Population Genetics Lecture

Introduction to Population Genetics

Learning changes everything.
Population Genetics is a branch of biology that studies genes and genotypes within populations. This includes:
- Understanding the extent of genetic variation.
- Exploring why variation exists and how it is maintained.
- Analyzing how genetic variation changes over generations.
- Understanding the relationship between genetic variation and phenotypic variation.

Key Concepts

Genes in Populations: Understanding the structure and variation of genes within populations.
Natural Selection: How advantageous traits enhance survival and reproduction.
Sexual Selection: Focused on traits that help in finding or selecting mates.
Genetic Drift: Random changes in allele frequencies that can lead to loss or fixation of alleles.
Migration: Movement between populations contributing to gene flow.
Nonrandom Mating: How mating choices affect genetic structure.

Genes in Populations

Population Genetics: Focuses on genes and genotypes in a population, emphasizing the study of genetic variation.;
Gene Pool: The complete set of genetic information within a population.
Focus: Genetic variation and its implications.

Definitions

Polymorphism: The presence of two or more variations of a character (phenotype) due to the existence of multiple alleles.
- Polymorphic Gene: A gene with two or more alleles.
- Monomorphic Gene: A gene predominantly featuring a single allele.
- Single Nucleotide Polymorphisms (SNPs): The smallest type of genetic change in a gene, contributing to 99% of variation in human gene sequences. SNP analysis aids personalized medicine by tailoring medical care to an individual's genotype.

Allele and Genotype Frequencies

Definitions:
- Allele Frequency: Proportion of a specific allele in the gene pool; calculated by:
  $\text{Allele Frequency} = \frac{\text{Number of copies of a specific allele}}{\text{Total number of all alleles for that gene}}$
- Genotype Frequency: Proportion of individuals with a specific genotype in the population; calculated by:
  $\text{Genotype Frequency} = \frac{\text{Number of individuals with a particular genotype}}{\text{Total number of individuals}}$

Example: Four O’clock Plants

Genetic Distribution:
- 49 red-flowered plants (genotype CRCR)
- 42 pink-flowered plants (genotype CRCW)
- 9 white-flowered plants (genotype CWCW)
Frequencies Calculation:
- Frequency of allele CW:
  $\text{Frequency of CW} = \frac{42+(2)(9)}{(2)(49)+(2)(42)+(2)(9)} = 0.3 \ or \ 30\%$
- Frequency of genotype CWCW:
  $\text{Frequency of CWCW} = \frac{(2)(49)+(2)(42)+(2)(9)}{49+42+9} = 0.09 \ or \ 9\%$

Hardy-Weinberg Equation

The equation:
- $p^2 + 2pq + q^2 = 1$
- Where:
- $p^2$ : Genotype frequency of homozygotes (CRCR)
- $2pq$ : Genotype frequency of heterozygotes (CRCW)
- $q^2$ : Genotype frequency of homozygotes (CWCW)
Example Values:
- Given: $p = 0.7$ and $q = 0.3$
- Frequencies:
- Frequency of CRCR: $p^2 = (0.7)² = 0.49$
- Frequency of CRCW: $2pq = 2(0.7)(0.3) = 0.42$
- Frequency of CWCW: $q^2 = (0.3)² = 0.09$

Hardy-Weinberg Equilibrium

Definition: Predicts allele and genotype frequencies remain constant over generations if conditions are met.
Conditions Required for Equilibrium:
- No new mutations occur.
- No natural selection occurs.
- Population must be large to negate random chance effects.
- No migration between populations occurs.
- Random mating occurs.
Implications: No actual population meets all these conditions; however, HW can be nearly approximated for some genes.

Microevolution

Definition: Changes in a population’s gene pool through generations due to various factors.
Sources of New Genetic Variation:
- Mutations: Introduces new alleles at a low rate (neutral, deleterious, or beneficial).
- Gene Duplication: Can result in gene family evolution.
- Horizontal Gene Transfer: Genes may move between species affecting genetic variation.
Evolutionary Mechanisms Affecting Allele Prevalence:
- Natural Selection: More fit traits survive and reproduce.
- Genetic Drift: Changes due to random chance, especially impactful in small populations.
- Migration: Alters allele frequencies by introducing new alleles.
- Nonrandom Mating: Selection based on phenotypes which affects genotype ratios.

Natural Selection

Definition: Process significantly altering allele frequencies over generations through survival of individuals with beneficial traits.
Outcomes: Leads to adaptations promoting survival in specific environments.

Reproductive Success

Definition: Likelihood of contributing offspring to the next generation governed by traits that aid in survival and reproductive capacities.
Fitness Measures: The relative likelihood of a genotype's contribution to the gene pool:
- Example:
- Genotypes: AA, Aa, aa with reproductive successes:
- AA: 5 offspring
- Aa: 4 offspring
- aa: 1 offspring
Fitness, denoted by ‘w’:
- Fitness(AA) = 1.0 (highest)
- Fitness(Aa) = 0.8
- Fitness(aa) = 0.2

Mean Fitness

Definition: The average reproductive success within a population.
Impact: As higher fitness individuals proliferate, mean fitness of the population increases.

Patterns of Natural Selection

Directional Selection: Favoring individuals at one extreme of a phenotype.
- Results from new advantageous alleles or environmental changes.
Stabilizing Selection: Favors intermediate phenotypes, extremes are selected against (e.g., clutch size).
Disruptive/Diversifying Selection: Promotes multiple forms/phenotypes in heterogeneous environments.
Balancing Selection: Maintains genetic diversity through mechanisms like heterozygote advantage or negative frequency-dependent selection.

Sexual Selection

A specialization of natural selection acting on traits affecting reproductive success.
- Often results in sexual dimorphism: differences in male and female traits.

Intrasexual Selection

Competition amongst the same sex (e.g., males) for mating rights.
- Traits: Horns, antlers, or physical size can be advantageous.

Intersexual Selection

Members of one sex (usually females) select mates based on traits, resulting in vibrant male characteristics.
Cryptic Female Choice: Females may select against genetically similar males.

Results of Sexual Selection

Explains characteristics that may reduce survival rates but improve reproductive success (Example: brightly colored guppies).
Predation impacts the distribution of these traits; brightly colored males are less common in predation-heavy environments.

Genetic Drift

Definition: Changes in allele frequencies occurring due to random events unrelated to fitness; results in either fixation or loss of alleles.
More pronounced in small populations.

Bottleneck Effect

Sudden reduction in population size affecting allele frequencies due to random survival which can reduce genetic variation.

Founder Effect

The establishment of a new population by a small number of individuals leads to potential disparity in genetic variation and allele frequency from the original population.

Neutral Theory of Evolution

Concept of non-Darwinian evolution, emphasizing that most genetic variation is due to random genetic drift rather than natural selection acting on phenotypes.
Neutral variations are often mutations that do not result in observable effects on phenotype.
Data indicates that nucleotide substitutions occur more frequently at the 3rd base of codons compared to the 1st or 2nd.

Migration and Nonrandom Mating

Gene Flow: Migration between populations equalizes allele frequencies, increasing genetic diversity.
Nonrandom Mating: Conditions deviation from Hardy-Weinberg equilibrium by selecting mates based on phenotypes or genotypes.

Assortative Mating

Preference for similar phenotypes increases homozygosity.

Disassortative Mating

Preference for dissimilar phenotypes increases heterozygosity.

Inbreeding

Mating based on genetic relatedness increasing the likelihood of homozygosity, potentially resulting in inbreeding depression, leading to lower population fitness.