BIO 150 Final Exam Notes

Measuring Biodiversity within Ecosystems

  • Alpha Diversity: "Species richness," which is the number of species in a certain area.
  • Beta Diversity: "Species turnover," referring to the unique species between different areas.
  • Gamma Diversity: Total biodiversity for the entire region.

Visualizing Biodiversity

  • Graphs are useful for showing trends but can be biased by leaving out data.

Variability Among Species

  • Species Richness: Number of species in an area.
  • Species Evenness: How close in number each species is.
  • Biodiversity is measured as a diversity index, considering both richness and evenness.

Novel Ecosystems

  • Novel ecosystems are made by humans and represent "engineered niches" of the Anthropocene.
  • They have no natural analogs.
  • Examples include the Titanic and pools filled with organisms and algae.

Invasive Species

  • Traits of invasives:
    • Introduced for a purpose.
    • Tend to be aggressive and very adaptive.
    • Possibly have no predators.
    • Out-compete the native species.
  • Some invasive species can't live away from humans, known as commensals.

Mutations

  • Mutations are random and naturally occur in populations.
  • Example: TCA GCT à TTA GCT
  • Most mutations don't lead to variation (many are neutral).
  • Mutations can be:
    • Repaired by specialized proteins.
    • Not repaired, leading to changes in amino acids and potentially protein function and traits.

Genetics and Population Genetics

  • Mendelian Genetics: Theory for the inheritance pattern for discrete traits.
    • Traits are clearly different (not continuous).
    • Autosomal (not on sex chromosome).
    • Includes a dominant allele.
  • Hardy-Weinberg Principle: Allele and genotype frequencies in a population will stay constant from generation to generation if evolutionary influences are absent.
    • Assumptions:
      • No natural selection (evolution).
      • Mate choice is random.
      • No mutation (no new alleles).
      • No gene flow (no migrants).
      • Large population size (no genetic drift).
    • Biological fit = more offspring.
    • No evolution occurring = null hypothesis.

Hardy-Weinberg Law Equation

  • Equation I: p + q = 1
  • Equation II: p^2 + 2pq + q^2 = 1
    • p = dominant allele
    • q = recessive allele
    • p^2 = % homozygous dominant individuals
    • 2pq = % heterozygous individuals
    • q^2 = % homozygous recessive individuals
  • Applies to the population as a whole.

Genetic Drift and Gene Flow

  • Genetic Drift: Removes alleles from the population.
  • Gene Flow: Brings alleles into the population from either direction, becoming part of the gene pool.
  • Effects of genetic drift are less drastic if gene flow is happening.
  • Gene flow can be one-way or two-way.

Modes of Natural Selection

  1. Stabilizing Selection:
    • Intermediate phenotypes have higher fitness than extreme phenotypes and become more frequent.
  2. Directional Selection:
    • Individuals with one of the extreme phenotypes have higher fitness than intermediate phenotypes.
  3. Disruptive Selection:
    • Both extreme phenotypes are favored, and intermediates are not.

Speciation Process

  • Cryptic Species: Species that look and sound similar but are genetically distinct.
    • Example: The howling mouse, where females' howls are different.

Models of Speciation

  • Allopatric Speciation:
    • Populations are in different homelands (split up geographically).
      • Colonization and dispersal.
      • Vicariance.
  • Sympatric Speciation:
    • Populations are in the same habitat/geographic area.
      • Ecological isolation.
      • Polyploidy.

Prokaryotes

  • To be successful, they need:
    • Many species.
    • Very diverse.
    • Large number of each species.
    • Good competitors in the local environment.
  • They are metabolically diverse, allowing them to live successfully in a wide range of environments.
  • Most species of bacteria are specialized for certain habitats.
  • Anaerobic cellular respiration:
    • Example: Bacteria making rusticles out of the Titanic.
    • Iron oxide created by bacteria = porous crust that lets water in, leading to more H2O contact with Fe and more corrosion.

Layers of Microbial Habitats

  • Blue-green pigment (Cyanobacteria):
    • Well-lit, O2-rich surface.
    • Oxygenic photosynthesis.
  • Purple pigment (purple sulfur bacteria):
    • Median lit, No O2 middle.
    • Anoxygenic photosynthesis.
  • No light, No O2 subsurface:
    • Anaerobic Cellular Respiration & Fermentation.

