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Classifying Organisms: The Three-Domain System

The five-kingdom system of classifying organisms has given way to a three-domain system that better reflects current evolutionary research. Domain Bacteria and Domain Archaea are offshoots of what was once Kingdom Monera. Domain Eukarya contains all four other kingdoms but subdivides what was once Kingdom Protista into five separate kingdoms: Archaezoa, Euglenozoa, Alveolata, Stramenopila, and Rhodophyta.


Domain Archaea

Consists of those prokaryotes that inhabit the harshest environments. Believed to be the ancestors of Kingdom Eukarya.

  1. Methanogens: Strict anaerobes (oxygen is fatal to them) that live in swamps and convert CO2 to methane (CH4).

  2. Extreme halophiles: Live in lakes saltier than the ocean.

  3. Extreme thermophiles: Live in hot deep-sea vents and sulfur springs.


Domain Bacteria

Consists of all other prokaryotes.


Domain Eukarya

Arose from prokaryotes through two evolutionary steps:

  1. An internal membranous system (including a nuclear envelope) derived from infoldings of the plasma membrane.

  2. Symbiosis with prokaryotes that later became mitochondria and chloroplasts.

Kingdom Archaezoa

Perhaps the oldest Eukarya; lack mitochondria, are flagellated, have dual nuclei and a simple cytoskeleton. Example: Giardia, a protist found in water.

Kingdom Euglenozoa

Flagellated unicellular protists with mitochondria. Examples: 1. Euglena (which has a flagella coming from an anterior folding); 2. kinetoplastids (which have a kinetoplast, a unique organelle that houses genetic material outside the nucleus).

Kingdom Alveolata

Characterized by alveoli (vesicles below the plasma membrane). Examples: 1. dinoflagellates (photosynthetic phytoplankton that cause algal blooms known as red tides); 2. Apicomplexa (animal parasites such as Plasmodium, which causes malaria); 3. ciliates (unicellular ciliated cells capable of binary fission or conjugation, such as Paramecium).

Kingdom Stramenopila

Characterized by flagella that have hairlike protrusions. Autotrophic stramenopila have chloroplasts that more closely resemble the original prokaryotic symbionts. Examples: 1. diatoms (unicellular protists with silicated exoskeletons); 2. brown and golden algae.

Kingdom Rhodophyta

Protists that evolved to lose their flagella. Example: red algae.

Kingdom Fungi

Decomposing organisms characterized by absorptive nutrition. Includes yeasts, which are unicellular, but also multicellular fungi that have the following features: 1. tubular units called hyphae with cell walls made of chitin, a plasma membrane, and eukaryotic organelles; 2. divisions between hyphae called septa, which separate hyphae into cells but also allow the passage of organelles from cell to cell; 3. multiple hyphae organized into a network called a mycelium.

  • Zygomycota: Terrestrial decomposers that have spores resistant to harsh environmental changes. Examples: 1. bread mold; 2. mycorrhizae (symbiosis between a fungus and the roots of plants, in which the fungus absorbs minerals that it passes to the roots in exchange for sugars from the plant).

  • Ascomycota: Terrestrial and aquatic decomposers that form spores in asci (which look like sacs) and have large fruiting bodies called ascocarps that release the asci. Examples: 1. truffles; 2. fruit molds; 3. lichens (symbiosis between a fungus and an algae); 4. some yeasts and also some mycorrhizae.

  • Basidiomycota: Club-shaped, sexually-reproducing decomposers that have large fruiting bodies called basidiocarps. Examples: 1. mushrooms; 2. some yeasts.

Kingdom Plantae

Muticellular eukaryotes characterized (with some exceptions) by photosynthetic nutrition. For classification, see Plants, next page.

Kingdom Animalia

Multicellular eukaryotes characterized by ingestive nutrition; generally reproduce sexually. All animals are believed to have originated from a single progenitor.

Major criteria for animal classification

  1. Parazoa vs. eumetazoa

    1. Parazoa lack true tissues; each cell is basically modular.

    2. Eumetazoa have true tissues (i.e., specialization of cells by function).

  2. Radiata vs. bilateria

    1. Radiata have radial symmetry, i.e., have a top and a bottom, but bodies are shaped like circles without a front or a back end. Have only two germ layers (embryonic cell layers that go on to constitute adult tissues): an ectoderm and an endoderm.

