Evolution and Population Genetics

Overview of Evolution and Genetic Diversity

Evolution is studied across several specific dimensions as outlined in the course chapters: * Chapter 20: Genes within populations (Population Genetics). * Chapter 21: Principles of evolution, processes, and supporting evidence. * Chapter 22: Origin of species, selection mechanisms, and biological diversity. * Chapter 23: Comparative biology. * Chapter 25: Diversity of the species.

Genetic Variation and Evolutionary Change (Chapter 20)

Evolutionary change is driven by the interaction between processes that act on genetic variation within populations.
Processes that cause evolutionary change include: * Mutation: Random changes in the DNA sequence. * Gene flow: The movement of alleles between populations (migration). * Nonrandom mating: Mating based on specific traits or preferences. * Genetic drift: Random fluctuations in allele frequencies, particularly in small populations. * Natural selection: Occurs when phenotypes differ in Fitness.
Fitness is determined by differences resulting from: * Survival. * Mating success. * The number of offspring produced per mating event.

Genetics Fundamentals and Nucleic Acids

Nucleic acids: Organic compounds responsible for holding and transmitting genetic information.
Nucleotide: The fundamental building block of nucleic acids. A nucleotide consists of: * A phosphate group ( $P$ ). * A sugar molecule (Deoxyribose in DNA or Ribose in RNA). * A nitrogen-containing base.
DNA (Deoxyribonucleic Acid): * Structure consists of a double helix with a sugar-phosphate backbone and nitrogenous base pairs held together by hydrogen bonds. * In DNA, the base pairs are Adenine with Thymine and Cytosine with Guanine ( $A=T, C \equiv G$ ).
RNA (Ribonucleic Acid): * Contains Uracil instead of Thymine.
Nitrogenous Base Categories: * Purines: Adenine ( $A$ ) and Guanine ( $G$ ). * Pyrimidines: Thymine ( $T$ ), Cytosine ( $C$ ), and Uracil ( $U$ ).

Genome Structure and Dimensions

DNA Length: When fully stretched out, a single strand of human DNA is approximately $1\,m$ long.
Genome Size Variation (measured in nucleotide pairs per haploid genome): * Bacteria (e.g., Mycoplasma, E. coli): Smallest genomes, ranging from $10^5$ to roughly $10^7$ nucleotide pairs; predominantly coding DNA. * Fungi (e.g., budding yeast): $10^7$ to $10^8$ nucleotide pairs. * Insects (e.g., Drosophila): $10^8$ to $10^9$ nucleotide pairs. * Mammals (e.g., humans): Approximately $3 \times 10^9$ nucleotide pairs. * Plants (e.g., Arabidopsis, lily) and Amphibians (e.g., newt, marbled lungfish): Can have massive genomes extending from $10^8$ to over $10^{12}$ nucleotide pairs, containing a high proportion of non-coding DNA. * Paris japonica and marbled lungfish represent some of the largest recorded genomes.

Genetic Terminology and Organization

Gene: The basic unit of heredity; a specific sequence of DNA nucleotides that codes for specific information.
Genome: The entire DNA sequence of an organism.
Genomics: The scientific study of genomes.
Phenotype: The physical expression or observable characteristics of genetic information.
Chromosomes: * Composed of DNA wound around Histones to form Nucleosomes. * Structure features include Telomeres (tips) and Centromeres (joining point for chromatids).
Ploidy Levels: * Diploid ( $2n$ ): Two sets of chromosomes. Humans are diploid with a total of $46$ chromosomes ( $23$ homologous pairs). * Haploid ( $n$ ): A single set of chromosomes. Gametes (egg and sperm) in humans are haploid. * Polyploid: Containing more than two sets of chromosomes.
Locus: The specific physical location of a gene on a chromosome.
Alleles: Different variations or versions of the same gene (e.g., $A$ vs. $a$ ). * Homozygous: An organism with two identical alleles for a trait ( $AA$ or $aa$ ). * Heterozygous: An organism with two different alleles for a trait ( $Aa$ ).

