Principles of Biology Final Examination Review

Evolution & Natural Selection

Definition of Natural Selection: This process occurs when individuals possessing certain traits are more likely to survive and reproduce compared to those who do not possess those traits.
Environmental Selection: The environment acts as the selector. Conditions in the surroundings—such as predators, climate, and food sources—favor specific traits. Over generations, animals with traits fitting that environment persist.
Individual vs. Population Impact:
* Natural selection acts on individuals, as an individual's specific combination of traits determines its survival and reproductive success.
* The evolutionary impact, however, is only visible in the changes within a population of organisms over a period of time.
Fundamental Rule of Evolution: Evolution occurs because natural selection favors individuals with beneficial traits, causing populations to change over generations. Natural selection does not change individuals; it changes the population.

Microevolution and Genetic Variation

Gene Pool: This consists of all copies of every type of allele at every locus in all members of a given population.
Microevolution: Defined as the change in allele frequencies within a population over generations, which leads to small-scale evolutionary updates within a species.
Causes of Microevolution:
    * Mutation: The creation of new genetic changes.
    * Natural Selection: The survival of the best-suited traits.
    * Genetic Drift: Random changes in allele frequencies.
    * Gene Flow: The movement of genes between different populations.
Genetic Drift (In-Depth): A random change in allele frequencies, most notably in small populations. It is driven by chance events rather than natural selection, causing unpredictable fluctuations in allele frequencies.
Mutation (In-Depth): The generation of new alleles via a change in the genetic information encoded within the nucleotide sequence of DNA. This serves as the ultimate source of genetic variation, providing the raw material for evolution.
Genetic Variation: The unique genome of every organism or person, which is reflected in their phenotypic variation.

Gene Flow and Darwin’s Theory

Gene Flow: The transfer of alleles between populations resulting from the movement and reproduction of individuals. This process increases genetic variation and serves to reduce genetic differences between populations.
Darwin’s Theory of Evolution:
    * States that all living species descend from ancestral species that differ from present-day species.
    * Natural selection is recognized as the main mechanism for evolutionary change.
    * Genetic changes over generations allow populations to become better adapted to their specific environments.
Mechanisms of Evolutionary Change:
* Selected traits increase in frequency from one generation to the next.
* Evolution is formally defined as a change in the allele frequencies of a population over time.

Key Evolutionary Concepts and Features

Speciation: The process that results in one species splitting into two or more descendant species.
Transitional Features: Traits found in a fossil species that are intermediate between ancestral species and derived species.
Constraints and Realities of Selection:
    * Lack of Goal-Direction: Evolution by natural selection is not purposeful; it is not goal-directed.
    * Problem Solving: Mutations do not occur to solve existing problems; they happen randomly.
    * Want vs. Need: Adaptations do not occur because an organism wants or needs them.
    * Fitness Trade-off: This is a compromise between traits regarding how those traits perform in the environment. Because selection acts on many traits simultaneously, every adaptation is viewed as a compromise.

Vestigial Traits and Homology

Vestigial Traits: Structures or features that performed important functions in an organism’s ancestors but now serve little to no function in the current organism.
Examples of Vestigial Traits:
    * Human appendix.
    * Whale pelvic bones.
    * Snake leg remnants (hip and leg bones).
    * Human tailbone ( $coccyx$ ) and goosebumps.
    * Reduced wings in flightless birds.
    * Eye sockets in eyeless cave-dwelling fish.
    * Brief eggshell formation and nonfunctional "egg teeth" in certain marsupials.
Homology: Similarity existing in species descended from a common ancestor. It is studied at three levels:
    1. Genetic Homology: Similarity in DNA nucleotide sequences, RNA nucleotide sequences, or amino acid sequences.
        * Example: The eyeless gene in fruit flies and the Aniridia gene in humans result in amino acid sequences that are $90\%$ identical.
    2. Developmental Homology: Similarities observed in the embryos of different species.
        * Example: Tails and gill pouches found in embryos of chickens, humans, and cats suggest a common vertebrate ancestor.
    3. Structural Homology: Similarity in adult morphology.
        * Example: The common structural plan in limb bones across most vertebrates.

