Chapter 23 - Population Genetics

Combined Analysis of HapMap CEU + YRI

Focused on genetic features of two populations: Europeans (CEU) and Africans (YRI). This section includes discussions on homozygote AA, homozygote aa, and heterozygote Aa, with detailed examinations of allele frequencies, mean Hardy-Weinberg expectation, and the effects of bottlenecking and servicing events on genetic composition. The analysis highlights the genetic diversity observed between these populations due to historical migration, natural selection, and adaptation to different environments.

Key Concepts in Population Genetics

• Natural Selection: A fundamental mechanism leading to changes in allele and phenotype frequencies in populations. Natural selection operates by favoring traits that improve survivability and reproductive success.

• Sexual Selection: A type of natural selection that focuses on traits that enhance mating success, often resulting in sexual dimorphism, where males and females exhibit different characteristics.

• Genetic Drift: A stochastic process causing random changes in allele frequencies, particularly significant in small populations where chance events can lead to the loss or fixation of alleles.

• Migration: The movement of alleles between populations, can introduce new genetic variation and increase overall genetic diversity.

• Nonrandom Mating: Occurs when individuals preferentially choose partners based on specific phenotypic traits, which can lead to an increased frequency of homozygosity in offspring.

Definition of a Population

• Population: A group of individuals of the same species occupying a specific environment and capable of interbreeding. Some species are widespread but fragmented into distinct populations; their sizes and distributions change over time, which impacts genetic diversity. The dynamics of population size, environmental conditions, and isolation are crucial for understanding these variations.

Population Genetics Overview

• Population Genetics: The study of genetic variation in populations and its implications for evolution, focusing on examining genetic variation's extent, maintenance, and the underlying factors driving changes over generations. Understanding these dynamics is vital for discerning how genetic variation correlates with phenotypic diversity, disease susceptibility, and adaptation to environmental pressures.

Gene Pool

• Gene Pool: The complete set of alleles in a population, reflecting genetic variation and changes passed from one generation to the next. It emphasizes the importance of allele variation among individuals, which is foundational for evolutionary processes.

Polymorphism and Genetic Diversity

• Polymorphism: Occurs when two or more variations exist for a character due to alleles influencing phenotype. Polymorphic genes consist of multiple alleles, while monomorphic genes predominantly feature a single allele. Single nucleotide polymorphisms (SNPs) are a significant source of genetic variation and can influence traits and disease susceptibility. Larger populations are generally associated with higher genetic diversity, essential for applications in personalized medicine, conservation biology, and understanding evolutionary processes.

Allele and Genotype Frequencies

• Genotype Frequency: Calculated as the number of individuals with a specific genotype divided by the total population.

• Allele Frequency: Determined by the number of copies of a specific allele divided by the total number of alleles in the population, providing insights into genetic diversity within populations and aiding in evolutionary studies.

Case Study: Four O’Clock Plants

An example illustrating the calculation of genotype frequencies of color variations among plants:

• 49 red-flowered plants

• 42 pink-flowered plants

• 9 white-flowered plantsAnalyzing the frequencies offers a practical application of Hardy-Weinberg calculations in studying phenotypic variation.

Hardy-Weinberg Equilibrium

• Hardy-Weinberg Principle: Predicts that allele and genotype frequencies will remain constant under specific conditions: no mutations, no natural selection, large population size, no migration, and random mating. If any conditions are not met, evolutionary mechanisms will influence gene and genotype frequencies, leading to changes over time.

Hardy-Weinberg Equation Calculation

Example with frequencies p = 0.7 and q = 0.3 leading to genotype frequencies:

• Frequency of CRCR (red flowers) = p^2 = 0.49.

• Frequency of CRCW (pink flowers) = 2pq = 0.42.

• Frequency of CWCW (white flowers) = q^2 = 0.09.