Cell Division and Inheritance

Mitosis: * Occurs in somatic cells. * The process involves phases: $G1, S, G2, M$ . * Results in two diploid daughter cells identical to the parent.
Meiosis: * Process for producing gametes. * Involves two rounds of division: Meiosis I (homologues segregate) and Meiosis II (sister chromatids segregate). * Features Chiasma where genetic material is exchanged. * Results in four haploid cells from one diploid parent cell.
Mendel’s Laws of Inheritance: 1. Law of Dominance: Dominant alleles mask the expression of recessive alleles. 2. Law of Segregation: Allele pairs separate during gamete formation. 3. Law of Independent Assortment: Genes for different traits can segregate independently during the formation of gametes.

Mutations and Frequency Change

Mutations: Changes or mistakes in DNA replication. * Somatic cell mutations: Occur in non-reproductive cells; not inherited by offspring. * Germline (Reproductive) mutations: Occur in gametes; these are hereditary mutations.
Evolution definition: The change in allele frequency within a population over time. * Allele frequency: The percentage of a specific allele in a population.
The 4 M’s that Alter Allele Frequency: 1. Mutation. 2. Migration (Gene flow). 3. Major events (Genetic drift/Bottlenecks). 4. Mating (Nonrandom mating patterns).

The Hardy-Weinberg Principle

Developed by W. Weinberg and G. H. Hardy to predict allele frequencies in a population.
Equilibrium Assumptions: 1. Mutations do not occur. 2. No immigration or emigration (gene flow) occurs. 3. Mating is strictly random. 4. The population size is very large. 5. No natural selection occurs.

The Hardy-Weinberg Equations

Sum of allele frequencies: $p + q = 1$ * $p$ : Frequency of the dominant allele (e.g., $B$ ). * $q$ : Frequency of the recessive allele (e.g., $b$ ).
Sum of genotype frequencies: $p^2 + 2pq + q^2 = 1$ * $p^2$ : Frequency of homozygous dominant genotype ( $BB$ ). * $2pq$ : Frequency of heterozygous genotype ( $Bb$ ). * $q^2$ : Frequency of homozygous recessive genotype ( $bb$ ).

Example Problem 1: Feral Cats

Population: $100$ cats.
Observed Phenotypes: White ( $16\%$ ), Black ( $84\%$ ).
Calculations: 1. White is homozygous recessive ( $bb$ ), so $q^2 = 0.16$ . 2. Solve for $q$ : $q = \sqrt{0.16} = 0.4$ . 3. Solve for $p$ using $p + q = 1$ : $p = 1 - 0.4 = 0.6$ . 4. Calculate genotype frequencies: * Expected $BB$ ( $p^2$ ): $(0.6)^2 = 0.36$ (or $36$ individuals). * Expected $Bb$ ( $2pq$ ): $2 \times (0.6) \times (0.4) = 0.48$ (or $48$ individuals). * Expected $bb$ ( $q^2$ ): $(0.4)^2 = 0.16$ (or $16$ individuals).

Example Problem 2: Red and White Flowers

Red is dominant ( $R$ ), White is recessive ( $r$ ).
Observed: $91\%$ are red ( $p^2 + 2pq$ ).
Calculations: 1. White flowers ( $rr$ ) make up $100\% - 91\% = 9\%$ . 2. $q^2 = 0.09 \rightarrow q = 0.3$ . 3. $p = 1 - 0.3 = 0.7$ . 4. The frequency of the red allele ( $p$ ) is $70\%$ .

Specific Agents of Evolutionary Change

Mutation: Changes the identity of alleles.
Gene Flow: Movement of alleles from one population to another.
Nonrandom Mating: * Assortative mating: Phenotypically similar individuals mate, increasing the proportion of homozygotes. * Disassortative mating: Phenotypically different individuals mate, increasing the proportion of heterozygotes.
Genetic Drift: * Founder Effect: A small group starts a new population. Example: The Amish community in Lancaster County, PA ( $1744$ ). Descendants of a single couple carry the recessive trait for Ellis-van Creveld Syndrome (six fingers and shortened limbs) which is now common due to inbreeding. * Bottleneck effect: A drastic reduction in population size (due to disaster, etc.). The surviving individuals may not represent the original genetic diversity.
Selection: Requires phenotype variation, reproductive success, and heritability.

