The Evolution of Seed Plants
I. General Characteristics of the Seed Plants
    A. The seed plants are the most recent group to appear in the evolution of the tracheophytes and are composed of the gymnosperms (such as pines and cycads) and the angiosperms (flowering plants).
    B. In seed plants, the gametophyte generation is reduced, with the haploid gametophyte being attached to and nutritionally dependent on the diploid sporophyte.
    C. The seed plants are heterosporous.
    D. The megaspores are not shed.
    E. In most species, only one of the meiotic products in the megasporangium survives.
        1. This surviving haploid nucleus produces a multicellular female gametophyte that is retained within the megasporangium, where it matures and is eventually fertilized.
        2. A protective integument composed of sterile sporophyte structures surrounds the megasporangium.
        3. Male gametophytes are called pollen grains and are formed by the division of microspores produced meiotically within the microsporangia.
    F. When a pollen grain reaches the appropriate surface of a sporophyte, it begins to develop further.
    G. A slender pollen tube is produced that elongates and digests its way through the sporophytic tissue toward the female gametophyte.
    H. When the tip of the pollen tube reaches the female gametophyte, two sperm are released and fertilization occurs.
    I. The resulting diploid zygote divides repeatedly until an embryonic stage is reached, at which stage growth is temporarily halted.
    J. The end product at this stage is a seed.
    K. A seed may contain tissues from three generations.
    L. The seed coat and megasporangium develop from tissues of the diploid sporophyte parent.
    M. Within the megasporangium is the haploid female gametophytic tissue of the next generation.
    N. The center of the seed package contains the third generation, in the form of the embryo of the new diploid sporophyte.
    O.The multicellular seed of a gymnosperm or an angiosperm is a well-protected resting stage.
    P. The possession of seeds is a major reason for the enormous evolutionary success of seed plants.
II. The Gymnosperms: Naked Seeds
    A. The gymnosperms are a group of seed plants that do not produce flowers.
    B. Gymnosperm means “naked-seeded.” This name is derived from the fact that their ovules and seeds are not protected by flower or fruit tissue.
    C. There are four phyla of living gymnosperms today.
        1. The cycads (phylum Cycadophyta) are palmlike plants of the tropics.
        2. The ginkgos (phylum Ginkgophyta) are represented today by a single genus and species, Ginkgo biloba.
        3. The phylum Gnetophyta consists of three very different genera sharing certain characteristics with angiosperms.
        4. The conifers (phylum Coniferophyta) are cone-bearing plants such as pines and redwoods.
    D. All gymnosperms exhibit secondary growth—their stems and roots grow larger in diameter.
    E. All gymnosperms but the Gnetophyta have only tracheids as water-conducting and support cells in their xylem.
    F. Wood is secondary xylem produced by gymnosperms.
    G. We know the early gymnosperms only as fossils
        1. The earliest fossil evidence of gymnosperms is found in Devonian rocks.
        2. The early gymnosperms had characteristics of both the rhyniophytes and the ferns, but also had tracheids like those found in modern gymnosperms.
        3. They also had thickened, woody stems that resulted from proliferation of xylem.
        4. Several new lines of gymnosperms had evolved by the Carboniferous period.
        5. The Permian period saw conifers and cycads flourish.
        6. The gymnosperm forests changed with time as the gymnosperms evolved.
        7. Gymnosperms dominated all forests until less than 100 million years ago, and they still dominate some present-day forests.
    H. Conifers have cones but no motile cells
        1. The trees of the great fir, cedar, spruce, and pine forests that cover much of the northern continental regions all belong to the phylum Coniferophyta.
        2. A cone is an axis bearing a tight cluster of scales or leaves specialized for reproduction.
        3. Megaspores and microspores are produced in separate seed and pollen cones.
        4. The ovule consists of the integument, the megasporangium inside it, and the tissue attaching it to the maternal sporophyte.
        5. Pollen grains enter through a small opening in the integument at the tip of the ovule called the micropyle.
        6. Conifer ovules are borne on the upper surfaces of modified branches called cone scales, which are tightly packed against each other within the cone.