Surface Area/Volume

  • Related to the size and shape of an organism.
  • Larger organisms have a lower ratio; smaller organisms have a higher ratio.
  • As cell size increases, SA/V decreases.
    • Larger volume: longer distance from surface to cell interior.
    • Needs more ATP and generates more waste.
  • Volume dictates energy needs and waste production, which must be met by movement through surface area.
  • V increases much faster than SA as cell size increases, making SA/V ratio decrease.
  • Surface area = cell membrane.

Characteristics of Eukaryotes

  • Membrane-bound organelles:
    • Prevent unwanted interactions by confining molecules to separate organelles.
    • Increase the chance of 2 molecules in a reaction interacting: reactants are concentrated.
  • Dynamic cytoskeleton:
    • Internal scaffolding (framework) of proteins; acts as support for fluid cell.

Cytoskeleton

  • Prokaryotic Cells:
    • Is present but not dynamic (not remodeled constantly).
    • Some functions:
      • Not as complex as in eukaryotes.
      • Internal transport is mostly done by diffusion.
        • This is sufficient (sort of) in prokaryotes because:
          • Cells are small.
          • Don’t need extensive cytoskeleton.
  • Eukaryotic Cells:
    • Can be remodeled quickly (extensive).
    • Moves items within the cells.
    • Changes the shape of the cell.
    • Moves chromosomes during cell division.
    • Moves vesicles containing proteins.
  • In Animals ONLY:
    • Cytoskeleton can cause: cell shape change.
    • Internal transport by diffusion alone isn't sufficient because cells are larger.

Being Multicellular: Success and Diversity

  • Simple multicellular organisms:
    • Example: Choanoflagellates.
    • Simple multicellular synapomorphies:
      • Composed of similar cells.
      • Have very few specialized cells or communication between cells.
      • Not much 3D structure.
      • Most cells are: in contact with the environment & acquire their own nutrients.
    • Possible advantage of evolving SIMPLE multicellularity:
      • Can filter food out of H2O.
      • Move water with coordinated beating of cilia.
  • Complex multicellular organisms:
    • Cells are specialized and interdependent (need each other).
    • Different cell types express different genes.
    • They have tissue, 3D structure (some cells not directly exposed to the environment).
    • The organism must:
      • Feed cells.
      • Pass signals from the environment to cells and back.

Thermoregulation

  • Organisms must respond to information from the environment and adjust so they can maintain stable conditions.
  • Most organisms (except humans, mammals, birds) have internal temperatures the same as the environment temperature.
  • Few species maintain high, stable internal temperature regardless of external temperature.
  • Most can't tolerate tissue freezing, but some have mechanisms to delay their body freezing despite below-freezing temperatures.
  • Animals try to avoid freezing temperatures by selecting a microhabitat that is above freezing.
  • Surface area/volume influences heat loss/gain.

Examples of Thermoregulation

  • Small lizards have a very high SA/V ratio and can't tolerate cold well because they have lots of surface to lose heat from and little volume to store heat.
  • Polar bears have a low SA/V ratio and can tolerate cold because they have relatively little surface to lose heat from and lots of volume to store it.

A. Stability of proteins (including enzymes):
* Heat – Thermal E can break bonds and destroy the structure of membranes and protein.
* High temperatures will render proteins nonfunctional.
* Breaks weak bonds in the 3D structure.
* Functional protein structure:
* Amino acid polymer folds into a complex 3D structure.
* 3D structure is needed for function.
* 3D structure is mostly held by noncovalent bonds (weak).
* Example: Indian zebu (domestic cattle) cells survive heat stress when heat shock proteins are elevated in level, helping to unfold/refold heat-stressed proteins.

Functional Plasma Membrane

B. Functional plasma membrane (permeability has limits to tolerance of temperature):
* Temperature effects membrane permeability.
* The composition of the cell membrane varies between species, affecting membrane permeability.
* Lipid bilayer: adaptations for hot/cold environments:
* One tail has one or more cis-double bonds and is an unsaturated fatty acid.
* The other tail does not have them and is a saturated fatty acid.
* Cold makes the cell membrane less permeable and more rigid.
* Heat makes the cell membrane more fluid (too fluid to function).
* Warm-adapted vs. cold-adapted species saturated vs. unsaturated fatty acids evolve to differ.
* Double bonds make it difficult to pack tail chains together à the bilayer is less likely to freeze.
* These adaptations are expressed in genes of organisms living in extreme temperatures.
* Cellular-level adaptations ultimately have more impact than behavioral adaptations.

