Genetic Drift, Gene Flow, and Population Genetics

Administrative Announcements and Schedule

Class Logistics: PLAs (Peer Learning Assistants) are distributing returned worksheets at the front of the room. The instructor is staying close to the microphone because a previous recording failed while they were walking around.
Energy Levels: The instructor is currently jet-lagged and has been re-recording lectures, resulting in a more "mellow" energy than usual on the recordings.
Upcoming Events: * Class Meal: On Friday of next week, there will be a group meal outside of Cedar C. Students must RSVP so the instructor knows the quantity of food to purchase. * Final Office Hours: * Wednesday after class (usual group session). * April 28 (Reading Day): Extra group office hour from $2:00\,\text{PM}$ to $3:30\,\text{PM}$ via a shared link. This is a voluntary session during a day with no classes. * Extra Credit: The opportunity involves filling out student/course evaluations and is due by April 28. This is calculated as bonus points and does not count toward the weighted base grade. * Exam Preparation: The exam discussion board is active on ELC. Students are encouraged to use it early, especially when practicing Hardy-Weinberg equations.

Clarifying Misconceptions: The Intentionality of Evolution

The "Chainsaw Beaver" Misconception: An exit ticket featured a cartoon of a beaver that evolved a chainsaw for a tail. This illustrates the common misconception that evolution provides organisms with exactly what they "need" as if it were an intentional, mechanical process.
Evolutionary Constraints: * Evolution is biological, not mechanical. Genes code for proteins, not electronic or electric parts. * Adaptation is neither perfect nor progressive; it involves modifications over millennia. * The most extreme natural adaptation for a beaver would be sharper teeth or claws, not electric tools. * There is no goal or intention in evolution; traits do not appear because an organism "wants" them. Evolution proceeds through random chance in mutations.
Selective Pressures: Natural selection itself is not random because it acts upon existing traits within a specific environment. A trait is only "good" for a specific location at a specific time.

Patterns of Natural Selection

Graph Interpretation: On a selection graph, the $y$-axis represents the number of individuals in a population, and the $x$-axis represents the value of a trait (e.g., weight, height, beak length).
Normal Distribution: In a standard population, alleles usually form a bell curve.
Directional Selection: * Occurs when selective pressures favor individuals at one end of the trait spectrum. * One extreme has low fitness while the other has high fitness. * The average value of the trait moves in one specific direction (e.g., towards larger size or towards smaller size).
Stabilizing Selection ("Goldilocks" Selection): * Occurs when the environment selects against both extremes of a trait distribution. * Individuals with the average (middle) trait have the highest fitness. * The result is a sharper, narrower curve with less variation at the extremes.
Disruptive (Diversifying) Selection: * The average trait is selected against, while both extreme traits are favored. * This disrupts the normal distribution and can split the population into two distinct phenotypic groups.

Genetic Drift: Evolution by Chance

Definition: Genetic drift is a random fluctuation in allele frequencies over time. Unlike natural selection, it has nothing to do with fitness or survival of the fittest; it is purely a matter of luck.
Mechanisms of Drift: Events such as a disaster (an earthquake or someone stepping on a bug) can randomly eliminate individuals regardless of their genetic advantages.
Population Size Sensitivity: * Small populations are affected much more drastically by genetic drift. * Example: If $1$ bird dies in a population of $20$, that is $5\%$ of the gene pool gone. In a population of $2,000$, $1$ death is only $0.05\%$ ($5.0 \times 10^{-4}$) of the gene pool. * Drift can lead to the random fixation of alleles (everyone has it) or the total loss of alleles (trait disappears) regardless of whether the trait is adaptive or deleterious.
Founder Effect: * A small group leaves a parent population to start a new colony (common on islands like Hawaii). * The "founding parents" carry only a small sample of the original population's genetic variety. * Example: The Afrikaner population in South Africa (Dutch settlers) experienced high incidences of Huntington’s disease (an autosomal dominant condition) and certain leukemias due to inbreeding and the founder effect.
Bottleneck Effect: * A disaster (e.g., volcano eruption) wipes out a large portion of a population randomly. * The remaining survivors do not represent the full genetic diversity of the original group, leading to a permanent loss of alleles.

