Genetic Variation and Natural Selection

Importance of Genetic Variation to Evolution

• Genetic variation (heritable variation) provides the raw material for natural selection, which drives evolution.
• Without genetic diversity, populations would not evolve over time.
• Genetic variation results in differences in an individual's traits.
• Some traits give a survival or reproductive edge therefore leading to differing reproductive success.
• Advantageous traits become more common over generations.
• Environmental pressures cause natural selection and favor the presence of certain traits over others.
• Heritable traits pass down via genes such as eye color and height.
• Acquired traits are developed due to environment or experience, like muscle growth from exercise or scars.

Natural Selection and Population Evolution

• Natural Selection alters allele frequencies over time.
• Natural Selection results in adaptations, which increases fitness in specific environments.
• Natural Selection can cause speciation, which is the formation of new species.

Hardy-Weinberg Equilibrium (HWE) Model

• The Hardy-Weinberg Equilibrium Model assumes no evolution is happening under five conditions.
• Condition 1: No mutation, thus no new alleles are introduced.
• Condition 2: No natural selection, thus all individuals reproduce equally.
• Condition 3: No gene flow, which means there is no migration into or out of the population.
• Condition 4: A large population size to prevents genetic drift.
• Condition 5: Random mating, therefore there's no preference in mate selection.

Allelic and Genotypic Frequencies

• Allelic Frequency Equation: p + q = 1
• Hardy-Weinberg Equation: p² + 2pq + q² = 1
• Calculating p and q from q²:
  • Find q² which the frequency of homozygous recessive individuals.
  • Solve for q, which means finding the square root of q².
  • Solve for p: p = 1 - q.
  • Calculate p², 2pq, and confirm that the population is in equilibrium.
• Calculations can only be used if a population is in Hardy-Weinberg equilibrium.

Difference Between Allelic and Genotypic Frequencies

• Allelic frequency refers to the frequency of an allele in the gene pool, e.g., p or q.
• Genotypic frequency refers to the frequency of a genotype in the population, e.g., p², 2pq, q².
• Use allele frequency when you examine individual alleles.
• Use genotypic frequency when you are dealing with organism-level inheritance.

Class Activities Review

• PTC, Thiourea, Sodium Benzoate Tasting Activity
  • Counted tasters vs. non-tasters.
  • Used Hardy-Weinberg calculations to determine gene frequencies.
• Electrophoresis Lab
  • Analyzed DNA fragment migration.
  • Found banding patterns to infer genetic differences.

Key Definitions

• Natural Selection: Where beneficial traits increase in frequency over generations.
• Gene Pool: The total genetic diversity in a population.
• Adaptation: A trait that increases the organism's fitness.
• Population Genetics: The study of genetic variation within populations.
• Hardy-Weinberg Equilibrium: it's the condition in which allele frequencies remain constant.
• Genetic Drift: Random changes to allele frequency, strongest in small populations.
  • Founder Effect: Occurs when genetic variation is lost when a small group starts a new population.
  • Bottleneck Effect: Occurs when a population size drastically reduces, decreasing genetic variation.
  • Fixation/Extinction of Alleles: Alleles can either disappear through extinction or become universal through fixation because of drift or selection.
• Recessive Refuge: Hidden recessive alleles persist in heterozygotes.
• Heterozygote Advantage: Heterozygotes have a fitness advantage, for example, the the sickle cell allele provides malaria resistance.

Prelab & Simulation Activities

• AlleleA1 Software was used for Simulations.
  • It Demonstrates allele frequency changes under different conditions.
  • The simulations can be re-run to properly understand genetic drift, selection, and mutation.

Factors Affecting Population Evolution

• Natural Selection: Selects advantageous traits.
• Sexual Selection: Mate preference affects allele frequency.
• Genetic Drift: Random changes, stronger in small populations.
• Gene Flow: Movement of alleles between populations.
• Mutation: Introduces new alleles.
• Fitness: Determines likelihood of survival and reproductive success.
• Fixation/Extinction of Alleles: Certain alleles can disappear or dominate.