        7. About half of the conifer species have fruitlike tissues associated with their seeds that may be eaten by animals, which in turn disperse the seeds in their feces.
        8. These tissues are not fruits.
II. The Angiosperms: Flowering Plants
    A. The phylum Angiospermae consists of the flowering plants, commonly known as the angiosperms.
        This phylum includes over 230,000 species.
    B. Angiosperm means “enclosed seed.”
    C. The angiosperms represent the current extreme of an evolutionary trend found in the tracheophytes—the sporophyte generation becomes larger and more independent of the gametophyte, while the gametophyte becomes smaller and more dependent on the sporophyte.
    D. The angiosperms differ from other plants in several ways:
        1. They produce triploid endosperm.
        2. They have double fertilization.
        3. Their ovules and seeds are enclosed in a carpel.
        4. They have flowers.
        5. They produce fruit.
        6. Their xylem contains vessel elements and fibers.
        7. Their phloem contains companion cells.
    E. In double fertilization, two male gametes participate in fertilization events within the megagametophyte.
        1. One sperm combines with the egg to produce a diploid zygote.
        2. The other sperm nucleus combines with two other haploid nuclei of the female gametophyte to form a triploid nucleus that gives rise to the endosperm, triploid tissue that nourishes the embryonic sporophyte during its early development.
    F. The carpel is a modified leaf that encloses the ovules and seeds of the angiosperms, offering protection and interacting with incoming pollen to prevent self-pollination.
    G. Vessel elements are specialized water-transporting cells present within the xylem of angiosperms.
    H. Fiber is another distinct cell type found in the xylem of angiosperms. It plays an important role in supporting the plant body.
    I. Companion cells are a unique type of cell found in angiosperm phloem.
    J. The sexual structures of angiosperms are flowers
        1. Stamens are microsporangia-bearing structures in a flower and are composed of a filament that bears an anther containing the pollen-producing microsporangia.
        2. The pistil is a structure composed of one carpel or two or more fused carpels. It has a swollen base that contains the megasporangia and is called the ovary.
        3. The style is the apical stalk of the pistil, and the terminal surface that receives pollen grains is called the stigma.
        4. Flowers often have several other specialized sterile leaves:
            a. The inner ones are called petals (collectively, the corolla).
            b. The outer ones are called sepals (collectively, the calyx).
                (1) These leaves often play roles in attracting animal pollinators to the flower.
                (2) The calyx commonly protects the immature flower in bud.
            c. From base to apex, the sepals, petals, stamens, and carpels are usually in circular arrangements called whorls and attached to a stalk called the receptacle.
        5. Flowers that have both microsporangia and megasporangia are referred to as perfect.
        6. Imperfect flowers contain either functional megasporangia or microsporangia, but not both.
            a. Monoecious angiosperm species produce both megasporangiate and microsporangiate flowers on the same plant.
            b. In dioecious angiosperm species, a given plant produces either megasporangiate or microsporangiate flowers but not both.
        7. Appendages on plants whose petals and sepals are indistinguishable are called tepals.
        8. Flowers may be single, or grouped together to form an inflorescence. Flower structure has evolved over time
        9. The flowers of the most evolutionarily ancient angiosperms have a large and variable number of tepals, carpels, and stamens.
            a. Evolution within the angiosperms has resulted in modifications of this early condition.
            b. Carpels and stamens are thought to have evolved from leaflike structures.
     K. Angiosperms have coevolved with animals
        1. Most angiosperms are animal-pollinated.
        2. Animals visit flowers to obtain nectar or pollen, and in the process often carry pollen from one plant to another.
        3. This contributes to the genetic diversity of the angiosperms.
        4. The animals have affected the evolution of plants, and plants have affected the evolution of animals.
        5. This coevolution has resulted in some highly specific interactions, with certain plant species being pollinated by only one or very few animal species.