Gene Flow and Speciation

Gene Flow: The transfer of alleles in and out of a population due to the migration of fertile individuals or gametes. It increases genetic variation within a population, providing more material for natural selection.
Barriers to Gene Flow: * If gene flow is restricted (isolation), it can lead to speciation (the formation of new species). * In Hawaii, lava flows can separate populations of insects into isolated groups. * Over centuries, these populations may evolve different behaviors, such as the "mating dance" in fruit flies. If the dance changes, females may no longer recognize males from the other population, preventing reproduction even if they are brought back together. This is a behavioral reproductive barrier.

Case Study: Natural Selection in Mice (Hopi Hoekstra)

Research Focus: Dr. Hopi Hoekstra studied the survival of mice in light and dark habitats.
Data Description (Figure 1): Measured mortality across time points for nonlocal mice (light mice in dark sites and dark mice in light sites). Mortality was significantly higher for nonlocal mice.
Interpretation: Mice that do not match the color of their habitat are selected against by predators. The local population is selected for matching the environment because that phenotype provides a fitness advantage (camouflage).
Genotype to Phenotype Correlation: A regression analysis of dorsal brightness (back fur color) showed that genotypes (Wild Type vs. Serine deletion) predicted the brightness of the coat. Homozygous recessive individuals for the serine allele were brighter, aiding survival in light-colored enclosures but decreasing fitness in dark ones.

Introduction to Population Genetics Math

Allele Frequency Definition: The proportion of a specific allele in the gene pool, reported as a value from $0$ to $1$ (0\text{%} to 100\text{%}).
Basic Formula (for Incomplete/Codominance): $\text{Frequency of Allele} = \frac{\text{Number of copies of that allele in the population}}{\text{Total number of copies of all alleles for that gene in the population}}$
Example: Dog Coat Types (Incomplete Dominance): * Curly (CC): $214$ dogs * Wavy (Cc): $327$ dogs * Straight (cc): $122$ dogs * Total dogs: $663$ . Total alleles: $2 \times 663 = 1326$ . * To find the frequency of $c$ : * From straight dogs: $122 \times 2 = 244$ alleles. * From wavy dogs: $327 \times 1 = 327$ alleles. * Numerator: $244 + 327 = 571$ . * Result: $\frac{571}{1326} \approx 0.43$ (or 43\text{%}).

The Hardy-Weinberg Equilibrium Equation

Concept: This acts as a "giant Punnett square" for an entire population to estimate genotype frequencies when you cannot distinguish between homozygous dominant and heterozygous individuals phenotypically (complete dominance).
The Allele Formula: $p + q = 1$ * $p$ : Frequency of the dominant allele. * $q$ : Frequency of the recessive allele.
The Genotype Formula: $p^2 + 2pq + q^2 = 1$ * $p^2$ : Frequency of homozygous dominant ( $AA$ ). * $2pq$ : Frequency of heterozygous ( $Aa$ ). * $q^2$ : Frequency of homozygous recessive ( $aa$ ).
Step-by-Step Calculation (Pea Plants): * Data: $1,000$ plants. $540$ are white ( $aa$ ), and $460$ are purple (can be $AA$ or $Aa$ ). * Step 1: Find $q^2$ . $q^2 = \frac{540}{1000} = 0.54$ . * Step 2: Find $q$ . Take the square root of $0.54$ , which is roughly $0.73$ . * Step 3: Find $p$ . Since $p + q = 1$ , then $p = 1 - 0.73 = 0.27$ . * Step 4: Use $p$ and $q$ to calculate the remaining genotype frequencies ( $p^2$ and $2pq$ ) if necessary.