SCIE201 - Essentials of Biology: Evolution and Biodiversity

Defining Life

• Life on Earth exhibits diverse forms, including humans, animals, insects, and bacteria.
• Living organisms share fundamental characteristics:
  • Composed of common chemical elements like Carbon, Hydrogen, and Oxygen.
  • Adhere to universal physical and chemical laws.
  • Organized into cells (unicellular or multicellular).

Characteristics of Living Things

• Living things possess a shared set of attributes:
  1. Organization: Exhibit hierarchical organization from atoms to the biosphere.
  2. Acquisition of Materials and Energy: Require energy and nutrients to sustain life processes.
  3. Response to Stimuli: React to environmental cues.
  4. Reproduction and Development: Capable of producing offspring and undergoing developmental changes.
  5. Adaptations: Evolve traits that enhance survival and reproduction in specific environments.

Levels of Biological Organization

The levels of biological organization are structured hierarchically:

• Atom: The smallest unit of an element composed of electrons, protons, and neutrons.
• Molecule: Union of two or more atoms of the same or different elements.
• Cell: The structural and functional unit of all living things.
• Tissue: A group of cells with a common structure and function.
• Organ: Composed of tissues functioning together for a specific task.
• Organ System: Composed of several organs working together.
• Organism: An individual; complex individuals contain organ systems.
• Population: Organisms of the same species in a particular area.
• Community: Interacting populations in a particular area.
• Ecosystem: A community plus the physical environment.
• Biosphere: Regions of the Earth's crust, waters, and atmosphere inhabited by living things.

Classification of Living Things

• Levels of classification from least to most inclusive:
  • Species, genus, family, order, class, phylum, kingdom, and domain.
• A level includes more species than the level below it, and fewer species than the one above it.
• Species is the fundamental unit of classification.
• Domain is the most inclusive category.
• Each level above species includes more types of organisms.
• Three Domains: Bacteria, Archaea, Eukarya.
• Example of classification:
  • Animals (Kingdom) are organisms able to move on their own.
  • Chordates (Phylum) are animals with a backbone.
  • Mammals (Class) are chordates with fur or hair and milk glands.
  • Primates (Order) are mammals with collar bones and grasping fingers.
  • Hominids (Family) are primates with relatively flat faces and three-dimensional vision.
  • Homo (Genus) are hominids with upright posture and large brains.
  • Homo sapiens (Species) are members of the genus Homo with a high forehead and thin skull bones.

Evolutionary Tree of Life

• The evolutionary tree illustrates the relationships between the three domains of life: Bacteria, Archaea, and Eukarya.
• All life shares a common ancestor.
• Eukarya and Archaea are more closely related than Bacteria.

Prokaryotes: Masters of Adaptation

• Prokaryotes inhabit diverse environments, including extreme conditions (acidic, salty, hot, or cold).
• They exhibit remarkable genetic diversity.
• Prokaryotes are classified into two domains: Bacteria and Archaea.

Adaptations Contributing to Prokaryotic Success

• Most prokaryotes are unicellular, although some form colonies.
• They are generally smaller than eukaryotic cells.
• Prokaryotic cells exhibit three common shapes: spheres (cocci), rods (bacilli), and spirals.

Genetic Variation in Prokaryotes

• Prokaryotes possess considerable genetic variation.
• Factors contributing to genetic diversity:
  • Rapid reproduction
  • Mutation (low rate)
  • Genetic recombination

Conjugation

• Conjugation is a process where genetic material is transferred between bacterial cells.
• Sex pili facilitate cell connection and DNA transfer.

Nutritional and Metabolic Adaptations in Prokaryotes

• Phototrophs obtain energy from light.
• Chemotrophs obtain energy from chemicals.
• Autotrophs require CO_2 as a carbon source.
• Heterotrophs require an organic nutrient to create organic compounds.
• Four major modes of nutrition:
  • Photoautotrophy
  • Chemoautotrophy
  • Photoheterotrophy
  • Chemoheterotrophy

Role of Oxygen in Metabolism

• Prokaryotic metabolism varies with respect to oxygen:
  • Obligate aerobes require O_2 for cellular respiration.
  • Obligate anaerobes are poisoned by O_2 and use fermentation or anaerobic respiration.
  • Facultative anaerobes can survive with or without O_2.

