BIO 102 Midterm Exam Study Guide: Phylogeny, Microbial Diversity, Plant and Animal Diversity

Chapter 26: Phylogeny

Key Concepts in Phylogeny

• Phylogeny: The evolutionary history and relationships among species or groups of organisms.

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

• Taxonomic Hierarchy: The order from broad to specific is Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

• Phylogenetic Trees: Diagrammatic hypotheses about the evolutionary relationships among organisms.

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

• Homology vs. Analogy: Homology is similarity due to shared ancestry; analogy is similarity due to convergent evolution.

• Clade: A group of species that includes an ancestral species and all its descendants.

• Monophyletic, Paraphyletic, Polyphyletic Groups:

  • Monophyletic: Includes ancestor and all descendants.

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

  • Polyphyletic: Does not include the most recent common ancestor.

• Ancestral vs. Derived Characteristics: Ancestral traits are inherited from distant ancestors; derived traits are new in a particular lineage.

• Maximum Parsimony: The simplest explanation (fewest evolutionary changes) is preferred.

• Phylogenetic Trees as Hypotheses: Trees are best guesses based on available data and may change with new evidence.

• Three Domains of Life: Bacteria, Archaea, Eukarya.

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

Chapter 27: Bacteria and Archaea

Prokaryotic Diversity and Structure

• Prokaryotes: Single-celled organisms lacking a nucleus (Bacteria and Archaea).

• Cell Wall: Maintains cell shape, protects, and prevents bursting in hypotonic environments.

• Plasmolysis: Shrinking of the cell membrane away from the cell wall due to water loss.

• Peptidoglycan: Polymer in bacterial cell walls; absent in Archaea.

• Bacterial vs. Archaeal Cell Walls: Bacteria have peptidoglycan; Archaea have distinct polysaccharides and proteins.

• Gram-Positive vs. Gram-Negative Bacteria:

  • Gram-positive: Thick peptidoglycan layer, stains purple.

  • Gram-negative: Thin peptidoglycan, outer membrane, stains pink/red.

• Endospores: Resistant cells formed by some bacteria for survival in harsh conditions.

• Fimbriae and Pili: Surface appendages for attachment (fimbriae) and DNA transfer (pili).

• Taxis: Directed movement toward or away from stimuli (e.g., chemotaxis).

• Internal Organization and DNA: Prokaryotes lack membrane-bound organelles; DNA is in a nucleoid region.

• Binary Fission: Asexual reproduction by cell division.

• Genetic Recombination:

  • Transformation: Uptake of foreign DNA from environment.

  • Transduction: Gene transfer by bacteriophages.

  • Conjugation: DNA transfer via direct contact (pili).

• Nutritional Modes (see Table below):

  • Phototrophs: Obtain energy from light.

  • Chemotrophs: Obtain energy from chemicals.

  • Autotrophs: Use CO2 as carbon source.

  • Heterotrophs: Require organic compounds for carbon.

• Aerobes vs. Anaerobes: Aerobes require oxygen; anaerobes do not (some are obligate, some are facultative).

• Biofilms: Surface-coating colonies of prokaryotes.

• Bacteria vs. Archaea: Differ in cell wall composition, membrane lipids, and some genetic machinery.

• Cyanobacteria: Photosynthetic bacteria; important for oxygen production.

• Extremophiles: Archaea living in extreme environments (e.g., extreme halophiles, extreme thermophiles).

• Decomposers: Break down dead organic matter.

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

• Exotoxins vs. Endotoxins:

  • Exotoxins: Secreted proteins causing disease.

  • Endotoxins: Released when Gram-negative bacteria die and cell walls break down.

• Bioremediation: Use of organisms to remove pollutants from environment.

Nutritional Mode	Energy Source	Carbon Source	Example Organisms
Photoautotroph	Light	CO2, HCO3-	Cyanobacteria, plants
Chemoautotroph	Inorganic chemicals	CO2, HCO3-	Unique to certain prokaryotes
Photoheterotroph	Light	Organic compounds	Some aquatic prokaryotes
Chemoheterotroph	Organic compounds	Organic compounds	Many prokaryotes, animals, fungi

Chapter 28: Protists

Protist Diversity and Classification

• Protists: Eukaryotes that are not plants, animals, or fungi; mostly unicellular.

• Phototrophs, Heterotrophs, Mixotrophs: Protists may obtain energy from light, organic compounds, or both.

• Endosymbiosis: Theory that eukaryotic organelles (mitochondria, chloroplasts) originated from symbiotic prokaryotes.

• Pseudopodia: Extensions of cytoplasm for movement and feeding.

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

Protist Taxonomy: Four Supergroups

• Excavata:

  • Diplomonads

  • Euglenazoans (Euglenids)

• SAR:

  • Stramenopiles: Diatoms, Brown Algae

  • Alveolata: Dinoflagellates, Apicomplexans, Ciliates

  • Rhizaria: Radiolarians, Foraminiferans

• Archaeplastida:

  • Red Algae

  • Green Algae (Charophytes)

  • Plants

• Unikonta:

  • Amoebozoa: Entamoebas

  • Opisthokonts: Animals, Fungi, Choanoflagellates

Chapter 29: Plant Diversity I

Origin and Evolution of Plants

• Green Algae (Charophytes) and Plants: Share traits such as cellulose synthesis, peroxisome enzymes, and flagellated sperm.

• Derived Traits of Plants: Alternation of generations, apical meristems, cuticle, stomata, multicellular gametangia.

