, the genotype frequencies would be:
  • Homozygous dominant (AA): $p^2 = 0.25$
  • Heterozygous (Aa): $2pq = 0.50$
  • Homozygous recessive (aa): $q^2 = 0.25$
• Step 5: Allele frequencies in this HW scenario would be: $p=0.5,\, q=0.5$
• Note: In real data, you would not deduce p and q from phenotype alone without additional information (e.g., counts of recessive phenotype), but this demonstrates how HW relationships can be used to check consistency with observations.

Gene Flow, Genetic Drift, and Speciation

• Gene flow (migration) tends to homogenize allele frequencies between populations and increase diversity within a population.
• Interruption of gene flow over time can lead to accumulation of differences and speciation (reproductive isolation).
• Genetic drift is random with respect to fitness and can cause allele frequencies to change by chance.
• Bottleneck effect: severe reduction in population size due to a random event leading to a non-representative surviving gene pool; often reduces genetic variation.
• Founder effect: a new population is established by a few individuals; the new population's allele frequencies may not reflect the original population's frequencies.
• Drift effects are stronger in small populations and can lead to fixation or loss of alleles, reducing genetic variation and potentially increasing susceptibility to environmental change.

Nonrandom Mating and Sexual Selection

• Nonrandom mating includes assortative mating (preference for similar phenotypes) and disassortative mating (prefer dissimilar phenotypes).
• Sexual selection can lead to increased frequency of particular homozygotes at chosen loci due to mate choice or competition.
• The good genes hypothesis and runaway selection explain why females may prefer certain traits that signal fitness, even if those traits incur costs.
• Typical pattern: males often display elaborate traits; females select based on fitness indicators; this can drive rapid trait elaboration and reproductive success.
• Example considerations: traits that increase visibility to predators may still indicate high fitness due to ability to survive in spite of risk.

Natural Selection Types and Examples

• Conditions for natural selection to occur:
  • Genetic variation exists
  • Variation is heritable
  • Differential survival and reproduction based on traits
• Types of natural selection:
  • Directional selection: one extreme trait is favored (e.g., longer giraffe necks)
  • Stabilizing selection: intermediate trait favored; extremes disfavored (e.g., optimal birth weight)
  • Disruptive selection: both extremes favored over the intermediate (e.g., light and dark snail morphs; intermediates suffer more predation)
• Illustrative examples:
  • Directional: bacteria evolving antibiotic resistance under antibiotic exposure
  • Stabilizing: human infant birth weight historically favored near an intermediate value due to survival rates
  • Disruptive: clams or snails with extreme color morphs may be favored in different microhabitats, while intermediates are more visible to predators
• Additional points:
  • Environmental differences produce polymorphism and multiple morphs within a population
  • Subspecies can exist when populations occupy different habitats but still interbreed; these differences reflect local environmental pressures and selection
  • Selection pressures are environment-dependent; what is favored in one habitat may be disfavored in another

The Role of Variation in Adaptation

• Maintenance of variation among population members has survival value when environments are variable.
• The Galápagos finches illustrate how beak size evolves with changing food supply across seasons: larger beaks favored when hard seeds predominate; smaller beaks favored when soft seeds prevail.
• Diploidy increases genetic variation because two allele copies exist per locus, allowing heterozygotes to display unique phenotypes.
• Balancing selection can maintain multiple alleles in a population (e.g., sickle cell trait in malaria regions).
• Heterozygote advantage: heterozygotes have higher fitness than either homozygote, preserving both alleles in the population.
• Substantial caution: balancing selection does not imply all traits are equally beneficial in all environments; it reflects trade-offs across environments and generations.

Implications for Real-World Scenarios

• Antibiotic resistance: directional selection in bacteria leads to resistant populations; improper antibiotic use accelerates resistance.
• Conservation and biodiversity: maintaining genetic variation is critical for resilience to environmental changes and disease.
• Human health and disease: malaria and sickle cell trait exemplify how evolutionary forces shape disease dynamics and population genetics in humans.
• Speciation and diversity: gene flow and drift can contribute to divergence; isolation can promote the emergence of distinct species or subspecies over time.