        6. Most plant–pollinator interactions are not highly specific.
    L. The angiosperm life cycle features double fertilization
        Cotyledons, or seed leaves, often serve as absorptive organs that digest the endosperm. In some plants, they enlarge and become photosynthetic when the seed germinates.
    M. Angiosperms produce fruits
        1. The ovary of a flowering plant develops into a fruit after fertilization.
        2. A fruit may consist only of the mature ovary and its seeds, or it may include other parts of the flower or structures associated with it.
        3. Simple fruits develop from a single carpel or several united carpels.
        4. Aggregate fruits develop from several separate carpels of a single flower.
        5. Multiple fruits are formed from a cluster of flowers.
        6. Accessory fruits are derived from parts in addition to the carpel and seeds.
    N. Determining the oldest living angiosperm lineage
        1. Until the close of the twentieth century, the two leading candidates for the most ancient angiosperm lineage were the magnolia family and the Chloranthaceae.
        2. A convergence of evidence led to the conclusion that the base of the angiosperm phylogenetic tree actually belonged to a single species of the genus Amborella.
        3. The xylem of this plant lacks vessel elements, which appeared later in angiosperm evolution.
        4. There are two large monophyletic groups of angiosperms
            a. The great majority of the angiosperm species are included in two large lineages: the monocots and the eudicots.
            b. The monocots have a single embryonic cotyledon; the eudicots have two.
        5. The origin of the angiosperms remains a mystery
            a. The question of how the angiosperms first arose is still unanswered.
            b. Several questions complicate investigators’ efforts to answer this question.
            c. What morphological characters should be selected as important?
            d. What algorithms should be applied to computerized analysis of data?
            e. Are all molecular differences and similarities significant?
            f. Which fossils should be chosen for comparisons?
            g. What is the likelihood that evidence of double fertilization can be found in ancient fossils?

Fungi: Recyclers, Killers, and Plant Partners
I. General Biology of the Fungi
     A. Fungi secrete digestive enzymes that break down large food molecules.
     B. They absorb the breakdown products.
     C. The kingdom Fungi encompasses heterotrophic organisms with absorptive nutrition.
         1. Some are saprobes (feeding on dead matter); others are parasites.
         2. A few have mutually beneficial (symbiotic) relationships with other organisms.
     D. All produce spores, but only one phylum (Chytridiomycota) has gametes with flagella.
     E. The cell walls of all fungi have at least some chitin.
     F. Some protists look superficially like fungi, but phagocytize their food.
 II. The kingdom Fungi consists of four phyla: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota.
     A. The four phyla are primarily distinguished by their methods and structures of reproduction.
     B. Some fungi reproduce asexually only.
         These are called imperfect fungi or deuteromycetes.
     C. Deuteromycetes are considered a "holding group" for species whose status has yet to be resolved.
III. Fossil evidence suggests that fungi have been present for at least 600 million years, and perhaps much longer.
IV. Some fungi are unicellular
     A. Unicellular forms are found in all of the fungal phyla.
     B. Those of the Zygomycota, Ascomycota, and Basidiomycota are called yeasts.
V. The body of a fungus is composed of hyphae
     A. The vegetative body of a fungus is called the mycelium (plural mycelia).
     B. The mycelium is composed of threadlike hyphae (singular hypha).
     C. Most fungi are not unicellular, but they are not exactly multicellular, either.
     D. Some hyphae have no internal separations into distinct cells, and organelles (even nuclei) can move around freely. These hyphae are said to be coenocytic hyphae
     E. Some hyphae are subdivided into cell-like compartments by incomplete cross-walls.
         1. These cross-walls are called septa (singular septum).
         2. Pores in septa still allow free movement of organelles and other materials.
     F. Rhizoids are modified hyphae, which anchor Chytridiomycota to a substrate.
     G. Some parasitic fungi may have modified hyphae that take up nutrients.
     H. Fungal parasites of plants can invade at wounds on plants and grow mycelium throughout the plant and their fruit.
     I. Fungi are in intimate contact with their environment
     J. The mycelium has a very high surface-to-volume ratio.
     K. Fungi are tolerant to highly hypertonic environments.
     L. Many can tolerate temperatures as low as 5 to 6oC below freezing. Some can tolerate temperatures as high as 50oC or more.
