Population Genetics and Hardy-Weinberg Equilibrium

Reading Materials

  • Chapter 26 Suggested Problems: Ch 26: 6, 9, Week 6 recitation packet

Terminology

  • Allele Frequency: The proportion of a specific allele among all allele copies in a given population.
  • Population: A group of individuals of the same species that interact and interbreed in a particular area.
  • Segregation Distorter: An allele that biases the segregation process, leading to a higher transmission rate than expected.
  • Hardy-Weinberg Equilibrium: A principle that states allele and genotype frequencies in a population will remain constant from generation to generation in the absence of evolutionary influences.

Learning Objectives

  • LO26: Calculate allele frequencies from genotype or phenotype frequencies; calculate genotype or phenotype frequencies from allele frequencies.
  • LO27: Use the Punnett square framework to derive the Hardy-Weinberg Equilibrium (HWE). Apply Hardy-Weinberg equilibrium formulas that relate allele and genotype frequencies to demonstrate why disease alleles are most commonly found in heterozygote carriers.
  • LO28: Apply the ext{χ}^2 test to determine whether a cross or a population deviates from our expectations under a null genetic model. Explain potential causes of deviation from these expectations.

Genetic Variation in Populations

  • Exam 1: Available through Sunday at the DLC Prep. Review assignment keys and work through recitation packets and learning objectives.

Chi-Square Test Practice

  • Data for Chi-Square Calculation:
    • Phenotype Observed vs. Expected:
    • Red, Brown: 100 observed, 90 expected
    • White, Brown: 12 observed, 30 expected
    • Red, Yellow: 10 observed, 30 expected
    • White, Yellow: 38 observed, 10 expected
    • Calculated values for the chi-square test:
    • ext{χ}^2 = 103.69
    • Degrees of freedom (df) = 3
    • Critical value = 16.27
    • Conclusion: p < 0.001 implies rejecting the null hypothesis, data inconsistent with independent assortment of alleles affecting body and eye color in flies. They are linked.

Causes for Model Inaccuracy

  • Traits can be inherited non-independently due to being on the same chromosome arm.
  • Chromosome segregation at meiosis can be non-random.
  • Segregation Distorter Alleles:
    • These alleles can lead to more than 50% of gametes in a heterozygote.
    • Segregation distorters in spermatogenesis often act as sperm killers.
    • Segregation distorters in oogenesis usually involve centromeres.

Mendelian Genetics and Population Variability

  • Mendelian genetics predicts the outcomes of crosses via independent assortment of alleles.
  • Why Populations Vary for Heritable Traits:
    • Variation arises due to mutation, independent assortment, recombination, and environmental influences.
    • Alleles in populations undergo evolution driven by mutation, migration, genetic drift, and selection.

Population Genetics Overview

  • Definition of Population Genetics: Describes, predicts, and infers patterns of alleles in populations.
  • Characteristics of Populations:
    • Populations carry multiple alleles at many loci, leading to genetic variability.
    • Many individuals may be heterozygous at various loci.

Genophytes and Their Effects on Phenotypes

  • Certain alleles impact phenotypic expressions; for example, different CCR5 genotypes lead to varying susceptibilities to HIV-1.

Allele Frequencies in Populations

  • Populations can be described with allele frequencies and genotype frequencies.
    • Example calculations from genotype data demonstrate allele proportions:
    • A alleles: 12/24 = 0.5
    • a alleles: 12/24 = 0.5
    • Genotype frequencies:
      • A/A genotypes: 3/12 = 0.25
      • A/a genotypes: 6/12 = 0.5
      • a/a genotypes: 3/12 = 0.25

Calculating Allele Frequencies

  • Example with C-C chemokine receptor-5 gene in humans:
    • Two alleles: 1 and $ ext{∆32}$.
    • Three genotypes: 1/1, 1/$\Delta$32, and $ ext{Δ32}/ ext{Δ32}$.
    • Assessing allele frequency can be achieved either by counting alleles or using genotype frequencies.

Hardy-Weinberg Equilibrium (HWE) Principles

  • The HWE describes expected diploid genotypes in a population:
    • If a population is large and individuals mate randomly, and no forces affect allele frequencies (e.g., mutation, migration, selection):
    • Allele frequencies (p and q) remain constant over time.
    • Genotype frequencies are:
      • A/A = p^2
      • A/a = 2pq
      • a/a = q^2

Applications of HWE

  • HWE serves as a null model to understand allele structuring into genotypes.
  • To calculate expected frequencies is particularly useful for assessing diseases:
    • Example of cystic fibrosis incidence = 1 in 2500 (0.0004) in Northern Europe:
    • Assess disease allele frequency: q = 0.02
    • Carrier frequency: 2pq = 0.044.

Chi-Square Test in Population Data

  • The test can assess whether diploid genotypes are present at frequencies expected by HWE:
    • Example data for CCR5 genotype:
    • Observed and expected values given for classes.

Next Steps

  • Next class requires reading Chapter 26, sections 4-8, and suggested practice problems from the Week 6 recitation packet.