Bio 102 Lecture 3: Population Genetics and Evolution

Lecture 3: Population Genetics and Evolution

Genes and Evolution

• Mendel's Explanation for Heritable Traits: This forms the basis of understanding how traits are passed down through generations.
• Darwin's Proposal of Evolution by Natural Selection: Provides a scientific explanation for adaptation.
• Genetic Variation and Evolution: Genetic variation is the raw material upon which evolution acts.

Darwin and Evolution

• Charles Darwin (1859): Published "On the Origin of Species."
• Central Question: Why are living things so well-adapted to their surroundings?
• Darwin's Theory: Proposed Evolution by Natural Selection as a scientific explanation for adaptation, based on natural laws rather than supernatural or religious actions.

The Voyage of the HMS Beagle (1831-1836)

• Darwin's observations during this voyage, particularly in the Galapagos Archipelago (September 15 to October 20, 1835), were crucial.
• Adaptive Radiation in Galapagos Finches: A key example observed, where an ancestral seed-eating finch diversified into various species with specialized beaks for different food sources (e.g., medium tree finch, small tree finch, large tree finch, mangrove finch, vegetarian finch, large cactus finch, cactus finch, sharps-beaked ground finch, large ground finch, small ground finch, medium ground finch, woodpecker finch, warbler finch, Cocos Island finch).
• The Large Ground-Finch (Geospiza magnirostris): Has the largest beak among Darwin's finches, adapted for cracking large, hard seeds, likely in dry conditions.

Evolutionary Theories Before Darwin

• Jean-Baptiste de Lamarck (1809): Proposed the first formal theory of evolution, based on the inheritance of acquired characters. This theory was later disproven.

Evolution by Natural Selection (Darwin & Wallace)

• Darwin's Theory (1858): "Descent with modification."
  • Concept: Over time, species accumulate differences, leading to descendants differing from their ancestors, and new species arising from existing ones.
• Key Principles of Natural Selection:
  1. Variation Among Individuals: Populations exhibit variable traits.
  2. Inheritance: Variable traits are heritable, passed from parent to offspring.
  3. Selective Pressures: Populations are under pressure to survive (e.g., limited resources, predators).
  4. Differential Survival and Reproduction: Individuals with traits best suited for survival are more likely to live, reproduce, and pass on their advantageous traits at higher rates to the next generation.

Genetic Variation and Evolution

• Genetic Variation: Differences in alleles of genes found within individuals in a population.
• Polymorphic Variation: Occurs when more than one allele exists at frequencies greater than mutation alone.
• Raw Material: Genetic variation is the essential raw material for natural selection.

Population Genetics

• Population Definition: Individuals of the same species living in the same area at the same time.
• Evolutionary Outcome: Evolution results in a change in the genetic composition of a population.
• Importance of Genetic Variation: Provides the raw material for selection.
• Definition of Evolution: The change in allele frequency in individuals that modifies the "fitness" of that population.
• Gene Pool: All gene copies at all gene loci in all individuals in the population.
• Genotype Frequencies: Percentages of individuals in a population possessing each genotype.
  • Each diploid organism has two copies of each gene (alleles), which can be the same or different.
• Allele Frequencies: Relative abundances of different alleles, which can be calculated.

Analyzing Change in Allele Frequencies: The Hardy-Weinberg Principle

• G. H. Hardy & W. Weinberg (1908): Developed a mathematical model to analyze the consequences of random matings within a population.
• Core Idea: All gametes produced in each generation contribute to a gene pool and combine randomly to predict offspring genotypes and their frequencies.
• Genetic Equilibrium: The principle specifies conditions under which a population of diploid organisms achieves genetic equilibrium, meaning neither allele frequencies nor genotype frequencies change across generations.

Hardy-Weinberg Equilibrium Assumptions

For proportions of genotypes not to change in a population, five conditions must be met:

1. No mutation: No new alleles are created.
2. No gene flow: No transfer of genes to or from other sources (no immigration or emigration).
3. Random mating: Mates are chosen irrespective of genotype.
4. Very large population size: Prevents random fluctuations in allele frequencies (genetic drift).
5. No selection: All genotypes have equal survival and reproductive rates.

• Null Model: Under these ideal conditions, microevolution does not occur. Natural populations rarely meet all five requirements.

