Chapter 26: Phylogeny and the Tree of Life

Phylogeny and Classification

Phylogeny is the evolutionary history of a species or group of related species. Understanding phylogeny helps biologists classify organisms and trace their evolutionary relationships.

• Carolus Linnaeus: Developed the two-part binomial system for naming species (Genus species).

• Taxonomic Hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.

• Phylogenetic Trees: Diagrams that represent evolutionary relationships; each branch point represents a common ancestor.

• Sister Taxa: Groups that share an immediate common ancestor.

Homology vs. Analogy

• Homology: Similarity due to shared ancestry (e.g., vertebrate forelimbs).

• Analogy: Similarity due to convergent evolution, not common ancestry (e.g., wings of birds and insects).

• Convergent Evolution: Independent evolution of similar traits in distantly related organisms.

Clades and Group Types

• Clade: A group of organisms that includes an ancestor and all its descendants.

• Monophyletic Group: Includes ancestor and all descendants.

• Paraphyletic Group: Includes ancestor and some, but not all, descendants.

• Polyphyletic Group: Includes taxa with different ancestors.

Character States and Tree Construction

• Ancestral Characteristics: Traits present in the ancestor.

• Derived Characteristics: Traits unique to a clade.

• Maximum Parsimony: Principle that the simplest explanation (fewest evolutionary events) is preferred.

• Phylogenetic Trees as Hypotheses: Trees are scientific hypotheses about relationships.

The Three Domains and Horizontal Gene Transfer

• Three Domains: Bacteria, Archaea, Eukarya.

• Horizontal Gene Transfer: Movement of genes between organisms other than by descent.

Chapter 27: Bacteria and Archaea

Prokaryotic Cell Structure

Prokaryotes are unicellular organisms lacking a nucleus. They have diverse cell wall structures and metabolic capabilities.

• Cell Wall: Maintains cell shape and protects against osmotic stress.

• Plasmolysis: Loss of water from a cell in a hypertonic environment.

• Peptidoglycan: Major component of bacterial cell walls; absent in archaea.

• Bacterial vs. Archaeal Cell Walls: Bacteria have peptidoglycan; archaea have unique polysaccharides and proteins.

• Gram Stain: Distinguishes gram-positive (thick peptidoglycan) from gram-negative (thin peptidoglycan, outer membrane) bacteria.

• Endospores: Resistant structures formed by some bacteria for survival.

• Fimbriae and Pili: Surface appendages for attachment and DNA transfer.

• Taxis: Directed movement toward or away from stimuli.

Internal Organization and Genetics

• Nucleoid: Region containing the prokaryotic chromosome.

• Binary Fission: Asexual reproduction by cell division.

• Transformation: Uptake of DNA from environment.

• Transduction: DNA transfer via bacteriophages.

• Conjugation: DNA transfer between cells via pili.

Metabolic Diversity

• Phototrophs: Use light as energy source.

• Chemotrophs: Use chemicals as energy source.

• Autotrophs: Use CO2 as carbon source.

• Heterotrophs: Use organic compounds as carbon source.

Table 27.1: Nutritional Modes of Prokaryotes

Oxygen and Environmental Adaptations

• Aerobes: Require oxygen.

• Anaerobes: Do not require oxygen; may be obligate or facultative.

• Biofilms: Surface-coating colonies of prokaryotes.

• Cyanobacteria: Only bacterial group covered; important photoautotrophs.

• Extremophiles: Archaea adapted to extreme environments (halophiles, thermophiles).

Ecological Roles and Interactions

• Decomposers: Break down dead organic matter.

• Symbiosis: Close association between organisms (mutualism, commensalism, parasitism).

• Exotoxins: Secreted toxins causing disease.

• Endotoxins: Toxins released when bacteria die.

• Bioremediation: Use of prokaryotes to remove pollutants.

Chapter 28: Protists

What are Protists?

Protists are a diverse group of mostly unicellular eukaryotes. They exhibit varied modes of nutrition and locomotion.

• Phototrophs: Obtain energy from light.

• Heterotrophs: Obtain energy from organic matter.

• Mixotrophs: Combine photosynthesis and heterotrophic nutrition.

• Endosymbiosis: Origin of some organelles (e.g., mitochondria, chloroplasts) from engulfed prokaryotes.

• Pseudopodia: Extensions of cytoplasm for movement and feeding.

• Cilia: Short, hair-like structures for movement.

Protist Taxonomy: Four Supergroups

• Excavata: Includes Diplomonads and Euglenazoans (e.g., Euglenids).

• SAR: Includes Stramenopiles (Diatoms, Brown Algae), Alveolata (Dinoflagellates, Apicomplexans, Ciliates), and Rhizaria (Radiolarians, Foraminiferans).

• Archaeplastida: Includes Red Algae, Green Algae (Charophytes), and Plants.

• Unikonta: Includes Amoebozoa (Entamoebas), Opisthokonts (Animals, Fungi, Choanoflagellates).

Chapter 29: Plant Diversity I

Origins and Traits of Plants

Plants evolved from green algae (charophytes) and share several derived traits.

• Derived Traits: Alternation of generations, apical meristems, cuticles, stomata, vascular tissue.

• Bryophytes: Non-vascular plants (liverworts, mosses, hornworts); dominant gametophyte, attached sporophyte.

• Seedless Vascular Plants: Dominant sporophyte, independent gametophyte (lycophytes, monilophytes).

• Rhizoids: Root-like structures in bryophytes.