VI. Fungi are absorptive heterotrophs
     A. The majority of fungi are saprobes, living on dead organisms.
     B. Saprobic fungi (along with bacteria) are Earth’s primary decomposers, recycling the elements used by living things.
     C. Fungi are the principal decomposers of cellulose and lignin, the major components of plant cell walls.
     D. Many fungi can use ammonium ions or nitrate as a sole source of nitrogen.
     E. Most fail to synthesize their own thiamin or biotin (two B vitamins), but they can synthesize some vitamins that animals cannot.
     F. Facultative parasites can be grown by themselves on defined media.
     G. Obligate parasites grow only on their specific host and must therefore have unusual nutritional requirements.
     H. Some fungi are active predators.
         1. Most predatory fungi secrete sticky substances from the hyphae.
         2. Trapped prey are penetrated by hyphae and eventually killed.
         3. Some species of Arthrobotrys, Dactylaria, and Dactylella form a ring with modified hyphae that constricts around nematodes.
         4. The crawling nematode triggers these rings to swell and trap. Fungal hyphae quickly invade and digest the worm.
     I. Lichens are associations of a fungus with either cyanobacteria or a unicellular photosynthetic eukaryote.
     J. Mycorrhizae are associations of fungi and plant roots.
         The fungus obtains organic compounds, while the plant is provided with readier access to soil minerals.
VII. Most fungi reproduce both asexually and sexually
     A. Both asexual and sexual reproduction are common among fungi.
         1. Asexual reproduction includes:
             a. The production of haploid spores within sporangia
             b. The production of naked spores (not within sporangia) called conidia, at the tips of hyphae
             c. Cell division by unicellular fungi
             d. Simple breakage of mycelium
         2. Sexual reproduction involves fusion between different mating types.
             a. Some fungi have more than two mating types.
             b. Mating types cannot be distinguished morphologically.
             c. Mating can only occur between different mating types.
                 This prevents self-fertilization.
     B. In many fungi, the zygote nuclei are the only diploid nuclei of the life cycle.
         1. These nuclei undergo meiosis, producing haploid nuclei.
         2. Haploid spores divide mitotically to form haploid hyphae.
    C. Many fungal life cycles include a dikaryon stage
         1. In some species, opposite mating types fuse to produce hyphae with two genetically different haploid nuclei.
         2. This type of hypha is called a dikaryon or heterokaryon.
         3. Later, when specialized fruiting structures form, dissimilar nuclei fuse to form zygotes.
         4. The zygote nucleus then undergoes meiosis, producing four haploid nuclei.
     D. Fungi have some other unusual reproduction features.
         1. There are no gamete cells, just gamete nuclei.
         2. There are no true diploid tissues, though for a long period the genes of both parents are present in the dikaryon and can be expressed.
         3. If the hypha is a dikaryon, a harmful recessive allele in one nucleus can be masked by a normal allele in the other nucleus.
         4. Zygomycota, Ascomycota, and Basidiomycota do not have motile gametes, so water is not required for fertilization.
VII. Some fungi are pathogens
     A. Fungal pathogens are a major cause of death among people with compromised immune systems.
         1. Most patients with AIDS die of fungal diseases such as Pneumocystis carinii.
         2. Candida albicans and other yeasts also cause severe diseases in those with AIDS.
     B. Other less severe and common diseases include ringworm and athlete's foot.
     C. Plant diseases include black stem rust and others.
VIII. Diversity in the Kingdom Fungi
    A. Chytrids probably resemble the ancestral fungi
         1. The chytrids are the earliest diverging fungal lineage.
         2. They are aquatic microorganisms and have sometimes been classed with protists.
         3. They are currently classed with fungi because of the chitin in their cell walls.
         4. Chytrids are either parasitic (on aquatic plants or invertebrates) or saprobic.
             The exceptions are those found in the rumen of ruminants, a mutualistic association.