Using the Hardy-Weinberg Equations

• p² + 2pq + q² = 1 is used to calculate genotypic frequencies.
• p + q = 1 is used to calculate allelic frequencies.
• Use p + q = 1 when focusing on alleles.
• Use p² + 2pq + q² = 1 when dealing with genotypes.

Heterozygote Advantage in Sickle-Cell Anemia and Malaria

• Heterozygote Advantage occurs when individuals with one normal allele (HbA) and one sickle-cell allele (HbS) have a survival benefit in a specific environment.
• In the case of sickle-cell anemia, carriers (HbA/HbS) are resistant to malaria, which explains why the HbS allele remains prevalent in regions with high malaria rates.
• Relationship Between Rainfall, Mosquitos, Malarial Transmission, and HbS Allele Frequency:
  • Rainfall: Higher rainfall increases stagnant water pools, which provide breeding grounds for mosquitoes.
  • Mosquito Population: More rainfall leads to more mosquitoes, which increases malaria transmission.
  • Malarial Transmission: As malaria spreads, selective pressure favors individuals with partial resistance (HbA/HbS carriers).
  • Frequency of HbS Allele: In malaria-endemic regions, the HbS allele is maintained at a higher frequency due to the survival advantage it provides against malaria.
  • Frequency of Sickle-Cell Anemia (HbS/HbS): Common HbS Allele leads to more cases of sickle-cell anemia, which is a severe and often deadly disorder.
• Why Do More Sickle-Cell Anemia Deaths Occur After a Large Malaria Outbreak?
  • After malaria outbreaks, carriers i.e (HbA/HbS) have a survival advantage and are more likely to reproduce.
  • This increases the HbS allele's frequency in the population.
  • Over generations, a higher HbS allele frequency means higher the chance of of two HbS alleles being inherited which results increased cases of sickle-cell anemia.
  • Sickle-cell anemia is a severe genetic disorder, and more individuals suffer from its complications, causing high mortality rates.

Identifying Blood Samples Under a Microscope

• It is important to be able to differentiate between normal blood, sickle-cell anemia, malaria infection, and carrier status which is important for diagnosis and understanding the genetic and environmental impacts on blood health.
• Sickle-Cell Anemia (HbS/HbS):
  • Red blood cells appear crescent or sickle-shaped.
  • Cells are elongated and rigid, leading to blockages in blood vessels.
  • Fewer healthy red blood cells are visible.
• Malaria Infection:
  • Normal-shaped red blood cells has Plasmodium parasites visible inside.
  • ring-like structures exist inside infected red blood cells.
  • Possible bursting of red blood cells due to parasitic infection.
• Completely Normal Blood (HbA/HbA):
  • Round, smooth, biconcave red blood cells.
  • Evenly distributed without deformities or inclusions.
• Possible Carrier for Sickle-Cell Anemia (HbA/HbS):
  • Mostly normal-shaped red blood cells.
  • rare sickle-shaped cells can be visible under stress conditions, for example low oxygen levels.
  • No malaria parasite structures present.

Key points regarding the samples

• Heterozygote Advantage: Carriers (HbA/HbS) have protection against malaria, this leads to the persistence of the HbS allele in certain populations.
• Environmental Impact: High rainfall leads to more mosquitoes, while increased malaria transmission influences the HbS allele frequency.
• Long-Term Consequences: Malaria outbreak can lead to an increase in future cases of sickle-cell anemia.
• Microscope Identification: Understanding the key differences in blood samples is essential to be able to make a diagnosis and in genetic studies.

Constructing a Cladogram or Phylogeny from a Character Matrix

• Character matrixes records the presence (1) or absence (0) of traits in various organisms.
• Steps to building a cladogram:
  • 1. Categorize traits and taxa.
  • 2. determine which traits the groups share.
  • 3. Identify an outgroup which is a taxon that shares the fewest derived trai
  • 4. Classify taxa based on shared synapomorphies sharing shared derived traits.
  • 5. Ensure the tree follows the principle of parsimony following the simplest explanation.

