II. Taxonomy

Key focus of this chapter: domains and kingdoms

This chapter reviews the three domains and the historical five-kingdom classification, with concise comparisons of major groups.

A. Chronological order of pre-biotic chemicals

* This diagram summarizes a proposed prebiotic sequence. Classic reducing-atmosphere experiments used CH₄, NH₃, H₂, and H₂O; some also included H₂S. These mixtures do not establish the actual composition of early Earth’s atmosphere.

B. Hierarchy

Domain – Eukarya, Bacteria, Archaea

Kingdom (historical five-kingdom scheme) – Monera, Protista, Fungi, Plantae, Animalia

Phylum – Chordata

Class – Mammalia

Order – Carnivora, Primates

Family – Hominidae

Genus – Homo

Species – Homo sapiens

** Human classification is indicated in bold

C. Three domains and five kingdoms

The five-kingdom scheme is historical: Monera grouped Bacteria and Archaea. Modern classification separates those domains; “Protista” is a traditional grouping, not a single evolutionary clade.

3 Domains	5 Kingdoms	Characteristics
Bacteria	Monera (historical)	• Unicellular microorganism • Reproduction by asexual binary fission • Some move using flagella; taxis is directed movement in response to a stimulus • DNA occurs in a chromosome; many also have plasmids • Some exchange DNA by conjugation or other horizontal transfer mechanisms • Eg/ cyanobacteria (blue-green algae)
Archaea	Monera (historical)
Eukarya	Protista	• Sexual or asexual reproduction • Photoautotrophs, heterotrophs, or mixotrophs • Endosymbiosis • Eg/ protozoa, slime molds, multicellular algae	Most unicellular
	Fungi	• Sexual or asexual reproduction • Heterotrophs and parasites • Mutualists and decomposers (Saprobes) • Eg/ Mold, yeast, mushroom	Most multicellular
	Plantae	• Photosynthetic organisms • Cell wall with cellulose • Alternation of generations	Most multicellular
	Animalia	• Heterotrophs • Most are motile during some stage of life	Multicellular

1. Domain Bacteria

Diverse, widespread microorganisms.
Common shapes are spiral, rod-shaped, and spherical.
Energy metabolism varies: bacteria may use respiration, fermentation, photosynthesis, or inorganic chemicals.
Eg/ Proteobacteria, Gram-positive and gram-negative bacteria, Blue-green algae (cyanobacteria), Spirochete, Chlamydias

2. Domain Archaea

Found in many ordinary environments; some are adapted to extreme conditions.
Eg/ Crenarchaeotes, euryarchaeotes, korarchaeotes, nanoarchaeotes, sulfolobus

D. Diversity of metabolic adaptations

Classification	Energy source	Carbon source	Organisms
Photoautotroph	Light		Cyanobacteria, Plant, algae
Photoheterotroph	Light	Organic compound	Chloroflexus, Rhodobacter
Chemoautotroph	Inorganic chemicals		Sulfolobus
Chemoheterotroph	Organic chemicals	Organic compound	Many prokaryotes and protists, fungi, animals

E. Kingdom Protista

Main Clade	Classification	Characteristics & Examples
Diplomonadida • Two nuclei • Lack plastids • Multiple flagella • Reduced mitochondria		• Eg/ Giardia
Parabasalids • Mutualists and parasites • Lack plastids • Reduced mitochondria		• Trichomonads – flagella and an undulating membrane • Some parabasalids live in termite guts • Eg/ Trichomonas
Euglenozoa • Predatory heterotrophs and photosynthetic autotrophs	Euglenids	• Most live in aquatic habitats • Flagellar pocket and eyespot • Some are photosynthetic; many are motile and lack a cell wall • Eg/ Euglena
	Kinetoplastids	• Kinetoplast – a concentrated region of mitochondrial DNA • Eg/ Trypanosoma
Alveolates • Alveoli membrane bound sacs	Apicomplexans	• Apical complex organelles • Sporozoites in plasmodium • Intricate life cycle • Eg/ Plasmodium (causing malaria)
	Ciliates	• Many cilia for movement and feeding • Micronuclei and macronuclei • Eg/ paramecium, stentor
	Dinoflagellates	• Many are planktonic; some cause harmful algal blooms • Symbiosis with coral or clam • Eg/ Ceratium, pfiesteria
Stramenopiles • Hairy flagella • Photosynthetic or heterotrophic	Oomycetes	• Cell walls made of cellulose • Having hyphae to absorb nutrients • Resembling fungi • Irish potato blight • Eg/ Water mold, downy mildews
	Diatoms	• Two shells made of silica • Eg/ Marine phytoplankton
	Golden algae	• Eg/ Dinobryon
	Brown algae	• Multicellular • Eg/ Seaweed, laminaria, macrocystis
Amoebozoans • Moving by pseudopodia	Gymnamoebas	• Live in soil, fresh water, or marine habitats • Eg/ Amoeba
	Entamoebas	• Parasites • Eg/ Entamoeba
	Myxogastrida	• Plasmodial slime molds • Multinucleate plasmodium • Acellular slime molds • Eg/ Physarum
	Dictyostelida	• Cellular slime molds • Fruiting bodies with asexual reproduction • Living independently as haploids • Dictyostelium
Rhodophyta	Red algae	• Mostly multicellular • Photosynthetic accessory pigment (phycoerythrin) • Alternation of generations with diverse life cycles • No flagellated stages • Eg/ Bonnemaisonia, palmaria
Chlorophyta	Green algae	• Green algae with chlorophyll a and b; land plants are most closely related to charophyte algae • Lichens (algae + fungi) • Eg/ Chlamydomonas, Ulva, Volvox, Caulerpa