         5. Most live in fresh water or moist soil; some live in marine environments.
         6. They reproduce both sexually and asexually.
         7. Allomyces display alternation of generations.
             a. A haploid zoospore comes to rest on dead matter.
             b. The zoospore germinates to form a small haploid organism, which later forms female and male gametangia. (Male are smaller than female.) Both are motile, using flagella.
             c. The female gametes produce a pheromone (a chemical signal) that attracts male gametes.
             d. The male and female gametes fuse.
             e. Cell division produces a small diploid organism, which produces numerous diploid flagellated zoospores.
             f. These disperse and produce more diploid organisms.
             g. These eventually produce resistant resting sporangia that can survive dry and freezing weather.
             h. The nuclei in sporangia eventually undergo meiosis to produce haploid zoospores.
             i. Chytrids are one of the few fungi with alternating generations (both a haploid and diploid life cycle).
         8. The early divergence of chytrids from the other fungi suggests that like chytrids, the protist ancestors of fungi had flagella.
    B. Zygomycetes reproduce sexually by fusion of two gametangia.
         1. Zygomycetes have coenocytic hyphae (no regular septa); they produce no motile cells and only one diploid cell, the zygote.
         2. Most do not form fleshy fruit, but just occasional stalked sporangiophores reaching up into the air.
         3. Almost 900 species have been described.
         4. These include the fungal species in the most common mycorrhizal associations.
         5. Black bread mold is Rhizopus stolonifer.
         6. Sporangiophores are the fruiting bodies.
             a. In Rhizopus stolonifer (black bread mold), each sporangiophore has a single sporangium at the tip, containing hundreds of spores.
             b. Other zygomycetes have many sporangia on each sporangiophore.
         7. Sexual reproduction occurs when adjacent hyphae of the same species but different mating types release pheromones, which stimulates them to fuse together.
         8. Zygospores may remain dormant for months, but eventually they undergo meiosis and sporangia sprout from the zygospore.
    C. The sexual reproductive structure of ascomycetes is an ascus
         1. The ascomycetes (phylum Ascomycota) are a large and diverse group distinguished from other fungi by the production of asci (singular ascus).
         2. The ascus contains the products of meiosis.
         3. Ascomycete hyphae are septated.
         4. A pore in each septum permits systolic movement, even of nuclei.
         5. There are so far about 30,000 species, which are divided into two groups based on whether asci are contained in special fruiting structures.
         6. Those with an ascocarp are called euascomycetes.
         7. Those without are called hemiascomycetes.
             a. Hemiascomycetes:
                 (1) Most hemiascomycetes are microscopic.
                 (2) Some are unicellular.
                 (3) Baker's or brewer's yeast (Saccharomyces cerevisiae) is an ascomycete. This yeast makes ethanol and CO2 from glucose.
                     (a) Bubbles of CO2 are responsible for making bread rise.
                     (b) The alcohol and bubbles in beer are produced by this yeast.
                 (4) Hemiascomycete yeasts reproduce asexually by budding or fission depending on the species.
                 (5) Sexual reproduction occurs when two haploid cells of opposite mating types fuse.
                 (6) In some species, diploid cells divide.
                 (7) In others, the zygote immediately undergoes meiosis. The entire cell becomes an ascus.
                 (8) Four or eight ascospores are produced depending on whether the cells divide once after meiosis.
             b. Euascomycetes:
                 (1) The euascomycetes include some of the fungi known as mold.
                 (2) Neurospora is pink bread mold.
                 (3) Many euascomycetes are plant parasites.
                 (4) Chestnut blight and Dutch elm disease are caused by euascomycetes.
                 (5) Powdery mildews infect cereals, lilacs, roses, and other plants.
                 (6) Cup fungi are euascomycetes. These produce huge numbers of spores and can be several centimeters in diameter.
                     a. Morels are edible cup fungi.
                     b. Truffles are cup fungi that grow underground, on the roots of some species of oak.
