Genetic Variation and Change: Level 2 Biology Study Guide

Overview of Genetic Variation and Change

• Achievement Standard (AS91157): This is a level 2 biology standard worth $4$ credits.

• Core Sections:

  • Sources of Variation: Focuses on how mutations and sexual reproduction lead to variations of traits in populations.

  • Meiosis: The process of cell division that facilitates variation.

  • Patterns of Inheritance: How genetic traits are passed from parents to offspring via predictable rules, involving dominant and recessive alleles.

  • Population Genetics: Factors that influence allele frequencies within a gene pool.

DNA Structure and Function

• DNA (Deoxyribonucleic Acid): A molecule composed of two strands forming a double helix.

  • Nucleotides: Each strand consists of nucleotides containing:

    • A phosphate group.

    • A deoxyribose sugar.

    • A nitrogenous base: Adenine ($A$), Thymine ($T$), Cytosine ($C$), or Guanine ($G$).

  • Complementary Base Pairing: Strands are held together by hydrogen bonds. $A$ pairs with $T$, and $C$ pairs with $G$.

• Functions of DNA:

  • Control of Cell Activities: Contains instructions for synthesizing proteins that regulate cellular functions.

  • Transmission of Genetic Information: Passes from one generation to the next to ensure the inheritance of traits.

Chromosomes, Genes, and Alleles

• Chromosomes: Long strands of DNA. Humans typically have $23$ pairs of chromosomes ($46$ total).

• Homologous Pairs: Chromosomes come in pairs that look similar and carry the same genes but are not identical. One is maternal (mother) and one is paternal (father).

• Gene: A section of DNA that holds the code for a particular characteristic or trait. Genes for specific characteristics are found at identical positions (loci) on chromosomes for all members of a species.

• Alleles: Alternative forms of a gene. They have slight differences in their base sequences, resulting in different genetic codes for the same trait.

  • Dominant Allele: Shown by an uppercase letter (e.g., $R$). It masks the effect of a recessive allele.

  • Recessive Allele: Shown by a lowercase letter (e.g., $r$). It is only expressed if two copies are present ($rr$).

• Genotype: The combination of alleles an individual possesses (e.g., $RR$, $Rr$, or $rr$).

• Phenotype: The physical characteristics or traits resulting from the genotype (e.g., brown eyes vs. blue eyes).

• Zygosity:

  • Homozygous: Having two of the same alleles ($RR$ or $rr$).

  • Heterozygous: Having two different alleles ($Rr$).

Sources of Genetic Variation

• Genetic Variation: The difference in DNA sequences between individuals within a species or population. This leads to different genotypes and phenotypes.

• Three Primary Sources:

  1. Mutation: Permanent changes in the base sequence of DNA. This is the only source of new alleles.

  2. Sexual Reproduction: Mixing of existing genes through meiosis and fertilization.

  3. Environmental Factors: External factors like nutrient availability or disease that affect the individual.

Reproduction Types

• Asexual Reproduction:

  • Requires only one parent.

  • Offspring are genetically identical clones.

  • Allows for rapid population growth but lacks variation, making the population vulnerable to environmental changes or disease.

  • Examples: Spider plants and aphids (the latter depends on environmental conditions).

• Sexual Reproduction:

  • Involves two parents and the fusion of gametes (sperm and egg) to form a zygote.

  • Produce offspring that vary from parents and each other due to new mixes of alleles.

  • Increases survival chances in changing environments.

  • Typically slower and requires more energy than asexual reproduction.

Mutations in Detail

• Mutation: A random and spontaneous permanent change to the base sequence of a section of DNA.

• Origins: Can occur due to errors during DNA replication or be induced by mutagens (UV light, X-rays, alcohol, processed foods, pathogens).

• Classification by Cell Type:

  • Somatic Mutations: Occur in body cells. They affect the individual (e.g., skin cancer) but are not passed to offspring.

  • Gametic Mutations: Occur during the formation of gametes (meiosis). These are inherited by offspring and can remain in the population.

• Effect on Survival:

  • Harmful: Negative impact; decreases survival chance.

  • Neutral/Silent: No effect on the organism.

  • Beneficial: Positive impact; increases survival chance (e.g., insecticide resistance).

• Structural Types:

  • Chromosomal (Block) Mutations: Large-scale changes to segments of a chromosome (Deletion, Inversion, Translocation, Duplication).

  • Gene (Point) Mutations: Small-scale changes to the base sequence within a single gene (Insertion, Deletion, Substitution).

Meiosis: The Process of Variation

• Definition: A type of cell division that produces four genetically unique haploid ($n$) gametes from one diploid ($2n$) parent cell.

• Stages:

  • Interphase: DNA is replicated to create sister chromatids.

  • Meiosis I: Homologous pairs separate. This includes Prophase I (crossing over), Metaphase I (independent assortment), Anaphase I (homologs move to poles), and Telophase I.

  • Meiosis II: Sister chromatids separate. Similar to mitosis, resulting in four haploid cells.

• Key Mechanisms for Variation:

  1. Independent Assortment: During Metaphase I, homologous pairs line up randomly at the cell equator. The orientation of one pair is independent of others, leading to $2^{23}$ possible combinations in humans (over $8$ million).