F. Kingdom Fungi

: heterotrophic organisms that break down molecules and absorb nutrients

Important roles in ecosystems and human welfare

– decomposers that recycle chemical elements

– symbionts (mycorrhizae, lichens)

– yeasts used in food production; edible fungi and antibiotic producers

Cell walls with chitin
Lack chloroplasts
Both asexual and sexual reproduction
Some fungi are human pathogens

1. Structure

Cell wall made of chitin
Mycelium: Interwoven mass of hyphae
Hyphae: Tubular filaments that collectively form a mycelium

– Septate hyphae: Divided by cross walls called septa

– Coenocytic hyphae: Continuous, multinucleate cytoplasm without septa

Mycorrhizae: Symbiotic mutual relationship with plants

– plants supply fungi with organic nutrients

– fungi improve the plant’s uptake of water and minerals

2. Classification

Phylum	Characteristics
Basidiomycota	• Club fungi • Fruiting bodies called basidiocarps in sexual reproduction • Eg/ Mushrooms, rusts, toadstools
Ascomycota	• Sac fungi • Production of sexual spores in sacs called asci • Fruiting bodies called ascocarps in production of sexual spores • Production of asexual spores called conidia • Many form lichens with photosynthetic partners • Eg/ Yeast, truffles, morels
Chytridiomycota	• Freshwater and terrestrial habitats • Saprobic or parasitic • Motile flagellated spores (zoospores) • Eg/ Chytridium
Glomeromycota	• Arbuscular mycorrhizal fungi • Symbiotic relationship with plants • Eg/ Arbuscular mycorrhizae
Former Zygomycota (historical)	• Resistant zygosporangium in sexual reproduction • Life cycle with black bread mold • Eg/ Rhizopus (black bread mold; now placed in Mucoromycota)

** Lichens are associations between a fungus and a photosynthetic alga or cyanobacterium; many colonize bare substrates.

G. Kingdom Plantae

1. Classification of plantae

Land plants	Classification		Characteristics & Examples
Bryophytes • Nonvascular plants • Gametophyte dominant	Liverworts		• Liver shaped gametophytes of Marchantia • Single-celled rhizoids
	Hornworts		• Gametophytes grow horizontally • Multicellular sporophyte
	Mosses		• Gametophytes grow vertically • Leaflike structures lacking vascular tissue
Vascular plants • Tracheophytes	Seedless Vascular Plants	Lycophytes	• An early-diverging vascular plant lineage • Eg/ Club mosses, spike mosses, quillworts
		Monilophytes	• Eg/ Ferns, horsetails
	Seed Plants	Gymnosperms	• Naked seeds • Eg/ Pines, ginkgo, cycads, conifers
		Angiosperms	• Monocots & dicots • Flowering plants • Produce fruit • Eg/ Maple, banana, lily, apple

2. Angiosperms

a. Monocot and dicot

“Dicot” is a traditional category; eudicots form its largest modern clade. The comparison below summarizes typical traits.