Nitrogen Metabolism

• Nitrogen fixation: Some prokaryotes convert N2 to NH3.
• Metabolic cooperation: Prokaryotes work together to use resources.
• Photosynthetic cells and nitrogen-fixing cells share nutrients.

Domain: Archaea

• Archaea are prokaryotes sharing traits with both bacteria and eukaryotes.
• Extremophiles thrive in extreme environments:
  • Extreme halophiles in highly saline environments.
  • Extreme thermophiles in very hot environments.

Ecological Roles of Prokaryotes

• Prokaryotes play crucial roles in the biosphere.
• They recycle nutrients between living and nonliving things.
• Decomposers break down dead organisms and waste.
• Nitrogen-fixing prokaryotes add usable nitrogen to the environment.
• Prokaryotes assist plants by increasing nitrogen, phosphorus, and potassium availability.
• Some prokaryotes can also limit nutrient availability.

Ecological Interactions

• Symbiosis: Two species live closely together (host & symbiont).
• Mutualism (+/+): Both benefit.
  • Example: Rhizobium bacteria provide nitrogen to legume plants; plants provide food & shelter.
• Commensalism (+/0): One benefits, the other is unaffected.
  • Example: Skin bacteria use sweat but don’t harm us.
• Parasitism (+/-): One benefits, the other is harmed.
  • Example: Disease-causing pathogens.

Uses of Prokaryotes

• Prokaryotes help in DNA technology research.
• Bioremediation: They clean up pollutants.
• Other uses:
  • Extracting metals from ores.
  • Making vitamins.
  • Producing antibiotics & hormones.

Protists

• Protists are mostly unicellular eukaryotes, but some are multicellular.
• They are highly diverse in structure and function.
• Nutritional types:
  • Photoautotrophs: Produce food using chloroplasts.
  • Heterotrophs: Consume organic matter.
  • Mixotrophs: Employ both photosynthesis and feeding.

Ecological Roles of Protists

• Protists fill diverse roles in aquatic ecosystems.
• Helpful protists (+/+):
  • Dinoflagellates support coral reefs.
  • Hypermastigotes aid termites in wood digestion.
• Harmful protists (+/-): Plasmodium causes malaria.

Plant Diversity

• Key sources of food, fuel, wood products, and medicine.
• Includes:
  • Nonvascular plants (bryophytes): Mosses, liverworts, hornworts
  • Vascular plants:
    • Seedless: Lycophytes, Monilophytes
    • Seed plants: Gymnosperms, Angiosperms

Ecological Advantage of Mosses

• Mosses may help retain Nitrogen in the soil, conferring an ecological advantage.

Threats to Plant Diversity

• Habitat destruction leads to plant species extinction.
• Loss of plant habitat results in the loss of animal species that rely on plants.
• Current habitat loss rates project 50% of Earth’s species extinction within 100–200 years.

Fungi

• Diverse and widespread, they decompose organic material and recycle nutrients in ecosystems.
• Heterotrophs: Absorb nutrients from their surroundings.
• Utilize enzymes to break down complex molecules into smaller compounds.
• Diverse lifestyles:
  • Decomposers/Saprophytes
  • Parasites (+ -)
  • Mutualists (+ +)

Practical Uses of Fungi

• Used for food, medicines, research, alternative fuels, and pest control.
• Play vital ecological roles by decomposing organic matter and breaking down minerals.
• Some fungi cause disease by absorbing nutrients and producing toxins.

Animal Diversity

• Multicellular, heterotrophic eukaryotes with tissues formed from embryonic layers.
• Approximately 1.3 million known species.
• Animal cells lack cell walls.
• Bodies are held together by proteins like collagen.
• Nervous tissue and muscle tissue are unique to animals.
• Most reproduce sexually, with the diploid stage dominating their life cycle.

Practical Uses of Animals

• Tilling agricultural fields.
• Providing wool for clothing.
• Providing milk, eggs, and meat for food.
• Serving as pets (dogs, cats).
• Helping humans in obtaining food.

Six Kingdoms

• Two are Prokaryotic (no nucleus):
  • Archaea
  • Bacteria
• Four are Eukaryotic (Domain Eukarya):
  • Protista: Algae, protozoans, slime molds, and water molds; complex single cell.
  • Fungi: Molds, mushrooms, yeasts, and ringworms; mostly multicellular filaments.
  • Plantae: Certain algae, mosses, ferns, conifers, and flowering plants; multicellular with specialized tissues.
  • Animalia: Sponges, worms, insects, fishes, frogs, turtles, birds, and mammals; multicellular with specialized tissues.

