Comprehensive Study Guide for Diversity of Species

Taxonomy and the Linnaean System

  • Foundational Classification: Carl Linnaeus developed the modern system of biological classification in the 18th century.
  • Hierarchical Organization: The system is hierarchical, meaning each level is nested within higher, more inclusive levels.
        * The Taxonomic Hierarchy (from most inclusive to least inclusive):
            * Domain: Eukarya (includes plants, insects, fish, rabbits, cats, foxes, jackals, wolves, and dogs).
            * Kingdom: Animalia (includes insects, fish, rabbits, cats, foxes, jackals, wolves, and dogs).
            * Phylum: Chordata (includes fish, rabbits, cats, foxes, jackals, wolves, and dogs).
            * Class: Mammalia (includes rabbits, cats, foxes, jackals, wolves, and dogs).
            * Order: Carnivora (includes cats, foxes, jackals, wolves, and dogs).
            * Family: Canidae (includes foxes, jackals, wolves, and dogs).
            * Genus: Canis (includes jackals, wolves, and dogs).
            * Species: Canis lupus (includes wolves and dogs).
            * Subspecies: Canis lupus familiaris (the domestic dog).

Biological Species and Binomial Nomenclature

  • Biological Species Concept: Defines a species as a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but are reproductively isolated from other such groups.
  • Binomial System: Every species is assigned a two-part scientific name in Latin.
        * Scientific Name Uniformity: These names are standardized and recognized globally to ensure uniform communication across different languages and regions.
        * Genus: The first part of the name, representing a group of closely related species. It is always capitalized and either italicized or underlined.
            * Examples include Felis (domestic cats and mountain lions), Homo (modern and prehistoric humans), and Sialia (bluebirds).
        * Species Epithet: The second part of the name, which refers to one specific species within a genus. It often describes a characteristic of the organism. It is always lowercase and either italicized or underlined.
  • Specific Nomenclature Examples:
        * Domestic Cat: Felis domesticus
        * Human: Homo sapiens
        * Western Bluebird: Sialia mexicana
        * Bluebird Variants: Eastern bluebird, Western bluebird, and Mountain bluebird.

Classification and Evolutionary Relationships

  • Phylogenetic Trees: Diagrams used to represent hypothesized evolutionary relationships among organisms. Branching points on the tree represent the most recent common ancestor between different lineages.
        * Example Tree (Primate lineage): Gibbons $\rightarrow$ Sumatran orangutan $\rightarrow$ Bornean orangutan $\rightarrow$ Mountain gorilla $\rightarrow$ Eastern lowland gorilla $\rightarrow$ Western gorilla $\rightarrow$ Human $\rightarrow$ Bonobo $\rightarrow$ Chimpanzee.
  • Homology vs. Analogy:
        * Homologous Characteristics: Traits that are similar due to shared ancestry.
        * Analogous Characteristics: Traits that are similar due to convergent evolution, not common ancestry (organisms evolve similar solutions to similar environmental pressures independently).

The Three Domains of Life

  • Historical Perspective: Early systems categorized all life as either plants or animals. This led to conflict where organisms like Euglena or fungi were incorrectly placed.
  • Modern Classification: Based largely on genomic studies of SSU rRNA (small subunit ribosomal RNA), life is now divided into three domains:
        1. Bacteria: Single-celled prokaryotes, including cyanobacteria, proteobacteria, and spirochetes.
        2. Archaea: Single-celled prokaryotes, many of which are known as extremophiles.
            * They can survive in high heat (thermophiles like Sulfolobus), high salt (halophiles), and high acidity (low pHpH).
            * Examples: Methanosarcina, Methanobacterium, Methanococcus, T.celer, Thermoproteus, Pyrodicticum.
        3. Eukarya: Organisms with membrane-bound organelles. Includes kingdoms such as Fungi, Plantae, and Animalia, along with diverse protist groups.

Evolution of Eukaryotes and Endosymbiosis

  • Organelle Development: There are two primary mechanisms for the origin of membrane-bound organelles:
        1. In-folding of the Plasma Membrane: Thought to have given rise to the nucleus, endoplasmic reticulum (ER), and Golgi apparatus.
        2. Endosymbiosis: The theory that certain organelles, specifically mitochondria and chloroplasts, originated as free-living prokaryotes that were consumed (but not digested) by an ancestral eukaryote.
            * Mitochondria: Resulted from an early endosymbiotic event where a proto-eukaryote consumed aerobic bacteria.
            * Chloroplasts: Resulted from a subsequent event where a heterotrophic eukaryote consumed photosynthetic bacteria (similar to cyanobacteria).
  • Evidence for Endosymbiosis:
        * Organelles are similar in size to prokaryotes.
        * Possess a double membrane (the inner membrane differs in composition from the outer membrane).
        * Contain their own circular DNA.
        * Molecular sequence comparisons show chloroplasts are highly similar to cyanobacteria.
  • Eukaryotic Kingdoms and Energy Acquisition:
        * Fungi: Multicellular, obtain energy through absorption.
        * Plants (Plantae): Multicellular, obtain energy through photosynthesis.
        * Animals (Animalia): Multicellular, obtain energy through ingestion.
        * These groups are all descendent from different protist lineages.

