Classification, Phylogeny, Systematics, & Cladistics

Overview of Classification, Phylogeny, and Systematics

• Goal of Classification: To identify and name organisms and organize the biosphere into groups to understand evolutionary links and predict shared characteristics.
• Foundational Review:     * Binomial System of Nomenclature: A two-name system for naming organisms developed by the Swedish botanist and physician Carolus (Carl) Linnaeus (1707-1778). Organisms are classified based on physical and social traits.     * Rules for Binomial Names:         * Example: Homo sapiens.         * The first name is the Genus and is always capitalized.         * The second name refers to the species and begins with a lowercase letter.         * Both words must be written in italics (or underlined if handwritten).     * Species Definition: The natural basic grouping of organisms which can interbreed and produce fertile offspring.     * Genus Definition: A group of similar species; every species is classified into a genus.     * Example Name: Armadillidium vulgare.

The Hierarchy of Taxa

• The Seven (plus) Levels of Classification:     1. Domain (Added above the original levels)     2. Kingdom     3. Phylum     4. Class     5. Order     6. Family     7. Genus     8. Species
• Classification Mnemonics:     * "King Phillip Came Over For Good Supper"     * "King Phillip Came Over For Good Soup"     * "Kissing Pretty Cute Otter Feels Gross Sometimes"
• Example: Animalia vs. Plantae Classification:     * Blue Whale: Kingdom Animalia, Phylum Chordata, Class Mammalia, Order Cetacea, Family Balaenopteridae, Genus Balaenoptera, Species musculus.     * Coast Redwood: Kingdom Plantae, Phylum Coniferophyta, Class Pinopsida, Order Pinales, Family Taxodiaceae, Genus Sequoia, Species sempervirens.

The Five Kingdom System and Domain System

• The Five Kingdoms:     1. Kingdom Plantae: Examples include cactus and moss.     2. Kingdom Animalia: Examples include spiders and humans.     3. Kingdom Fungi: Examples include slime molds and molds.     4. Kingdom Protoctista: Examples include protozoa, algae, and seaweed.     5. Kingdom Prokaryotae (aka Kingdom Monera): Examples include bacteria, paramecium, and amoebas.
• Alternative Systems and Modern Taxonomy:     * Three-Domain System: Bacteria, Archaea, and Eukarya.     * Complexity: Domain Bacteria is divided into 5 kingdoms; Domain Archaea into 4 kingdoms; Eukarya includes Kingdom Plantae, Animalia, Fungi, and Protista (which is sometimes divided into 8 kingdoms).     * Reclassification Examples: The Giant Panda and bears; the Red Panda and raccoons.

Characteristics of Plant Phyla

• Bryophyta (e.g., Mosses, Liverworts, Hornworts):     * General: Short stature (max height of $0.5\,m$).     * Vegetative: Non-vascular (lacks xylem and phloem); no roots, only rhizoids (resemble root hairs); no true leaves or stems.     * Reproductive: No flowers or seeds; produce spores in capsules at the end of stalks; transported by rainwater and ground humidity.
• Filicinophyta (e.g., Ferns, Horsetails):     * General: Max height of $15\,m$.     * Vegetative: Vascular; true roots, leaves, and non-woody stems; leaves are usually curled in a bud and often pinnate (divided into pairs).     * Reproductive: Spores produced in sporangia, usually on the underside of leaves.
• Coniferophyta (e.g., Cedar, Juniper, Fir, Pine):     * General: Max height of $100\,m$.     * Vegetative: Shrubs or trees with roots, leaves, and woody stems; leaves are narrow and thick with a waxy cuticle; vascular tissue present.     * Reproductive: Male cones produce pollen; female cones produce ovules on scales. Pollinated by wind. Seeds develop from fertilized eggs within ovules.
• Angiospermophyta (Flowering Plants):     * General: Max height of $100\,m$.     * Vegetative: Roots, leaves, and stems with vascular tissue.     * Reproductive: Male stamens produce pollen; female pistils produce ovaries containing eggs. Pollinated by wind, animals, or insects. Seeds develop in ovules; fruits develop from ovaries to disperse seeds.