Key Terms in Phylogenetics

• Apomorphy is a derived trait that is unique to a particular taxon or clade.
• Plesiomorphy is an ancestral trait shared by multiple taxa.
• Synapomorphy is a clade-defining, shared derived trait.
• Autapomorphy is a derived trait unique to a single taxon.
• Symplesiomorphy is a shared ancestral trait (rarely used term).
• Sister Taxa are two taxa sharing an immediate common ancestor.
• Node: A point on a cladogram representing a common ancestor
• Clade: A group of organisms including the ancestor and all descendants.
• Ancestor: A hypothetical inferred common ancestor from shared traits.
• Analogous Trait/Convergent Evolution: Traits that appear similar due to adaptation and not shared ancestry (e.g., wings in birds and bats).
• Monophyletic Clade: Includes a common ancestor and all its descendants.
• Paraphyletic Clade: Includes an ancestor and some, but not all, of its descendants.
• Polyphyletic Clade: Includes taxa with similar traits but different ancestors grouping by analogy not homology).

Importance of an Outgroup

• Outgroups determine which traits are ancestral (0s in the matrix) and those that are derived (1s).
• Outgroups also establish a baseline for evolutionary relationships.
• In character matrices, the outgroup gets all "0"s regardless of it has a trait to distinguish ancestral from derived states.

Convergent Evolution vs. Synapomorphies

• Convergent Evolution occurs when unrelated species evolve similar traits as a result of environmental pressures.
• Synapomorphies are traits that are shared because of common ancestry.
  • To differentiate traits make sure to check for common ancestry.
  • Examine if the trait appears independently in multiple clades.

Principle of Parsimony

• The most valid most explanation often has the fewest evolutionary changes.
• Reduces unnecessary assumptions when phylogenies are being constructed..

Interpreting a Cladogram

• Node: A branching point presenting a common ancestor.
• Y-Axis or X-Axis in digital trees: Representing time or the evolutionary divergence.
• Autapomorphies are terminal branch unique traits.
• Synapomorphies: Traits shared among taxa existing at branch points.

Skull Morphology and Classification

• Useful skull traits:
  • Cranial structure
  • Tooth morphology
  • Foramen magnum position
  • Zygomatic arch size
  • Nasal cavity structure

Using MEGA Software for Phylogenetic Analysis

• Steps to use MEGA:
  • 1. Import the sequence data.
  • 2. Align sequences.
  • 3. Generate the distance matrix.
  • 4. Construct the phylogenetic tree using neighbor-joining or maximum parsimony.
  • 5. Read the resulting tree.

Understanding Character Matrices

• "0" presents an ancestral trait, while "1" presents derived trait.
• The outgroup is assigned all "0"s to determine which traits are derived.

Distance Matrices and Phylogenetic Trees

• Distance matrixmeasures genetic or morphological differences between taxa.
• Phylogenetic treessupport complex evolutionary relationships and are based on these distances..

Why Trees Based on 1-2 Genes May Be Inaccurate

• Evolutionary history is complex: one or two genes cannot reflect the entire genome.
• Due to different genes evolving at different rates and some they have to undergo horizontal gene transfer.
• A concensus tree integrates various data sources which makes concensus trees more reliable.

The Three Domains of Life

• The three domains of living organisms are Bacteria, Archaea, and Eukarya and each domain has unique characteristics.

Domain Bacteria

• Bacteria is Prokaryotic which means there is no Nucleaus or membrane-bound organelles.
• Bacteria's cell walls consists of peptidoglycan.
• Bacteria reproduce by binary fission
• Some Bacteria can perform photosynthesis, for example cyanobacteria.
• Bacteria can be pathogenic, beneficial, or decomposers in ecosystems.

Domain Archea

• Archea's are Prokaryotic by genetically different from Bacteria.
• Archea's cell walls have no peptidoglycan.
• Many Archeas live in extreme environments such as extremophiles.
  • Thermophiles love heat.
  • Halophiles love salt.
  • Methanogens love anaerobic methane.
• Archeas Membranes are made up of unique lipid compositions.