Plant Diversity and Adaptations

  • Origin: Land plants evolved from green algae.
  • Terrestrial Adaptations: To survive on land and avoid desiccation (drying out), plants developed:
        * Protected Embryos.
        * Sporangia: Structures where spores develop.
        * Gametangia: Structures where gametes (egg and sperm) develop.
  • Alternation of Generations: A life cycle including two multicellular forms:
        * Gametophyte (nn): Haploid form; develops from a spore; produces gametes through mitosis.
        * Sporophyte (2n2n): Diploid form; develops from a zygote (fertilization of egg and sperm); produces spores through meiosis via structures like sori containing sporangia.
  • Major Plant Groups:
        1. Nonvascular Plants (Bryophytes): Small plants lacking vascular tissue (e.g., Liverworts and Mosses). They require wet habitats due to flagellated sperm.
        2. Vascular Plants: Contain specialized tissues for transport:
            * Xylem: Transports water and inorganic nutrients.
            * Phloem: Transports organic nutrients (sugars).
            * They possess true roots and leaves.
        3. Seedless Vascular Plants: Reproduce via spores and require wet habitats for flagellated sperm (e.g., Ferns, horsetails, club mosses).
        4. Seed Plants: Split into two groups:
            * Gymnosperms: Seeds develop in cones.
            * Angiosperms: Seeds develop in flowers.

Animal Diversity and Body Plans

  • Core Characteristics: Multicellular heterotrophs, lack cell walls, possess unique muscle cells and neurons.
  • Body Symmetry:
        * Asymmetrical: No symmetry (e.g., Sponges/Encrusting sponge).
        * Radial Symmetry: Body parts arranged around a central axis (e.g., Cnidaria).
        * Bilateral Symmetry: Has a distinct anterior (front), posterior (back), and a single plane of symmetry.
  • Embryonic Development and Tissues:
        * Parazoa: No true tissues (Sponges).
        * Eumetazoa: Specialized tissues developed during embryo development.
            * Gastrulation: Process where the blastula (hollow ball of cells) folds inward to form the gastrula and germ layers.
        * Diploblastic: Two tissue layers (Ectoderm - outer covering/nervous system; Endoderm - digestive lining).
        * Triploblastic: Three tissue layers (Ectoderm, Endoderm, and Mesoderm - internal organs).
  • Bilateral Animal Divisions (Protostomes vs. Deuterostomes):
        * Cleavage: Spiral and determinate in Protostomes; Radial and indeterminate in Deuterostomes.
        * Coelom Formation: Splitting of mesoderm in Protostomes; Out-pocketing of the gut in Deuterostomes.
        * Blastopore Fate: Becomes the mouth in Protostomes; becomes the anus in Deuterostomes.

Major Animal Groups

  • Protostomes:
        * Ecdysozoans: Animals that molt their cuticle.
            * Arthropods: Segmented bodies, jointed skeletons. Includes Insects (6 legs), Arachnids (8 legs), Crustacea (variable legs), and Myriapoda (many legs).
            * Nematodes (Roundworms): Unsegmented, move with longitudinal muscles in a whip-like motion. Examples: Heartworms.
        * Lophotrochozoans: Defined by special feeding structures (Lophophore) or larvae (Trochophore).
            * Flatworms: Gastrovascular cavity with one opening. Includes Planaria, flukes, and tapeworms.
            * Annelids: Segmented worms like earthworms, leeches, and polychaetes.
            * Mollusks: Body plan includes visceral mass, foot, and mantle. Includes snails, sea slugs, octopus, squid, nautilus, scallops, and mussels.
  • Deuterostomes:
        * Echinoderms: Feature a water vascular system and tube feet. Includes sea stars, sea urchins, and sea cucumbers.
        * Chordates:
            * Invertebrate Chordates: Lancelets and Tunicates.
            * Vertebrates: Developed adaptations for land, including walking legs and the amniotic egg. Birds are classified as specialized reptiles.

Biodiversity and Conservation

  • Current Species Estimates: Approximately 1.51.5 million species have been named. Estimates suggest a total of 10−1310-13 million species exist, mostly insects. Prokaryote diversity may be significantly higher, with new techniques revealing over 1,0001,000 species in the human gut alone.
  • Importance of Biodiversity:
        * Ecosystem Services: Nutrient cycling, drought and flood control, decomposition, detoxification, pest control, and weather modification.
        * Economic value: New medicines (≈50%\approx 50\% of prescription drugs are derived from plant chemicals) and new food sources.
        * Other values: Aesthetics, recreation, quality of life, and moral obligations.
  • The Extinction Crisis:
        * Extinction is natural; 95%95\% of all historically existing species are extinct.
        * Five Major Extinction Events: Historical mass extinctions (end-Ordovician, end-Devonian, end-Permian, end-Triassic, end-Cretaceous).
        * Current Human-Caused Rate: Estimates put current extinction at 100−10,000100-10,000 times the background rate.
  • Threats to Biodiversity:
        1. Habitat Destruction: The leading cause of extinction.
        2. Over-harvesting: Hunting (e.g., Dodo bird, Passenger pigeon [noted as bird in transcript], Buffalo), plant collection (Orchids), and fisheries decline.
        3. Predator/Pest Control: Elimination of species like the Carolina parakeet and wolves.
        4. Nonnative Species: Invasive species like rats in Hawaii, snakes in Guam, and zebra mussels.
        5. Pollution: Includes Bioaccumulation and Biomagnification.
            * Lipid-soluble molecules (e.g., DDT and PCBs) accumulate in tissue and increase in concentration up the food chain.
            * DDT Concentration Example: Water (0.000003 ppm0.000003\,ppm) $\rightarrow$ Zooplankton (0.04 ppm0.04\,ppm) $\rightarrow$ Minnows (0.5 ppm0.5\,ppm) $\rightarrow$ Needle fish (2 ppm2\,ppm) $\rightarrow$ Ospreys (25 ppm25\,ppm).
            * Affected species: Osprey, brown pelicans, bald eagles, prairie falcon, sparrow hawk, peregrine falcon.
        6. Climate Change: Visualized through glacial retreat (e.g., Glacier National Park archives from 1938 to 2009).