Endotherms and Hibernation

  • Most animals can thermoregulate.

    • Ectotherms depend on the temperature of the environment but can move to a micro-habitat, so they have some control.
      • Most animals are "ectotherms."
    • Endotherms regulate internal temperature.
      • Generate internal heat, depending on how much energy (food) they get.
      • Homeostasis: Maintain stable core temperature.
      • Found in birds and mammals, but NOT all endotherms: Heterotherms
    • Hibernation – only true hibernators drop their body temperature to ~freezing.
      • These mammals must be small, such as chipmunks and groundhogs.
      • Larger mammals (bears) can't hibernate = too much stress on the heart.

  • Instead of hibernation, bears enter a state of Torpor:

    • Hypothermia
    • Hypometabolism
    • Denning behavior: northern climates
    • Associated with delayed implantation
    • Gestation in bears is weeks long.
    • Cubs are tiny when born (1/270th of mom’s weight).

  • Heterotherms (once called poikilotherms):

    • Body temperature variable but often still higher than ambient temperature.
    • Anteaters: 91ºF core temp, sleep 15 hours a day.

How Animals Regulate Temperature

  1. Whether ectotherm or endotherm, it pays to:
    • Migrate to a more comfortable habitat/climate.
    • Create a microhabitat.
    • Change orientation.
  2. Structural adaptations for thermoregulation:
    • Change coloring to regulate heat absorption:
      • Polar bear (black skin absorbs).
      • Gazelle – tan/light coat reflects UV (heat).
    • Use sweat glands for evaporative cooling:
      • Only mammals (not all over body) – humans have them all over.
    • Insulation (heat and cold):
      • Decrease the difference between internal temperature and external.
      • Can use hair, feathers, fat, brown fat (have when born then disperses as you get older).
  3. Physiological adaptations:
    • Endotherms: ability to burn food to keep warm.
      • Most animals are not endotherms.
      • They are expensive organisms (eat 8-10x more than ectotherms).
    • When cold or hot (endo and ecto):
      • Torpor (cold)
      • Hibernation
      • Estivation (hot)
  • Ectotherms can live where there is little food.
    • Most can’t live in colder habitats.
  • Endotherms can live in colder places.
    • Most can’t live without an abundant food source.

Physiological Adaptations for Thermoregulation

  • How plants regulate temperature:
    • Temperature extremes are usually correlated with limited H20.
    • Plants can’t move between microhabitats to cope.
    • Since they are stationary, they can’t thermoregulate extensively.
  • Ways they can:
    • Move to the area with external temperature closest to optimum (with seeds).
    • Re-orient leaves (fold, turn directions).
    • Add epidermal “hairs” to leaves (reflect more light à tissue stays cooler).
  • In hot conditions, the rate of bulk flow is high; this allows evaporative cooling.
  • Since H20 is limited, plants have evolved mechanisms to reduce H20 loss:
    • a) Drop leaves when H20 is unavailable (frozen).
    • b) When it gets too cold/hot: survive in a dormant state (ex. seeds).
    • c) Unlike animals, this may occur over the lifetime of 1 plant.
    • If a plant lives where temperatures are seasonal, it can increase the unsaturated fatty acid content of the membrane as the temperature drops.
    • If a plant is native to where there is little temperature change (ex. tropics), it can’t change the membrane movement of large amounts of fluid in one direction).

Regulation of Water

  • Organisms are constantly faced with challenges in the environment.
  • Organisms need to ADAPT (during life via behavior/regulation or through offspring) to cope with challenges.
  • Natural selection à adaptations to meet those challenges if a species is to survive.
  • Heritable adaptations include: the habitat a species lives in has a huge effect.
  • Ex. effect on water regulation:
    • Freshwater
    • Marine
    • Land
  • Mobility makes a huge difference: plants have limited movement.
  • Single-celled organisms: at the mercy of water currents.
  • Regulation of water content in unicellular species: adaptations to survive in freshwater.
  • Prokaryotes & unicellular algae (eukaryotes) have a cell wall:
    • Adaptation to stop bursting/lysing.

Regulation of Water (cont.)

  • Unicellular eukaryotes without a cell wall have another structure to help expel H20.
  • Marine H20 is hypotonic relative to the cell.
  • Hypotonic

Regulation of Water – Multicellular

  • Osmocenformers: cell osmolarity is the same as water.
  • Osmolarity: ratio of solute/solvent or salts/H20 in cells.