Hardy-Weinberg Equation

• Allele Frequencies for Two Alleles: Represented by $p$ and $q$.
• Total Allele Frequency: Since there are only two alleles, their frequencies must sum to 1:
  $p + q = 1$
• Genotype Frequencies: Represented by $p^2$, $2pq$, and $q^2$.
  • $p^2$: Frequency of homozygous dominant genotype.
  • $q^2$: Frequency of homozygous recessive genotype.
  • $2pq$: Frequency of heterozygous genotype.
• Total Genotype Frequency: The sum of all genotype frequencies must also equal 1, representing 100% of the population:
  $p^2 + 2pq + q^2 = 1$
• Predictive Power: If allele frequencies are $p = 0.6$ and $q = 0.4$ in generation one:
  • Genotype frequencies in generation two would be:
    $p^2 (BB) + 2pq (Bb) + q^2 (bb) = (0.6)^2 + 2(0.6)(0.4) + (0.4)^2 = 0.36 + 0.48 + 0.16 = 1$
  • Allele frequencies in generation two would be:
    p = 0.36 + rac{1}{2}(0.48) = 0.60 (unchanged)
    q = 0.16 + rac{1}{2}(0.48) = 0.40 (unchanged)
• Conclusion: When alleles are transmitted via random combination of gametes, their frequencies do not change over time under Hardy-Weinberg assumptions. Evolution requires other factors.
• Testing for Evolution: The Hardy-Weinberg principle is used to test the null hypothesis (no change, no evolution). If genotype frequencies deviate from Hardy-Weinberg proportions, it indicates that evolution or nonrandom mating is occurring.

Agents of Evolution

Gene Flow

• Definition: Movement of alleles from one population to another.
• Mechanisms: Animal movement, drifting of gametes or immature stages, mating between adjacent populations.
• Effect: Homogenizes populations by reducing genetic differences between them.

Mutations: Creating Genetic Variations

• Definition: Spontaneous and heritable changes in DNA.
• Rate: Generally low.
• Immediate Effect: Little or no immediate effect on allele frequencies due to low rates.
• Ultimate Source: The ultimate source of all genetic variation.
• Restoration of Diversity: While most evolutionary mechanisms reduce diversity, mutation restores it by creating new alleles.
• Role in Evolution: Not goal-directed; natural selection acts on existing variation.
• Benefit:
  • Often result in little or no benefit, or are harmful, especially when selective pressures are low.
  • Can be highly beneficial when selective pressures are high (e.g., antibiotic resistance in bacteria).
• Example: Antibiotic Resistance in M. tuberculosis:
  • A single point mutation in the rpoB gene (changing TCG to TTG) for RNA polymerase.
  • The mutated RNA polymerase has a altered shape, reducing rifampin's ability to bind tightly.
  • This allows efficient transcription even in the presence of rifampin, leading to resistance.
• Take-Home Messages:
  • Ultimate source of new genetic variations and new alleles.
  • Mutation alone is usually inconsequential in changing allele frequencies at a particular gene.

Genetic Drift

• Definition: Random changes in allele frequencies due to chance, prevalent in small populations.
• Magnitude: Negatively related to population size (stronger in smaller populations).
• Effect: Alters allele frequencies, can lead to the loss of alleles in isolated populations.
• Types:
  • Founder Effect: Occurs when a small group establishes a new population in a new area. The allele frequencies of this new, smaller population differ randomly from the source population.
    • Common in the colonization of isolated habitats.
  • Bottleneck Effect: A drastic reduction in a population's size due to a chance event (e.g., natural disaster, hunting).
    • The surviving individuals may constitute a random genetic sample of the original population.
    • Leads to a significant loss of genetic variability.
    • Case Study: Northern Elephant Seal: Nearly hunted to extinction in the 19th century. Although the population rebounded to tens of thousands, it lost almost all genetic variation due to the bottleneck.