• Flagellated Sperm: Require water for fertilization.

• Peat Moss: Used for fuel, soil conditioning; stores carbon.

• Roots and Leaves: Types of leaves (microphylls, megaphylls); roots anchor and absorb.

• Megaspores vs. Microspores: Megaspores develop into female gametophytes; microspores into male.

• Spores vs. Seeds: Spores are single-celled; seeds are multicellular, with stored food.

Chapter 30: Plant Diversity II

Seed Plants: Gymnosperms and Angiosperms

Seed plants have adaptations for reproduction and dispersal, including seeds, pollen, and flowers.

• Seeds: Embryo, food supply, protective coat.

• Megasporophylls vs. Microsporophylls: Female vs. male spore-producing structures.

• Ovule: Structure containing female gametophyte.

• Pollen: Male gametophyte; pollen tubes deliver sperm.

• Advantages of Seeds: Protection, nourishment, dispersal.

• Gymnosperms: Seed plants without flowers (cycads, ginkgo, gnetophytes, conifers).

• Angiosperms: Flowering plants; produce fruit.

• Flowers: Modified leaves; female (carpels) and male (stamens) parts.

• Double Fertilization: One sperm fertilizes egg, another forms endosperm.

• Cotyledons: Seed leaves; monocots (one), dicots (two).

• Endosperm: Food for embryo.

• Monocots vs. Dicots: Monocots have parallel veins, scattered vascular tissue; dicots have net-like veins, ringed vascular tissue.

Table: Monocots vs. Dicots (Fig 30.16)

Chapter 32: Animal Diversity

What are Animals?

Animals are multicellular, heterotrophic eukaryotes with specialized tissues and complex development.

• Development: Cleavage → blastula → gastrula → larva → metamorphosis.

• Choanoflagellates: Closest living relatives to animals.

• Cambrian Explosion: Rapid diversification of animal forms.

• Symmetry: Asymmetrical, radial, bilateral.

• Tissues: Ectoderm, endoderm, mesoderm.

• Diploblastic: Two tissue layers; Triploblastic: Three layers.

• Coelom: Body cavity lined by mesoderm.

• Hemocoel: Body cavity with blood-like fluid.

• Protostome vs. Deuterostome: Differences in embryonic development.

• Archenteron: Primitive gut.

• Blastopore: Opening in gastrula; becomes mouth or anus.

Major Animal Relationships

• Eumetazoa: Animals with true tissues.

• Bilaterians: Bilateral symmetry, three tissue layers.

• Deuterostomia, Ecdysozoa, Lophotrochozoa: Major clades within Bilateria.

Chapter 33: Invertebrates

Invertebrate Diversity

Invertebrates are animals without a backbone, comprising the vast majority of animal species.

• Phylum Porifera: Sponges; sessile, filter feeders, lack true tissues, have choanocytes.

• Eumetazoa: All animals with true tissues.

• Phylum Cnidaria: Corals, jellies, hydra; radial symmetry, diploblastic, gastrovascular cavity, polyps and medusa, cnidocytes and nematocysts.

• Lophotrochozoa: Includes Platyhelminthes, Mollusca, Annelida.

• Phylum Platyhelminthes: Flatworms; bilateral symmetry, no body cavity, planarians (free-living), trematodes and tapeworms (parasitic).

• Phylum Mollusca: Snails, clams, squids, octopuses; foot, visceral mass, mantle, radula, chitons, gastropods, bivalves, cephalopods.

• Phylum Annelida: Segmented worms; coelom, errantians (marine), sedentarians (leeches, earthworms).

• Ecdysozoa: Includes Nematoda and Arthropoda; cuticle, ecdysis (molting).

• Phylum Nematoda: Roundworms; no circulatory system, only longitudinal muscles.

• Phylum Arthropoda: Exoskeleton, jointed appendages, trilobites, chelicerates (spiders, scorpions), myriapods (centipedes, millipedes), pancrustaceans (insects, crustaceans).

• Metamorphosis: Incomplete (nymphs) vs. complete (larval stages).

• Deuterostomia: Includes Echinodermata and Chordata.

• Phylum Echinodermata: Sea stars, sea urchins, sand dollars; bilateral symmetry as larvae, water vascular system, tube feet.

Chapter 34: Vertebrates

Vertebrate Characteristics and Taxonomy

Vertebrates are animals with a backbone, belonging to Phylum Chordata. They exhibit complex structures and diverse adaptations.

• Phylum Chordata: Bilateral, deuterostomes; four key traits: notochord, dorsal hollow nerve cord, pharyngeal slits/clefts, post-anal tail.

• Cephalochordata: Lancelets.

• Urochordata: Tunicates (sea squirts).

• Vertebrata: All vertebrates.

• Jawless Vertebrates: Hagfish, lampreys.

• Gnathostomata: Jawed vertebrates; jaws evolved from pharyngeal slits.

• Chondrichthyes: Sharks, rays, ratfish; cartilaginous skeleton, oily liver for buoyancy.

• Ray-finned Fishes (Actinopterygii): Most fish; bony endoskeleton, operculum, swim bladder.

• Lobe-finned Fishes (Sarcopterygii): Coelacanths, lungfishes, tetrapods.

• Tetrapods: Evolved from lobe-finned fishes; four limbs, Tiktaalik as transitional fossil.

• Amphibians: Salamanders (paedomorphosis), frogs (development), caecilians (no limbs); tied to water for reproduction.

• Amniotes: Amniotic egg allows reproduction away from water.