    2. Bilateria have bilateral symmetry, i.e., have dorsal (top), ventral (bottom), anterior (front), and posterior (back) sides. Are characterized by cephalization (sensory organs face the anterior end). Have three germ layers (including a mesoderm between the ectoderm and endoderm).

  3. Acoelomates vs. pseudocoelomates vs. coelomates

    1. Acoelomates have no body cavity separating the digestive tract from the rest of the body.

    2. Pseudocoelomates have a simple body cavity, but it is not completely lined by mesodermal tissue.

    3. Coelomates have a body cavity completely lined with mesodermal tissue that suspends the digestive tract and internal organs in fluid.

  4. Protostomes vs. deuterostomes

    1. Protostomes have embryonic cells that divide in pattern known as spiral cleavage. Cells are determinate (i.e., each dividing cell has a specific fate in forming the adult body). During embryonic cleavage, the mouth is formed from the blastospore (embryonic cellular infolding).

    2. Deuterostome embryonic cells divide in pattern of radial cleavage. Cells are indeterminate (i.e., each cell, if separated, could form its own embryo). During embryonic cleavage, the anus is formed from the blastopore.

Animal phyla

  • Phylum Porifera (sponges): Sessile (attached by a base) suspension feeders with no true tissues or organs. Spongocoel (central cavity) draws in water through osculum (large hole); food is siphoned out. Amoebocytes digest food, carry nutrients to other cells.

  • Phylum Cnidaria (sea anemones, jellyfish): Have a saclike body plan with a single opening as both mouth and anus. Polyps are sessile with mouths facing up; medusas are free-floating with mouths facing down. Both have cnidae, organelles that shoot off nematocysts (stinging barbs).

  • Phylum Ctenophora (comb jellies): Similar in appearance to cnidarians; named for comblike plates of cilia used for motion. Tentacles have colloblasts (sticky threads for capturing food).

  • Phylum Platyhelminthes (flatworms): Can be terrestrial or marine; some are parasitic. Have true muscle tissue but, like radiata, have only one digestive tract opening that serves as both mouth and anus. Examples: planaria, tapeworms.

  • Phylum Rotifera (rotifers): Tiny multicellular organisms with a digestive tract that has two openings (mouth and anus). Have a wheel-like crown of cilia at the mouth, used to suck in water.

  • Phylum Nematoda (roundworms): Worms without segments. Covered with a protective cuticle. Reproduce sexually, with internal fertilization of eggs. No circulatory system, so nutrients transported through fluid of the pseudocoelom.

  • Phylum Nemertea (proboscis or ribbon worms): Acoelomate but have a full digestive tract and closed circulatory system. Capture prey using a fluid-filled sac that operates a proboscis.

  • Phyla Bryozoa, Phoronida, Brachiopoda (lophophorates): Sessile aquatic suspension feeders with lophophores, fold of ciliated tentacles that draw water into the mouth. No true head. Bryozoans look like mosses; their hard exoskeletons create reefs. Phoronids are aquatic worms that build hard chitinous tubes. Brachiopods are sessile marine creatures that look like clams and live like Bryozoa.

  • Phylum Mollusca (mollusks): Have a three-part body: a muscular foot (for moving), a visceral mass (containing the organs), and a mantle (tissue covering the visceral mass that may produce a shell). Many feed using a radula, a scraping organ that drags for nutrients. Examples: 1. snails (gastropoda); 2. clams, mussels (bivalvia); 3. squids, octopus (cephalopoda).

  • Phylum Annelida (segmented worms): True coelomates; have a digestive tract with specialized regions, nerves, and a closed circulatory system. Each segment has metanephridia, excretory tubes that remove wastes. Examples: 1. earthworms (oligochaeta); 2. leeches (hirudinea).

  • Phylum Arthropoda (arthropods): Have a chitinous exoskeleton, specialized appendages with joints, and segmented bodies, and grow by molting their exoskeletons to form increasingly larger ones. Have an open circulatory system with a heart, and sensory organs for touch, smell, and sight.

    • Subphylum Chelicerata (scorpions and spiders): Feed with clawlike chelicerae. Most have simple rather than compound eyes. Spiders (arachnids) have book lungs, stacks of organs that carry out gas exchange.

