Population Genetics: Allele Frequencies & Mechanisms (Lecture 9)

• Population Genetics and mechanisms that change allele frequencies in populations are the subject.
• The lecture aims to explain the principles of population genetics.
• The lecture aims to explain how the Hardy-Weinberg equilibrium and its applications.
• The lecture aims to allow you to explore genetic drift and its effects.

Key Concepts

• A population is a group of individuals of the same species living in the same area that interbreed and produce fertile offspring.
• Population genetics studies processes changing allele and genotype frequencies in populations.
• Hardy-Weinberg equilibrium is a state where allele frequencies remain constant across generations under specific conditions.
• Genetic drift includes random changes in allele frequencies, especially in small populations.
• Bottlenecks and founder effects are cases of genetic drift resulting from population reduction or founding events.

Basics of Population Genetics

• Population genetics focuses on how allele frequencies change in populations, and why.
• Evolution, at its core, involves changes in allele frequencies in populations.
• Four major processes of evolutionary change: mutation, genetic drift, gene flow/migration, and natural selection.
• Mutations are a source of new genetic variation.
• Genetic drift causes random changes in allele frequencies.
• Gene flow/migration involves movement of alleles between populations.
• Natural selection increases the frequency of adaptive alleles.
• Only natural selection leads to adaptation.
• Alleles are different versions of a gene, like A and a.
• Genotype refers to allelic combinations such as AA, Aa, or aa.
• Phenotype means observable traits resulting from the interaction of genotype and environment.
• A gene pool includes all alleles from all gametes in a population.

Hardy-Weinberg Principle

• The Hardy-Weinberg principle gives a mathematical framework for understanding population genetics.
• The Hardy-Weinberg principle was developed independently by Hardy and Weinberg in 1908.
• The Hardy-Weinberg principle extends Mendel's approach from individual matings to entire populations.
• The Hardy-Weinberg principle assumes a hypothetical gene pool where all gametes mix randomly.
• The fundamental equation for the Hardy-Weinberg principle: p² + 2pq + q² = 1, where p and q are allele frequencies.
• In Hardy-Weinberg equilibrium, allele frequencies remain constant across generations.
• Key conditions for equilibrium include diploid organisms, no overlapping generations, and no mutation.
• Key conditions for equilibrium include an infinitely large population, no gene flow, no natural selection, and random mating.

Applying Hardy-Weinberg

• The Hardy-Weinberg principle can be used in detecting evolutionary forces that act on a population.
• Example using snapdragons with incomplete dominance to illustrate applications of the principle.
• Example, there were 430 red flowers (CRCR), 510 pink flowers (CRCW), and 60 white flowers (CWCW).
• The calculated allele frequencies for the snapdragons were CR(p) = 0.685, CW(q) = 0.315.
• The expected genotype frequencies for the snapdragons were 0.469 for red, 0.432 for pink, and 0.099 for white.
• With these frequencies, you would expect 469 red plants, 432 pink plants, and 99 white plants.
• Differences between observed and expected counts indicate evolutionary forces at work.
• In this example, there is an excess of heterozygotes and a deficit of homozygotes

Genetic Drift

• Genetic drift causes random changes in allele frequencies as a result of sampling error.
• Genetic drift is similar to randomly sampling colored beads from a container.
• Population size is the key factor that affects the magnitude of genetic drift.
• Buri's 1956 experiment with fruit flies illustrates genetic drift.
• Buri's experiment started with 107 populations with identical allele frequencies.
• After 19 generations in Buri's experiment, populations diverged dramatically.
• In Buri's experiment, some populations became fixed for one allele while others became fixed for the alternative allele.
• Computer simulations show that for smaller populations, fixation happens sooner.
• When N=5, all populations fixed within ~20 generations in computer simulations.
• When N=50, most populations fixed by 500 generations in computer simulations.
• When N=500,000, almost no change occurred over 500 generations in computer simulations.
• Fixation occurs when an allele reaches 100% frequency in a population.
• Heterozygosity is a measure of genetic variation in a population.

Bottlenecks and Founder Effects

• Bottlenecks and founder effects offer dramatic examples of genetic drift.
• A genetic bottleneck occurs when population size is drastically reduced.
• Northern elephant seals' population was reduced to 30 individuals in the 1890s due to hunting.
• The current population of northern elephant seals is 124,000, but it has almost no genetic variation.
• Northern elephant seals have only 2 variable sites in 300bp of mitochondrial DNA, versus 23 sites in southern elephant seals.
• The Founder Effect occurs when a small number of individuals establish a new population.
• Zebra finches on the Lesser Sundas Islands: 9 founders led to a population of 26,750.
• Pennsylvania Amish: 100 founders led to a current population of 300,000.
• Ellis-van Crevald syndrome (polydactyly) occurs in 7% of the Amish population, which is hundreds of times higher than the greater general population.
• The high number of Ellis-van Crevald is likely due to two heterozygous carriers among the founders.