Natural Selection

• Definition: A process where heritable traits that allow some organisms to survive and reproduce better become more common in subsequent generations.
• Outcome: Individuals pass on their alleles (both favorable and unfavorable) to the next generation based on their success.
• Relative Fitness: The number of surviving offspring an individual produces compared with others in the population.
  • Differences in relative fitness are the essence of natural selection.
• Components of Fitness:
  • Survival
  • Sexual selection (attracting mates)
  • Number of offspring per mating
  • Traits favored for one component might be disadvantageous for others.
• Phenotypic Selection: Selection favors phenotypes with the greatest fitness (i.e., those that produce the greatest number of offspring).
• Three Conditions for Natural Selection:
  1. Variation: Must exist among individuals in a population.
  2. Differential Reproduction: Variation must lead to differences in the number of offspring surviving.
  3. Heritability: Variation must be genetically inherited.
• Gene Interaction: Many traits are affected by multiple genes; selection operates on all genes for a trait, changing the population based on which genotypes are favored.
• Distinction: Natural Selection vs. Artificial Selection.

Types of Natural Selection

1. Directional Selection: Acts to eliminate one extreme phenotype.
   • Occurs when the environment changes, favoring individuals at one end of the phenotypic range.
   • Example: In Drosophila, artificial selection for flies that moved toward light.
2. Stabilizing Selection: Acts to eliminate both extreme phenotypes.
   • Makes intermediate phenotypes more common by favoring the average.
   • Example: Higher survival rates for human infants with intermediate birth weight.
3. Disruptive Selection: Acts to eliminate intermediate phenotypes.
   • Favors individuals at both extremes of the phenotypic range.
   • Example: Birds with intermediate-sized beaks are at a disadvantage; they cannot efficiently open large seeds or process small seeds, favoring birds with very small or very large beaks.

Natural Selection vs. Evolution

• Natural Selection: A process—one of several processes that can lead to evolution.
• Evolution: The historical record or outcome of change through time.
• Result: Evolution driven by natural selection leads to populations becoming better adapted to their environment.

Evolution and Adaptation

• Adaptation: A "heritable trait" that increases an individual's fitness in a particular environment relative to individuals lacking that trait.
• Evolution: The change in "heritable traits" in individuals over time that modifies population "fitness."
• Example of Natural Selection: Pocket Mice Coat Color:
  • Populations living on dark lava rocks favor dark coat color.
  • Populations living on light sand favor light coat color.
  • This provides camouflage, making dark mice vulnerable on sand and light mice vulnerable on lava rock.

Interactions Between Evolutionary Forces

• Selection vs. Genetic Drift:
  • Drift may decrease an allele favored by selection.
  • Selection usually overwhelms drift, except in very small populations.
• Selection vs. Gene Flow:
  • Constructive: Can spread beneficial mutations to other populations.
  • Constraining: Can impede adaptation by the continual flow of inferior alleles from other populations.
• Selection vs. Mutations:
  • In nature, mutation rates are rarely high enough to effectively counter selection.

Frequency-Dependent Selection

• Definition: The fitness of a phenotype depends on its frequency within the population.
• Negative Frequency-Dependent Selection: Rare phenotypes are favored by selection.
  • Example: When predators focus on the most common type of prey, a rare phenotype gains a selective advantage (e.g., water boatmen colors—common forms were eaten at a disproportionately high rate, uncommon forms at a disproportionately low rate).
• Positive Frequency-Dependent Selection: Favors the common form.

Heterozygote Advantage

• Explanation: Maintaining alleles that might seem deleterious from one perspective.
• Example: Sickle Cell Allele (HbS):
  • The HbS allele, while causing sickle cell anemia in homozygotes ($HbS HbS$), confers resistance to malaria in heterozygotes ($HbA HbS$).
  • This heterozygote advantage maintains the HbS allele in populations where malaria is prevalent, preventing its elimination despite its negative effects in homozygotes.

Inheritance, Evolution, and Natural Selection

• Mendelian Inheritance: "Particulate inheritance" (genes as discrete units) works in conjunction with Darwin's natural selection, as opposed to the disproven "blending inheritance."
• Evolution Recap: Change in allele frequency in individuals modifying population fitness.
• Mechanisms of Evolution: Natural selection is not the only mechanism; mutations and gene shuffling also contribute to genetic variation and, therefore, evolution.

Review of Key Points

• Evolutionary Mechanism for Adaptation: Natural selection produces adaptation, occurring when individuals with certain alleles produce the most surviving offspring.
• Genetic Drift vs. Gene Flow:
  • Genetic drift causes random fluctuations in allele frequencies.
  • Gene flow equalizes allele frequencies between populations.
• Nonrandom Mating and Allele Frequencies: Nonrandom mating does not change allele frequencies directly; it only changes genotype frequencies.