Case Studies and Examples of Selection

Predatory Avoidance: Pocket mice living on light sand are light-colored. Mice living on dark lava rock are dark-colored. Selection favors the color matching the substrate.
Pesticide Resistance: * pen gene: Decreased uptake of pesticides across the insect cell membrane. * kdr gene: Decreased number of target sites for the pesticide.
Antibiotic Resistance: Bacteria with resistant genes survive treatment, multiply into the vacant space, and can transfer resistance to other bacteria via horizontal gene transfer.
Fitness and Reproductive Strategy: * Fitness involves the number of surviving grandchildren, not just children. * Parental Investment: Energy expended on reproduction. * Water Strider Study: * Larger females ( $16\,mm$ ) lay more eggs per day (approx. $13$ ) and more eggs in a lifetime (approx. $200$ ) but have shorter lifespans (approx. $12$ days). * Smaller females ( $12\,mm$ ) lay fewer eggs but live longer (approx. $45$ days).

Sexual Selection and Variation Maintenance

Intrasexual selection: Competition between members of the same sex (e.g., males fighting).
Intersexual selection: Mate choice (e.g., females choosing specific males).
Sensory Exploitation: Male signals evolve to exploit pre-existing sensory biases in females. * Example: Egg-spots in Cichlid fish. Females prefer males with virtual egg-spots on their anal fins. This may be linked to a bias for high-quality food (carotenoids).
Frequency-Dependent Selection: * Negative frequency dependency: Rare phenotypes have higher fitness (e.g., distinct search images for predators). * Positive frequency dependency: Rare phenotypes have lower fitness (common phenotypes are favored).
Oscillating Selection: Selection favors different phenotypes at different times. * Example: Medium ground finch of the Galápagos. During droughts, birds with big bills ( $10.5\,mm$ beak depth) are favored. In wet years, smaller bills ( $8.0\,mm$ ) are favored.
Heterozygote Advantage: Maintains both alleles in a population. * Example: Sickle cell anemia. * $AA$ : Susceptible to malaria; no sickle cell. * $Aa$ : Resistant to malaria; mild sickle cell effects. (Favored in malaria-zones). * $aa$ : Resistant to malaria; fatal sickle cell disease.

Types of Selection on Traits Affected by Multiple Genes

Disruptive Selection: Selection for both extremes (small and large) and against the average. Creates two peaks.
Directional Selection: Selection for one extreme, shifting the population peak in that direction. * Example: Phototaxis in flies (tendency to fly toward light). Over $20$ generations, the average tendency shifted from a score of $6$ to nearly $11$ .
Stabilizing Selection: Selection for the mid-size or average individuals, narrowing the distribution. * Example: Human birth weight. Mortality is highest at very low weight ( $<3\,lbs$ ) and very high weight ( $>10\,lbs$ ), favoring an average weight around $7\,lbs$ .

Natural Selection in Guppies (Poecilia reticulata)

Field Study (NE South America): High predation environments vs. low predation (above waterfalls).
Vulnerability: Predators like Crenicichla alta influence color.
Observations: * Above waterfalls (no predators): Males are vibrantly colored to attract mates. * Below waterfalls (predators present): Males are drab/dull to avoid being eaten. * Experimental result: Moving guppies to low-predation environments increases the number of spots per fish from approximately $9$ to over $13$ in $12$ months.

Interactions and Limits to Selection

Evolutionary forces can work in opposition. * Example: Copper tolerance in bent grass (Agrostis tenuis). Plants on mine sites develop tolerance, but gene flow (pollen) from non-tolerant windward populations limits the perfection of the adaptation.
Epistasis: Interaction between two or more genes to control a single phenotype (e.g., varied comb shapes in chickens).
Pleiotropy: A single allele affects multiple aspects of a phenotype. * Example: The Frizzle gene in chickens causes curled feathers but also impacts egg laying, body temperature, metabolism, and digestion.
These factors (gene interactions) place biological limits on how much a specific trait can be altered by selection.