Evolution and Population Genetics Notes

Introduction to Evolution

• The lecture series covers evolution, starting with population genetics (Chapter 20), principles, processes, and evidence of evolution (Chapter 21), the origin of species, selection, and biological diversity (Chapter 22), comparative biology (Chapter 23), and the diversity of species (Chapter 25).

Genes within Populations (Chapter 20)

• This chapter focuses on genetic variation within populations and the processes that drive evolutionary change.

Genetic Variation and Evolutionary Change

• Genetic variation in populations is acted upon by processes that cause evolutionary change.

• These processes include:

  • Mutation

  • Gene flow

  • Nonrandom mating

  • Genetic drift

  • Natural selection

• Natural selection occurs when phenotypes differ in fitness.

• Fitness differences result from:

  • Survival

  • Mating success

  • Number of offspring per mating event

Lecture Outline

• 20.1 Genetic Variation and Evolution

• 20.2 Changes in Allele Frequency

• 20.3 Five Agents of Evolutionary Change

• 20.4 Quantifying Natural Selection

• 20.5 Reproductive Strategies

• 20.6 Natural Selection’s Role in Maintaining Variation

• 20.7 Selection Acting on Traits Affected by Multiple Genes

• 20.8 Experimental Studies of Natural Selection

• 20.9 Interactions Among Evolutionary Forces

• 20.10 The Limits of Selection

Genetic Review

• Nucleic acids are organic compounds that hold genetic information.

• A nucleotide is the building block for nucleic acids.

Nucleic Acids

• Nucleotides consist of a sugar-phosphate backbone and a nitrogen-containing base.

• DNA uses the bases Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

• RNA uses Uracil (U) instead of Thymine (T).

• Base pairs:

  • A pairs with T in DNA ($A=T$)

  • C pairs with G in DNA ($C=G$)

DNA vs RNA

• DNA (Deoxyribonucleic acid) contains Thymine.

• RNA (Ribonucleic Acid) contains Uracil.

Genome Size

• Genome sizes vary greatly across different organisms. The number of nucleotide pairs per haploid genome can range from 10^5 in Mycoplasma to 10^12 in Paris japonica.

• Bacteria (e.g., Mycoplasma, E. coli) have mostly coding DNA.

• Eukaryotes (fungi, protists, plants, animals) contain varying amounts of non-coding DNA.

• Genome size does not directly correlate with organismal complexity.

Terminology

• Gene: The basic unit of heredity; a sequence of DNA nucleotides that codes for specific information.

• Genome: The entire DNA sequence of an organism.

• Genomics: The study of genomes.

• Phenotype: The expression of genetic information.

Chromosomes

• DNA is organized into chromosomes within the cell nucleus.

• Key components of a chromosome include:

  • Telomeres: Protective caps at the end of chromosomes.

  • Centromere: The region where sister chromatids are joined.

  • Nucleosomes: DNA wrapped around histone proteins.

• Base pairing rules: T=A, C=G

Chromosomes - Ploidy

• Diploid (2n): Two sets of chromosomes.

• Haploid (n): One set of chromosomes.

• Polyploid: More than two sets of chromosomes.

• Humans are diploid, with 46 chromosomes (23 homologous pairs).

• Gametes (egg and sperm) are haploid.

Alleles and Locus

• Locus: Location of a gene on a chromosome.

• Alleles: Variations of the same gene.

• Homozygous: Organism with two identical alleles (AA or aa).

• Heterozygous: Organism with two different alleles (Aa).

Mitosis

• Mitosis is a process of cell division that results in two identical diploid cells.

• It involves the separation of sister chromatids.

Meiosis

• Meiosis is a process of cell division that results in four haploid cells (gametes).

• It involves two rounds of division: Meiosis I and Meiosis II.

• Homologous chromosomes separate in Meiosis I, and sister chromatids separate in Meiosis II.

• Chiasma: site of crossing over

Mendel’s Laws of Inheritance

• Law of Dominance

• Law of Segregation

• Law of Independent Assortment

Mutations

• Mutations are mistakes in DNA replication.

• Somatic cell mutations: Non-reproductive mutations.

• Hereditary mutations: Reproductive or germline mutations.

Genetic Variation and Evolution

• Genetic variability is a key component of evolution.

• Evolution is defined as changes in allele frequency over time.

• Allele frequency (% of an allele in a population) can be estimated and used to predict phenotypic expression.

• Frequencies can change over time, leading to evolution.

Consequences of Allele Frequency Changes

• Changes in allele frequency can be perpetuated in the population and lead to genetic variability.

• Four main factors alter allele frequency (4 M’s):

  • Mutation

  • Migration

  • Major events (Genetic drift)

  • Mating (Non-random)

Genetic Variability Prerequisite

• Genetic variability is required for evolution to occur.

Hardy-Weinberg Principle

• The Hardy-Weinberg principle allows for a prediction of allele frequencies within a given population.

• Assumptions of Hardy-Weinberg:

  • Mutations do not occur.

  • Immigration or emigration does not occur.

  • Mating is random.

  • Population is large.

  • No selection.

Hardy-Weinberg Equation

• $p$ represents the probability of allele B.

• $q$ represents the probability of allele b.

• $p + q = 1$ (The sum of allele frequencies for a particular gene must equal 1).

• $BB + Bb + bb = 1$ (The sum of genotype frequencies in the population must equal 1).