Darwin’s Four Postulates

Individual Variation: Individuals within a population vary in their traits.
Inheritability: Some differences are heritable and are passed on to offspring.
Variable Survival/Reproduction: In each generation, more offspring are produced than can survive. Only some survive long enough to reproduce, and some produce more offspring than others.
Differential Success: Individuals with certain heritable traits are more likely to survive and reproduce.

Summary: Heritable variation leads to differential reproductive success.

Biological Definitions and Driving Forces

Phylogenetic Tree: A diagram illustrating the ancestor-descendant relationships among various taxa.
Biological Fitness: The ability of an individual to produce surviving, fertile offspring relative to the ability of other individuals in the population.
Selection: Differential reproduction resulting from heritable variation.
Adaptation vs. Acclimatization:
* Adaptation: A heritable trait that increases individual fitness in a specific environment relative to those lacking the trait. It involves changes in allele frequencies in a population.
* Acclimatization: An individual's phenotype changes in response to environmental changes. The genotype remains fixed, and changes are not passed to offspring because no alleles have changed.
Forces of Evolution:
    1. Natural Selection: Beneficial traits increase in frequency (e.g., antibiotic-resistant bacteria).
    2. Mutation: Random DNA changes; the original source of new variation. Most are neutral or harmful; some are beneficial.
    3. Gene Flow (Migration): Movement of genes via reproduction (e.g., pollen moving between plant populations).
    4. Genetic Drift: Random changes, strongest in small populations.
        * Bottleneck Effect: Population is suddenly and drastically reduced.
        * Founder Effect: A small group starts a new, isolated population.
    5. Non-random Mating (Sexual Selection): Choosing mates based on specific traits, which can increase those traits even if they do not aid survival (e.g., bright feathers in birds).

Ecology: Fundamentals and Levels

Definition: The study of how organisms interact with their environment.
Adaptation to Abiotic Factors: To be successful, organisms must adapt to non-living factors, including:
    * Energy sources.
    * Temperature.
    * Presence of water.
    * Inorganic nutrients.
    * Other aquatic and terrestrial factors.
Five Levels of Ecology:
    1. Organism: A single individual.
    2. Population: A group of individuals of the same species living in the same area.
    3. Community: Different species living and interacting together.
    4. Ecosystem: The combination of living (biotic) and non-living (abiotic) factors (water, soil, sunlight, climate).
    5. Biosphere: All life on Earth.

Biotic and Abiotic Interactions

Biotic Factors: Living components of the environment.
Abiotic Factors: Non-living components (e.g., temperature and water).
Influence on Distribution: These factors determine where organisms grow, survive, and reproduce. Abiotic factors set limits, while biotic interactions like competition and predation further restrict species distribution.
Climate vs. Weather:
* Weather: Short-term atmospheric conditions.
* Climate: Long-term patterns of temperature and precipitation.

Biomes

Definition: A large ecological region defined by its climate and the specific types of plants and animals resident there.
Aquatic Biomes:
    * Pelagic Realm: Open ocean water; contains phytoplankton, fish, and zooplankton.
    * Benthic Realm: The seafloor (bottom); inhabited by worms, crabs, and bottom feeders.
    * Photic Zone: Area where sunlight reaches, allowing for photosynthesis. Home to phytoplankton, zooplankton, and coral reefs.
    * Aphotic Zone: Areas with no sunlight and no photosynthesis. Organisms must consume others or use chemical energy.
Terrestrial Biomes (Defined by temperature and precipitation):
    * Tropical Forests: Equatorial, warm, $11-12$ hour days, variable rainfall. High species diversity; endangered by human destruction.
    * Savannas: Warm year-round, $30-50\,cm$ annual rainfall, dramatic seasonal variation, dominated by grasses/scattered trees and insect herbivores.
    * Deserts: Driest biomes, low/unpredictable rainfall. Can be hot or cold. Desertification is a major problem.
    * Chaparral: Dense, spiny shrubs with evergreen leaves. Mild, rainy winters; hot, dry summers. Adapted to periodic fires.
    * Tundra: Arctic region between taiga and polar ice. Treeless, characterized by permafrost (frozen subsoil) and low precipitation.
    * Temperate Grasslands: Mostly treeless, cold winters, $25-75\,cm$ rain/year, periodic droughts. Historically grazed by bison/pronghorn; now mostly farms.
    * Temperate Broadleaf Forests: Sufficient moisture for large trees ( $75-150\,cm$ rain), range of temperatures (seasonality), $5-6$ month growing season. Open canopy compared to rainforests.
    * Taiga: Northern hemisphere, cold, forested, long winters and short summers, characterized by coniferous trees.