Monocot	Dicot
• One cotyledon • Flower parts usually in multiples of three • Parallel leaf veins • Scattered vascular bundles • Fibrous root system • Typical vascular cambium secondary growth is usually absent (Such as bark and wood)	• Two cotyledons • Flower parts usually in multiples of four or five • Reticulated leaf veins • Vascular bundles arranged in a ring • Taproot with lateral roots • Secondary growth usually present

b. Structures and functions of flower

Structures	Classification	Functions
Female part (Carpel)	Stigma	• Receives pollen during pollination
	Style	• Connects stigma to ovary and provides a path for pollen tubes
	Ovary	• Contains ovules; the ovary usually develops into fruit
Male part (Stamen)	Anther	• Produces pollen in pollen sacs
Male part (Stamen)	Filament	• Holding the anther
Other parts	Petal	• Often attracts pollinators
	Receptacle	• Flower’s attachment to the stalk which sometimes becomes part of the fruit after fertilization
	Sepal	• Small leaves under the flower -protecting flower during budding

c. Plant tissues

Plant tissues	Functions and features
Parenchyma cells	• Thin and flexible primary cell wall • Metabolic functions, photosynthesis, and storing organic molecules • Eg/ Mesophyll
Collenchyma cells	• Thicker and flexible primary cell walls • Supports young plant tissues • Living cells
Sclerenchyma cells	• Thicker and rigid secondary cell wall • Containing lignin • Supporting elements of plant • Usually dead at maturity

d. Anatomy of leaf

Structures	Functions
Guard cell	• Controlling the size of opening
Stoma	• A pore for exchanging gas
Cuticle	• Wax layer for protecting epidermal cells
Epidermis	• Produces wax for the cuticle • Secreting metabolic materials
Mesophyll	• Parenchyma and chlorenchyma tissues • Primary site for photosynthesis
Bundle sheath	• Surrounds vascular bundles containing xylem and phloem • Regulates exchange between vascular tissue and mesophyll

** Transpiration

– loss of water vapor, chiefly through stomata; temperature, wind, and light influence its rate

– this creates tension that helps pull water upward through xylem.

e. Anatomy of stem

Structures	Functions
Periderm	• Secondary protective tissue: cork, cork cambium, and phelloderm
Cork cambium	• Produces cork outward and phelloderm inward • Undifferentiated, actively dividing cells
Phloem	• Transporting nutrients and sugars through sieve tubes (both up and down direction) • Pressure-driven bulk flow from sources to sinks; loading and unloading help establish the gradient • Composed of living cells (companion cells and sieve tubes) • Sieve plate and plasmodesmata
Vascular cambium	• Produces secondary xylem inward and secondary phloem outward • Undifferentiated, actively dividing cells
Xylem	• Transports water and minerals mainly from roots to shoots • Composed of dead cells (vessel elements and tracheids) • Transpiration-driven tension and water cohesion • Pit pairs
Pith	• Parenchyma ground tissue • Located in the center of vascular tissues (ground tissues)

f. Modified stems

Modified stems	Features
Bulbs	• Short and vertical underground stem • Stores food in enlarged, fleshy leaves • Eg/ onions
Stolons	• Horizontal stem along the surface of the ground • Produces rooted plantlets at nodes • Eg/ strawberry and spider plant
Tubers	• Underground storage stem • Enlarged ends of rhizomes • Eg/ potatoes
Rhizomes	• Horizontal stem along or below the surface of ground • Eg/ ginger

g. Plant hormones

Hormones	Functions
Auxin	• Phototropism – shoot growing toward light • Gravitropism (geotropism) - roots grow downward in response to gravity (positive gravitropism) - shoots grow upward against gravity (negative gravitropism) • Hydrotropism – growing toward water
Cytokinins	• Stimulate cell division and growth
Gibberellins	• Stem elongation • Stimulate flowering
Abscisic acid	• Inhibits growth • Promotes seed dormancy and stomatal closure during water stress
Ethylene	• Promotes fruit ripening
Kinins (older term for cytokinins)	• Promote cell division

h. Life cycle of angiosperm

H. Kingdom Animalia

1. Pedigree and summary

Some vertebrate labels below are traditional teaching groups: “Agnatha” is a historical grade, bony vertebrates include tetrapods, and birds are nested within reptiles.

