BIO 102 Exam 1 Study Guide: Phylogeny, Prokaryotes, Protists, Plant Diversity, and Fungi

Phylogeny and the Tree of Life

Key Concepts in Phylogeny

Phylogeny is the study of the evolutionary relationships among organisms. It is fundamental to understanding biological diversity and classification.

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

• 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; branches indicate lineage splits.

• 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 organisms that includes an ancestor and all its descendants.

• Monophyletic, Paraphyletic, Polyphyletic Groups: Monophyletic includes ancestor and all descendants; paraphyletic excludes some descendants; polyphyletic includes unrelated organisms.

• Ancestral vs. Derived Characteristics: Ancestral traits are inherited from distant ancestors; derived traits are recent adaptations.

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

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

• Three Domains: Bacteria, Archaea, Eukarya.

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

Bacteria and Archaea

Prokaryotic Diversity and Structure

Bacteria and Archaea are prokaryotes, organisms without a membrane-bound nucleus. They exhibit diverse metabolic and structural adaptations.

• Prokaryotes: Single-celled organisms lacking a nucleus.

• Cell Wall: Provides shape and protection; composition differs between bacteria (peptidoglycan) and archaea.

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

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

• Gram-Positive vs. Gram-Negative: Gram-positive have thick peptidoglycan; gram-negative have thin peptidoglycan and an outer membrane. Gram stain differentiates them.

• 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: Prokaryotes lack organelles; DNA is in the nucleoid region.

• Binary Fission: Asexual reproduction by cell division.

• Transformation, Transduction, Conjugation: Mechanisms of genetic exchange.

• Phototrophs vs. Chemotrophs: Phototrophs use light; chemotrophs use chemicals for energy.

• Autotrophs vs. Heterotrophs: Autotrophs use CO2 as carbon source; heterotrophs use organic compounds.

• Aerobes vs. Anaerobes: Aerobes require oxygen; anaerobes do not.

• Biofilms: Communities of prokaryotes attached to surfaces.

• Bacteria vs. Archaea: Differ in cell wall composition, membrane lipids, and genetics.

• Cyanobacteria: Photosynthetic bacteria; important for oxygen production.

• Extremophiles: Organisms thriving in extreme environments (halophiles, thermophiles).

• Decomposers: Break down dead organic matter.

• Symbiosis: Close association between organisms.

• Exotoxins vs. Endotoxins: Exotoxins are secreted; endotoxins are part of cell wall.

• Bioremediation: Use of organisms to clean up pollutants.

Nutritional Modes of Prokaryotes

Energy Source	Carbon Source	Example
Photoautotroph	Light	CO2	Cyanobacteria
Chemoautotroph	Inorganic chemicals	CO2	Some Archaea
Photoheterotroph	Light	Organic compounds	Some bacteria
Chemoheterotroph	Organic chemicals	Organic compounds	Most bacteria

Protists

Protist Diversity and Classification

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

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

• Phototrophs, Heterotrophs, Mixotrophs: Phototrophs use light; heterotrophs consume organic matter; mixotrophs combine both.

• Endosymbiosis: Theory explaining origin of mitochondria and chloroplasts.

• Pseudopodia: Extensions of cytoplasm for movement.

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

Protist Supergroups and Key Taxa

• Excavata: Includes Diplomonads and Euglenazoans (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) and Opisthokonts (Animals, Fungi, Choanoflagellates).

Plant Diversity I: How Plants Colonized Land

Key Concepts in Early Plant Evolution

Plants evolved from green algae (charophytes) and share several derived traits that enabled them to colonize land.

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

• Bryophytes: Non-vascular plants; dominant gametophyte stage; sporophytes attached.

• Seedless Vascular Plants: Dominant sporophyte stage; independent gametophytes.

• Rhizoids: Root-like structures in bryophytes.

• Flagellated Sperm: Require water for fertilization.

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

• Roots and Leaves: Evolution of roots and leaves increased plant size and complexity.

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

• Spores vs. Seeds: Spores are single cells; seeds are multicellular and contain an embryo.

Bryophyte Groups

• Liverworts

• Mosses

• Hornworts

Seedless Vascular Plant Groups

• Lycophyta: Club mosses, spike mosses, quillworts.

• Monilophyta: Ferns, horsetails, whisk ferns.

Plant Diversity II: The Evolution of Seed Plants

Key Concepts in Seed Plant Evolution

Seed plants evolved reproductive adaptations including seeds, pollen, and flowers, leading to the dominance of gymnosperms and angiosperms.

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

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

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

• Pollen and Pollen Tubes: Pollen delivers sperm to ovule; pollen tube facilitates fertilization.

• Advantages of Seed Reproduction: Protection, dispersal, dormancy.

• Gymnosperms: Seed plants with "naked" seeds (not enclosed in fruit).

• Angiosperms: Seed plants with seeds enclosed in fruit; produce flowers.

• Flowers and Fruit: Flowers facilitate pollination; fruit aids seed dispersal.

• Modified Flower Leaves: Sepals, petals, stamens, carpels.

• Female and Male Flower Parts: Carpels (female), stamens (male).

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

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

• Endosperm: Nutrient-rich tissue for embryo.

• Monocots vs. Dicots: Monocots have parallel veins, one cotyledon; dicots have netted veins, two cotyledons.

Gymnosperm Groups

• Cycadophyta

• Ginkophyta

• Gnetophyta: Welswitchia, Ephreda

• Coniferophyta

Angiosperm Groups

• Monocots

• Dicots

Fungi

Fungal Biology and Ecology

Fungi are heterotrophic eukaryotes that absorb nutrients from their environment. They play essential roles as decomposers, mutualists, and pathogens.

• Taxonomy: Use lecture taxonomy; not all phyla are equally emphasized.

• Nutrient Acquisition: Fungi absorb nutrients via external digestion.

• Roles in Ecosystems: Decomposers, mutualists (mycorrhizae, lichens), parasites.

• Filaments and Hyphae: Hyphae are thread-like structures; collectively form mycelium.

• Chitin: Structural polysaccharide in fungal cell walls.

• Mycelium: Network of hyphae; increases surface area for absorption.

• Mycorrhizae: Symbiotic association with plant roots.

• Spores: Reproductive cells; can be sexual or asexual.

• Yeast and Bud Cells: Unicellular fungi; reproduce by budding.

• Opisthokonts: Clade including fungi, animals, and related protists.

• Decomposers: Break down organic matter.

• Mutualism: Lichens (fungi + algae/cyanobacteria), mycorrhizae.

• Parasites: Cause disease in plants and animals.

• Mycosis: Fungal infection.

Fungal Phyla

• Chytridiomycota (Chytrids): Affect amphibians.

• Zygomycota: Parasites of insects.

• Ascomycota (Sac Fungi): Includes yeasts, molds, truffles.

• Basidiomycota (Club Fungi): Includes mushrooms, shelf fungi.

• Glomeromycota: Not emphasized for this exam.

Example: Yeasts are unicellular ascomycetes used in baking and brewing; Chytrids are implicated in amphibian declines.

Additional info: Fungi reproduce via spores, which can be dispersed by air, water, or animals. Lichens are important bioindicators of air quality.