Darwin's Conclusions

• Prior to Darwin, scientists believed species remained unchanged since creation, and variation was imperfection.
• Darwin developed the theory of natural selection, explaining evolution and species changes over time.

Natural Selection

• Process leading to adaptation of a population to biotic and abiotic environments.
• Darwin’s mechanism for adaptation.
• Fitter individuals become more common in a population.
• Leads to change in population over time.
• Fitter individuals reproduce more due to better adaptation.
• Example: High elevation allele in Tibetans.

Evolutionary Thought before Darwin

• Environments can drive evolution.

Natural Selection Requirements

• Evolution by natural selection involves:
  1. Variation: Members of a population differ.
  2. Inheritance: Many differences are heritable genetic differences.
  3. Increased fitness: Better-adapted individuals reproduce more, and their offspring form a larger share of the next generation.

Types of Selection

• Most traits are polygenic, controlled by multiple alleles at different gene loci.
• Traits have a range of phenotypes resembling a bell-shaped curve.
• Natural selection reduces detrimental phenotypes and favors those better adapted.
• Types of selection:
  • Stabilizing selection
  • Directional selection
  • Disruptive selection

Stabilizing Selection

• Intermediate phenotype favored.
• Extreme phenotypes selected against; average is favored.
• Most common; the average individual is well-adapted.
• Example: Swiss starlings lay four to five eggs for highest survival rate.

Directional Selection

• Extreme phenotype is favored.
• Distribution curve shifts in that direction.
• Occurs when adapting to a changing environment.
• Examples:
  • Drug resistance in bacteria
  • Pesticide resistance in insects
  • Malaria—Plasmodium becoming resistant to chloroquine and mosquitoes resistant to DDT
  • Industrial melanism

Industrial Melanism

• Increased frequency of a dark phenotype due to pollution.
• Light moths were common before soot darkened tree trunks.
• Dark-colored moths became more common post-industry.
• Natural selection can occur quickly.
• Change in gene pool frequencies is microevolution.

Disruptive Selection

• Two or more extreme phenotypes are favored over any intermediate phenotype.
• Favors polymorphism—different forms in a population of the same species.

Adaptations Are Not Perfect

• Natural selection doesn't produce perfectly adapted organisms.
• Evolution is limited by available variations.
• Environment changes as adaptations evolve.

Maintenance of Variations

• Populations always show some genotypic variations.
• Limited variation may prevent adaptation to changing environments.
• Forces promoting variation:
  • Mutations (random DNA changes)
  • Recombination (mixing of genes during reproduction)
  • Independent assortment (random gene distribution in gametes)
  • Fertilization (genes from two parents combined)
  • Gene flow (genes moving between populations)
• Natural selection favors some phenotypes, but others remain.
• Diploidy (two gene copies) and heterozygosity

Heterozygote Advantage

• Heterozygotes can protect recessive alleles.
• Balanced polymorphism—natural selection favors the ratio of two or more phenotypes across generations.
• Sickle-cell disease illustrates heterozygote advantage in malaria-prone areas.

Sickle-Cell Disease

• Sickle-cell disease (HbS HbS) can be deadly at a young age.
• Heterozygotes (HbA HbS) have sickle-cell trait, with symptoms only in low oxygen.
• Normally, HbA HbA is best.
• In malaria-prone regions, HbS is more common because it provides some protection against malaria.
• Malaria is caused by a parasite that attacks normal red blood cells.

Microevolution

• Individuals don’t evolve; evolution occurs via traits passed to future generations.
• Evolution is change in heritable traits within a population over time.
• A population is all individuals of a species in a specific area that reproduce together.
• Microevolution is changes in allele frequencies within a population across generations.
• Microevolution involves small, measurable genetic changes from one generation to the next.

