Genes & Evolution

Diversity of Organisms

• Diversity Example:
  • 1,000 bat species.
  • 5,000 mammal species.
  • 40,000 vertebrate species.
  • 250,000 flowering plant species.
  • 350,000 beetle species.
• Different Forms:
  • Bacteria, fungi, trees, whales showcase the variety of life.
• Many Similar Yet Different:
  • Dogs, wolves, foxes, and coyotes demonstrate variations within related groups.

Common Mechanisms

• Many mechanisms are common to different organisms:
  • Chemical pathways.
  • Energy metabolism.
  • The genetic code.
  • Molecules.
• These common mechanisms allow organisms to thrive in different environments and be well-adapted to these environments.

Evolutionary Questions

• Key questions in evolution include:
  • Why are there so many species, and what is their origin?
  • How are species so well-adapted to their environments?

Definition of Evolution

• Evolution is defined as a change in a species over time.
• This change occurs in the genetic makeup of the species.
• Specifically, evolution is a change in the allele frequency of a population over time.

Chromosomes, Genes, and Alleles

• Alleles are different forms of a gene (e.g., allele for purple flowers vs. allele for white flowers).
• The locus is the specific location of a gene on a chromosome.
• Example: PTC receptor gene with tasting and non-tasting alleles.
  • Individuals with at least one tasting allele can taste PTC.
  • Individuals with two non-tasting alleles cannot taste PTC.

Time and Evolutionary Change

• Changes in a species require time.
• The rate of change is correlated with generation time.
• Antibiotic resistance is a common example of rapid evolutionary change.

Examples of Antimicrobial Resistance

• Examples include:
  • Antibiotic-Resistant Mycobacterium tuberculosis (TB).
  • Methicillin-Resistant Staphylococcus aureus (MRSA).
  • Vancomycin-Resistant Enterococci (VRE).
  • Neisseria gonorrhoeae (Gonorrhea).
  • Clostridium difficile.
  • Gram-negative Bacteria.

Sickle Cell Anemia

• Sickle cell trait is a genetic abnormality affecting red blood cells.
• Ryan Clark, a Steelers safety, had issues playing in Denver due to the altitude affecting his sickle cell trait.
• Normal Red Blood Cells:
  • Normal hemoglobin.
  • RBCs flow freely within blood vessels.
• Abnormal, Sickled, Red Blood Cells (Sickle Cells):
  • Abnormal hemoglobin forms strands, causing the sickle shape.
  • Sickle cells block blood flow.

DNA, mRNA, and Protein in Normal Cells

• Normal Cells:
  • DNA sequence: $CAA\, GTA \,AAC\, ATA\, GGA\, CTT\, CTT$
  • mRNA sequence: $GUU\, CAU\, UUG\, UAU\, CCU\, GAA\, GAA$
  • Protein sequence: Val-His-Leu-Thr-Pro-Glu-Glu

DNA, mRNA, and Protein in Sickle Cells

• Sickle Cells:
  • DNA Sequence: $CAA\, GTA\, AAC\, ATA\, GGA\, CAT\, CTT$
  • mRNA Sequence: $GUU\, CAU\, UUG\, UAU\, CCU\, GUA\, GAA$
  • Protein sequence: Val-His-Leu-Thr-Pro-Val-Glu
• The single amino acid change from glutamic acid (Glu) to valine (Val) causes sickle cell anemia.

Heterozygote Advantage: Malaria and the Sickle-Cell Allele

• The distribution of malaria, caused by Plasmodium falciparum, correlates with the frequencies of the sickle-cell allele.
• Areas with higher malaria rates have higher frequencies of the sickle-cell allele.
• Heterozygotes (carriers of one sickle-cell allele) are more resistant to malaria, providing a selective advantage.

Gene Pools and Allele Frequencies

• A population is a localized group of individuals capable of interbreeding and producing fertile offspring.
• A gene pool consists of all the alleles for all loci in a population.
• A locus is fixed if all individuals in a population are homozygous for the same allele.

Definition of Evolution Revisited

• Evolution is the change in allele frequency in a population over time.