    • Subphylum Uniramia (centipedes, millipedes, insects): Have compound rather than simple eyes. Have antennae and feed with jawlike mandibles. Insects (Insecta) have a three-part body with a head, thorax, and abdomen. Remove waste with Malpighian tubules and breathe using a tracheal system that lets oxygen directly into cells. Many insects can fly and also undergo metamorphosis, a changing of the body from a larval to an adult stage.

    • Subphylum Crustacea (crabs, shrimp, lobsters, barnacles): Have jawlike mandibles (as opposed to chelicerae) and two pairs of antennae. Have many pairs of appendages on the abdomen (unlike insects, which have appendages on the thorax), and can regenerate appendages.

  • Phylum Echinodermata (echinoderms): Marine organisms radially symmetrical in adult form but bilaterally symmetrical in larval form. Endoskeletons derive from the mesoderm. Water vascular system powers tube feet used in movement and feeding. Examples: 1. sea stars (Asteroidea); 2. sea urchins, sand dollars (Echinoidea); 3. sea cucumbers (Holothuroidea).

  • Phylum Chordata (chordates): Have an embryonic notochord for skeletal support and a hollow dorsal nerve cord (all other animals have solid ventral nerve cords) that develops into a brain and spinal chord. Pharyngeal slits filter out water without its continuing through the entire digestive tract: in aquatic vertebrates, these have evolved toward gas exchange; in higher animals, used for jaw support and auditory sensation. Have a postanal tail originally used for aquatic propulsion (other animals’ digestive tracts extend throughout the body).

Vertebrate classes

  • Superclass Agnatha: Jawless vertebrates lacking paired appendages. Skeleton made of cartilage; notochord exists throughout life. Examples: hagfishes, lampreys.

  • Superclass Gnathostomata: All other vertebrates. Have hinged jaws and vertebrae that replace the notochord. Are divided between the fish and the tetrapods (“four feet”).

    • Class Chondrichthyes (cartilaginous fishes): Have cartilage skeletons, jaws. Breathe using gills derived from the pharyngeal slits. Fertilization is internal. Lateral line system is a sensory system that detects changes in pressure or vibrations in the water. Examples: sharks, rays.

    • Class Osteichthyes (bony fishes): Have bone skeletons. Breathe through gills that are covered with a protective layer called the operculum. Fertilization is internal. Stay afloat via air-filled swim bladders. Examples: tuna, salmon.

    • Class Amphibia (amphibians): Oldest tetrapods; most live close to water, Have damp skin used in gas exchange and shell-less eggs that must be laid in water. Frogs undergo metamorphosis between an aquatic larval stage and a terrestrial adult stage. The adult stage marks the loss of gills and of the lateral line system. Examples: 1. frogs, toads (Anura); 2. salamanders (Urodela); 3. caecilians (Apoda).

    • Class Reptilia (reptiles): Eggs are amniotic, with a protective water-filled sac (amnion) in which the embryo grows alongside a repository of nutrients (yolk). Eggs have leathery shells and are laid on land. Have protective keratinized scales for skin, breathe using lungs, and are ectothermic (control temperature via behavioral or environmental rather than metabolic regulations). Examples: 1. turtles, tortoises (Chelonia); 2. lizards, snakes (Squamata); 3. crocodiles, alligators (Crocodilia).

    • Class Aves (birds): Evolved from reptiles. Have wings, specialized bones; beaks, feathers made of keratin; no teeth; instead grind food in a gizzard. Lay amniotic eggs with hard shells. Four-chambered heart. Endothermic (regulate temperature metabolically). Examples: pigeons, eagles.

    • Class Mammalia (mammals): Also evolved from reptiles. Endothermic; have hair made of keratin and make milk from mammary glands. Have large brains, specialized teeth, and an inner ear derived from the pharyngeal slits.

      • Subclass Monotremata (monotremes): Hatch from eggs. Examples: platypuses, echidnas.

      • Subclass Marsupialia (marsupials): Fertilization is internal; embryo develops inside the uterus. The embryo continues to develop after birth, as the fledgling organism nurses inside the mother’s external protective pouch. Examples: koalas, kangaroos.

      • Subclass Placentalia (placental mammals): Fertilization is internal; embryo develops inside the uterus. A protective and nurturing complex called the placenta forms around the embryo, which develops fully inside the uterus before birth. Examples: mice, dogs, cats, horses, whales, humans.