Phylum	Class	Animals and Distinctive features
Porifera - no true tissues or organs - respiration and excretion by diffusion		Sponge • Choanocytes – creating a water current through water channels to get food particles
Cnidaria - most radial symmetry - tentacles - gastrovascular cavity - two body types (polyps and medusa) - nerve net present		Hydra • Cnidocyte – containing nematocyst (stinging capsule) • Many polyps reproduce by asexual budding • Medusae in many cnidarians reproduce sexually; Hydra lacks a medusa stage
Platyhelminthes - body flattened dorsoventrally - incomplete digestive system; absent in tapeworms - pair of anterior ganglia with longitudinal nervous system	Turbellaria (traditional)	Planaria • Protonephridia- containing flame bulbs, excretory system
	Cestoda	Tapeworm • Scolex – hooks and sucker
Mollusca - mantle cavity	Gastropoda	Snail • Open circulation system • Gills in aquatic forms; a lunglike mantle cavity in many land snails • Embryonic torsion • Radula
	Bivalvia	Clams, mussels, oysters • Open circulation system • Two valves • Adductor muscles • Breathing with gills and mantle • Siphons
	Cephalopoda	Octopus & Squid • Cephalization - concentration of sensory organs and nervous tissue at the anterior end. • Closed circulatory system • Tentacles for grasping or movement
Annelida - complete digestive system (one way) - closed circulatory system - double ventral nerve cord		Earthworm • Metanephridia – filter coelomic fluid and excrete through external pores • Septa – dividing coelom cavities
Arthropoda - jointed appendages - exoskeleton of cuticle - well developed sensory structures - open circulatory system - metamorphosis	Insecta	Grasshopper • Malpighian tubules – excretion waste from hemolymph to gut • Breathing by tracheal tubes • Three body divisions (head, thorax, abdomen) • 3 pairs of legs; adults often have 2 pairs of wings
	Diplopoda	Millipedes (centipedes belong to Chilopoda) • Mandible – jaw like structure for eating food
	Arachnida	Spider • Simple eyes; spiders often have eight • 4 pairs legs • Respiration by book lungs and/or tracheae
Echinodermata - adults usually pentaradial; larvae bilateral - water vascular system - endoskeleton of dermal calcareous ossicles - nervous system with a circular ring and radial nerves		Sea star • Tube feet – water vascular system • Madreporite • Ampulla
Chordata	Agnatha	Jawless fishes (lampreys, hagfishes) • Naked skin • Heart with two main chambers; single circulation • No paired appendages
	Chondrichthyes	Cartilaginous fishes (sharks, skates, rays) • Jaws present • Ventral mouth and two olfactory sacs • Skin with scales or naked • No swim bladder; gas exchange through gills • Lateral line senses water movement
	Osteichthyes	Bony fishes • Most have an operculum • Many bony fishes have a swim bladder
	Amphibia	Frog, toads, salamanders • Typically a three-chambered heart with partial double circulation • Usually four limbs • Respiration varies with species and stage: lungs, skin, and/or gills • Metamorphosis
	Reptilia	Snakes, lizards, turtles, alligators, crocodiles • Skin covered with keratinized epidermal scales
	Aves	Birds • Four-chambered heart with double circulation • Epidermal covering of feathers and leg scales • Beak, no teeth
	Mammalia	• Brain highly developed • Most females have estrous cycles; some primates have menstrual cycles

2. Diagram of pedigree

I. Animal Reproduction

1. Asexual reproduction

Budding: new individual arises from parent body
Fission: the separation of a parent body into two parts
Fragmentation: A parent breaks into pieces that develop into new individuals.
Regeneration: Replacement of lost body parts; it does not always produce a new individual.
Parthenogenesis: Development of an individual from an unfertilized egg

2. Sexual reproduction

Reproduction of vertebrates	Descriptions
Oviparity	• Fertilized eggs are laid and hatched outside mother’s body. • Eg/ All birds
Ovoviviparity	• Eggs are retained within the mother and hatch there • Young obtain nourishment from egg yolk • Eg/ Some sharks and snakes
Viviparity	• Fertilized eggs develop within the mother’s body • Embryos receive nutrients from the mother, often through a placenta • Eg/ Almost all mammals

** Duck-billed platypus: an egg-laying (oviparous) mammal, a monotreme.

3. Sexual and asexual reproduction

Hermaphroditism: Each individual organism has both male and female reproductive systems

J. Life cycle of animals, plants, and fungi

Many fungi have haploid-dominant cycles, often with a dikaryotic stage; protist life cycles vary.
Plants: Alternation of multicellular haploid gametophyte and diploid sporophyte generations
Animal: Diploid life cycle dominates