Regulation of Water - Plants

  • Bryophytes: plants without vascular tissue or roots (mosses) because there are no roots:
    • Moss cells are pressed up against the moist substrate.
    • H20 is taken up by diffusion.
    • Internal transport is relatively slow (compared to bulk flow).
    • Mosses must:
      • Grow to only ~1inch tall.
      • Grow in moist places.
  • Bryophytes are non-vascular plants, but if a plant has vascular tissue, it can live in more terrestrial habitats (dry).

Terrestrial Plants

  • Water transport:

    • Xylem tissue: straw-like but full of holes.
    • Terrestrial plant leaves have little ”mouths” called stomata.

  • Transpiration:

    • Water moves through xylem from roots to crown.
    • Process like sucking on a straw full of holes.
    • Pull from soil (roots) is created by stomata opening à leads to evaporation.
    • Stomata are closed: there is not enough H20 in the habitat (soil).

  • Cuticle: waxy layer that prevents water loss from stems and leaves.

    • Cuticle thickness varies with climate.
    • Dramatically preventing H20 loss to surrounding air.
    • Also, a barrier to pathogens.

  • Desert plants have a thicker cuticle than tropical plants.

    • Desert plants: small/no leaves, thick cuticles.
    • Tropical plants: thin cuticles, many have drip tips.

Acquiring Nutrients

  • All organisms need:
    • Energy
    • Carbon (food source)
  • The energy source comes first in the name:
    • Organisms that use light: Photo…..
    • Organisms that use organic carbon: Chemo….
  • The carbon source comes second in the name:
    • Organisms that use elements/minerals from the carbon source: Auto….
      • Synthesize organic C from inorganic C = makes its own resources.
    • Organisms that use other organisms: Hetero….
      • Must obtain organic C from others: eat other organisms (ex. humans).
  • Nutrients are substances that provide nourishment & growth & maintain life.
    • Phototroph: energy source is light (photosynthesis).
    • Autotroph: self-feeders (synthesize their own reduced, organic compounds from inorganic carbon).
    • Chemoorganotroph: energy gained from the oxidation of reduced carbon molecules (ex. glucose).
    • Heterotroph: eat others (carbon source is organic carbon compounds produced by others).

Macromolecules

  • Carbohydrates
  • Lipids
  • Fats
  • Nucleic acids (DNA & RNA)
  • Contains macronutrients: (CHNOPS)
    • Carbon
    • Hydrogen
    • Nitrogen
    • Oxygen
    • Phosphorous
    • Sulfur
  • Some macronutrients are not macromolecules:
    • Fe (iron)
  • Adaptation provides advantage: can chew through hard things.

Nutrient Uptake in Roots

  • Root = organ of a plant.
  • Roots are partly made up of vascular tissue.
  • Selectively & actively uptake in nutrients.
  • How roots work:
    • Absorb H20 from the soil, along with minerals dissolved in water and amino acids.
  • How can roots be more efficient (more surface area)?
    • Plant roots need help from fungi: more specifically, fungi’s mycorrhizae (cloud of filaments) to absorb additional nutrients.
  • Fungal Mycorrhizae: have a mutualistic relationship with most angiosperms (flowering plants) and gymnosperms (cone-bearing plants).
  • Some plants have root nodules.
  • Potential source of N in the atmosphere: N2 (Nitrogen gas).
    • Only N-fixing bacteria have the ability to break the N2 bond with an enzyme.
    • Some are free-living soil microbes.
    • Some live in symbiosis with a plant.

Reproduction Adaptations

  • Pre-zygotic isolating mechanisms:
    • Mating doesn’t occur à No zygote.
  • Post-zygotic isolating mechanisms:
    • Might get an organism, but it may not reproduce.
  • Specific reproductive adaptation (pre-zygotic):
    • Deer
      • Structures for mating: antlers, tusks
    • White-tailed deer
      • Structures for mating: glands (near foot and legs).
      • Associated behaviors: rubbing scent.
      • Flehmen
        • Behavioral response: potential mates nearby.
        • Connected with reproduction/scent markers.
      • These can be unique to species in 2 ways:
        • Species have unique pheromones.
        • Pheromones have unique chemical compounds.