Allele Frequency Calculation

• To calculate allele frequencies::
  • Count the number of each allele in the population.
  • Divide by the total number of alleles.
• Example:
  • 10 plants (20 alleles total).
  • 5 RR individuals = 10 R alleles.
  • 4 Rr individuals = 4 R alleles.
  • 14 R alleles / 20 total alleles.
  • $p$ (frequency of R allele) = $14/20 = 0.7$
  • $q$ (frequency of r allele) = $1-p = 0.3$
  • $p + q = 1$

Allele Frequency Problems

• Problem 1:
  • Given 10 individuals with various RR, Rr, and rr genotypes, calculate $p$ and $q$.
  • If R = 10/20, then $p = 0.5$.
  • If r = 10/20, then $q = 0.5$.
• Problem 2:
  • For population 1 (mostly homozygotes): $N<em>{AA} = 90$, $N</em>{Aa} = 40$, and $N_{aa} = 70$. Total individuals = 200, total alleles = 400.
  • Total Dominant Alleles = $(2 \times 90) + (1 \times 40) = 220$.
  • $p = 220/400 = 0.55$, therefore $q = 0.45$.
• Problem 3:
  • For population 2 (mostly heterozygotes): $N<em>{AA} = 45$, $N</em>{Aa} = 130$, and $N_{aa} = 25$. Total individuals = 200, total alleles = 400.
  • Total Dominant Alleles = $(2 \times 45) + (1 \times 130) = 220$.
  • $p = 220/400 = 0.55$, therefore $q = 0.45$.
• Problem 4:
  • A plant species has flowers that are either red (dominant) or pink (recessive). In one population, this trait has become fixed for pink.
  • Population fixed for pink – no dominant red alleles.
  • All alleles are recessive (pink), thus $p=0$ and $q=1$.

Calculating Allele Frequencies

• In any population:
  • Frequency of allele A: $p = (2N<em>{AA} + N</em>{Aa}) / (2N)$
  • Frequency of allele a: $q = (2N<em>{aa} + N</em>{Aa}) / (2N)$
  • Where $N$ is the total number of individuals in the population.

The Hardy-Weinberg Principle

• Frequencies of alleles and genotypes in a population remain constant from generation to generation only in a population that is not evolving.
• If a population does not meet the criteria of the Hardy-Weinberg principle, it can be concluded that the population is evolving.

Hardy-Weinberg Equilibrium

• Hardy-Weinberg Equilibrium describes the constant frequency of alleles in a gene pool.
• If $p$ and $q$ represent the relative frequencies of the two possible alleles in a population, then:
  • $p^2 + 2pq + q^2 = 1$
    • $p^2$ = frequency of the homozygous dominant genotype.
    • $q^2$ = frequency of the homozygous recessive genotype.
    • $2pq$ = frequency of the heterozygous genotype.
  • Important to contrast this from $p$ and $q$ which represent allele frequencies.

Hardy-Weinberg Calculation Example

• A plant species has flowers that are either red (dominant) or pink (recessive). In a population of 100 plants, 49 have pink flowers. What is the frequency of the dominant allele?
  • $p^2 + 2pq + q^2 = 1$
  • $q^2 = 0.49$
  • $q = 0.7$
  • $p = 0.3$

Mechanisms of Evolutionary Change

• Hardy-Weinberg equilibrium is a null hypothesis that assumes evolutionary forces are absent.
• Known evolutionary mechanisms include:
  • Mutation
  • Gene flow
  • Genetic drift
  • Nonrandom mating
  • Natural selection

Mutation

• Any change in the nucleotide sequences of DNA.
• Mutations are random with respect to the adaptive needs of an organism.
• Selection acting on the random variation results in adaptation.

Gene Flow

• Migration of individuals between populations.
• Movements of gametes between populations.
• New individuals can:
  • Add new alleles to the gene pool.
  • Change allele frequencies.

Genetic Drift

• Random changes in allele frequencies.
• Harmful alleles may increase in frequency.
• Rare advantageous alleles may be lost.
• Example: Greater prairie chicken (Tympanuchus cupido) with only a few hundred left.

Founder Effect

• Population of the pitcher plant Sarracenia purpurea in central Ohio arose from a single individual planted in 1912.
• Today, there is only one detectable polymorphic locus in its entire genome.