Earth's Tilt and Climate

Tilt: Earth is tilted at approximately $23.5^{\circ}$ .
Sunlight Distribution: This tilt leads to uneven sunlight. The equator receives direct sunlight (hotter), while the poles receive indirect sunlight (colder).
Temperature Zones: Tropical (hot), Temperate (moderate), and Polar (cold).
Seasons: The tilt causes seasonal shifts affecting rainfall and temperature, which ultimately defines the types of biomes found at various latitudes.

Biodiversity and Conservation

Biodiversity: The variety of life types (species, genes, ecosystems).
Importance: Maintains ecosystem stability, provides resources, supports pollination and nutrient cycling.
Conservation Needs: Threatened by habitat destruction, pollution, climate change, and invasive species. Loss leads to extinction, ecosystem collapse, and loss of resources.
Measuring Genetic Diversity:
1. Number of Alleles: More alleles indicate higher diversity.
2. Heterozygosity: Measurement of individuals with two different alleles ( $Aa$ ). High heterozygosity indicates high diversity.
Species Metrics:
* Species Richness: A count of species present in a defined region.
* Species Diversity: A weighted measure incorporating richness and evenness (relative abundance). High evenness increases diversity; dominance by one species lowers it.
Ecosystem metrics:
    * Horizontal Diversity: Number of species in each trophic level.
    * Vertical Diversity: Number of trophic levels.
    * Ecosystem Function: Sum of biological and chemical processes (primary production, nitrogen cycling, decomposition, carbon cycling).
Energy Transfer: Only about $10\%$ of energy is transferred to the next trophic level; the rest is lost as heat. This limits the number of organisms at higher trophic levels (energy pyramid).

Threats to Biodiversity

Endangered Species: Species whose numbers have decreased drastically, making extinction likely without intervention.
Categories of Threats:
    1. Habitat Destruction: Caused by logging, burning, livestock grazing, damming rivers, filling wetlands, mining, and road building.
    2. Overexploitation: Unsustainable removal of organisms. Overharvesting is the main threat to marine species (two-thirds of harvestable species are depleted). Overhunting affects African mammals (bushmeat, ivory, skin). Pet trade is also a factor.
    3. Exotic and Invasive Species: Non-native species that grow to large sizes and disrupt ecosystems by eating natives, competing for resources, or carrying disease.
    4. Pollution: Industrial pollutants (acid rain, greenhouse gases), pharmaceuticals (via human urine), nutrient runoff (eutrophication), and garbage.
    5. Climate Change: Melting ice caps/glaciers leading to loss of habitat and rising sea levels that inundate biodiversity hotspots.
Community Reaction:
* Resistance: Measure of how much a community is affected by a disturbance.
* Resilience: Measure of how quickly a community recovers after a disturbance.

Case Studies in Endangered Species

Southern Resident Killer Whales (SRKW):
    * Main Threats: Decline of Chinook salmon (starvation), noise pollution from ships/boats, and chemical pollution.
    * Biomagnification: Toxins build up in the food chain: small organisms -> fish -> whales. Results in weak immune systems and reproductive failure.
    * Vessel Effects: Noise disrupts echolocation (hunting) and communication, causing stress.
    * Biggest Threat: Starvation due to lack of Chinook salmon.
Black-footed Ferrets:
    * Main Threats: Loss of prairie dog populations (primary food and shelter source), habitat destruction of grasslands, and disease (plague).
    * Reason for Near Extinction: Extermination of prairie dogs.
    * Current Biggest Threat: Lack of genetic diversity in the recovering population.
    * Conservation Efforts: Habitat restoration, disease management, captive breeding, and reintroduction.
Orangutans:
* Main Threats: Deforestation (specifically for palm oil plantations), habitat fragmentation, and illegal hunting.
* Impact: Loss of food/habitat, isolation of populations, and population decline.