Basics of Reproduction

  • Which eukaryotes, when does mitotic cell division occur?
    • Unicellular eukaryotes:
      • Mitosis is needed for asexual reproduction.
    • Multicellular eukaryotes:
      • Mitosis is needed in most species for cell replacement (skin cells) and wound repair.
      • Cells are continually replaced, like red blood cells.
      • Some species for asexual reproduction.
  • In multicellular eukaryotes:
    • Budding in animals: a tiny copy of the parent forms on the parent and then breaks off to live on its own.
    • Fission: one sea anemone divides down the middle to form 2.
    • Fragmentation: a piece of sponge breaks off and grows into new tissue.
    • Vegetative reproduction – plants: some succulent offspring – grow on the parent leaf and fall off.

Asexual Reproduction

  • Cell division in eukaryotic cells can be by mitosis or meiotic cell division.
  • Paradox of sex:
    • Asexual reproduction could be considered more efficient: make a lot of offspring from 1.
    • All things being equal, sexual reproduction puts organisms at a disadvantage don’t multiple as efficient as asexual organisms.

Asexual and Sexual Reproduction

  • Asexual: no gametes formed.
  • Sexual: 2 types of gametes are formed.
    • Hermaphrodites: both types of gametes are produced by the same individual.
      • Self-fertilize: sperm fertilizes the egg made in the same individual.
      • Cross-fertilization: egg fertilized by the sperm of a different individual.
    • Dioecious – 1 type of gamete produced by each sex (ex. humans).

Population Ecology Overview

  • A viable population must have the possibility for genetic exchange (gene flow) in contiguous areas of inhabitation.
  • Population ecology is the study of fluctuations in population size and the regulatory factors causing those fluctuations.
  • Population properties:
    • Population size and density.
    • Population (N) – number of individuals in an area.
    • Population (D) – D = N/A
  • Life strategies = two main strategies:
    • Species are one of these 2 types: r or K species.

r Species

  • r species: like rats, roaches, and rabbits.
    • Cheap to make (many offspring).
    • Small size.
    • Prey population size does not depend on density; instead, it depends on resources.
  • Normally, an “r” species population fluctuates dramatically.
  • Rabbit Island:
    • An r species has a high population.
    • 8 rabbits were released (1971).
    • Unlimited resources were brought by tourists.
    • K species are missing.
    • The environment is unstable.
    • Arsenic was found in the groundwater.
    • Perfect for an opportunist.
    • Adaptations have probably crept into the population already.
  • Opportunists:
    • If times are good: hoard resources and reproduce.
    • If times are bad: the population can crash.

K Species

  • Body species are usually median to large.
  • Reproduce relatively slowly.
  • More effort is put into offspring.
  • Mature later than r species.
  • Lifespan is relatively long.
  • Population does depend on density.

Regulation of Population Growth

  • Population growth is often classified as being density-dependent or density-independent.

  1. Density-dependent factors:

    • Regulatory factors that have a greater impact as density goes up (increases).

    • Ex. Resources become limited: competition and population declines.

    • Dependent factors can affect the mortality rate (how many die off).

      • Ex. Gobies die off if their reef gets too crowded.

    • Affect birth rate.

    • Carrying capacity: the number of individuals that a habitat can support.

  2. Density-independent factors:

    • The population is affected by abiotic factors.

    • Ex. Volcanoes, forest fires, droughts, floods.

Community Ecology

  • Convergent evolution: eco-morphs (same niche).
  • Ecological Niches:
    • The niche of a species: specific habitat requirements of that species: food, space, temperature.
    • The ecological role of species in a community.
  • The niche is affected by:
    • Abiotic factors: soil type, weather, sun amount.
    • Biotic factors: competition with species.
  • Factors lead to adaptations (natural selection).
  • Adaptations allow for species to coexist: every species has its own niche but often overlaps with other niches.
    • Creates potential competition between the same/other species.

Niche

  • Fundamental Niche:

    • Right conditions.

    • Where you could live, how much you could eat.

  • Realized niche:

    • Most common.

    • The niche a species actually occupies.

  • How interspecies (within) competition affects niches?

    • One species eats seeds of a certain size range.

    • Species 2 can eat some of the same seeds as species 1.

  • What happens when niche overlap is incomplete?

    • Competition occurs at overlap.

    • Natural selection acts on weaker species to reduce competition.

    • Results for one or both species: moves to a smaller realized niche.