Nonrandom Mating

• Occurs when individuals choose mates with particular phenotypes.
• If individuals choose the same genotype as themselves, homozygote frequencies will increase.

Types of Nonrandom Mating

• Assortative Mating: Preference (e.g., humans choosing mates based on height).
• Inbreeding: Common in small populations.
• Sexual Selection: Based on best genes/resources.

Natural Selection

• One of the primary mechanisms of evolution.

How Natural Selection Results in Evolution

• Natural selection acts on the phenotype (not the genotype).
• Example: Distribution of malaria and sickle-cell allele frequencies, where heterozygotes have a survival advantage in malaria-prone regions.

Fitness

• Fitness is a function of:
  • The probability of individuals surviving.
  • The average number of offspring they produce.

Fitness Examples

• Fitness is determined by the relative rates of survival and reproduction of individuals.

Single vs. Multiple Loci

• Most characters are influenced by alleles at more than one locus and often show quantitative variation instead of qualitative variation.
• Example: The distribution of body size of individuals in a population is likely to resemble a bell-shaped curve.

Modes of Natural Selection

• Natural selection can act on characters with quantitative variation in three ways:
  • Stabilizing selection
  • Directional selection
  • Disruptive selection

Stabilizing Selection

• Reduces variation in a population but does not change the mean.
• Rates of evolution are slow because natural selection is usually stabilizing.

Stabilizing Selection Example

• Human birth weight is influenced by stabilizing selection, with optimal birth weights having the lowest mortality rates.

Directional Selection

• Individuals at one extreme are more successful.
• May result in favoring a particular genetic variant (positive selection for that variant).

Directional Selection Example

• Peccaries consume cacti with fewer spines, leading to directional selection favoring cacti with more spines.

Disruptive Selection

• Individuals at either extreme are more successful.
• Example: Bill size in black-bellied seedcrackers.

Disruptive Selection Example: Bill Size in Black-Bellied Seedcrackers

• Birds with large bills can crack the hard seeds of one plant species, while birds with small bills feed efficiently on the soft seeds of a different species.

Sexual Selection

• Ability to compete for mates (intrasexual selection).
• Ability to be more attractive to the opposite sex (intersexual selection).
• Favors traits that:
  • Enhance chances of reproduction.
  • Reduce its chances of survival.

Sexual Selection Example

• Male widowbirds with artificially lengthened tails fathered the most offspring, demonstrating sexual selection favoring long tails.

How Genetic Variation Is Maintained within Populations

• Genetic variation is maintained through several mechanisms.

Mechanisms for Maintaining Genetic Variation

• Many mutations do not affect the function of the resulting proteins.
• An allele that does not affect fitness is a neutral allele and tends to accumulate in a population.

Sexual Reproduction

• Sexual reproduction results in new combinations of genes through:
  • Crossing over
  • Independent assortment
  • The combination of gametes.
• Sexual recombination increases evolutionary potential.

Frequency-Dependent Selection

• Polymorphism is maintained when fitness depends on frequency in population.
• Example: Scale-eating fish in Lake Tanganyika, where "left-mouthed" and "right-mouthed" individuals are both favored.

Heterozygote Advantage

• Example: Colias butterflies in environments with temperature extremes.
• Population polymorphic for an enzyme that influences flight at different temperatures.
• Heterozygotes are favored because they can fly over a larger temperature range.

Constraints on Evolution

• Evolution is subject to various constraints.

Lack of Genetic Variation as a Constraint

• Lack of genetic variation prevents evolution of potentially favorable traits.
• If an allele for a trait does not exist in a population, that trait cannot evolve, even if it would be favored by natural selection.

Universal Constraints on Evolution

• Evolution must work within the boundaries of universal constraints:
  • Cell size: Constrained by surface area-to-volume ratios.
  • Protein folding: Constrained by the types of bonding that can occur.
  • Thermodynamics: Constrain energy transfers.

Developmental Processes as Constraints

• Developmental processes also constrain evolution.
• All evolutionary innovations are modifications of previously existing traits.
• Example: Stingray vs. Flounder, showing how existing body plans are modified during evolution.