Characteristics of Major Animal Phyla

• The 9 Major Animal Phyla and Identification Keys:     * Porifera (Sponges): Simple marine animals; no clear symmetry; sessile (attached to surfaces); body wall pierced by pores; filter feed by pumping water; no mouth, anus, muscle, nerves, or internal organs.     * Cnidaria (Corals, Jellyfish, Anemones): Radial symmetry; tentacles with stinging cells; gastric pouch with one opening (mouth, no anus).     * Platyhelminthes (Flat worms, Planaria, Tapeworms): Bilateral symmetry; unsegmented, flat body; gut with one opening (mouth, no anus); no heart or lungs; flat shape allows gas exchange via diffusion through the surface.     * Annelida (Segmented worms like Earthworms): Bilateral symmetry; segmented body; bristles often present; mouth and anus with intestines.     * Mollusca (Slugs, Snails, Clams, Squids): Muscular foot and mantle; shell usually present; segmentation not visible; mouth and anus.     * Arthropoda (Insects, Spiders, Crabs, Millipedes): Bilateral symmetry; exoskeleton made of chitin; segmentation; jointed appendages.     * Echinodermata: Body hard, spiny, or leathery; shaped like a "warty hot dog."     * Nematoda: Body long, slender, smooth, and worm-like.     * Chordata: Gills present and conspicuous, or appendages in 2 pairs; includes snakes, fish, and mammals.

Dichotomous Keys

• Definition: A tool used to identify species by characterizing organisms through a series of choices between two statements.
• Usage Procedure:     1. Read the first pair of sentences describing a characteristic.     2. Check the organism for the characteristic.     3. If yes, follow the number at the end of the line to the next set of statements.     4. If no, move to the second statement in the current pair and follow that number.     5. Repeat until a name is reached instead of a number.
• Construction: Start by grouping items, identifying why they belong in those groups, and inventing statements that split groups into two parts iteratively.

Phylogeny and Systematics

• Phylogeny: The study of how living and extinct organisms are related to one another; "taxonomy from an evolutionary past."
• Phylogenetic Systematics: Placing organisms into higher taxa whose members are more closely related to each other than to any other group.
• Evidence for Relationships: Homologous structures and molecular differences (amino acid sequences, cytochrome c, Hemoglobin vs. Chlorophyll).
• Evolutionary Clock: Concept that changes in polypeptide sequences accumulate steadily and gradually over time as mutations occur. This estimates how far back in time two species split from a common ancestor. Tools include Mitochondrial DNA, DNA hybridization, and radioactive fossil dating.

Cladistics and Cladograms

• Cladistics: A system of classification grouping taxa according to recently evolved characteristics (common descent).
• Trait Types:     * Primitive Traits (Plesiomorphic): Structures/functions that evolved early on (e.g., leaves with vascular tissue).     * Derived Traits (Amorphic): Structures/functions that evolved more recently as modifications (e.g., flowers with vascular tissue).
• Key Terminology:     * Cladogram: An illustration showing evolutionary relationships.     * Clade: An evolutionary branch including a single (monophyletic) common ancestor and all its descendants.     * Lineage: A series of ancestor and descendant populations shown as a line on a time axis.     * Node: A point where a lineage divides into two; represents a common ancestor.     * Root: The base of the cladogram representing the common ancestor of all represented taxa.     * Sister Clades: Groups that share an immediate common ancestor.     * Outgroup: A group that defines the ancestral characters and is less related than the rest.
• Types of Clades:     1. Monophyletic: Contains an ancestor and ALL descendants.     2. Paraphyletic: Includes an ancestor but not all descendants; does not meet cladistic criteria.     3. Polyphyletic: Grouping of various species that lack a recent common ancestor; does not meet cladistic criteria.
• Cladogram Construction Steps:     1. Compile a table of characters (e.g., vertebrae, lungs, mammary glands).     2. Construct a Venn diagram (biggest circle for the most shared characteristic).     3. Convert the Venn diagram into a branching cladogram.
• Branching Rules: The shape and order of terminal nodes (e.g., switching human and chimp positions at a final node) do not change the meaning of the relationship. Branches can be scaled (length indicates amount of evolutionary change) or unscaled.