• Alternation of Generations: Life cycle alternates between multicellular haploid gametophyte and diploid sporophyte.

• Apical Meristems: Regions of cell division at plant tips.

• Cuticle: Waxy covering to prevent water loss.

• Stomata: Pores for gas exchange.

• Vascular Tissue: Specialized for transport of water and nutrients; defines vascular plants.

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

• Seedless Vascular Plants: Lycophyta (club mosses, etc.), Monilophyta (ferns, etc.); dominant sporophyte generation.

• Rhizoids: Root-like structures in bryophytes.

• Flagellated Sperm: Require water for fertilization.

• Peat Moss: Important for carbon storage and as a soil additive.

• Roots and Leaves: Roots anchor and absorb; leaves increase photosynthetic area.

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

• Spores vs. Seeds: Spores are single cells; seeds are multicellular, with stored food and protective coat.

Chapter 30: Plant Diversity II

Seed Plants: Gymnosperms and Angiosperms

• Seeds: Embryo, food supply, and protective coat; allow for dispersal and dormancy.

• Megasporophylls vs. Microsporophylls: Structures bearing megaspores (female) or microspores (male).

• Ovule: Structure that develops into a seed after fertilization.

• Pollen and Pollen Tubes: Male gametophyte; pollen tube delivers sperm to ovule.

• Advantages of Seeds: Protection, nourishment, dispersal, dormancy.

• Gymnosperms: "Naked seeds" not enclosed in fruit (e.g., conifers).

• Angiosperms: Flowering plants; seeds enclosed in fruit.

• Flowers and Fruit: Flowers for reproduction; fruit aids seed dispersal.

• Double Fertilization: One sperm fertilizes egg, another forms endosperm (nutritive tissue).

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

• Monocots vs. Dicots: Differ in leaf veins, root systems, flower parts, and vascular tissue arrangement.

Feature	Monocots	Dicots (Eudicots)
Cotyledons	One	Two
Leaf Veins	Parallel	Net-like
Vascular Bundles	Scattered	Ring
Root System	Fibrous	Taproot
Flower Parts	Multiples of 3	Multiples of 4 or 5

• Gymnosperm Groups: Cycadophyta, Ginkophyta, Gnetophyta (Welwitschia, Ephedra), Coniferophyta.

• Angiosperm Groups: Monocots and Dicots.

Chapter 32: Animal Diversity

Animal Characteristics and Development

• Animals: Multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers.

• Development: Zygote undergoes cleavage, forms blastula, then gastrula.

• Larva and Metamorphosis: Many animals have a larval stage that undergoes metamorphosis to become an adult.

• Choanoflagellates: Closest protist relatives of animals.

• Cambrian Explosion: Rapid diversification of animal body plans ~535 million years ago.

• Symmetry: Asymmetrical, radial, or bilateral.

• Tissues: Ectoderm (outer), endoderm (inner), mesoderm (middle; only in triploblasts).

• Diploblastic vs. Triploblastic: Two vs. three germ layers.

• Coelom: Body cavity lined by mesoderm.

• Hemocoel: Body cavity containing hemolymph (in some invertebrates).

• Protostome vs. Deuterostome: Differences in cleavage, coelom formation, and fate of blastopore.

• Archenteron: Primitive gut formed during gastrulation.

• Blastopore: Opening of the archenteron; becomes mouth in protostomes, anus in deuterostomes.

• Eumetazoa: Animals with true tissues.

• Bilaterians: Animals with bilateral symmetry and three germ layers.

• Major Clades: Deuterostomia, Ecdysozoa, Lophotrochozoa.

Chapter 33: Invertebrates

Invertebrate Diversity

• Invertebrates: Animals without a backbone; comprise most animal species.

Major Invertebrate Phyla

• Phylum Porifera (Sponges): Sessile, filter feeders, lack true tissues; have choanocytes.

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

• Lophotrochozoa:

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

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

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

• Ecdysozoa:

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

  • Phylum Arthropoda: Most diverse; exoskeleton (chitin), jointed appendages, includes chelicerates (spiders, scorpions), myriapods (centipedes, millipedes), pancrustaceans (insects, crustaceans).

• Deuterostomia:

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

Chapter 34: Vertebrates

Vertebrate Diversity and Evolution

• Phylum Chordata: Bilateral, deuterostome animals with notochord, dorsal hollow nerve cord, pharyngeal slits/clefts, post-anal tail.

• Cephalochordata: Lancelets.

• Urochordata: Tunicates (sea squirts).

• Vertebrata: Chordates with a backbone.

• Jawless Vertebrates: Hagfish and lampreys.

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

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

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

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

• Tetrapods: Evolved from lobe-finned fishes; four limbs, includes amphibians, reptiles, mammals.

• Amphibians: Salamanders, frogs, caecilians; tied to water for reproduction.

• Amniotes: Reptiles, birds, mammals; have amniotic egg for terrestrial reproduction.

• Reptiles: Turtles, lepidosaurs (lizards, snakes), archosaurs (crocodilians, birds); ectotherms (most), endotherms (birds).

• Mammals: Hair, mammary glands, specialized teeth; monotremes (egg-laying), marsupials (pouch), eutherians (placental).

• Primates: Opposable thumbs, depth perception; includes lemurs, tarsiers, monkeys, apes (gibbons, orangutans, gorillas, chimpanzees, humans).

• Homo sapiens: Derived characters include bipedalism, large brain, language; misconceptions about human evolution addressed.