Evolution in a Genetic Context

• Gene pool—the various alleles at all the gene loci in all individuals of a population.
• Described in terms of genotype and allele frequency.
• Peppered moth color example:
  • D = dark color, d = light color.
• From genotype frequencies you calculate allele frequencies.
• If there are 2 alleles at a locus, p and q represent their frequencies.
• The frequency of all alleles in a population will add up to 1:
  • p + q = 1

Hardy-Weinberg Principle

• Describes an ideal population that isn’t evolving.
• The closer a population is to the Hardy-Weinberg criteria, the more stable it is.
• Calculating Genotype Frequencies:
  • p^2 + 2pq + q^2 = 1
    • where p^2 and q^2 represent the frequencies of the homozygous genotypes, and 2pq represents the frequency of the heterozygous genotype.

Methods For Allelic Frequency Calculation

• Method 1 using gene counting
• Method 2 using genotype frequency
  • Given genotype frequencies, calculate allele frequencies in a gene pool!
• Alleles = A, a
• Genotypes AA, Aa, aa
• Frequency of allele A:
  • f(A) = f (AA) + mfrac{1}{2} f (Aa)
• Frequency of allele a:
  • f(a) = f (aa) + mfrac{1}{2} f (Aa)

Natural Selection and Change in Allelic Frequency

• Natural selection can cause changes in the frequencies of alleles in a population.

Hardy-Weinberg Equilibrium

• Required conditions are rarely (if ever) met.
• Changes in gene pool frequencies are likely.
• When gene pool frequencies change, microevolution has occurred.
• Deviations from a Hardy-Weinberg equilibrium indicate that evolution has taken place.

Speciation and Macroevolution

• Macroevolution—larger scale changes in a population over a very long period of time which often results in speciation
• Speciation—splitting of one species into two or more new species due to evolving many adaptations and accumulating them over time.

Types of Evolution

• Divergent Evolution: occurs when two close species gradually become increasingly different.
  • When closely related species diversify due to new habitats.
  • Responsible for current diversity from first living cells and also human evolution
• Convergent Evolution: occur when species of different ancestry begin to share analogous traits
  • Due to shared environment or other selection pressure.
  • For example, whales and fish have some similar characteristics since both had to evolve methods of moving through the same medium: water.

Parallel Evolution

• Parallel Evolution: Two species evolve independently but remain similar.
• It occurs in unrelated species that live in different habitats.
• Example: Marsupials in Australia and placental mammals elsewhere evolved similarly.
• Australian marsupials resemble wolves, cats, mice, and moles due to adaptation to similar lifestyles.

Biological Species Concept

• Not based on appearance.
• Members of a species:
  • Interbreed.
  • Have a shared gene pool.
  • Each species reproductively isolated from every other species.
• Gene flow occurs between populations of a species but not between populations of different species.
• Category of classification below rank of genus Species in the same genus share a recent common ancestor.

Reproductive Barriers

• Isolating Mechanisms: Prevent different species from producing fertile offspring.
• Prezygotic Isolation (before fertilization, no zygote forms):
  • Habitat Isolation: Species live in different environments (e.g., flycatchers).
  • Temporal Isolation: Species breed at different times (e.g., frogs mating in different seasons or water depths).
  • Behavioral Isolation: Unique courtship behaviors prevent mating (e.g., chemical signals, movement displays).
  • Mechanical Isolation: Physical incompatibility of reproductive structures (common in insects and plants).
  • Gamete Isolation: Sperm cannot fertilize the egg due to incompatibility (e.g., species-specific egg receptors).

Postzygotic Isolating Mechanism

• Postzygotic barriers occur after zygote formation, preventing hybrid offspring from developing or breeding.
• Zygote mortality: The zygote is not viable due to mismatched chromosomes and fails to continue mitosis.
• Hybrid sterility: The hybrid develops into a sterile adult because chromosome misalignment during meiosis prevents the production of viable gametes.

Domain Eukarya

The Eukaryotes, which have a nucleus, form a third domain, and comprise 4 additional kingdoms:

• Protista – Eukaryotic unicells: protozoa, algae, water molds, slime molds (use spores to reproduce)
• Fungi – Yeasts, mildew, molds, and mushrooms – Nonphotosynthetic: heterotrophs
• Plantae – Complex organization – Nonvascular (mosses) and vascular (ferns, conifers, flowering) plants – Many photosynthetic, make carbohydrate from H2O & CO2 – Stiff outer cuticle with cell walls
• Animalia – Multicellular heterotrophs – Complex tissues and organs, capacity for movement