Genotype Frequencies

• The probability of the homozygote BB = $p * p = p^2$

• The probability of the homozygote bb = $q * q = q^2$

Heterozygote Frequency

• There are two ways an offspring can be a heterozygote (Bb):

  • Possibility 1: offspring gets a B from mom and b from dad. Probability = $p*q$

  • Possibility 2: offspring gets a b from mom and B from dad. Probability = $q*p$

• Therefore, the probability of an offspring being heterozygote Bb = $pq + qp = 2pq$

Hardy-Weinberg Equation

• $(q + p)^2 = p^2 + 2pq + q^2$

• Probability of BB = $p^2$

• Probability of Bb = $2pq$

• Probability of bb = $q^2$

• $1 = p^2 + 2pq + q^2$

Hardy-Weinberg Example

• Population of 100 feral cats: White = 16%, Black = 84%.

• 16% of the white cats (homozygous recessive) have the genotype of bb.

• $q^2 = 0.16$

• $q = \sqrt{0.16} = 0.4$

• Since $q + p = 1$, then $p = 1 - q = 1 - 0.4 = 0.6$

• The frequency of the b allele is 0.4, and the frequency of the B allele is 0.6.

Solving for Genotype Frequencies

• Given $p = 0.6$ and $q = 0.4$:

• $p^2 + 2pq + q^2 = (0.6)^2 + 2(0.6)(0.4) + (0.4)^2 = 0.36 + 0.48 + 0.16 = 1$

• Expected number of individuals:

  • BB: $0.36 * 100 = 36$

  • Bb: $0.48 * 100 = 48$

  • bb: $0.16 * 100 = 16$

Practice Problems

• In a population of red and white flowers (red dominant) in Hardy-Weinberg equilibrium, the frequency of red flowers is 91%. What is the frequency of the red allele?

• 91% of flowers are red (RR or Rr), so 9% are white (rr).

• $q^2 = 0.09$

• $q = \sqrt{0.09} = 0.3$

• $p + q = 1$, so $p = 1 - 0.3 = 0.7$

• The frequency of the red allele is 70%.

Agents of Evolutionary Change

• Mutation changes alleles.

• Gene flow occurs when alleles move between populations.

• Nonrandom mating shifts genotype frequencies:

  • Assortative mating: Increases homozygotes.

  • Disassortative mating: Increases heterozygotes.

  • Mate selection.

Genetic Drift

• Founder Effect: A few individuals from a population start a new population with a different allele frequency than the original population.

• Bottleneck Effect: A drastic reduction in population size reduces genetic diversity.

Selection

• Variation in phenotype must be present.

• There must be reproductive success.

• The phenotypic trait must be heritable.

Examples of Selection

• Predatory Avoidance: Coat color in pocket mice is selected based on the environment (light sand vs. black lava rock).

• Pesticide Resistance: Insects develop resistance to pesticides through decreased uptake or decreased number of target sites.

• Antibiotic Resistance: Bacteria evolve resistance to antibiotics, which can then spread to other bacteria.

Quantifying Natural Selection: Fitness

• Fitness measures the reproductive success of individuals (children, grandchildren).

• Higher fitness results in more offspring.

Reproductive Strategies

• Parental investment = energy expended on reproduction.

• Costs and Benefits: There are trade-offs between lifespan, egg size, and number of eggs laid.

Sexual Selection

• Sexual selection: competition for mates.

  • Intrasexual selection: competition between members of one sex.

  • Intersexual selection: mate choice.

  • Sensory exploitation.

Natural Selection’s Role in Maintaining Variation

• There is natural variation within populations.

• Selection can be frequency dependent.

  • Negative frequency dependency: rare phenotypes have higher fitness.

  • Positive frequency dependency: rare phenotypes have a lower fitness.

Oscillating Selection

• Selection can favor one phenotype at one time and another phenotype at another time.

• Example: Medium ground finch of Galápagos Islands.

  • Birds with big bills favored during drought.

  • Birds with smaller bills favored in wet conditions.

Heterozygote Advantage

• Heterozygotes are favored over homozygotes.

• Works to maintain both alleles in the population (variation).

• Example: Sickle cell anemia.

  • Hereditary disease affecting hemoglobin.

  • Homozygotes for sickle cell allele usually die before reproducing (without medical treatment).

  • Heterozygotes are resistant to malaria and have only mild sickle cell disease, giving them a selective advantage in malaria-prone regions.

Types of Selection

• Directional Selection: Selection for larger individuals.

• Stabilizing Selection: Selection for mid-size individuals. The distribution gets narrower.

• Disruptive Selection: Selection for small and large individuals. Two peaks form.

Experimental Studies of Natural Selection

• Biologists traditionally investigated past events using fossils or DNA evidence.

• Organisms with short lifespans are often used to study evolution.

• Laboratory studies on fruit flies (40-day lifespan) are common.

• Experiments can be run in the field or in the lab.

Natural Selection in Guppies Example

• Male guppies above the waterfall (no predator) have vibrant colors.

• Male guppies below the waterfall (predator) have drab colors.

• Introducing a predator above the waterfall would lead to a decrease of spots per fish over time.

Interactions Among Evolutionary Forces

• Evolutionary processes can work together or in opposition.

Copper Tolerance in Plants Example

• Copper tolerance in bent grass near mine sites is an example of selection pressure.

• Gene flow (pollen dispersal) from non-mine sites can introduce non-tolerant alleles, opposing selection for copper tolerance.

Limitations to Selection: Interactions between genes

• Epistasis: Interaction between two or more genes to control a single phenotype.

Epistasis Example

• New comb shapes appeared in F2 generation indicating that more than one gene controls comb shape.

Limitations to Selection: Multiple effects of alleles

• Pleiotropy: One allele affects many aspects of a phenotype.

Pleiotropy Example

• Frizzle gene causes curled feathers in chickens but also affects other aspects of phenotype:

  • Fewer eggs

  • Abnormal body temperature

  • Altered metabolism and blood flow

  • Greater digestive capacity