Domain Eukarya

• Eukaryotes are have a Nucleus and membrane-bound organelles are present.
• Eukaryotes encompass most of the protists, fungi, plants, and animals.
• Eukaryotes can exist as unicellular or multicellular.
• Eukaryotes tend to have more complex genetics, regulation and organization.

Bacterial Morphology (Shapes)

• Bacteria are typically found in Coccus which means their spherical, some examples are: Streptococcus which creates chains and Staphylococcus which forms in clusters.
• Bacteria are Bacillus which means rod-shaped, an example of this is Escherichia coli.
• Bacteria are Spirillum which means spiral-shaped, an example of this is Spirillum volutans

Compound Microscope

• Objective Lenses are 4X, 10X, 40X, and 100X when using oil immersion..
• Ocular Lens is usually 10X and is also called is the Eyepiece. Total Magnification: Eyepiece X Objective Lens
• Use Coarse adjustment during low power, use fine adjustment for high power.
• Proper Lighting: Adjust diaphragm for contrast of the image.
• Oil Immersion is Used for 100X magnification to improve resolution

Horizontal Gene Transfer (HGT) and Phylogeny of Single-Celled Organisms

• HGT allows organisms to transfer genes even if they are between different species.
• This can occur through three mechanisms:
  • 1: Transformation or intake of foreign DNA from the environment.
  • 2: Transduction or DNA transfer through viruses, bacteriophages.
  • 3: Conjugation or by direct transfer of DNA between a pilis.. HGT complicates phylogenetic classification because genetic relationships may not follow traditional lineage-based evolution.

Unique Features of Domain Bacteria

• Cell walls include peptidoglycan which is a Gram-positive bacteria with thick layers;
• Gram-negative bacteria also have thin layers and an outer membrane).
• Some bacteria form endospores such as Bacillus, and Clostridium due to survival in harsh conditions
• Bacteria have been shown to display diverse metabolic abilities such as photosynthesis, as well as nitrogen fixation, and decomposition

Aerobic, Anaerobic, and Facultative Anaerobic Bacteria

• Aerobic Bacteria which require oxygen for survival as exemplified best by Mycobacterium tuberculosis).
• Anaerobic Bacteria which Can't are unable to survive in oxygen-rich environment, for example Clostridium botulinum.
• Facultative Anaerobic Bacteria which Can switch between aerobic and anaerobic and exemplified best by E. coli).

Ecological Importance of Cyanobacteria

• Cyanobacteria Photosynthetic which aids in production of oxygen an oxygenated Earth's atmosphere.
• Nitrogen fixation assists in changing atmospheric nitrogen to usable plant forms (e.g., Anabaena).
• Cyanobacteria are primary producers in aquatic ecosystems.
• With nutrient pollution, cynobacteria can form harmful algal blooms.

Distinguishing Cyanobacteria from Other Bacteria

• Most cyanobacteria are larger than other bacterias.
• Cyanobacteria are known for their blue-green from chlorophyll and phycobilins .
• Cyanobacteria can Form filaments and or colonies from organisms such as: Nostoc and Anabaena.
• Heterocysts are present in nitrogen-fixing species .

Endosymbiosis and Secondary Endosymbiosis

• Theory is that Eukaryotic organelles which includes the mitochondria and chloroplastss originated fromprokaryotic cells engulfed by ancestral eukaryotes.
• Endosymbiosis can be Evidenced by the follow:
  • A: Mitochondria and chloroplasts also have their own DNA and double membranes
  • B: Being similar in size to bacteria
  • C: Reproducing through binary fission.
  • D: Having Ribosomes that are similar to prokaryotes.
• Secondary Endosymbiosis:
  • A: Occurs when a eukaryotic cell engulfs another eukaryotic cell that alreadyunderwent primary endosymbiosis.
  • B: Explaining the Diversity of the known algae and all protists with this e.g., dinoflagellates, euglenids, and the famous brown algae