  2. Crossing Over: During Prophase I, non-sister chromatids of homologous chromosomes exchange DNA segments at points called chiasma. This produces recombinant chromosomes with new combinations of alleles.

  3. Segregation: The separation of homologous chromosomes (Meiosis I) and then sister chromatids (Meiosis II) ensures each gamete receives only one allele per gene. This makes every daughter cell genetically unique.

Mitosis versus Meiosis comparison

Patterns of Inheritance

• Monohybrid Cross: A cross looking at one trait. Follows Mendel’s Law of Dominance, where the dominant allele masks the recessive.

• Pure Breeding: Individuals that are homozygous for a trait ($AA$ or $aa$) and consistently pass the trait to offspring.

• Test Cross: Breeding an individual with an unknown genotype (showing the dominant phenotype) with a homozygous recessive individual ($aa$).

  • If any offspring show the recessive phenotype, the parent was heterozygous ($Aa$).

  • If all offspring show the dominant phenotype, the parent is likely homozygous dominant ($AA$).

• Pedigree Charts: Track inheritance through generations.

  • Squares = Males; Circles = Females; Shaded = Affected individuals.

  • Used to determine if a trait is dominant or recessive (e.g., if two unaffected parents have an affected child, the trait must be recessive).

• Incomplete Dominance: Neither allele is dominant; a blend/intermediate phenotype is produced (e.g., Red $RR$ + White $rr$ = Pink $Rr$).

• Co-dominance: Both alleles are fully and simultaneously expressed (e.g., speckled chickens or tortoiseshell cats).

• Multiple Alleles: More than two alleles exist for a gene (e.g., Blood groups $I^A, I^B, I^O$). $I^A$ and $I^B$ are co-dominant, and both are dominant over $I^O$.

• Lethal Alleles: Mutations in essential genes that cause death or drastically reduce life expectancy. Often change the expected $3:1$ phenotypic ratio to $2:1$.

  • Examples: Lethal White Overo ($LWO$) in horses, Manx cats, and yellow coat color in mice.

• Dihybrid Cross: Tracking two traits simultaneously ($4 \times 4$ Punnett square). If unlinked, heterozygous parents ($AaBb \times AaBb$) produce a phenotypic ratio of $9:3:3:1$.

• Linked Genes: Genes located close together on the same chromosome. They do not assort independently and are usually inherited together unless separated by crossing over. They reduce genetic variation.

• Sex-Linked Inheritance: Genes located on sex chromosomes ($X$ or $Y$).

  • X-linked recessive traits are more common in males (hemizygous) because they have only one $X$ chromosome and no second allele to mask a recessive one.

  • Examples: Red-green color blindness, hemophilia.

Population Genetics and Evolution

• Evolution: The change in the genetic makeup (allele frequencies) of a population over long periods of time.

• Gene Pool: The total number of alleles present in a population at a given time.

• Allele Frequency: The proportion of a specific allele within the gene pool calculated as: $\frac{\text{Number of particular allele}}{\text{Total number of alleles}} \times 100$.

• Natural Selection: Individuals with phenotypes better suited to their environment (fitness) are more likely to survive and reproduce, passing beneficial alleles to the next generation.

  1. Stabilizing Selection: Favors average phenotypes; selects against extremes. Reduces variation.

  2. Directional Selection: Favors one extreme phenotype. Occurs during environmental changes.

  3. Disruptive Selection: Favors both extreme phenotypes; selects against the intermediate. Occurs in varied environments.

• Non-Random Mating:

  • Sexual Selection: Choosing mates based on specific traits.

  • Artificial Selection: Humans selecting desirable traits (e.g., high-yield cows, dog breeds).

• Gene Flow (Migration):

  • Immigration: Individuals entering; increases variation.

  • Emigration: Individuals leaving; decreases variation.

• Genetic Drift: Random change in allele frequency due to chance events, affecting small populations more significantly.

  • Founder Effect: A small group isolates itself to start a new population; has a non-representative gene pool and lower diversity.

  • Bottleneck Effect: A catastrophic event (disaster, hunting) drastically reduces population size, leading to the loss of alleles and decreased diversity (e.g., tara iti, kākāpō, northern elephant seals).

Case Studies and Applications

• Darwin’s Finches: Finches adapted different beak shapes for food sources, illustrating natural selection and speciation.

• Peppered Moths: Shift from light to dark coloration during the Industrial Revolution due to directional selection.

• Skin Color (Melanin): Influenced by natural selection. Near the equator, high melanin (dark skin) protects against UV-induced mutations. At high latitudes, low melanin (light skin) allows for sufficient Vitamin D absorption.

• Kākāpō: Suffered a bottleneck ($51$ individuals in $1995$). Interestingly, the Stewart Island population lost harmful mutations despite inbreeding, likely because natural selection removed individuals with disadvantageous alleles from the small gene pool.

• Tara Iti (Fairy Tern): Critical bottleneck with fewer than $40$ individuals remaining. Facing challenges of low genetic diversity and higher risk from recessive deleterious alleles.

• Japanese Quail: Population bottleneck in the $1940s$ led to high rates of hatching failure ($20\%$) due to a lethal recessive variant of the $EL-1$ gene.