                 (7) Penicillium is a genus of green molds.
                     a. Some produce the antibiotic penicillin.
                     b. P. roquefortii and P. camembertii provide the flavors to the cheeses Roquefort and Camembert.
                 (8) Brown molds of the genus Aspergillus are used in food preparation.
                     a. A. tamarii is used to ferment soybeans to make soy sauce.
                     b. A. oryzae is used in brewing the Japanese alcoholic beverage sake.
                     c. Some Aspergillus species that contaminate peanuts and pecans produce powerful mutagens called aflatoxins.
                 (9) Euascomycetes reproduce asexually using conidia that form at the tips of specialized hyphae.
                     a. Small chains of conidia are produced by the millions and can survive for weeks.
                     b. Sexual reproduction of euascomycetes includes formation of a dikaryon.
                     c. The nuclei from a male structure on one hypha enter a female mating structure.
                     d. Ascogenous hyphae develop from the dikaryotic female.
                     e. Asci form at the tips of ascogenous hyphae. Both fusion of nuclei and meiosis occur within individual asci.
                     f. Meiotic products are incorporated into ascospores.
    D. The sexual reproductive structure of basidiomycetes is a basidium
         1. About 25,000 species of basidiomycetes have been described.
         2. They produce a wide variety of fruiting structures: puffballs, mushrooms, and giant bracket fungi.
         3. There are more than 3,250 species of mushrooms.
             a. Agaricus bisporus is the common edible one; some Amanita mushrooms are deadly poisonous.
             b. Bracket fungi are tree parasites.
             c. Smut fungi parasitize cereal grains.
         4. Basidiomycetes are septated.
         5. Basidia are swollen cells at the tips of hyphae.
             a. Nuclear fusion and meiosis occur within basidia.
             b. The elaborate fruiting structures of some, such as the gill mushroom, are topped with a cap called a pileus.
             c. Vast numbers of spores form between the gills.
    E. Imperfect fungi lack a sexual stage
         1. Fungi not yet placed in any existing phyla are grouped as imperfect fungi (deuteromycetes). Deuteromycetes currently include 25,000 species.
         2. The sexual cycle has yet to be observed in these species.
         3. DNA sequences can now be used to determine actual relationships between deuteromycetes and other fungi.
IX. Fungal Associations
    A. Mycorrhizae are essential to many plants
         1. Almost all tracheophytes have mycorrhizae.
         2.The fungi help make water and minerals more available to the plant.
         3. In ectomycorrhizae, the fungus wraps around the root tips and acts as a sponge.
         4. Endomycorrhizae infect the interior of the root.
         5. The fungi get sugars, amino acids, and some vitamins from the plant; the plants get improved water and mineral supplies from the fungus.
         6. The fungus might supply hormones as well.
         7. Fungal–plant root interactions have existed for hundreds of millions of years.
    B. Lichens grow where no eukaryote has succeeded
         1. Lichens are a meshwork of two different organisms.
         2. One organism is a fungus, and the other is a photosynthetic organism.
         3. Lichens can survive harsh environments.
         4. The flora of Antarctica has 100 times more species of lichens than plants.
         5. Lichens are sensitive to air pollution.
         6. The fungi of most lichens are ascomycetes.
         7. The photosynthetic component might be either a cyanobacterium or a unicellular green alga.
         8. There are about 13,500 "species" of lichens.
         9. The reindeer of the arctic, subarctic, and boreal regions use lichens in their diets.
         10. The photosynthetic cells from lichens grow more rapidly on their own than when combined with a fungus.
         11. Lichens can reproduce simply by fragmentation of the vegetative body called the thallus.
         12. They can also reproduce by means of specialized structures called soredia (singular soredium).
         13. These are composed of fungal hyphae and a few photosynthetic cells.
         14. If the fungal partner is an ascomycete or a basidiomycete, the fungus might undergo a sexual process, but the spores are released alone into the environment and fail to reestablish the lichen relationship.