Microevolution

• Microevolution: Refers to small-scale changes in allele frequencies within populations from generation to generation, driven by the introduction of new genetic variations (e.g., mutations, gene duplications) and evolutionary mechanisms like natural selection, genetic drift, and migration. These processes contribute to the gradual evolution of populations over time, facilitating adaptation to changing environments.

Natural Selection

• Natural Selection: The process by which certain heritable traits become more common in a population due to those traits' favorable impact on survival and reproduction. Important mechanisms of reproductive success include:

  • Traits enhancing survival until reproduction.

  • Traits linked directly to reproductive success.

Evolutionary Fitness

• Fitness: The relative chance of a genotype contributing to the next generation's gene pool compared to others. Mean fitness of the population is derived from metrics of reproductive success. An example illustrating different fitness values among genotypes based on offspring yield:

  • AA genotype - 5 offspring (fitness wAA = 1.0).

  • Aa genotype - 4 offspring (fitness wAa = 0.8).

  • aa genotype - 1 offspring (fitness waa = 0.2).

Limits of Natural Selection

Natural selection is not goal-oriented and must work within existing variations present in the population. Various constraints arise from historical factors influencing past evolution, trade-offs in trait advantages, and inherent limitations in predicting perfection in evolutionary outcomes, leading to suboptimal solutions in certain contexts.

Patterns of Natural Selection

• Directional Selection: Favors one extreme phenotype affecting reproductive success—e.g., industrial melanism seen in peppered moths.

• Stabilizing Selection: Promotes intermediate phenotypes, favoring individuals with average trait values (e.g., optimal clutch size in birds).

• Disruptive Selection: Favors extreme phenotypes in heterogeneous environments, leading to greater phenotypic variance.

• Balancing Selection: Maintains genetic variation through mechanisms like heterozygote advantage (where heterozygous individuals have a fitness benefit) and negative frequency-dependent selection.

Sexual Selection

A type of natural selection focusing on traits that increase the likelihood of finding or securing mates. This form of selection is often more pronounced in males, leading to distinctive traits that enhance mating success but may reduce survival.

Sexual Selection Mechanisms

• Intrasexual Selection: Involves competition among individuals of the same sex for access to mates, often leading to the evolution of traits that enhance combat effectiveness.

• Intersexual Selection: Involves preferences shown by one sex (often females) for specific traits in the opposite sex, influencing partner choice and driving the development of elaborate traits and displays.

Results of Sexual Selection

This can lead to traits that enhance reproductive success but might be detrimental to survival. For example, brightly colored male guppies may attract females effectively but simultaneously increase their visibility to predators, exemplifying the trade-offs in evolution.

Genetic Drift

• Genetic Drift: Refers to changes in allele frequency due to random chance, particularly affecting small populations where the effects of random sampling can lead to the loss of alleles or fixation of others.

• Bottleneck Effect: A sudden reduction in population size that results in altered allele frequencies, often leading to decreased genetic diversity.

• Founder Effect: Occurs when a small group starts a new population, potentially carrying different allele frequencies than the source population, leading to unique genetic traits in the new population.

Neutral Theory of Evolution

This theory posits that the majority of genetic variation within populations is due to genetic drift rather than natural selection, suggesting many mutations are neutral and do not confer a selective advantage or disadvantage.

Migration and Gene Flow

Migration serves to modify allele frequencies between populations, facilitating gene flow that can enhance genetic diversity within and between groups, impacting evolutionary trajectories.

Nonrandom Mating and Its Types

• Nonrandom Mating: Violates Hardy-Weinberg conditions and can lead to increased homozygosity, affecting levels of genetic fitness.

  • Assortative Mating: Preference for similar phenotypes, leading to increased similarity among mated pairs.

  • Disassortative Mating: Preference for dissimilar phenotypes, increasing genetic diversity.

  • Inbreeding: Occurs when mates are chosen based on genetic similarities, potentially raising homozygosity and revealing deleterious genetic effects.